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Sample records for related quantitative traits

  1. Quantitative trait locus (QTL) analysis of pod related traits in different ...

    African Journals Online (AJOL)

    Administrator

    2011-09-26

    Sep 26, 2011 ... assistant breeding selection. Key words: Soybean, pod traits, QTL, different environments. INTRODUCTION. Yield related traits in soybean are generally controlled by multiple genes and environmental dependent (Kwon and. Torrie, 1964). Epigenetics of genes controlling these traits also affect the yield.

  2. Comparative mapping of quantitative trait loci for tassel-related traits ...

    Indian Academy of Sciences (India)

    QIANG YI

    2018-03-15

    Mar 15, 2018 ... in maize have evaluated flowering-related traits (Li et al. ... with Upadyayula et al. (2006). The measurements taken were TTL, the length (cm) of the tassel ...... M. Banziger, H. R. Mickelson and C. B. Penã–Valdivia), pp.

  3. Quantitative Trait Loci in Inbred Lines

    NARCIS (Netherlands)

    Jansen, R.C.

    2001-01-01

    Quantitative traits result from the influence of multiple genes (quantitative trait loci) and environmental factors. Detecting and mapping the individual genes underlying such 'complex' traits is a difficult task. Fortunately, populations obtained from crosses between inbred lines are relatively

  4. Variation in CHI3LI in relation to type 2 diabetes and related quantitative traits.

    Directory of Open Access Journals (Sweden)

    Camilla Noelle Rathcke

    Full Text Available CHI3LI encoding the inflammatory glycoprotein YKL-40 is located on chromosome 1q32.1. YKL-40 is involved in inflammatory processes and patients with Type 2 Diabetes (T2D have elevated circulating YKL-40 levels which correlate with their level of insulin resistance. Interestingly, it has been reported that rs10399931 (-329 G/A of CHI3LI contributes to the inter-individual plasma YKL-40 levels in patients with sarcoidosis, and that rs4950928 (-131 C/G is a susceptibility polymorphism for asthma and a decline in lung function. We hypothesized that single nucleotide polymorphisms (SNPs or haplotypes thereof the CHI3LI locus might influence risk of T2D. The aim of the present study was to investigate the putative association between SNPs and haplotype blocks of CHI3LI and T2D and T2D related quantitative traits.Eleven SNPs of CHI3LI were genotyped in 6514 individuals from the Inter99 cohort and 2924 individuals from the outpatient clinic at Steno Diabetes Center. In cas-control studies a total of 2345 T2D patients and 5302 individuals with a normal glucose tolerance test were examined. We found no association between rs10399931 (OR, 0.98 (CI, 0.88-1.10, p = 0.76, rs4950928 (0.98 (0.87-1.10, p = 0.68 or any of the other SNPs with T2D. Similarly, we found no significant association between any of the 11 tgSNPs and T2D related quantitative traits, all p>0.14. None of the identified haplotype blocks of CHI3LI showed any association with T2D, all p>0.16.None of the examined SNPs or haplotype blocks of CHI3LI showed any association with T2D or T2D related quantitative traits. Estimates of insulin resistance and dysregulated glucose homeostasis in T2D do not seem to be accounted for by the examined variations of CHI3LI.

  5. Variation in CHI3LI in relation to type 2 diabetes and related quantitative traits

    DEFF Research Database (Denmark)

    Rathcke, Camilla Noelle; Holmkvist, Johan; Jørgensen, Torben

    2009-01-01

    BACKGROUND: CHI3LI encoding the inflammatory glycoprotein YKL-40 is located on chromosome 1q32.1. YKL-40 is involved in inflammatory processes and patients with Type 2 Diabetes (T2D) have elevated circulating YKL-40 levels which correlate with their level of insulin resistance. Interestingly...... in 6514 individuals from the Inter99 cohort and 2924 individuals from the outpatient clinic at Steno Diabetes Center. In cas-control studies a total of 2345 T2D patients and 5302 individuals with a normal glucose tolerance test were examined. We found no association between rs10399931 (OR, 0.98 (CI, 0...... (SNPs) or haplotypes thereof the CHI3LI locus might influence risk of T2D. The aim of the present study was to investigate the putative association between SNPs and haplotype blocks of CHI3LI and T2D and T2D related quantitative traits. METHODS/PRINCIPAL FINDINGS: Eleven SNPs of CHI3LI were genotyped...

  6. Genetic disparity and relationship among quantitatively inherited yield related traits in diallel crosses of upland cotton

    International Nuclear Information System (INIS)

    Bibi, M.; Khan, N.U.; Mohammad, F.; Gul, R.; Idrees, M.; Sayal, O.U.; Khakwani, A.A.; Khan, I.A.

    2011-01-01

    In quantitative genetics, development of high yielding genotypes from parental cultivars of same ancestry is some what confusing as compared to genetically diverse parents. However, sufficient recombinations through allelic variations in mating of closely-related populations result in superior agronomic performance. Development of improved cotton genotypes is one of the prime objectives of any cotton breeding programmes. Genetic divergence and yield potential of parental cotton genotypes versus their diallel hybrids, relationship of yield with various morpho-yield traits and their heritability were studied in 8 X 8 F/sub 1/ diallel hybrids and their parental cultivars in Gossypium hirsutum L. during 2008-09 at Khyber Pakhtunkhwa Agricultural University, Peshawar, Pakistan. Highly significant (p less than or equal to 0.01) differences were observed among parental genotypes and F/sub 1/ populations for all the traits. Results revealed that F/sub 1/ hybrids i.e., CIM-506 X CIM-554, CIM-473 X CIM-554, CIM-446 X CIM-496 and CIM-446 X CIM-554 produced significantly higher number of sympodia, bolls per populations showed incredible performance for plant height, locules per boll and seeds plant and seed cotton yield. Some F/sub 1/ per locule. Seed cotton yield manifested positive association with morpho-yield traits which also accounted for greater genetic variations to yield being dependent trait. Heritabilities (broad sense) were moderate to high in magnitude for all populations with larger genetic potential, positive relationship between yield and yield traits. Results revealed that F1 contributing traits and moderate to high heritability can guide intensive selection and improvement per se in segregating populations. (author)

  7. Quantitative trait local analysis of growth-related traits in a new Arabidopsis recombinant inbred population

    NARCIS (Netherlands)

    El-Lithy, M.E.M.; Clerkx, E.J.M.; Ruijs, G.J.; Koornneef, M.; Vreugdenhil, D.

    2004-01-01

    Arabidopsis natural variation was used to analyze the genetics of plant growth rate. Screening of 22 accessions revealed a large variation for seed weight, plant dry weight and relative growth rate but not for water content. A positive correlation was observed between seed weight and plant area 10 d

  8. Analysis of heterosis and quantitative trait loci for kernel shape related traits using triple testcross population in maize.

    Directory of Open Access Journals (Sweden)

    Lu Jiang

    Full Text Available Kernel shape related traits (KSRTs have been shown to have important influences on grain yield. The previous studies that emphasize kernel length (KL and kernel width (KW lack a comprehensive evaluation of characters affecting kernel shape. In this study, materials of the basic generations (B73, Mo17, and B73 × Mo17, 82 intermated B73 × Mo17 (IBM individuals, and the corresponding triple testcross (TTC populations were used to evaluate heterosis, investigate correlations, and characterize the quantitative trait loci (QTL for six KSRTs: KL, KW, length to width ratio (LWR, perimeter length (PL, kernel area (KA, and circularity (CS. The results showed that the mid-parent heterosis (MPH for most of the KSRTs was moderate. The performance of KL, KW, PL, and KA exhibited significant positive correlation with heterozygosity but their Pearson's R values were low. Among KSRTs, the strongest significant correlation was found between PL and KA with R values was up to 0.964. In addition, KW, PL, KA, and CS were shown to be significant positive correlation with 100-kernel weight (HKW. 28 QTLs were detected for KSRTs in which nine were augmented additive, 13 were augmented dominant, and six were dominance × additive epistatic. The contribution of a single QTL to total phenotypic variation ranged from 2.1% to 32.9%. Furthermore, 19 additive × additive digenic epistatic interactions were detected for all KSRTs with the highest total R2 for KW (78.8%, and nine dominance × dominance digenic epistatic interactions detected for KL, LWR, and CS with the highest total R2 (55.3%. Among significant digenic interactions, most occurred between genomic regions not mapped with main-effect QTLs. These findings display the complexity of the genetic basis for KSRTs and enhance our understanding on heterosis of KSRTs from the quantitative genetic perspective.

  9. Quantitative traits and diversification.

    Science.gov (United States)

    FitzJohn, Richard G

    2010-12-01

    Quantitative traits have long been hypothesized to affect speciation and extinction rates. For example, smaller body size or increased specialization may be associated with increased rates of diversification. Here, I present a phylogenetic likelihood-based method (quantitative state speciation and extinction [QuaSSE]) that can be used to test such hypotheses using extant character distributions. This approach assumes that diversification follows a birth-death process where speciation and extinction rates may vary with one or more traits that evolve under a diffusion model. Speciation and extinction rates may be arbitrary functions of the character state, allowing much flexibility in testing models of trait-dependent diversification. I test the approach using simulated phylogenies and show that a known relationship between speciation and a quantitative character could be recovered in up to 80% of the cases on large trees (500 species). Consistent with other approaches, detecting shifts in diversification due to differences in extinction rates was harder than when due to differences in speciation rates. Finally, I demonstrate the application of QuaSSE to investigate the correlation between body size and diversification in primates, concluding that clade-specific differences in diversification may be more important than size-dependent diversification in shaping the patterns of diversity within this group.

  10. Fine mapping and candidate gene prediction of a pleiotropic quantitative trait locus for yield-related trait in Zea mays.

    Directory of Open Access Journals (Sweden)

    Ruixiang Liu

    Full Text Available The yield of maize grain is a highly complex quantitative trait that is controlled by multiple quantitative trait loci (QTLs with small effects, and is frequently influenced by multiple genetic and environmental factors. Thus, it is challenging to clone a QTL for grain yield in the maize genome. Previously, we identified a major QTL, qKNPR6, for kernel number per row (KNPR across multiple environments, and developed two nearly isogenic lines, SL57-6 and Ye478, which differ only in the allelic constitution at the short segment harboring the QTL. Recently, qKNPR6 was re-evaluated in segregating populations derived from SL57-6×Ye478, and was narrowed down to a 2.8 cM interval, which explained 56.3% of the phenotypic variance of KNPR in 201 F(2∶3 families. The QTL simultaneously affected ear length, kernel weight and grain yield. Furthermore, a large F(2 population with more than 12,800 plants, 191 recombinant chromosomes and 10 overlapping recombinant lines placed qKNPR6 into a 0.91 cM interval corresponding to 198Kb of the B73 reference genome. In this region, six genes with expressed sequence tag (EST evidence were annotated. The expression pattern and DNA diversity of the six genes were assayed in Ye478 and SL57-6. The possible candidate gene and the pathway involved in inflorescence development were discussed.

  11. Quantitative trait loci controlling leaf appearance and curd initiation of cauliflower in relation to temperature.

    Science.gov (United States)

    Hasan, Yaser; Briggs, William; Matschegewski, Claudia; Ordon, Frank; Stützel, Hartmut; Zetzsche, Holger; Groen, Simon; Uptmoor, Ralf

    2016-07-01

    QTL regions on chromosomes C06 and C09 are involved in temperature dependent time to curd induction in cauliflower. Temperature is the main environmental factor influencing curding time of cauliflower (Brassica oleracea var. botrytis). Temperatures above 20-22 °C inhibit development towards curding even in many summer cultivars. To identify quantitative trait loci (QTL) controlling curding time and its related traits in a wide range of different temperature regimes from 12 to 27 °C, a doubled haploid (DH) mapping population segregating for curding time was developed and days to curd initiation (DCI), leaf appearance rate (LAR), and final leaf number (FLN) were measured. The population was genotyped with 176 single nucleotide polymorphism (SNP) markers. Composite interval mapping (CIM) revealed repeatedly detected QTL for DCI on C06 and C09. The estimated additive effect increased at high temperatures. Significant QTL × environment interactions (Q × E) for FLN and DCI on C06 and C09 suggest that these hotspot regions have major influences on temperature mediated curd induction. 25 % of the DH lines did not induce curds at temperatures higher than 22 °C. Applying a binary model revealed a QTL with LOD >15 on C06. Nearly all lines carrying the allele of the reliable early maturing parental line (PL) on that locus induced curds at high temperatures while only half of the DH lines carrying the allele of the unreliable PL reached the generative phase during the experiment. Large variation in LAR was observed. QTL for LAR were detected repeatedly in several environments on C01, C04 and C06. Negative correlations between LAR and DCI and QTL co-localizations on C04 and C06 suggest that LAR has also effects on development towards curd induction.

  12. Variation in CAPN10 in relation to type 2 diabetes, obesity and quantitative metabolic traits

    DEFF Research Database (Denmark)

    Jensen, Dorit P; Urhammer, Søren A; Eiberg, Hans

    2006-01-01

    = 4659 normoglycemic and glucose-tolerant control subjects), however, no significant associations of the SNP43 or the SNP44 variant with T2D were found. Neither were the two variants associated with obesity, and no association of either variant with diabetes-related quantitative traits was found......The first type 2 diabetes (T2D) gene to be identified in a genome wide scan followed by positional cloning was CAPN10 encoding the cysteine protease calpain-10. Subsequently, a large number of studies have investigated variation in CAPN10 in relation to T2D. Two CAPN10 single nucleotide...... in a study involving a population-based sample of 5698 middle-aged subjects. Meta-analyses, however, of the present and previously published studies involving 15,368 (SNP43) or 13,628 (SNP44) subjects yielded odds ratios of 1.09 (95% CI 1.02-1.16, p = 0.007) and 1.15 (1.07-1.23, p = 0.0002), respectively...

  13. Quantitative genetics of disease traits.

    Science.gov (United States)

    Wray, N R; Visscher, P M

    2015-04-01

    John James authored two key papers on the theory of risk to relatives for binary disease traits and the relationship between parameters on the observed binary scale and an unobserved scale of liability (James Annals of Human Genetics, 1971; 35: 47; Reich, James and Morris Annals of Human Genetics, 1972; 36: 163). These two papers are John James' most cited papers (198 and 328 citations, November 2014). They have been influential in human genetics and have recently gained renewed popularity because of their relevance to the estimation of quantitative genetics parameters for disease traits using SNP data. In this review, we summarize the two early papers and put them into context. We show recent extensions of the theory for ascertained case-control data and review recent applications in human genetics. © 2015 Blackwell Verlag GmbH.

  14. Quantitative trait loci and metabolic pathways

    Science.gov (United States)

    McMullen, M. D.; Byrne, P. F.; Snook, M. E.; Wiseman, B. R.; Lee, E. A.; Widstrom, N. W.; Coe, E. H.

    1998-01-01

    The interpretation of quantitative trait locus (QTL) studies is limited by the lack of information on metabolic pathways leading to most economic traits. Inferences about the roles of the underlying genes with a pathway or the nature of their interaction with other loci are generally not possible. An exception is resistance to the corn earworm Helicoverpa zea (Boddie) in maize (Zea mays L.) because of maysin, a C-glycosyl flavone synthesized in silks via a branch of the well characterized flavonoid pathway. Our results using flavone synthesis as a model QTL system indicate: (i) the importance of regulatory loci as QTLs, (ii) the importance of interconnecting biochemical pathways on product levels, (iii) evidence for “channeling” of intermediates, allowing independent synthesis of related compounds, (iv) the utility of QTL analysis in clarifying the role of specific genes in a biochemical pathway, and (v) identification of a previously unknown locus on chromosome 9S affecting flavone level. A greater understanding of the genetic basis of maysin synthesis and associated corn earworm resistance should lead to improved breeding strategies. More broadly, the insights gained in relating a defined genetic and biochemical pathway affecting a quantitative trait should enhance interpretation of the biological basis of variation for other quantitative traits. PMID:9482823

  15. Quantitative Trait Loci Affecting Calving Traits in Danish Holstein Cattle

    DEFF Research Database (Denmark)

    Thomasen, J R; Guldbrandtsen, B; Sørensen, P

    2008-01-01

    The objectives of this study were 1) to detect quantitative trait loci (QTL) affecting direct and maternal calving traits at first calving in the Danish Holstein population, 2) to distinguish between pleiotropic and linked QTL for chromosome regions affecting more than one trait, and 3) to detect...

  16. Quantitative trait loci for behavioural traits in chicken

    NARCIS (Netherlands)

    Buitenhuis, A.J.; Rodenburg, T.B.; Siwek, M.Z.; Cornelissen, S.J.B.; Nieuwland, M.G.B.; Crooijmans, R.P.M.A.; Groenen, M.A.M.; Koene, P.; Bovenhuis, H.; Poel, van der J.J.

    2005-01-01

    The detection of quantitative trait loci (QTL) of behavioural traits has mainly been focussed on mouse and rat. With the rapid development of molecular genetics and the statistical tools, QTL mapping for behavioural traits in farm animals is developing. In chicken, a total of 30 QTL involved in

  17. Quantitative trait loci (QTL) mapping for inflorescence length traits in ...

    African Journals Online (AJOL)

    Lablab purpureus (L.) sweet is an ancient legume species whose immature pods serve as a vegetable in south and south-east Asia. The objective of this study is to identify quantitative trait loci (QTLs) associated with quantitative traits such as inflorescence length, peduncle length from branch to axil, peduncle length from ...

  18. Quantitative Autism Traits in First Degree Relatives: Evidence for the Broader Autism Phenotype in Fathers, but Not in Mothers and Siblings

    Science.gov (United States)

    De la Marche, Wouter; Noens, Ilse; Luts, Jan; Scholte, Evert; Van Huffel, Sabine; Steyaert, Jean

    2012-01-01

    Autism spectrum disorder (ASD) symptoms are present in unaffected relatives and individuals from the general population. Results are inconclusive, however, on whether unaffected relatives have higher levels of quantitative autism traits (QAT) or not. This might be due to differences in research populations, because behavioral data and molecular…

  19. Quantitative variation in obesity-related traits and insulin precursors linked to the OB gene region on human chromosome 7

    Energy Technology Data Exchange (ETDEWEB)

    Duggirala, R.; Stern, M.P.; Reinhart, L.J. [Univ. of Texas Health Science Center, San Antonio, TX (United States)] [and others

    1996-09-01

    Despite the evidence that human obesity has strong genetic determinants, efforts at identifying specific genes that influence human obesity have largely been unsuccessful. Using the sibship data obtained from 32 low-income Mexican American pedigrees ascertained on a type II diabetic proband and a multipoint variance-components method, we tested for linkage between various obesity-related traits plus associated metabolic traits and 15 markers on human chromosome 7. We found evidence for linkage between markers in the OB gene region and various traits, as follows: D7S514 and extremity skinfolds (LOD = 3.1), human carboxypeptidase A1 (HCPA1) and 32,33-split proinsulin level (LOD = 4.2), and HCPA1 and proinsulin level (LOD = 3.2). A putative susceptibility locus linked to the marker D7S514 explained 56% of the total phenotypic variation in extremity skinfolds. Variation at the HCPA1 locus explained 64% of phenotypic variation in proinsulin level and {approximately}73% of phenotypic variation in split proinsulin concentration, respectively. Weaker evidence for linkage to several other obesity-related traits (e.g., waist circumference, body-mass index, fat mass by bioimpedance, etc.) was observed for a genetic location, which is {approximately}15 cM telomeric to OB. In conclusion, our study reveals that the OB region plays a significant role in determining the phenotypic variation of both insulin precursors and obesity-related traits, at least in Mexican Americans. 66 refs., 3 figs., 4 tabs.

  20. Quantitative trait loci mapping for stomatal traits in interspecific ...

    Indian Academy of Sciences (India)

    M. Sumathi

    2018-02-23

    Feb 23, 2018 ... Journal of Genetics, Vol. ... QTL analysis was carried out to identify the chromosomal regions affecting ... Keywords. linkage map; quantitative trait loci; stomata; stress ..... of India for providing financial support for the project.

  1. An empirical Bayes method for updating inferences in analysis of quantitative trait loci using information from related genome scans.

    Science.gov (United States)

    Zhang, Kui; Wiener, Howard; Beasley, Mark; George, Varghese; Amos, Christopher I; Allison, David B

    2006-08-01

    Individual genome scans for quantitative trait loci (QTL) mapping often suffer from low statistical power and imprecise estimates of QTL location and effect. This lack of precision yields large confidence intervals for QTL location, which are problematic for subsequent fine mapping and positional cloning. In prioritizing areas for follow-up after an initial genome scan and in evaluating the credibility of apparent linkage signals, investigators typically examine the results of other genome scans of the same phenotype and informally update their beliefs about which linkage signals in their scan most merit confidence and follow-up via a subjective-intuitive integration approach. A method that acknowledges the wisdom of this general paradigm but formally borrows information from other scans to increase confidence in objectivity would be a benefit. We developed an empirical Bayes analytic method to integrate information from multiple genome scans. The linkage statistic obtained from a single genome scan study is updated by incorporating statistics from other genome scans as prior information. This technique does not require that all studies have an identical marker map or a common estimated QTL effect. The updated linkage statistic can then be used for the estimation of QTL location and effect. We evaluate the performance of our method by using extensive simulations based on actual marker spacing and allele frequencies from available data. Results indicate that the empirical Bayes method can account for between-study heterogeneity, estimate the QTL location and effect more precisely, and provide narrower confidence intervals than results from any single individual study. We also compared the empirical Bayes method with a method originally developed for meta-analysis (a closely related but distinct purpose). In the face of marked heterogeneity among studies, the empirical Bayes method outperforms the comparator.

  2. Induced mutations for quantitative traits in rice

    International Nuclear Information System (INIS)

    Chakrabarti, B.N.

    1974-01-01

    The characteristics and frequency of micro-mutations induced in quantitative traits by radiation treatment and the extent of heterozygotic effects of different recessive chlorophyll-mutant-genes on quantitative trait has been presented. Mutagenic treatments increased the variance for quantitative traits in all cases although the magnitude of increase varied depending on the treatment and the selection procedure adopted. The overall superiority of the chlorophyll-mutant heterozygotes over the corresponding wild homozygotes, as noted in consecutive two seasons, was not observed when these were grown at a high level of nitrogen fertiliser. (author)

  3. Quantitative traits in wheat (Triticum aestivum L

    African Journals Online (AJOL)

    MSS

    2012-11-13

    Nov 13, 2012 ... Of the quantitative traits in wheat, spike length, number of spikes per m2, grain mass per spike, number ... design with four liming variants along with three replications, in which the experimental field .... The sampling was done.

  4. Quantitative Trait Loci for Fertility Traits in Finnish Ayrshire Cattle

    DEFF Research Database (Denmark)

    Schulman, Nina F; Sahana, Goutam; Lund, Mogens S

    2008-01-01

    A whole genome scan was carried out to detect quantitative trait loci (QTL) for fertility traits in Finnish Ayrshire cattle. The mapping population consisted of 12 bulls and 493 sons. Estimated breeding values for days open, fertility treatments, maternal calf mortality and paternal non-return rate...... combinations, which were observed significant in the regression method. Twenty-two chromosome-wise significant QTL were detected. Several of the detected QTL areas were overlapping with milk production QTL previously identified in the same population. Multi-trait QTL analyses were carried out to test...... if these effects were due to a pleiotropic QTL affecting fertility and milk yield traits or to linked QTL causing the effects. This distinction could only be made with confidence on BTA1 where a QTL affecting milk yield is linked to a pleiotropic QTL affecting days open and fertility treatments...

  5. Quantitative trait loci (QTL) mapping for inflorescence length traits in ...

    African Journals Online (AJOL)

    User

    2011-05-02

    May 2, 2011 ... character affected by ecological surroundings, growth ... developed from each F2 by bud self-pollination for QTL analysis. ... Quantitative traits measured for the each individual plant in F2 the population and F3 families ..... sex and parental interactions (Liu et al., 1996). ... evolution of solanaceous species.

  6. Quantitative trait loci for fertility traits in Finnish Ayrshire cattle

    Directory of Open Access Journals (Sweden)

    Viitala Sirja M

    2008-03-01

    Full Text Available Abstract A whole genome scan was carried out to detect quantitative trait loci (QTL for fertility traits in Finnish Ayrshire cattle. The mapping population consisted of 12 bulls and 493 sons. Estimated breeding values for days open, fertility treatments, maternal calf mortality and paternal non-return rate were used as phenotypic data. In a granddaughter design, 171 markers were typed on all 29 bovine autosomes. Associations between markers and traits were analysed by multiple marker regression. Multi-trait analyses were carried out with a variance component based approach for the chromosomes and trait combinations, which were observed significant in the regression method. Twenty-two chromosome-wise significant QTL were detected. Several of the detected QTL areas were overlapping with milk production QTL previously identified in the same population. Multi-trait QTL analyses were carried out to test if these effects were due to a pleiotropic QTL affecting fertility and milk yield traits or to linked QTL causing the effects. This distinction could only be made with confidence on BTA1 where a QTL affecting milk yield is linked to a pleiotropic QTL affecting days open and fertility treatments.

  7. Implications of central obesity-related variants in LYPLAL1, NRXN3, MSRA, and TFAP2B on quantitative metabolic traits in adult Danes.

    Directory of Open Access Journals (Sweden)

    Dorthe S Bille

    Full Text Available Two meta-analyses of genome-wide association studies (GWAS have suggested that four variants: rs2605100 in lysophospholipase-like 1 (LYPLAL1, rs10146997 in neuroxin 3 (NRXN3, rs545854 in methionine sulfoxide reductase A (MSRA, and rs987237 in transcription factor activating enhancer-binding protein 2 beta (TFAP2B associate with measures of central obesity. To elucidate potential underlying phenotypes we aimed to investigate whether these variants associated with: 1 quantitative metabolic traits, 2 anthropometric measures (waist circumference (WC, waist-hip ratio, and BMI, or 3 type 2 diabetes, and central and general overweight and obesity.The four variants were genotyped in Danish individuals using KASPar®. Quantitative metabolic traits were examined in a population-based sample (n = 6,038 and WC and BMI were furthermore analyzed in a combined study sample (n = 13,507. Case-control studies of diabetes and adiposity included 15,326 individuals. The major G-allele of LYPLAL1 rs2605100 associated with increased fasting serum triglyceride concentrations (per allele effect (β = 3%(1;5(95%CI, p(additive = 2.7×10(-3, an association driven by the male gender (p(interaction = 0.02. The same allele associated with increased fasting serum insulin concentrations (β = 3%(1;5, p(additive = 2.5×10(-3 and increased insulin resistance (HOMA-IR (β = 4%(1;6, p(additive = 1.5×10(-3. The minor G-allele of rs10146997 in NRXN3 associated with increased WC among women (β = 0.55cm (0.20;0.89, p(additive = 1.7×10(-3, p(interaction = 1.0×10(-3, but showed no associations with obesity related metabolic traits. The MSRA rs545854 and TFAP2B rs987237 showed nominal associations with central obesity; however, no underlying metabolic phenotypes became obvious, when investigating quantitative metabolic traits. None of the variants influenced the prevalence of type 2 diabetes.We demonstrate that several of the central

  8. Estimating rice yield related traits and quantitative trait loci analysis under different nitrogen treatments using a simple tower-based field phenotyping system with modified single-lens reflex cameras

    Science.gov (United States)

    Naito, Hiroki; Ogawa, Satoshi; Valencia, Milton Orlando; Mohri, Hiroki; Urano, Yutaka; Hosoi, Fumiki; Shimizu, Yo; Chavez, Alba Lucia; Ishitani, Manabu; Selvaraj, Michael Gomez; Omasa, Kenji

    2017-03-01

    Application of field based high-throughput phenotyping (FB-HTP) methods for monitoring plant performance in real field conditions has a high potential to accelerate the breeding process. In this paper, we discuss the use of a simple tower based remote sensing platform using modified single-lens reflex cameras for phenotyping yield traits in rice under different nitrogen (N) treatments over three years. This tower based phenotyping platform has the advantages of simplicity, ease and stability in terms of introduction, maintenance and continual operation under field conditions. Out of six phenological stages of rice analyzed, the flowering stage was the most useful in the estimation of yield performance under field conditions. We found a high correlation between several vegetation indices (simple ratio (SR), normalized difference vegetation index (NDVI), transformed vegetation index (TVI), corrected transformed vegetation index (CTVI), soil-adjusted vegetation index (SAVI) and modified soil-adjusted vegetation index (MSAVI)) and multiple yield traits (panicle number, grain weight and shoot biomass) across a three trials. Among all of the indices studied, SR exhibited the best performance in regards to the estimation of grain weight (R2 = 0.80). Under our tower-based field phenotyping system (TBFPS), we identified quantitative trait loci (QTL) for yield related traits using a mapping population of chromosome segment substitution lines (CSSLs) and a single nucleotide polymorphism data set. Our findings suggest the TBFPS can be useful for the estimation of yield performance during early crop development. This can be a major opportunity for rice breeders whom desire high throughput phenotypic selection for yield performance traits.

  9. A Quantitative Genomic Approach for Analysis of Fitness and Stress Related Traits in a Drosophila melanogaster Model Population

    Directory of Open Access Journals (Sweden)

    Palle Duun Rohde

    2016-01-01

    Full Text Available The ability of natural populations to withstand environmental stresses relies partly on their adaptive ability. In this study, we used a subset of the Drosophila Genetic Reference Panel, a population of inbred, genome-sequenced lines derived from a natural population of Drosophila melanogaster, to investigate whether this population harbors genetic variation for a set of stress resistance and life history traits. Using a genomic approach, we found substantial genetic variation for metabolic rate, heat stress resistance, expression of a major heat shock protein, and egg-to-adult viability investigated at a benign and a higher stressful temperature. This suggests that these traits will be able to evolve. In addition, we outline an approach to conduct pathway associations based on genomic linear models, which has potential to identify adaptive genes and pathways, and therefore can be a valuable tool in conservation genomics.

  10. A Quantitative Genomic Approach for Analysis of Fitness and Stress Related Traits in a Drosophila melanogaster Model Population

    DEFF Research Database (Denmark)

    Rohde, Palle Duun; Krag, Kristian; Loeschcke, Volker

    2016-01-01

    , to investigate whether this population harbors genetic variation for a set of stress resistance and life history traits. Using a genomic approach, we found substantial genetic variation for metabolic rate, heat stress resistance, expression of a major heat shock protein, and egg-to-adult viability investigated......The ability of natural populations to withstand environmental stresses relies partly on their adaptive ability. In this study, we used a subset of the Drosophila Genetic Reference Panel, a population of inbred, genome-sequenced lines derived from a natural population of Drosophila melanogaster...... at a benign and a higher stressful temperature. This suggests that these traits will be able to evolve. In addition, we outline an approach to conduct pathway associations based on genomic linear models, which has potential to identify adaptive genes and pathways, and therefore can be a valuable tool...

  11. Multivariate analysis of quantitative traits can effectively classify rapeseed germplasm

    Directory of Open Access Journals (Sweden)

    Jankulovska Mirjana

    2014-01-01

    Full Text Available In this study, the use of different multivariate approaches to classify rapeseed genotypes based on quantitative traits has been presented. Tree regression analysis, PCA analysis and two-way cluster analysis were applied in order todescribe and understand the extent of genetic variability in spring rapeseed genotype by trait data. The traits which highly influenced seed and oil yield in rapeseed were successfully identified by the tree regression analysis. Principal predictor for both response variables was number of pods per plant (NP. NP and 1000 seed weight could help in the selection of high yielding genotypes. High values for both traits and oil content could lead to high oil yielding genotypes. These traits may serve as indirect selection criteria and can lead to improvement of seed and oil yield in rapeseed. Quantitative traits that explained most of the variability in the studied germplasm were classified using principal component analysis. In this data set, five PCs were identified, out of which the first three PCs explained 63% of the total variance. It helped in facilitating the choice of variables based on which the genotypes’ clustering could be performed. The two-way cluster analysissimultaneously clustered genotypes and quantitative traits. The final number of clusters was determined using bootstrapping technique. This approach provided clear overview on the variability of the analyzed genotypes. The genotypes that have similar performance regarding the traits included in this study can be easily detected on the heatmap. Genotypes grouped in the clusters 1 and 8 had high values for seed and oil yield, and relatively short vegetative growth duration period and those in cluster 9, combined moderate to low values for vegetative growth duration and moderate to high seed and oil yield. These genotypes should be further exploited and implemented in the rapeseed breeding program. The combined application of these multivariate methods

  12. Nonparametric functional mapping of quantitative trait loci.

    Science.gov (United States)

    Yang, Jie; Wu, Rongling; Casella, George

    2009-03-01

    Functional mapping is a useful tool for mapping quantitative trait loci (QTL) that control dynamic traits. It incorporates mathematical aspects of biological processes into the mixture model-based likelihood setting for QTL mapping, thus increasing the power of QTL detection and the precision of parameter estimation. However, in many situations there is no obvious functional form and, in such cases, this strategy will not be optimal. Here we propose to use nonparametric function estimation, typically implemented with B-splines, to estimate the underlying functional form of phenotypic trajectories, and then construct a nonparametric test to find evidence of existing QTL. Using the representation of a nonparametric regression as a mixed model, the final test statistic is a likelihood ratio test. We consider two types of genetic maps: dense maps and general maps, and the power of nonparametric functional mapping is investigated through simulation studies and demonstrated by examples.

  13. Identification of distinct quantitative trait loci associated with defence against the closely related aphids Acyrthosiphon pisum and A. kondoi in Medicago truncatula

    KAUST Repository

    Guo, Su-Min; Kamphuis, Lars G.; Gao, Ling-Ling; Klingler, John P.; Lichtenzveig, Judith; Edwards, Owain; Singh, Karam B.

    2012-01-01

    and the more resistant line Jester. The results show that PA resistance in A17 involves both antibiosis and tolerance, and that resistance is phloem based. Quantitative trait locus (QTL) analysis using a recombinant inbred line (RIL) population (n=114) from a

  14. Association of genetic variants of the incretin-related genes with quantitative traits and occurrence of type 2 diabetes in Japanese.

    Science.gov (United States)

    Enya, Mayumi; Horikawa, Yukio; Iizuka, Katsumi; Takeda, Jun

    2014-01-01

    None of the high frequency variants of the incretin-related genes has been found by genome-wide association study (GWAS) for association with occurrence of type 2 diabetes in Japanese. However, low frequency and rare and/or high frequency variants affecting glucose metabolic traits remain to be investigated. We screened all exons of the incretin-related genes ( GCG , GLP1R , DPP4 , PCSK1 , GIP , and GIPR ) in 96 patients with type 2 diabetes and investigated for association of genetic variants of these genes with quantitative metabolic traits upon test meal with 38 young healthy volunteers and with the occurrence of type 2 diabetes in Japanese subjects comprising 1303 patients with type 2 diabetes and 1014 controls. Two mutations of GIPR , p.Thr3Alafsx21 and Arg183Gln, were found only in patients with type 2 diabetes, and both of them were treated with insulin. Of ten tagSNPs, we found that risk allele C of SNP393 (rs6235) of PCSK1 was nominally associated with higher fasting insulin and HOMA-R ( P  = 0.034 and P  = 0.030), but not with proinsulin level, incretin level or BMI. The variant showed significant association with occurrence of type 2 diabetes after adjustment for age, sex, and BMI ( P  = 0.0043). Rare variants of GIPR may contribute to the development of type 2 diabetes, possibly through insulin secretory defects. Furthermore, the genetic variant of PCSK1 might influence glucose homeostasis by altered insulin resistance independently of BMI, incretin level or proinsulin conversion, and may be associated with the occurrence of type 2 diabetes in Japanese.

  15. Variance Component Quantitative Trait Locus Analysis for Body Weight Traits in Purebred Korean Native Chicken

    Directory of Open Access Journals (Sweden)

    Muhammad Cahyadi

    2016-01-01

    Full Text Available Quantitative trait locus (QTL is a particular region of the genome containing one or more genes associated with economically important quantitative traits. This study was conducted to identify QTL regions for body weight and growth traits in purebred Korean native chicken (KNC. F1 samples (n = 595 were genotyped using 127 microsatellite markers and 8 single nucleotide polymorphisms that covered 2,616.1 centi Morgan (cM of map length for 26 autosomal linkage groups. Body weight traits were measured every 2 weeks from hatch to 20 weeks of age. Weight of half carcass was also collected together with growth rate. A multipoint variance component linkage approach was used to identify QTLs for the body weight traits. Two significant QTLs for growth were identified on chicken chromosome 3 (GGA3 for growth 16 to18 weeks (logarithm of the odds [LOD] = 3.24, Nominal p value = 0.0001 and GGA4 for growth 6 to 8 weeks (LOD = 2.88, Nominal p value = 0.0003. Additionally, one significant QTL and three suggestive QTLs were detected for body weight traits in KNC; significant QTL for body weight at 4 weeks (LOD = 2.52, nominal p value = 0.0007 and suggestive QTL for 8 weeks (LOD = 1.96, Nominal p value = 0.0027 were detected on GGA4; QTLs were also detected for two different body weight traits: body weight at 16 weeks on GGA3 and body weight at 18 weeks on GGA19. Additionally, two suggestive QTLs for carcass weight were detected at 0 and 70 cM on GGA19. In conclusion, the current study identified several significant and suggestive QTLs that affect growth related traits in a unique resource pedigree in purebred KNC. This information will contribute to improving the body weight traits in native chicken breeds, especially for the Asian native chicken breeds.

  16. Quantile-Based Permutation Thresholds for Quantitative Trait Loci Hotspots

    NARCIS (Netherlands)

    Neto, Elias Chaibub; Keller, Mark P.; Broman, Andrew F.; Attie, Alan D.; Jansen, Ritsert C.; Broman, Karl W.; Yandell, Brian S.; Borevitz, J.

    Quantitative trait loci (QTL) hotspots (genomic locations affecting many traits) are a common feature in genetical genomics studies and are biologically interesting since they may harbor critical regulators. Therefore, statistical procedures to assess the significance of hotspots are of key

  17. The IBO germination quantitative trait locus encodes a phosphatase 2C-related variant with a nonsynonymous amino acid change that interferes with abscisic acid signaling.

    Science.gov (United States)

    Amiguet-Vercher, Amélia; Santuari, Luca; Gonzalez-Guzman, Miguel; Depuydt, Stephen; Rodriguez, Pedro L; Hardtke, Christian S

    2015-02-01

    Natural genetic variation is crucial for adaptability of plants to different environments. Seed dormancy prevents precocious germination in unsuitable conditions and is an adaptation to a major macro-environmental parameter, the seasonal variation in temperature and day length. Here we report the isolation of IBO, a quantitative trait locus (QTL) that governs c. 30% of germination rate variance in an Arabidopsis recombinant inbred line (RIL) population derived from the parental accessions Eilenburg-0 (Eil-0) and Loch Ness-0 (Lc-0). IBO encodes an uncharacterized phosphatase 2C-related protein, but neither the Eil-0 nor the Lc-0 variant, which differ in a single amino acid, have any appreciable phosphatase activity in in vitro assays. However, we found that the amino acid change in the Lc-0 variant of the IBO protein confers reduced germination rate. Moreover, unlike the Eil-0 variant of the protein, the Lc-0 variant can interfere with the activity of the phosphatase 2C ABSCISIC ACID INSENSITIVE 1 in vitro. This suggests that the Lc-0 variant possibly interferes with abscisic acid signaling, a notion that is supported by physiological assays. Thus, we isolated an example of a QTL allele with a nonsynonymous amino acid change that might mediate local adaptation of seed germination timing. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  18. Quantitative genetic analysis of anxiety trait in bipolar disorder.

    Science.gov (United States)

    Contreras, J; Hare, E; Chavarría, G; Raventós, H

    2018-01-01

    Bipolar disorder type I (BPI) affects approximately 1% of the world population. Although genetic influences on bipolar disorder are well established, identification of genes that predispose to the illness has been difficult. Most genetic studies are based on categorical diagnosis. One strategy to overcome this obstacle is the use of quantitative endophenotypes, as has been done for other medical disorders. We studied 619 individuals, 568 participants from 61 extended families and 51 unrelated healthy controls. The sample was 55% female and had a mean age of 43.25 (SD 13.90; range 18-78). Heritability and genetic correlation of the trait scale from the Anxiety State and Trait Inventory (STAI) was computed by using the general linear model (SOLAR package software). we observed that anxiety trait meets the following criteria for an endophenotype of bipolar disorder type I (BPI): 1) association with BPI (individuals with BPI showed the highest trait score (F = 15.20 [5,24], p = 0.009), 2) state-independence confirmed after conducting a test-retest in 321 subjects, 3) co-segregation within families 4) heritability of 0.70 (SE: 0.060), p = 2.33 × 10 -14 and 5) genetic correlation with BPI was 0.20, (SE = 0.17, p = 3.12 × 10 -5 ). Confounding factors such as comorbid disorders and pharmacological treatment could affect the clinical relationship between BPI and anxiety trait. Further research is needed to evaluate if anxiety traits are specially related to BPI in comparison with other traits such as anger, attention or response inhibition deficit, pathological impulsivity or low self-directedness. Anxiety trait is a heritable phenotype that follows a normal distribution when measured not only in subjects with BPI but also in unrelated healthy controls. It could be used as an endophenotype in BPI for the identification of genomic regions with susceptibility genes for this disorder. Published by Elsevier B.V.

  19. Effects of normalization on quantitative traits in association test

    Science.gov (United States)

    2009-01-01

    Background Quantitative trait loci analysis assumes that the trait is normally distributed. In reality, this is often not observed and one strategy is to transform the trait. However, it is not clear how much normality is required and which transformation works best in association studies. Results We performed simulations on four types of common quantitative traits to evaluate the effects of normalization using the logarithm, Box-Cox, and rank-based transformations. The impact of sample size and genetic effects on normalization is also investigated. Our results show that rank-based transformation gives generally the best and consistent performance in identifying the causal polymorphism and ranking it highly in association tests, with a slight increase in false positive rate. Conclusion For small sample size or genetic effects, the improvement in sensitivity for rank transformation outweighs the slight increase in false positive rate. However, for large sample size and genetic effects, normalization may not be necessary since the increase in sensitivity is relatively modest. PMID:20003414

  20. Effects of normalization on quantitative traits in association test

    Directory of Open Access Journals (Sweden)

    Yap Von Bing

    2009-12-01

    Full Text Available Abstract Background Quantitative trait loci analysis assumes that the trait is normally distributed. In reality, this is often not observed and one strategy is to transform the trait. However, it is not clear how much normality is required and which transformation works best in association studies. Results We performed simulations on four types of common quantitative traits to evaluate the effects of normalization using the logarithm, Box-Cox, and rank-based transformations. The impact of sample size and genetic effects on normalization is also investigated. Our results show that rank-based transformation gives generally the best and consistent performance in identifying the causal polymorphism and ranking it highly in association tests, with a slight increase in false positive rate. Conclusion For small sample size or genetic effects, the improvement in sensitivity for rank transformation outweighs the slight increase in false positive rate. However, for large sample size and genetic effects, normalization may not be necessary since the increase in sensitivity is relatively modest.

  1. Major Quantitative Trait Loci and Putative Candidate Genes for Powdery Mildew Resistance and Fruit-Related Traits Revealed by an Intraspecific Genetic Map for Watermelon (Citrullus lanatus var. lanatus)

    Science.gov (United States)

    Kim, Kwang-Hwan; Hwang, Ji-Hyun; Han, Dong-Yeup; Park, Minkyu; Kim, Seungill; Choi, Doil; Kim, Yongjae; Lee, Gung Pyo; Kim, Sun-Tae; Park, Young-Hoon

    2015-01-01

    An intraspecific genetic map for watermelon was constructed using an F2 population derived from ‘Arka Manik’ × ‘TS34’ and transcript sequence variants and quantitative trait loci (QTL) for resistance to powdery mildew (PMR), seed size (SS), and fruit shape (FS) were analyzed. The map consists of 14 linkage groups (LGs) defined by 174 cleaved amplified polymorphic sequences (CAPS), 2 derived-cleaved amplified polymorphic sequence markers, 20 sequence-characterized amplified regions, and 8 expressed sequence tag-simple sequence repeat markers spanning 1,404.3 cM, with a mean marker interval of 6.9 cM and an average of 14.6 markers per LG. Genetic inheritance and QTL analyses indicated that each of the PMR, SS, and FS traits is controlled by an incompletely dominant effect of major QTLs designated as pmr2.1, ss2.1, and fsi3.1, respectively. The pmr2.1, detected on chromosome 2 (Chr02), explained 80.0% of the phenotypic variation (LOD = 30.76). This QTL was flanked by two CAPS markers, wsb2-24 (4.00 cM) and wsb2-39 (13.97 cM). The ss2.1, located close to pmr2.1 and CAPS marker wsb2-13 (1.00 cM) on Chr02, explained 92.3% of the phenotypic variation (LOD = 68.78). The fsi3.1, detected on Chr03, explained 79.7% of the phenotypic variation (LOD = 31.37) and was flanked by two CAPS, wsb3-24 (1.91 cM) and wsb3-9 (7.00 cM). Candidate gene-based CAPS markers were developed from the disease resistance and fruit shape gene homologs located on Chr.02 and Chr03 and were mapped on the intraspecific map. Colocalization of these markers with the major QTLs indicated that watermelon orthologs of a nucleotide-binding site-leucine-rich repeat class gene containing an RPW8 domain and a member of SUN containing the IQ67 domain are candidate genes for pmr2.1 and fsi3.1, respectively. The results presented herein provide useful information for marker-assisted breeding and gene cloning for PMR and fruit-related traits. PMID:26700647

  2. Major Quantitative Trait Loci and Putative Candidate Genes for Powdery Mildew Resistance and Fruit-Related Traits Revealed by an Intraspecific Genetic Map for Watermelon (Citrullus lanatus var. lanatus).

    Science.gov (United States)

    Kim, Kwang-Hwan; Hwang, Ji-Hyun; Han, Dong-Yeup; Park, Minkyu; Kim, Seungill; Choi, Doil; Kim, Yongjae; Lee, Gung Pyo; Kim, Sun-Tae; Park, Young-Hoon

    2015-01-01

    An intraspecific genetic map for watermelon was constructed using an F2 population derived from 'Arka Manik' × 'TS34' and transcript sequence variants and quantitative trait loci (QTL) for resistance to powdery mildew (PMR), seed size (SS), and fruit shape (FS) were analyzed. The map consists of 14 linkage groups (LGs) defined by 174 cleaved amplified polymorphic sequences (CAPS), 2 derived-cleaved amplified polymorphic sequence markers, 20 sequence-characterized amplified regions, and 8 expressed sequence tag-simple sequence repeat markers spanning 1,404.3 cM, with a mean marker interval of 6.9 cM and an average of 14.6 markers per LG. Genetic inheritance and QTL analyses indicated that each of the PMR, SS, and FS traits is controlled by an incompletely dominant effect of major QTLs designated as pmr2.1, ss2.1, and fsi3.1, respectively. The pmr2.1, detected on chromosome 2 (Chr02), explained 80.0% of the phenotypic variation (LOD = 30.76). This QTL was flanked by two CAPS markers, wsb2-24 (4.00 cM) and wsb2-39 (13.97 cM). The ss2.1, located close to pmr2.1 and CAPS marker wsb2-13 (1.00 cM) on Chr02, explained 92.3% of the phenotypic variation (LOD = 68.78). The fsi3.1, detected on Chr03, explained 79.7% of the phenotypic variation (LOD = 31.37) and was flanked by two CAPS, wsb3-24 (1.91 cM) and wsb3-9 (7.00 cM). Candidate gene-based CAPS markers were developed from the disease resistance and fruit shape gene homologs located on Chr.02 and Chr03 and were mapped on the intraspecific map. Colocalization of these markers with the major QTLs indicated that watermelon orthologs of a nucleotide-binding site-leucine-rich repeat class gene containing an RPW8 domain and a member of SUN containing the IQ67 domain are candidate genes for pmr2.1 and fsi3.1, respectively. The results presented herein provide useful information for marker-assisted breeding and gene cloning for PMR and fruit-related traits.

  3. Unraveling possible association between quantitative trait loci (QTL ...

    African Journals Online (AJOL)

    Unraveling possible association between quantitative trait loci (QTL) for partial resistance and nonhost resistance in food barley ( Hordeum vulgaris L.) ... Abstract. Many quantitative trait loci (QTLs) in different barley populations were discovered for resistance to Puccinia hordei and heterologous rust species. Partial ...

  4. Identification of distinct quantitative trait loci associated with defence against the closely related aphids Acyrthosiphon pisum and A. kondoi in Medicago truncatula

    KAUST Repository

    Guo, Su-Min

    2012-03-21

    Aphids are a major family of plant insect pests. Medicago truncatula and Acyrthosiphon pisum (pea aphid, PA) are model species with a suite of resources available to help dissect the mechanism underlying plant-aphid interactions. A previous study focused on monogenic and relatively strong resistance in M. truncatula to PA and other aphid species. In this study a moderate resistance to PA was characterized in detail in the M. truncatula line A17 and compared with the highly susceptible line A20 and the more resistant line Jester. The results show that PA resistance in A17 involves both antibiosis and tolerance, and that resistance is phloem based. Quantitative trait locus (QTL) analysis using a recombinant inbred line (RIL) population (n=114) from a cross between A17 and A20 revealed that one locus, which co-segregated with AIN (Acyrthosiphon-induced necrosis) on chromosome 3, is responsible for the reduction of aphid biomass (indicator of antibiosis) for both PA and bluegreen aphid (BGA, A. kondoi), albeit to a lesser degree for PA than BGA. Interestingly, two independent loci on chromosomes 5 and 3 were identified for the plant biomass reduction (indicator of plant tolerance) by PA and BGA, respectively, demonstrating that the plant\\'s tolerance response to these two closely related aphid species is distinct. Together with previously identified major resistant (R) genes, the QTLs identified in this study are powerful tools to understand fully the spectrum of plant defence against sap-sucking insects and provide opportunities for breeders to generate effective and sustainable strategies for aphid control. 2012 The Author.

  5. Studies of variations of the cyclin-dependent kinase inhibitor 1C and the cyclin-dependent kinase 4 genes in relation to type 2 diabetes mellitus and related quantitative traits

    DEFF Research Database (Denmark)

    Nielsen, Eva-Maria D; Hansen, Lars; Stissing, Trine

    2005-01-01

    diabetes or changes in related quantitative phenotypes among glucose-tolerant subjects. Mutation analyses of the two genes in 62 type 2 diabetic patients resulted in the discovery of seven variants of CDKN1C and two variants of CDK4. In a case-control study comprising 717 type 2 diabetic patients and 518...... glucose-tolerant subjects the most frequent variants did not show any difference in allele frequencies between the type 2 diabetic patients and the control subjects. However, in two genotype-quantitative trait correlation studies involving 206 glucose-tolerant offspring of type 2 diabetic patients and 359...... in the pathogenesis of the Beckwith-Wiedemann syndrome, a disorder characterized by neonatal hyperinsulinaemic hypoglycaemia and pre- and post-natal overgrowth. The aim of this study was to investigate if variations in the proximal promoter and the coding region of the CDKN1C and CDK4 genes are associated with type 2...

  6. Quantitative trait loci analysis of osteocondrosis traits in the elbow joint of pigs

    DEFF Research Database (Denmark)

    Christensen, O F; Busch, M E; Gregersen, V R

    2010-01-01

    Osteochondrosis is a growth disorder in the cartilage of young animals and is characterised by lesions found in the cartilage and bone. This study identified quantitative trait loci (QTLs) associated with six osteochondrosis lesion traits in the elbow joint of finishing pigs. The traits were: thi...

  7. Quantitative trait loci (QTL mapping for growth traits on bovine chromosome 14

    Directory of Open Access Journals (Sweden)

    Marcelo Miyata

    2007-03-01

    Full Text Available Quantitative trait loci (QTL mapping in livestock allows the identification of genes that determine the genetic variation affecting traits of economic interest. We analyzed the birth weight and weight at 60 days QTL segregating on bovine chromosome BTA14 in a F2 resource population using genotypes produced from seven microsatellite markers. Phenotypes were derived from 346 F2 progeny produced from crossing Bos indicus Gyr x Holstein Bos taurus F1 parents. Interval analysis to detect QTL for birth weight revealed the presence of a QTL (p < 0.05 at 1 centimorgan (cM from the centromere with an additive effect of 1.210 ± 0.438 kg. Interval analysis for weight at 60 days revealed the presence of a QTL (p < 0.05 at 0 cM from the centromere with an additive effect of 2.122 ± 0.735 kg. The region to which the QTL were assigned is described in the literature as responsible for some growth traits, milk yield, milk composition, fat deposition and has also been related to reproductive traits such as daughter pregnancy rate and ovulation rate. The effects of the QTL described on other traits were not investigated.

  8. Quantitative trait loci mapping for stomatal traits in interspecific ...

    Indian Academy of Sciences (India)

    Dr.YASODHA

    seedling raising, field planting and maintenance of the mapping population. ... tereticornis and production of interspecific hybrids displaying hybrid vigour in terms of .... A total of 114, 115 and 129 SSR, ISSR and SRAP markers were generated .... stomatal traits with yield and adaptability would help to improve productivity of ...

  9. Quantitative trait loci analysis of swine meat quality traits

    DEFF Research Database (Denmark)

    Li, H D; Lund, M S; Christensen, O F

    2010-01-01

    loss, and the Minolta color measurements L*, a*, and b* representing meat lightness, redness, and yellowness, respectively. The families consist of 3,883 progenies of 12 Duroc boars that were evaluated to identify the QTL. The linkage map consists of 462 SNP markers on 18 porcine autosomes...... were estimated from a posterior distribution of the QTL position. In total, 31 QTL for the 6 meat quality traits were found to be significant at the 5% chromosome-wide level, among which 11 QTL were significant at the 5% genome-wide level and 5 of these were significant at the 0.1% genome-wide level...... will be helpful for fine mapping and identifying genes affecting meat quality traits, and tightly linked markers may be incorporated into marker-assisted selection programs...

  10. Mapping of quantitative trait loci controlling Orobanche foetida Poir ...

    African Journals Online (AJOL)

    Mapping of quantitative trait loci controlling Orobanche foetida Poir. resistance in faba bean (Vicia faba L.) R Díaz-Ruiz, A Torres, MV Gutierrez, D Rubiales, JI Cubero, M Kharrat, Z Satovic, B Román ...

  11. Implications of central obesity-related variants in LYPLAL1, NRXN3, MSRA, and TFAP2B on quantitative metabolic traits in adult Danes

    DEFF Research Database (Denmark)

    Bille, Dorthe S; Banasik, Karina; Justesen, Johanne M

    2011-01-01

    Background Two meta-analyses of genome-wide association studies (GWAS) have suggested that four variants: rs2605100 in lysophospholipase-like 1 (LYPLAL1), rs10146997 in neuroxin 3 (NRXN3), rs545854 in methionine sulfoxide reductase A (MSRA), and rs987237 in transcription factor activating enhancer...... diabetes, and central and general overweight and obesity. Methodology/Principal Findings The four variants were genotyped in Danish individuals using KASPar®. Quantitative metabolic traits were examined in a population-based sample (n = 6,038) and WC and BMI were furthermore analyzed in a combined study...... sample (n = 13,507). Case-control studies of diabetes and adiposity included 15,326 individuals. The major G-allele of LYPLAL1 rs2605100 associated with increased fasting serum triglyceride concentrations (per allele effect (ß) = 3%(1;5(95%CI)), padditive = 2.7×10-3), an association driven by the male...

  12. High-resolution mapping of a fruit firmness-related quantitative trait locus in tomato reveals epistatic interactions associated with a complex combinatorial locus.

    Science.gov (United States)

    Chapman, Natalie H; Bonnet, Julien; Grivet, Laurent; Lynn, James; Graham, Neil; Smith, Rebecca; Sun, Guiping; Walley, Peter G; Poole, Mervin; Causse, Mathilde; King, Graham J; Baxter, Charles; Seymour, Graham B

    2012-08-01

    Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Fir(s.p.)QTL2.1 to Fir(s.p.)QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Fir(s.p.)QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Fir(s.p.)QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus.

  13. Association of genetic variants of the incretin-related genes with quantitative traits and occurrence of type 2 diabetes in Japanese

    OpenAIRE

    Mayumi Enya; Yukio Horikawa; Katsumi Iizuka; Jun Takeda

    2014-01-01

    Background: None of the high frequency variants of the incretin-related genes has been found by genome-wide association study (GWAS) for association with occurrence of type 2 diabetes in Japanese. However, low frequency and rare and/or high frequency variants affecting glucose metabolic traits remain to be investigated. Method: We screened all exons of the incretin-related genes (GCG, GLP1R, DPP4, PCSK1, GIP, and GIPR) in 96 patients with type 2 diabetes and investigated for association of...

  14. Quantitative trait loci at the 11q23.3 chromosomal region related to dyslipidemia in the population of Andhra Pradesh, India.

    Science.gov (United States)

    Pranavchand, Rayabarapu; Reddy, Battini Mohan

    2017-06-13

    Given the characteristic atherogenic dyslipidemia of south Indian population and crucial role of APOA1, APOC3, APOA4 and APOA5 genes clustered in 11q23.3 chromosomal region in regulating lipoprotein metabolism and cholesterol homeostasis, a large number of recently identified variants are to be explored for their role in regulating the serum lipid parameters among south Indians. Using fluidigm SNP genotyping platform, a prioritized set of 96 SNPs of the 11q23.3 chromosomal region were genotyped on 516 individuals from Hyderabad, India, and its vicinity and aged >45 years. The linear regression analysis of the individual lipid traits viz., TC, LDLC, HDLC, VLDL and TG with each of the 78 SNPs that confirm to HWE and with minor allele frequency > 1%, suggests 23 of those to be significantly associated (p ≤ 0.05) with at least one of these quantitative traits. Most importantly, the variant rs632153 is involved in elevating TC, LDLC, TG and VLDLs and probably playing a crucial role in the manifestation of dyslipidemia. Additionally, another three SNPs rs633389, rs2187126 and rs1263163 are found risk conferring to dyslipidemia by elevating LDLC and TC levels in the present population. Further, the ROC (receiver operating curve) analysis for the risk scores and dyslipidemia status yielded a significant area under curve (AUC) = 0.675, suggesting high discriminative power of the risk variants towards the condition. The interaction analysis suggests rs10488699-rs2187126 pair of the BUD13 gene to confer significant risk (Interaction odds ratio = 14.38, P = 7.17 × 10 5 ) towards dyslipidemia by elevating the TC levels (β = 37.13, p = 6.614 × 10 5 ). On the other hand, the interaction between variants of APOA1 gene and BUD13 and/or ZPR1 regulatory genes at this region are associated with elevated TG and VLDL. The variants at 11q23.3 chromosomal region seem to determine the quantitative lipid traits and in turn dyslipidemia in the population of Hyderabad

  15. Quantitative trait loci associated with seed and seedling traits in Lactuca.

    Science.gov (United States)

    Argyris, Jason; Truco, María José; Ochoa, Oswaldo; Knapp, Steven J; Still, David W; Lenssen, Ger M; Schut, Johan W; Michelmore, Richard W; Bradford, Kent J

    2005-11-01

    Seed and seedling traits related to germination and stand establishment are important in the production of cultivated lettuce (Lactuca sativa L.). Six seed and seedling traits segregating in a L. sativa cv. Salinas x L. serriola recombinant inbred line population consisting of 103 F8 families revealed a total of 17 significant quantitative trait loci (QTL) resulting from three seed production environments. Significant QTL were identified for germination in darkness, germination at 25 and 35 degrees C, median maximum temperature of germination, hypocotyl length at 72 h post-imbibition, and plant (seedling) quality. Some QTL for germination and early seedling growth characteristics were co-located, suggestive of pleiotropic loci regulating these traits. A single QTL (Htg6.1) described 25 and 23% of the total phenotypic variation for high temperature germination in California- and Netherlands-grown populations, respectively, and was significant between 33 and 37 degrees C. Additionally, Htg6.1 showed significant epistatic interactions with other Htg QTL and a consistent effect across all the three seed production environments. L. serriola alleles increased germination at these QTL. The estimate of narrow-sense heritability (h2) of Htg6.1 was 0.84, indicating potential for L. serriola as a source of germination thermotolerance for lettuce introgression programs.

  16. Genome-Wide Mapping of Growth-Related Quantitative Trait Loci in Orange-Spotted Grouper (Epinephelus coioides) Using Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq).

    Science.gov (United States)

    Yu, Hui; You, Xinxin; Li, Jia; Liu, Hankui; Meng, Zining; Xiao, Ling; Zhang, Haifa; Lin, Hao-Ran; Zhang, Yong; Shi, Qiong

    2016-04-06

    Mapping of quantitative trait loci (QTL) is essential for the discovery of genetic structures that related to complex quantitative traits. In this study, we identified 264,072 raw SNPs (single-nucleotide polymorphisms) by double digest restriction site associated DNA sequencing (ddRADseq), and utilized 3029 of these SNPs to construct a genetic linkage map in orange-spotted grouper (Epinephelus coioides) using a regression mapping algorithm. The genetic map contained 24 linkage groups (LGs) spanning a total genetic distance of 1231.98 cM. Twenty-seven significant growth-related QTLs were identified. Furthermore, we identified 17 genes (fez2, alg3, ece2, arvcf, sla27a4, sgk223, camk2, prrc2b, mchr1, sardh, pappa, syk, tert, wdrcp91, ftz-f1, mate1 and notch1) including three (tert, ftz-f1 and notch1) that have been reported to be involved in fish growth. To summarize, we mapped growth-related QTLs in the orange-spotted grouper. These QTLs will be useful in marker-assisted selection (MAS) efforts to improve growth-related traits in this economically important fish.

  17. Quantitative trait loci for milk production and functional traits in two Danish Cattle breeds

    DEFF Research Database (Denmark)

    Mai, M D; Rychtarova, J; Zink, V

    2010-01-01

    Quantitative trait loci (QTL) in Danish Jersey and Danish Red cattle were independently mapped by least squares regression analysis. For Jersey breed, five grandsire families were genotyped for 186 markers on 16 chromosomes (BTAs). Eight traits analysed were milk yield (MY), fat percentage (FP), ...

  18. Whole genome scan in chickens for quantitative trait loci affecting carcass traits

    NARCIS (Netherlands)

    Kaam, van J.B.C.H.M.; Groenen, M.A.M.; Bovenhuis, H.; Veenendaal, A.; Vereijken, A.L.J.; Arendonk, van J.A.M.

    1999-01-01

    An experiment was conducted to enable quantitative trait loci (QTL) mapping for carcass traits. The population consisted of 10 full-sib families originating from a cross between male and female founders chosen from two different outcross broiler lines. Founder animals, parents, offspring, and

  19. Statistical mechanics and the evolution of polygenic quantitative traits

    NARCIS (Netherlands)

    Barton, N.H.; De Vladar, H.P.

    The evolution of quantitative characters depends on the frequencies of the alleles involved, yet these frequencies cannot usually be measured. Previous groups have proposed an approximation to the dynamics of quantitative traits, based on an analogy with statistical mechanics. We present a modified

  20. Marker-assisted selection for quantitative traits

    Directory of Open Access Journals (Sweden)

    Ivan Schuster

    2011-01-01

    Full Text Available Although thousands of scientific articles have been published on the subject of marker-assisted selection (MAS andquantitative trait loci (QTL, the application of MAS for QTL in plant breeding has been restricted. Among the main causes for thislimited use are the low accuracy of QTL mapping and the high costs of genotyping thousands of plants with tens or hundreds ofmolecular markers in routine breeding programs. Recently, new large-scale genotyping technologies have resulted in a costreduction. Nevertheless, the MAS for QTL has so far been limited to selection programs using several generations per year, wherephenotypic selection cannot be performed in all generations, mainly in recurrent selection programs. Methods of MAS for QTL inbreeding programs using self-pollination have been developed.

  1. Studies of a genetic variant in HK1 in relation to quantitative metabolic traits and to the prevalence of type 2 diabetes

    Directory of Open Access Journals (Sweden)

    Bonnefond Amélie

    2011-07-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs within the gene encoding Hexokinase 1 (HK1 are associated with changes in glycated haemoglobin (HbA1c levels. Our aim was to investigate the effect of HK1 rs7072268 on measures of glucose- and lipid-metabolism in a Danish non-diabetic population and combine the outcome of these analyses in a meta-analysis with previously published results. Furthermore, our aim was to perform a type 2 diabetes case-control analysis and meta-analysis with two previous case-control studies. Methods SNP rs7072268 was genotyped in 9,724 Danes. The quantitative trait study included 5,604 non-diabetic individuals from the Inter99 cohort. The case-control study included 4,449 glucose tolerant individuals and 3,398 patients with type 2 diabetes. Meta-analyses on quantitative traits included 24,560 Caucasian individuals and 30,802 individuals were included in the combined analysis of present and previous type 2 diabetes case-control studies. Results Using an additive model, we confirmed that the T-allele of rs7072268 associates with increased HbA1c of 0.6% (CI: 0.4 - 0.9, p = 3*10-7 per allele. The same allele associated with an increased area under the curve (AUC for glucose of 5.0 mmol/l*min (0.1 - 10.0, p = 0.045 following an oral glucose tolerance test (OGTT and increased fasting levels of cholesterol of 0.06 mmol/l (0.03 - 1.0, p = 0.001 and triglycerides of 2.0% (0.2 - 3.8, p = 0.03 per allele in the same study sample of non-diabetic individuals from the Inter99 cohort. However, the T-allele did not show any association with estimates of insulin release or insulin sensitivity neither in Inter99 nor in combined analyses. The prevalence of type 2 diabetes was increased among carriers of the rs7072268 T-allele both in the Danish study-population with an OR of 1.11 (1.02-1.21 and in a meta-analysis including the two additional sample sets with an OR of 1.06 (1.02-1.11. However, after Bonferroni correction the T

  2. Evidences of local adaptation in quantitative traits in Prosopis alba (Leguminosae).

    Science.gov (United States)

    Bessega, C; Pometti, C; Ewens, M; Saidman, B O; Vilardi, J C

    2015-02-01

    Signals of selection on quantitative traits can be detected by the comparison between the genetic differentiation of molecular (neutral) markers and quantitative traits, by multivariate extensions of the same model and by the observation of the additive covariance among relatives. We studied, by three different tests, signals of occurrence of selection in Prosopis alba populations over 15 quantitative traits: three economically important life history traits: height, basal diameter and biomass, 11 leaf morphology traits that may be related with heat-tolerance and physiological responses and spine length that is very important from silvicultural purposes. We analyzed 172 G1-generation trees growing in a common garden belonging to 32 open pollinated families from eight sampling sites in Argentina. The multivariate phenotypes differ significantly among origins, and the highest differentiation corresponded to foliar traits. Molecular genetic markers (SSR) exhibited significant differentiation and allowed us to provide convincing evidence that natural selection is responsible for the patterns of morphological differentiation. The heterogeneous selection over phenotypic traits observed suggested different optima in each population and has important implications for gene resource management. The results suggest that the adaptive significance of traits should be considered together with population provenance in breeding program as a crucial point prior to any selecting program, especially in Prosopis where the first steps are under development.

  3. Quantitative Trait Loci Associated with Drought Tolerance in Brachypodium distachyon

    Directory of Open Access Journals (Sweden)

    Yiwei Jiang

    2017-05-01

    Full Text Available The temperate wild grass Brachypodium distachyon (Brachypodium serves as model system for studying turf and forage grasses. Brachypodium collections show diverse responses to drought stress, but little is known about the genetic mechanisms of drought tolerance of this species. The objective of this study was to identify quantitative trait loci (QTLs associated with drought tolerance traits in Brachypodium. We assessed leaf fresh weight (LFW, leaf dry weight (LDW, leaf water content (LWC, leaf wilting (WT, and chlorophyll fluorescence (Fv/Fm under well-watered and drought conditions on a recombinant inbred line (RIL population from two parents (Bd3-1 and Bd1-1 known to differ in their drought adaptation. A linkage map of the RIL population was constructed using 467 single nucleotide polymorphism (SNP markers obtained from genotyping-by-sequencing. The Bd3-1/Bd1-1 map spanned 1,618 cM and had an average distance of 3.5 cM between adjacent single nucleotide polymorphisms (SNPs. Twenty-six QTLs were identified in chromosome 1, 2, and 3 in two experiments, with 14 of the QTLs under well-watered conditions and 12 QTLs under drought stress. In Experiment 1, a QTL located on chromosome 2 with a peak at 182 cM appeared to simultaneously control WT, LWC, and Fv/Fm under drought stress, accounting for 11–18.7% of the phenotypic variation. Allelic diversity of candidate genes DREB2B, MYB, and SPK, which reside in one multi-QTL region, may play a role in the natural variation in whole plant drought tolerance in Brachypodium. Co-localization of QTLs for multiple drought-related traits suggest that the gene(s involved are important regulators of drought tolerance in Brachypodium.

  4. Quantitative trait loci for yield and morphological traits in maize under drought stress

    Directory of Open Access Journals (Sweden)

    Nikolić Ana

    2011-01-01

    Full Text Available Drought is one of the most important factors contributing to crop yield loss. In order to develop maize varieties with drought tolerance, it is necessary to explore the genetic basis. Mapping quantitative trait loci (QTL that control the yield and associate agronomic traits is one way of understanding drought genetics. QTLs associated with grain yield (GY, leaf width (LW3, LW4 plant height (PH, ear height (EH, leaf number (NL, tassel branch number (TBN and tassel length (TL were studied with composite interval mapping. A total of 43 QTLs were detected, distributed on all chromosomes, except chromosome 9. Phenotypic variability determined for the identified QTLs for all the traits was in the range from 20.99 to 87.24%. Mapping analysis identified genomic regions associated with two traits in a manner that was consistent with phenotypic correlation among traits, supporting either pleiotropy or tight linkage among QTLs.

  5. Two-part zero-inflated negative binomial regression model for quantitative trait loci mapping with count trait.

    Science.gov (United States)

    Moghimbeigi, Abbas

    2015-05-07

    Poisson regression models provide a standard framework for quantitative trait locus (QTL) mapping of count traits. In practice, however, count traits are often over-dispersed relative to the Poisson distribution. In these situations, the zero-inflated Poisson (ZIP), zero-inflated generalized Poisson (ZIGP) and zero-inflated negative binomial (ZINB) regression may be useful for QTL mapping of count traits. Added genetic variables to the negative binomial part equation, may also affect extra zero data. In this study, to overcome these challenges, I apply two-part ZINB model. The EM algorithm with Newton-Raphson method in the M-step uses for estimating parameters. An application of the two-part ZINB model for QTL mapping is considered to detect associations between the formation of gallstone and the genotype of markers. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Statistical equivalent of the classical TDT for quantitative traits and ...

    Indian Academy of Sciences (India)

    sion model to test the association for quantitative traits based on a trio design. We show that the method ... from the analyses and only one transmission is considered. Keywords. .... use the sample mean or median of Y, as an estimator of c in.

  7. Genomic value prediction for quantitative traits under the epistatic model

    Directory of Open Access Journals (Sweden)

    Xu Shizhong

    2011-01-01

    Full Text Available Abstract Background Most quantitative traits are controlled by multiple quantitative trait loci (QTL. The contribution of each locus may be negligible but the collective contribution of all loci is usually significant. Genome selection that uses markers of the entire genome to predict the genomic values of individual plants or animals can be more efficient than selection on phenotypic values and pedigree information alone for genetic improvement. When a quantitative trait is contributed by epistatic effects, using all markers (main effects and marker pairs (epistatic effects to predict the genomic values of plants can achieve the maximum efficiency for genetic improvement. Results In this study, we created 126 recombinant inbred lines of soybean and genotyped 80 makers across the genome. We applied the genome selection technique to predict the genomic value of somatic embryo number (a quantitative trait for each line. Cross validation analysis showed that the squared correlation coefficient between the observed and predicted embryo numbers was 0.33 when only main (additive effects were used for prediction. When the interaction (epistatic effects were also included in the model, the squared correlation coefficient reached 0.78. Conclusions This study provided an excellent example for the application of genome selection to plant breeding.

  8. Quantitative trait loci associated with anthracnose resistance in sorghum

    Science.gov (United States)

    With an aim to develop a durable resistance to the fungal disease anthracnose, two unique genetic sources of resistance were selected to create genetic mapping populations to identify regions of the sorghum genome that encode anthracnose resistance. A series of quantitative trait loci were identifi...

  9. Genome Scan Detects Quantitative Trait Loci Affecting Female Fertility Traits in Danish and Swedish Holstein Cattle

    DEFF Research Database (Denmark)

    Höglund, Johanna Karolina; Guldbrandtsen, B; Su, G

    2009-01-01

    Data from the joint Nordic breeding value prediction for Danish and Swedish Holstein grandsire families were used to locate quantitative trait loci (QTL) for female fertility traits in Danish and Swedish Holstein cattle. Up to 36 Holstein grandsires with over 2,000 sons were genotyped for 416 mic...... for QTL segregating on Bos taurus chromosome (BTA)1, BTA7, BTA10, and BTA26. On each of these chromosomes, several QTL were detected affecting more than one of the fertility traits investigated in this study. Evidence for segregation of additional QTL on BTA2, BTA9, and BTA24 was found...

  10. Quantitative trait loci for udder conformation and other udder traits in Finnish Ayrshire cattle

    Directory of Open Access Journals (Sweden)

    N.F. SCHULMAN

    2008-12-01

    Full Text Available Udder traits are important due to their correlation with clinical mastitis which causes major economic losses to the dairy farms. Chromosomal areas associated with udder conformation traits, milking speed and leakage could be used in breeding programs to improve both udder traits and mastitis resistance. Quantitative trait loci (QTL mapping for udder traits was carried out on bovine chromosomes (BTA 9, 11, 14, 18, 20, 23, and 29, where earlier studies have indicated QTL for mastitis. A granddaughter design with 12 Ayrshire sire families and 360 sons was used. The sires and sons were typed for 35 markers. The traits analysed were udder depth, fore udder attachment, central ligament, distance from udder to floor, body stature, fore teat length, udder balance, rear udder height, milking speed, and leakage. Associations between markers and traits were analysed with multiple marker regression. Five genome-wise significant QTL were detected: stature on BTA14 and 23, udder balance on BTA23, rear udder height on BTA11, and central ligament on BTA23. On BTA11 and 14 the suggested QTL positions for udder traits are at the same position as previously detected QTL for mastitis and somatic cell count.;

  11. Quantile-based permutation thresholds for quantitative trait loci hotspots.

    Science.gov (United States)

    Neto, Elias Chaibub; Keller, Mark P; Broman, Andrew F; Attie, Alan D; Jansen, Ritsert C; Broman, Karl W; Yandell, Brian S

    2012-08-01

    Quantitative trait loci (QTL) hotspots (genomic locations affecting many traits) are a common feature in genetical genomics studies and are biologically interesting since they may harbor critical regulators. Therefore, statistical procedures to assess the significance of hotspots are of key importance. One approach, randomly allocating observed QTL across the genomic locations separately by trait, implicitly assumes all traits are uncorrelated. Recently, an empirical test for QTL hotspots was proposed on the basis of the number of traits that exceed a predetermined LOD value, such as the standard permutation LOD threshold. The permutation null distribution of the maximum number of traits across all genomic locations preserves the correlation structure among the phenotypes, avoiding the detection of spurious hotspots due to nongenetic correlation induced by uncontrolled environmental factors and unmeasured variables. However, by considering only the number of traits above a threshold, without accounting for the magnitude of the LOD scores, relevant information is lost. In particular, biologically interesting hotspots composed of a moderate to small number of traits with strong LOD scores may be neglected as nonsignificant. In this article we propose a quantile-based permutation approach that simultaneously accounts for the number and the LOD scores of traits within the hotspots. By considering a sliding scale of mapping thresholds, our method can assess the statistical significance of both small and large hotspots. Although the proposed approach can be applied to any type of heritable high-volume "omic" data set, we restrict our attention to expression (e)QTL analysis. We assess and compare the performances of these three methods in simulations and we illustrate how our approach can effectively assess the significance of moderate and small hotspots with strong LOD scores in a yeast expression data set.

  12. Functional mapping imprinted quantitative trait loci underlying developmental characteristics

    Directory of Open Access Journals (Sweden)

    Li Gengxin

    2008-03-01

    Full Text Available Abstract Background Genomic imprinting, a phenomenon referring to nonequivalent expression of alleles depending on their parental origins, has been widely observed in nature. It has been shown recently that the epigenetic modification of an imprinted gene can be detected through a genetic mapping approach. Such an approach is developed based on traditional quantitative trait loci (QTL mapping focusing on single trait analysis. Recent studies have shown that most imprinted genes in mammals play an important role in controlling embryonic growth and post-natal development. For a developmental character such as growth, current approach is less efficient in dissecting the dynamic genetic effect of imprinted genes during individual ontology. Results Functional mapping has been emerging as a powerful framework for mapping quantitative trait loci underlying complex traits showing developmental characteristics. To understand the genetic architecture of dynamic imprinted traits, we propose a mapping strategy by integrating the functional mapping approach with genomic imprinting. We demonstrate the approach through mapping imprinted QTL controlling growth trajectories in an inbred F2 population. The statistical behavior of the approach is shown through simulation studies, in which the parameters can be estimated with reasonable precision under different simulation scenarios. The utility of the approach is illustrated through real data analysis in an F2 family derived from LG/J and SM/J mouse stains. Three maternally imprinted QTLs are identified as regulating the growth trajectory of mouse body weight. Conclusion The functional iQTL mapping approach developed here provides a quantitative and testable framework for assessing the interplay between imprinted genes and a developmental process, and will have important implications for elucidating the genetic architecture of imprinted traits.

  13. Uncovering the Genetic Architectures of Quantitative Traits

    Directory of Open Access Journals (Sweden)

    James J. Lee

    2016-01-01

    Full Text Available The aim of a genome-wide association study (GWAS is to identify loci in the human genome affecting a phenotype of interest. This review summarizes some recent work on conceptual and methodological aspects of GWAS. The average effect of gene substitution at a given causal site in the genome is the key estimand in GWAS, and we argue for its fundamental importance. Implicit in the definition of average effect is a linear model relating genotype to phenotype. The fraction of the phenotypic variance ascribable to polymorphic sites with nonzero average effects in this linear model is called the heritability, and we describe methods for estimating this quantity from GWAS data. Finally, we show that the theory of compressed sensing can be used to provide a sharp estimate of the sample size required to identify essentially all sites contributing to the heritability of a given phenotype.

  14. Detection and characterization of quantitative trait loci for meat quality traits in pigs

    NARCIS (Netherlands)

    Koning, de D.J.; Harlizius, B.; Rattink, A.P.; Groenen, M.A.M.; Brascamp, E.W.; Arendonk, van J.A.M.

    2001-01-01

    In an experimental cross between Meishan and Dutch Large White and Landrace lines, 785 F2 animals with carcass information and their parents were typed for molecular markers covering the entire porcine genome. Linkage was studied between these markers and eight meat quality traits. Quantitative

  15. An international collaborative family-based whole genome quantitative trait linkage scan for myopic refractive error

    DEFF Research Database (Denmark)

    Abbott, Diana; Li, Yi-Ju; Guggenheim, Jeremy A

    2012-01-01

    To investigate quantitative trait loci linked to refractive error, we performed a genome-wide quantitative trait linkage analysis using single nucleotide polymorphism markers and family data from five international sites....

  16. Relating Stomatal Conductance to Leaf Functional Traits.

    Science.gov (United States)

    Kröber, Wenzel; Plath, Isa; Heklau, Heike; Bruelheide, Helge

    2015-10-12

    Leaf functional traits are important because they reflect physiological functions, such as transpiration and carbon assimilation. In particular, morphological leaf traits have the potential to summarize plants strategies in terms of water use efficiency, growth pattern and nutrient use. The leaf economics spectrum (LES) is a recognized framework in functional plant ecology and reflects a gradient of increasing specific leaf area (SLA), leaf nitrogen, phosphorus and cation content, and decreasing leaf dry matter content (LDMC) and carbon nitrogen ratio (CN). The LES describes different strategies ranging from that of short-lived leaves with high photosynthetic capacity per leaf mass to long-lived leaves with low mass-based carbon assimilation rates. However, traits that are not included in the LES might provide additional information on the species' physiology, such as those related to stomatal control. Protocols are presented for a wide range of leaf functional traits, including traits of the LES, but also traits that are independent of the LES. In particular, a new method is introduced that relates the plants' regulatory behavior in stomatal conductance to vapor pressure deficit. The resulting parameters of stomatal regulation can then be compared to the LES and other plant functional traits. The results show that functional leaf traits of the LES were also valid predictors for the parameters of stomatal regulation. For example, leaf carbon concentration was positively related to the vapor pressure deficit (vpd) at the point of inflection and the maximum of the conductance-vpd curve. However, traits that are not included in the LES added information in explaining parameters of stomatal control: the vpd at the point of inflection of the conductance-vpd curve was lower for species with higher stomatal density and higher stomatal index. Overall, stomata and vein traits were more powerful predictors for explaining stomatal regulation than traits used in the LES.

  17. Quantitative Trait Loci for Mercury Tolerance in Rice Seedlings

    Directory of Open Access Journals (Sweden)

    Chong-qing WANG

    2013-05-01

    Full Text Available Mercury (Hg is one of the most toxic heavy metals to living organisms and its conspicuous effect is the inhibition of root growth. However, little is known about the molecular genetic basis for root growth under excess Hg2+ stress. To map quantitative trait loci (QTLs in rice for Hg2+ tolerance, a population of 120 recombinant inbred lines derived from a cross between two japonica cultivars Yuefu and IRAT109 was grown in 0.5 mmol/L CaCl2 solution. Relative root length (RRL, percentage of the seminal root length in +HgCl2 to –HgCl2, was used for assessing Hg2+ tolerance. In a dose-response experiment, Yuefu had a higher RRL than IRAT109 and showed the most significant difference at the Hg2+ concentration of 1.5 μmol/L. Three putative QTLs for RRL were detected on chromosomes 1, 2 and 5, and totally explained about 35.7% of the phenotypic variance in Hg2+ tolerance. The identified QTLs for RRL might be useful for improving Hg2+ tolerance of rice by molecular marker-assisted selection.

  18. Quantitative trait loci linked to PRNP gene controlling health and production traits in INRA 401 sheep

    Directory of Open Access Journals (Sweden)

    Brunel Jean-Claude

    2007-07-01

    Full Text Available Abstract In this study, the potential association of PrP genotypes with health and productive traits was investigated. Data were recorded on animals of the INRA 401 breed from the Bourges-La Sapinière INRA experimental farm. The population consisted of 30 rams and 852 ewes, which produced 1310 lambs. The animals were categorized into three PrP genotype classes: ARR homozygous, ARR heterozygous, and animals without any ARR allele. Two analyses differing in the approach considered were carried out. Firstly, the potential association of the PrP genotype with disease (Salmonella resistance and production (wool and carcass traits was studied. The data used included 1042, 1043 and 1013 genotyped animals for the Salmonella resistance, wool and carcass traits, respectively. The different traits were analyzed using an animal model, where the PrP genotype effect was included as a fixed effect. Association analyses do not indicate any evidence of an effect of PrP genotypes on traits studied in this breed. Secondly, a quantitative trait loci (QTL detection approach using the PRNP gene as a marker was applied on ovine chromosome 13. Interval mapping was used. Evidence for one QTL affecting mean fiber diameter was found at 25 cM from the PRNP gene. However, a linkage between PRNP and this QTL does not imply unfavorable linkage disequilibrium for PRNP selection purposes.

  19. Linkage Map Construction and Quantitative Trait Locus Analysis of Agronomic and Fiber Quality Traits in Cotton

    Directory of Open Access Journals (Sweden)

    Michael A. Gore

    2014-03-01

    Full Text Available The superior fiber properties of L. serve as a source of novel variation for improving fiber quality in Upland cotton ( L., but introgression from has been largely unsuccessful due to hybrid breakdown and a lack of genetic and genomic resources. In an effort to overcome these limitations, we constructed a linkage map and conducted a quantitative trait locus (QTL analysis of 10 agronomic and fiber quality traits in a recombinant inbred mapping population derived from a cross between TM-1, an Upland cotton line, and NM24016, an elite line with stabilized introgression from . The linkage map consisted of 429 simple-sequence repeat (SSR and 412 genotyping-by-sequencing (GBS-based single-nucleotide polymorphism (SNP marker loci that covered half of the tetraploid cotton genome. Notably, the 841 marker loci were unevenly distributed among the 26 chromosomes of tetraploid cotton. The 10 traits evaluated on the TM-1 × NM24016 population in a multienvironment trial were highly heritable, and most of the fiber traits showed considerable transgressive variation. Through the QTL analysis, we identified a total of 28 QTLs associated with the 10 traits. Our study provides a novel resource that can be used by breeders and geneticists for the genetic improvement of agronomic and fiber quality traits in Upland cotton.

  20. Principal Component Analysis of Some Quantitative and Qualitative Traits in Iranian Spinach Landraces

    Directory of Open Access Journals (Sweden)

    Mohebodini Mehdi

    2017-08-01

    Full Text Available Landraces of spinach in Iran have not been sufficiently characterised for their morpho-agronomic traits. Such characterisation would be helpful in the development of new genetically improved cultivars. In this study 54 spinach accessions collected from the major spinach growing areas of Iran were evaluated to determine their phenotypic diversity profile of spinach genotypes on the basis of 10 quantitative and 9 qualitative morpho-agronomic traits. High coefficients of variation were recorded in some quantitative traits (dry yield and leaf area and all of the qualitative traits. Using principal component analysis, the first four principal components with eigen-values more than 1 contributed 87% of the variability among accessions for quantitative traits, whereas the first four principal components with eigen-values more than 0.8 contributed 79% of the variability among accessions for qualitative traits. The most important relations observed on the first two principal components were a strong positive association between leaf width and petiole length; between leaf length and leaf numbers in flowering; and among fresh yield, dry yield and petiole diameter; a near zero correlation between days to flowering with leaf width and petiole length. Prickly seeds, high percentage of female plants, smooth leaf texture, high numbers of leaves at flowering, greygreen leaves, erect petiole attitude and long petiole length are important characters for spinach breeding programmes.

  1. Inheritance of quantitative traits in opium poppy (Papaver somniferum L.

    Directory of Open Access Journals (Sweden)

    Yadav H.K.

    2011-01-01

    Full Text Available Generation mean analysis was carried out using five parameter model on five cross combinations with five generations i.e. parents, F1s, F2s, and F3s randomly selected from partial diallel breeding experiment. The aim of study was to investigate the mode of gene actions involved in the inheritance of quantitative traits viz. days to 50% flowering, plant height, leaves/plant, capsules/plant, capsule size, capsule weight/plant, seed yield/plant and opium yield/plant. C and D scaling test showed the presence of non allelic interaction in the inheritance for all the traits except for plant height, seed yield/plant (ND1001xIS13 and capsule size (NBR5xND1002 which showed non interacting mode of inheritance. In general, the interaction effect together i.e. additive x additive [i] and dominance x dominance [l] found in higher magnitude than the combined main effects of additive [d] and dominance [h] effects for all the traits in all the five crosses. Dominance effect [h] was found pronounced for most of the traits except days to 50% flowering where additive effect [d] was found prevalent. Among the interaction effects dominance x dominance [l] was predominant over additive x additive [i] for all traits in all the five crosses except capsules/plant and capsule size in cross ND1001xNBRI11 and leaves/plant and opium yield/plant in cross NBRI5xND1002. As per sign of dominance (h and dominance x dominance (l duplicate epistasis were noticed for all the traits except plant height and leaves/plant in cross ND1001xUO1285. Potence ratio indicated presence of over dominance for almost all the traits. Substantial amount of realized heterosis, residual heterosis in F2 and F3 progenies and high heritability with moderate to high genetic advance in F2 progeny and significant correlation among important traits in desirable direction were observed. A breeding strategy of diallel selective mating or biparental mating in early segregating generation followed by recurrent

  2. MAPPING AND GENETIC EFFECT ANALYSIS ON QUANTITATIVE TRAIT LOCI RELATED TO FEED CONVERSION RATIO OF COMMON CARP (CYPRINUS CARPIO L.)%鲤饲料转化率性状的QTL定位及遗传效应分析

    Institute of Scientific and Technical Information of China (English)

    王宣朋; 张晓峰; 李文升; 张天奇; 李超; 孙效文

    2012-01-01

    The common carp (Cyprinus carpio L.), one of the most important species for aquaculture in China, is a widespread freshwater fish of eutrophic waters in lakes and large rivers. The wild populations are considered vulnerable to extinction, but the species has also been domesticated and introduced into environments worldwide, and is often considered as an invasive species. However, genetic degeneration, such as low growth rate, small body size, weak disease-resistance, etc., emerged in common carp with the rapid development of its farming scale. Quantitative traits (for example, the feed conversion ratio of common carp) refer to phenotypes that vary in degree and can be attributed to polygenic effects, I.e., product of two or more genes, and their environment. Quantitative trait loci (QTLs) are stretches of DNA containing or linked to the genes that underlie a quantitative trait. Mapping regions of the genome that contain genes involved in specifying a quantitative trait is done using molecular tags such as SSR, EST or more commonly SNPs. This is an early step in identifying and sequencing the actual genes underlying trait variation. Researches of genetic diversity, kin discrimination, strain identification, genetic linkage map construction, trait-related marker screening, genetic evaluation and QTL are the effective way to solve these problems of breeding in common carp. In this paper, a group of F2 hybrids German mirror carp including 68 individuals was used to construct a linkage map by using 560 markers (174 SSR markers, 41EST-SSR markers and 345 SNP markers). Quantitative traits loci (QTLs) associated with feed conversion ratio were identified by interval mapping and MQM mapping of the software MapQTL5.0. A linkage group wide permutation test (1000 replicates) determined the significance of the maximum LOD value over the various intervals analyzed for each linkage group. The results indicated that fifteen QTLs were identified for feed conversion ratio on nine

  3. Detection of quantitative trait loci on chromosomes 1,2,3,12,14,15, X in pigs: performance characteristics

    NARCIS (Netherlands)

    Paixao, D.M.; Carneiro, P.L.S.; Paiva, S.R.; Sousa, K.R.S.; Verardo, L.L.; Braccini Neto, J.; Pinto, A.P.G.; Marubayashi Hidalgo, A.; Nascimento, C.; Périssé, I.V.; Lopes, P.S.; Guimaraes, S.E.F.

    2013-01-01

    The accomplishment of the present study had the objective of mapping Quantitative Trait Loci (QTL) related to performance traits in a F2 pig population developed by mating two Brazilian Piau breed sires with 18 dams from a commercial line (Landrace × Large White × Pietrain). The linkage map for this

  4. Marker-assisted selection for improving quantitative traits of forage crops

    International Nuclear Information System (INIS)

    Dolstra, O.; Denneboom, C.; Vos, Ab L.F. de; Loo, E.N. van

    2007-01-01

    This chapter provides an example of using marker-assisted selection (MAS) for breeding perennial ryegrass (Lolium perenne), a pasture species. A mapping study had shown the presence of quantitative trait loci (QTL) for seven component traits of nitrogen use efficiency (NUE). The NUE-related QTL clustered in five chromosomal regions. These QTL were validated through divergent marker selection in an F 2 population. The criterion used for plant selection was a summation index based on the number of positive QTL alleles. The evaluation studies showed a strong indirect response of marker selection on NUE. Marker selection using a summation index such as applied here proved to be very effective for difficult and complex quantitative traits such as NUE. The strategy is easily applicable in outbreeding crops to raise the frequency of several desirable alleles simultaneously. (author)

  5. The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci

    Directory of Open Access Journals (Sweden)

    Xavier Suresh R

    2006-06-01

    Full Text Available Abstract Background Many important agricultural traits such as weight gain, milk fat content and intramuscular fat (marbling in cattle are quantitative traits. Most of the information on these traits has not previously been integrated into a genomic context. Without such integration application of these data to agricultural enterprises will remain slow and inefficient. Our goal was to populate a genomic database with data mined from the bovine quantitative trait literature and to make these data available in a genomic context to researchers via a user friendly query interface. Description The QTL (Quantitative Trait Locus data and related information for bovine QTL are gathered from published work and from existing databases. An integrated database schema was designed and the database (MySQL populated with the gathered data. The bovine QTL Viewer was developed for the integration of QTL data available for cattle. The tool consists of an integrated database of bovine QTL and the QTL viewer to display QTL and their chromosomal position. Conclusion We present a web accessible, integrated database of bovine (dairy and beef cattle QTL for use by animal geneticists. The viewer and database are of general applicability to any livestock species for which there are public QTL data. The viewer can be accessed at http://bovineqtl.tamu.edu.

  6. Mapping of quantitative trait loci (QTL) for production, resistance and tolerance traits in Salix. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Roennberg-Waestljung, Ann Christin; Bertholdsson, Nils-Ove; Glynn, Carolyn; Weih, Martin; Aahman, Inger [SLU, Uppsala (Sweden). Dept. of Plant Biology and Forest Genetics

    2004-05-01

    Quantitative trait loci (QTL) for growth traits, water use efficiency and tolerance/resistance against metals and herbivores have been identified. A hybrid F2 population originating from a cross between a Salix dasyclados-clone (SW901290) and a S. viminalis-clone ('Jorunn') was used for the different studies in this project. The growth response was analyzed in a greenhouse experiment with two water treatments, normal and drought. In addition, three field experiments with contrasting soils and climates were established. QTL specific for each treatment or field environment but also QTL stable over the treatments or field environments were detected. Each QTL explained from 8 to 29 % of the phenotypic variation depending on trait, treatment or field environment. Clusters of QTL for different traits were mapped indicating a common genetic base or tightly-linked QTL. Stable QTL identified for dryweight can be useful tools for early selection in Salix. In a separate greenhouse experiment, with a subset of ten genotypes from the F2 population, we show that genotype is more important than irrigation treatment for production of phenolic substances as well as for resistance to herbivory by P vulgatissima.

  7. Integrative genomic analysis identifies ancestry-related expression quantitative trait loci on DNA polymerase β and supports the association of genetic ancestry with survival disparities in head and neck squamous cell carcinoma.

    Science.gov (United States)

    Ramakodi, Meganathan P; Devarajan, Karthik; Blackman, Elizabeth; Gibbs, Denise; Luce, Danièle; Deloumeaux, Jacqueline; Duflo, Suzy; Liu, Jeffrey C; Mehra, Ranee; Kulathinal, Rob J; Ragin, Camille C

    2017-03-01

    African Americans with head and neck squamous cell carcinoma (HNSCC) have a lower survival rate than whites. This study investigated the functional importance of ancestry-informative single-nucleotide polymorphisms (SNPs) in HNSCC and also examined the effect of functionally important genetic elements on racial disparities in HNSCC survival. Ancestry-informative SNPs, RNA sequencing, methylation, and copy number variation data for 316 oral cavity and laryngeal cancer patients were analyzed across 178 DNA repair genes. The results of expression quantitative trait locus (eQTL) analyses were also replicated with a Gene Expression Omnibus (GEO) data set. The effects of eQTLs on overall survival (OS) and disease-free survival (DFS) were evaluated. Five ancestry-related SNPs were identified as cis-eQTLs in the DNA polymerase β (POLB) gene (false discovery rate [FDR] ancestry (P = .002). An association was observed between these eQTLs and OS (P ancestry-related alleles could act as eQTLs in HNSCC and support the association of ancestry-related genetic factors with survival disparities in patients diagnosed with oral cavity and laryngeal cancer. Cancer 2017;123:849-60. © 2016 American Cancer Society. © 2016 American Cancer Society.

  8. Functional linear models for association analysis of quantitative traits.

    Science.gov (United States)

    Fan, Ruzong; Wang, Yifan; Mills, James L; Wilson, Alexander F; Bailey-Wilson, Joan E; Xiong, Momiao

    2013-11-01

    Functional linear models are developed in this paper for testing associations between quantitative traits and genetic variants, which can be rare variants or common variants or the combination of the two. By treating multiple genetic variants of an individual in a human population as a realization of a stochastic process, the genome of an individual in a chromosome region is a continuum of sequence data rather than discrete observations. The genome of an individual is viewed as a stochastic function that contains both linkage and linkage disequilibrium (LD) information of the genetic markers. By using techniques of functional data analysis, both fixed and mixed effect functional linear models are built to test the association between quantitative traits and genetic variants adjusting for covariates. After extensive simulation analysis, it is shown that the F-distributed tests of the proposed fixed effect functional linear models have higher power than that of sequence kernel association test (SKAT) and its optimal unified test (SKAT-O) for three scenarios in most cases: (1) the causal variants are all rare, (2) the causal variants are both rare and common, and (3) the causal variants are common. The superior performance of the fixed effect functional linear models is most likely due to its optimal utilization of both genetic linkage and LD information of multiple genetic variants in a genome and similarity among different individuals, while SKAT and SKAT-O only model the similarities and pairwise LD but do not model linkage and higher order LD information sufficiently. In addition, the proposed fixed effect models generate accurate type I error rates in simulation studies. We also show that the functional kernel score tests of the proposed mixed effect functional linear models are preferable in candidate gene analysis and small sample problems. The methods are applied to analyze three biochemical traits in data from the Trinity Students Study. © 2013 WILEY

  9. An improved procedure of mapping a quantitative trait locus via the ...

    Indian Academy of Sciences (India)

    Data on the quantitative trait under consideration and several codominant genetic markers with known genomic locations are collected from members of families and statistically .... Although the primary aim is to estimate , since the trait.

  10. Genetic and Molecular Mechanisms of Quantitative Trait Loci Controlling Maize Inflorescence Architecture.

    Science.gov (United States)

    Li, Manfei; Zhong, Wanshun; Yang, Fang; Zhang, Zuxin

    2018-03-01

    The establishment of inflorescence architecture is critical for the reproduction of flowering plant species. The maize plant generates two types of inflorescences, the tassel and the ear, and their architectures have a large effect on grain yield and yield-related traits that are genetically controlled by quantitative trait loci (QTLs). Since ear and tassel architecture are deeply affected by the activity of inflorescence meristems, key QTLs and genes regulating meristematic activity have important impacts on inflorescence development and show great potential for optimizing grain yield. Isolation of yield trait-related QTLs is challenging, but these QTLs have direct application in maize breeding. Additionally, characterization and functional dissection of QTLs can provide genetic and molecular knowledge of quantitative variation in inflorescence architecture. In this review, we summarize currently identified QTLs responsible for the establishment of ear and tassel architecture and discuss the potential genetic control of four ear-related and four tassel-related traits. In recent years, several inflorescence architecture-related QTLs have been characterized at the gene level. We review the mechanisms of these characterized QTLs.

  11. Quantitative autistic trait measurements index background genetic risk for ASD in Hispanic families.

    Science.gov (United States)

    Page, Joshua; Constantino, John Nicholas; Zambrana, Katherine; Martin, Eden; Tunc, Ilker; Zhang, Yi; Abbacchi, Anna; Messinger, Daniel

    2016-01-01

    Recent studies have indicated that quantitative autistic traits (QATs) of parents reflect inherited liabilities that may index background genetic risk for clinical autism spectrum disorder (ASD) in their offspring. Moreover, preferential mating for QATs has been observed as a potential factor in concentrating autistic liabilities in some families across generations. Heretofore, intergenerational studies of QATs have focused almost exclusively on Caucasian populations-the present study explored these phenomena in a well-characterized Hispanic population. The present study examined QAT scores in siblings and parents of 83 Hispanic probands meeting research diagnostic criteria for ASD, and 64 non-ASD controls, using the Social Responsiveness Scale-2 (SRS-2). Ancestry of the probands was characterized by genotype, using information from 541,929 single nucleotide polymorphic markers. In families of Hispanic children with an ASD diagnosis, the pattern of quantitative trait correlations observed between ASD-affected children and their first-degree relatives (ICCs on the order of 0.20), between unaffected first-degree relatives in ASD-affected families (sibling/mother ICC = 0.36; sibling/father ICC = 0.53), and between spouses (mother/father ICC = 0.48) were in keeping with the influence of transmitted background genetic risk and strong preferential mating for variation in quantitative autistic trait burden. Results from analysis of ancestry-informative genetic markers among probands in this sample were consistent with that from other Hispanic populations. Quantitative autistic traits represent measurable indices of inherited liability to ASD in Hispanic families. The accumulation of autistic traits occurs within generations, between spouses, and across generations, among Hispanic families affected by ASD. The occurrence of preferential mating for QATs-the magnitude of which may vary across cultures-constitutes a mechanism by which background genetic liability

  12. Detection of Quantitative Trait Loci Affecting Fat Deposition Traits in Pigs

    Directory of Open Access Journals (Sweden)

    B. H. Choi

    2012-11-01

    Full Text Available Quantitative trait loci (QTL associated with fat deposition traits in pigs are important gene positions in a chromosome that influence meat quality of pork. For QTL study, a three generation resource population was constructed from a cross between Korean native boars and Landrace sows. A total of 240 F2 animals from intercross of F1 were produced. 80 microsatellite markers covering chromosomes 1 to 10 were selected to genotype the resource population. Intervals between adjacent markers were approximately 19 cM. Linkage analysis was performed using CRIMAP software version 2.4 with a FIXED option to obtain the map distances. For QTL analysis, the public web-based software, QTL express (http://www.qtl.cap.ed.ac.uk was used. Two significant and two suggestive QTL were identified on SSC 6, 7, and 8 as affecting body fat and IMF traits. For QTL affecting IMF, the most significant association was detected between marker sw71 and sw1881 on SSC 6, and a suggestive QTL was identified between sw268 and sw205 on SSC8. These QTL accounted for 26.58% and 12.31% of the phenotypic variance, respectively. A significant QTL affecting IMF was detected at position 105 cM between markers sw71 and sw1881 on SSC 6.

  13. A Strategy for Identifying Quantitative Trait Genes Using Gene Expression Analysis and Causal Analysis

    Directory of Open Access Journals (Sweden)

    Akira Ishikawa

    2017-11-01

    Full Text Available Large numbers of quantitative trait loci (QTL affecting complex diseases and other quantitative traits have been reported in humans and model animals. However, the genetic architecture of these traits remains elusive due to the difficulty in identifying causal quantitative trait genes (QTGs for common QTL with relatively small phenotypic effects. A traditional strategy based on techniques such as positional cloning does not always enable identification of a single candidate gene for a QTL of interest because it is difficult to narrow down a target genomic interval of the QTL to a very small interval harboring only one gene. A combination of gene expression analysis and statistical causal analysis can greatly reduce the number of candidate genes. This integrated approach provides causal evidence that one of the candidate genes is a putative QTG for the QTL. Using this approach, I have recently succeeded in identifying a single putative QTG for resistance to obesity in mice. Here, I outline the integration approach and discuss its usefulness using my studies as an example.

  14. A family-based joint test for mean and variance heterogeneity for quantitative traits.

    Science.gov (United States)

    Cao, Ying; Maxwell, Taylor J; Wei, Peng

    2015-01-01

    Traditional quantitative trait locus (QTL) analysis focuses on identifying loci associated with mean heterogeneity. Recent research has discovered loci associated with phenotype variance heterogeneity (vQTL), which is important in studying genetic association with complex traits, especially for identifying gene-gene and gene-environment interactions. While several tests have been proposed to detect vQTL for unrelated individuals, there are no tests for related individuals, commonly seen in family-based genetic studies. Here we introduce a likelihood ratio test (LRT) for identifying mean and variance heterogeneity simultaneously or for either effect alone, adjusting for covariates and family relatedness using a linear mixed effect model approach. The LRT test statistic for normally distributed quantitative traits approximately follows χ(2)-distributions. To correct for inflated Type I error for non-normally distributed quantitative traits, we propose a parametric bootstrap-based LRT that removes the best linear unbiased prediction (BLUP) of family random effect. Simulation studies show that our family-based test controls Type I error and has good power, while Type I error inflation is observed when family relatedness is ignored. We demonstrate the utility and efficiency gains of the proposed method using data from the Framingham Heart Study to detect loci associated with body mass index (BMI) variability. © 2014 John Wiley & Sons Ltd/University College London.

  15. A Strategy for Identifying Quantitative Trait Genes Using Gene Expression Analysis and Causal Analysis.

    Science.gov (United States)

    Ishikawa, Akira

    2017-11-27

    Large numbers of quantitative trait loci (QTL) affecting complex diseases and other quantitative traits have been reported in humans and model animals. However, the genetic architecture of these traits remains elusive due to the difficulty in identifying causal quantitative trait genes (QTGs) for common QTL with relatively small phenotypic effects. A traditional strategy based on techniques such as positional cloning does not always enable identification of a single candidate gene for a QTL of interest because it is difficult to narrow down a target genomic interval of the QTL to a very small interval harboring only one gene. A combination of gene expression analysis and statistical causal analysis can greatly reduce the number of candidate genes. This integrated approach provides causal evidence that one of the candidate genes is a putative QTG for the QTL. Using this approach, I have recently succeeded in identifying a single putative QTG for resistance to obesity in mice. Here, I outline the integration approach and discuss its usefulness using my studies as an example.

  16. Joint analysis of quantitative trait loci and majoreffect causative mutations affecting meat quality and carcass composition traits in pigs

    OpenAIRE

    Cherel, Pierre; Pires, José; Glénisson, Jérôme; Milan, Denis; Iannuccelli, Nathalie; Herault, Frédéric; Damon, Marie; Le Roy, Pascale

    2011-01-01

    Abstract Background Detection of quantitative trait loci (QTLs) affecting meat quality traits in pigs is crucial for the design of efficient marker-assisted selection programs and to initiate efforts toward the identification of underlying polymorphisms. The RYR1 and PRKAG3 causative mutations, originally identified from major effects on meat characteristics, can be used both as controls for an overall QTL detection strategy for diversely affected traits and as a scale for detected QTL effect...

  17. Dynamic Quantitative Trait Locus Analysis of Plant Phenomic Data.

    Science.gov (United States)

    Li, Zitong; Sillanpää, Mikko J

    2015-12-01

    Advanced platforms have recently become available for automatic and systematic quantification of plant growth and development. These new techniques can efficiently produce multiple measurements of phenotypes over time, and introduce time as an extra dimension to quantitative trait locus (QTL) studies. Functional mapping utilizes a class of statistical models for identifying QTLs associated with the growth characteristics of interest. A major benefit of functional mapping is that it integrates information over multiple timepoints, and therefore could increase the statistical power for QTL detection. We review the current development of computationally efficient functional mapping methods which provide invaluable tools for analyzing large-scale timecourse data that are readily available in our post-genome era. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Quantitative Trait Loci Analysis of Allelopathy in Rice

    DEFF Research Database (Denmark)

    Jensen, L B; Courtois, B; Olofsdotter, M

    2008-01-01

    The allelopathic potential of rice (Oryza sativa L.) against Echinochloa crus-galli (L.) Beauv. was investigated under both laboratory and greenhouse conditions. A population of 150 recombinant inbred lines (RILs) was derived through single-seed descent from a cross between the indica cultivar AC...... the population phenotype was normally distributed. Two quantitative trait loci (QTLs) were located on chromosomes 4 and 7, explaining 20% of the phenotypic variation. A second relay seeding experiment was set up, this time including charcoal in the perlite. This screening showed that the allelopathic rice...... varieties did not have any effect on the weed species when grown with charcoal, the charcoal reversing the effect of any potential allelochemicals exuded from the rice roots. The second phenotypic experiment was conducted under greenhouse conditions in pots. Thirteen QTLs were detected for four different...

  19. Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping

    Directory of Open Access Journals (Sweden)

    Xu Shizhong

    2011-05-01

    Full Text Available Abstract Background The Bayesian shrinkage technique has been applied to multiple quantitative trait loci (QTLs mapping to estimate the genetic effects of QTLs on quantitative traits from a very large set of possible effects including the main and epistatic effects of QTLs. Although the recently developed empirical Bayes (EB method significantly reduced computation comparing with the fully Bayesian approach, its speed and accuracy are limited by the fact that numerical optimization is required to estimate the variance components in the QTL model. Results We developed a fast empirical Bayesian LASSO (EBLASSO method for multiple QTL mapping. The fact that the EBLASSO can estimate the variance components in a closed form along with other algorithmic techniques render the EBLASSO method more efficient and accurate. Comparing with the EB method, our simulation study demonstrated that the EBLASSO method could substantially improve the computational speed and detect more QTL effects without increasing the false positive rate. Particularly, the EBLASSO algorithm running on a personal computer could easily handle a linear QTL model with more than 100,000 variables in our simulation study. Real data analysis also demonstrated that the EBLASSO method detected more reasonable effects than the EB method. Comparing with the LASSO, our simulation showed that the current version of the EBLASSO implemented in Matlab had similar speed as the LASSO implemented in Fortran, and that the EBLASSO detected the same number of true effects as the LASSO but a much smaller number of false positive effects. Conclusions The EBLASSO method can handle a large number of effects possibly including both the main and epistatic QTL effects, environmental effects and the effects of gene-environment interactions. It will be a very useful tool for multiple QTL mapping.

  20. Detection of quantitative trait loci for carcass composition traits in pigs

    Directory of Open Access Journals (Sweden)

    Renard Christine

    2002-11-01

    Full Text Available Abstract A quantitative trait locus (QTL analysis of carcass composition data from a three-generation experimental cross between Meishan (MS and Large White (LW pig breeds is presented. A total of 488 F2 males issued from six F1 boars and 23 F1 sows, the progeny of six LW boars and six MS sows, were slaughtered at approximately 80 kg live weight and were submitted to a standardised cutting of the carcass. Fifteen traits, i.e. dressing percentage, loin, ham, shoulder, belly, backfat, leaf fat, feet and head weights, two backfat thickness and one muscle depth measurements, ham + loin and back + leaf fat percentages and estimated carcass lean content were analysed. Animals were typed for a total of 137 markers covering the entire porcine genome. Analyses were performed using a line-cross (LC regression method where founder lines were assumed to be fixed for different QTL alleles and a half/full sib (HFS maximum likelihood method where allele substitution effects were estimated within each half-/full-sib family. Additional analyses were performed to search for multiple linked QTL and imprinting effects. Significant gene effects were evidenced for both leanness and fatness traits in the telomeric regions of SSC 1q and SSC 2p, on SSC 4, SSC 7 and SSC X. Additional significant QTL were identified for ham weight on SSC 5, for head weight on SSC 1 and SSC 7, for feet weight on SSC 7 and for dressing percentage on SSC X. LW alleles were associated with a higher lean content and a lower fat content of the carcass, except for the fatness trait on SSC 7. Suggestive evidence of linked QTL on SSC 7 and of imprinting effects on SSC 6, SSC 7, SSC 9 and SSC 17 were also obtained.

  1. Evaluation of Quantitative and Qualitative Traits of 18 Potato Clones

    Directory of Open Access Journals (Sweden)

    A. R Bolandi

    2016-10-01

    to those of check. Based on results of this experiment, the clones 397003-7, 396151-27 and 397045-100 could be selected for Ardebil region. The objective of this research was to evaluate the quantitative and qualitative traits of cultivars and advanced potato clones in spring cultivation (Jolge-e-Rokh region. Materials and Methods In this research, 18 potato clones for the quantitative and qualitative traits were compared with three check cultivars including: Agria (suitable for French-fries, Marfona (suitable for boiled eating and Lady Rosetta (suitable for chips in Jolge-Rokh Agriculture Research Station, the location 35'¸ 50° north latitude and 59° east longitude and 1721 m above sea level, in crop year 2011. Experimental design was Randomized Complete Block Design (RCBD with three replications. Treatment consisted of 18 advanced potato clones: 396151-8, 397045-4, 397045-10, TP12-13, TP21-29, TP12-8, 397007-16, 397007-17, 396140-6, 397009-8, 397015-14, 397003-7, 396151-27, 397045-100, 397097-9, 396151-20, 397045-7 and 69 indigenous with three control cultivars (Agria, Marfona and Lady Rosetta. Tubers were planted on two rows with 6 meters length. Distance between row and plants on the row were 75 and 25 cm, respectively. Area of each plot was 9 square meter. The evaluated characters were total yield, marketable yield, eye number, dry matter percentage, tuber number per plant, tuber weight per plant and mean of tuber weight. In order to measure total yield, after maturity, and remove the aerial organs, all of the tubers were harvested and the fresh weight was obtained. After removal of the tumor in bad shape, with soft rot and smaller than 30 mm that cannot be sold as part of the marketable yield, rest of them were used to measure marketable yield. Tuber dry matter percentage (TDM% was determined from the relationship between fresh and dry weights of sub-sample of 8-10 thinly sliced tubers dried for 48 h at 80° C. Data were analyzed using SAS 9.1 software. The

  2. Comparative mapping reveals quantitative trait loci that affect spawning time in coho salmon (Oncorhynchus kisutch

    Directory of Open Access Journals (Sweden)

    Cristian Araneda

    2012-01-01

    Full Text Available Spawning time in salmonids is a sex-limited quantitative trait that can be modified by selection. In rainbow trout (Oncorhynchus mykiss, various quantitative trait loci (QTL that affect the expression of this trait have been discovered. In this study, we describe four microsatellite loci associated with two possible spawning time QTL regions in coho salmon (Oncorhynchus kisutch. The four loci were identified in females from two populations (early and late spawners produced by divergent selection from the same base population. Three of the loci (OmyFGT34TUF, One2ASC and One19ASC that were strongly associated with spawning time in coho salmon (p < 0.0002 were previously associated with QTL for the same trait in rainbow trout; a fourth loci (Oki10 with a suggestive association (p = 0.00035 mapped 10 cM from locus OmyFGT34TUF in rainbow trout. The changes in allelic frequency observed after three generations of selection were greater than expected because of genetic drift. This work shows that comparing information from closely-related species is a valid strategy for identifying QTLs for marker-assisted selection in species whose genomes are poorly characterized or lack a saturated genetic map.

  3. Using genetic markers to orient the edges in quantitative trait networks: the NEO software.

    Science.gov (United States)

    Aten, Jason E; Fuller, Tova F; Lusis, Aldons J; Horvath, Steve

    2008-04-15

    Systems genetic studies have been used to identify genetic loci that affect transcript abundances and clinical traits such as body weight. The pairwise correlations between gene expression traits and/or clinical traits can be used to define undirected trait networks. Several authors have argued that genetic markers (e.g expression quantitative trait loci, eQTLs) can serve as causal anchors for orienting the edges of a trait network. The availability of hundreds of thousands of genetic markers poses new challenges: how to relate (anchor) traits to multiple genetic markers, how to score the genetic evidence in favor of an edge orientation, and how to weigh the information from multiple markers. We develop and implement Network Edge Orienting (NEO) methods and software that address the challenges of inferring unconfounded and directed gene networks from microarray-derived gene expression data by integrating mRNA levels with genetic marker data and Structural Equation Model (SEM) comparisons. The NEO software implements several manual and automatic methods for incorporating genetic information to anchor traits. The networks are oriented by considering each edge separately, thus reducing error propagation. To summarize the genetic evidence in favor of a given edge orientation, we propose Local SEM-based Edge Orienting (LEO) scores that compare the fit of several competing causal graphs. SEM fitting indices allow the user to assess local and overall model fit. The NEO software allows the user to carry out a robustness analysis with regard to genetic marker selection. We demonstrate the utility of NEO by recovering known causal relationships in the sterol homeostasis pathway using liver gene expression data from an F2 mouse cross. Further, we use NEO to study the relationship between a disease gene and a biologically important gene co-expression module in liver tissue. The NEO software can be used to orient the edges of gene co-expression networks or quantitative trait

  4. A general mixture model for mapping quantitative trait loci by using molecular markers

    NARCIS (Netherlands)

    Jansen, R.C.

    1992-01-01

    In a segregating population a quantitative trait may be considered to follow a mixture of (normal) distributions, the mixing proportions being based on Mendelian segregation rules. A general and flexible mixture model is proposed for mapping quantitative trait loci (QTLs) by using molecular markers.

  5. A Major Locus for Quantitatively Measured Shank Skin Color Traits in Korean Native Chicken

    Directory of Open Access Journals (Sweden)

    S. Jin

    2016-11-01

    Full Text Available Shank skin color of Korean native chicken (KNC shows large color variations. It varies from white, yellow, green, bluish or grey to black, whilst in the majority of European breeds the shanks are typically yellow-colored. Three shank skin color-related traits (i.e., lightness [L*], redness [a*], and yellowness [b*] were measured by a spectrophotometer in 585 progeny from 68 nuclear families in the KNC resource population. We performed genome scan linkage analysis to identify loci that affect quantitatively measured shank skin color traits in KNC. All these birds were genotyped with 167 DNA markers located throughout the 26 autosomes. The SOLAR program was used to conduct multipoint variance-component quantitative trait locus (QTL analyses. We detected a major QTL that affects b* value (logarithm of odds [LOD] = 47.5, p = 1.60×10−49 on GGA24 (GGA for Gallus gallus. At the same location, we also detected a QTL that influences a* value (LOD = 14.2, p = 6.14×10−16. Additionally, beta-carotene dioxygenase 2 (BCDO2, the obvious positional candidate gene under the linkage peaks on GGA24, was investigated by the two association tests: i.e., measured genotype association (MGA and quantitative transmission disequilibrium test (QTDT. Significant associations were detected between BCDO2 g.9367 A>C and a* (PMGA = 1.69×10−28; PQTDT = 2.40×10−25. The strongest associations were between BCDO2 g.9367 A>C and b* (PMGA = 3.56×10−66; PQTDT = 1.68×10−65. However, linkage analyses conditional on the single nucleotide polymorphism indicated that other functional variants should exist. Taken together, we demonstrate for the first time the linkage and association between the BCDO2 locus on GGA24 and quantitatively measured shank skin color traits in KNC.

  6. A Simple Linear Regression Method for Quantitative Trait Loci Linkage Analysis With Censored Observations

    OpenAIRE

    Anderson, Carl A.; McRae, Allan F.; Visscher, Peter M.

    2006-01-01

    Standard quantitative trait loci (QTL) mapping techniques commonly assume that the trait is both fully observed and normally distributed. When considering survival or age-at-onset traits these assumptions are often incorrect. Methods have been developed to map QTL for survival traits; however, they are both computationally intensive and not available in standard genome analysis software packages. We propose a grouped linear regression method for the analysis of continuous survival data. Using...

  7. Design database for quantitative trait loci (QTL) data warehouse, data mining, and meta-analysis.

    Science.gov (United States)

    Hu, Zhi-Liang; Reecy, James M; Wu, Xiao-Lin

    2012-01-01

    A database can be used to warehouse quantitative trait loci (QTL) data from multiple sources for comparison, genomic data mining, and meta-analysis. A robust database design involves sound data structure logistics, meaningful data transformations, normalization, and proper user interface designs. This chapter starts with a brief review of relational database basics and concentrates on issues associated with curation of QTL data into a relational database, with emphasis on the principles of data normalization and structure optimization. In addition, some simple examples of QTL data mining and meta-analysis are included. These examples are provided to help readers better understand the potential and importance of sound database design.

  8. Quantitative genetic analysis of life-history traits of Caenorhabditis elegans in stressful environments

    Directory of Open Access Journals (Sweden)

    Shorto Alison

    2008-01-01

    Full Text Available Abstract Background Organisms live in environments that vary. For life-history traits that vary across environments, fitness will be maximised when the phenotype is appropriately matched to the environmental conditions. For the free-living nematode Caenorhabditis elegans, we have investigated how two major life-history traits, (i the development of environmentally resistant dauer larvae and (ii reproduction, respond to environmental stress (high population density and low food availability, and how these traits vary between lines and the genetic basis of this variation. Results We found that lines of C. elegans vary in their phenotypic plasticity of dauer larva development, i.e. there is variation in the likelihood of developing into a dauer larva for the same environmental change. There was also variation in how lifetime fecundity and the rate of reproduction changed under conditions of environmental stress. These traits were related, such that lines that are highly plastic for dauer larva development also maintain a high population growth rate when stressed. We identified quantitative trait loci (QTL on two chromosomes that control the dauer larva development and population size phenotypes. The QTLs affecting the dauer larva development and population size phenotypes on chromosome II are closely linked, but are genetically separable. This chromosome II QTL controlling dauer larva development does not encompass any loci previously identified to control dauer larva development. This chromosome II region contains many predicted 7-transmembrane receptors. Such proteins are often involved in information transduction, which is clearly relevant to the control of dauer larva development. Conclusion C. elegans alters both its larval development and adult reproductive strategy in response to environmental stress. Together the phenotypic and genotypic data suggest that these two major life-history traits are co-ordinated responses to environmental stress

  9. Remote Sensing of plant functional types: Relative importance of biochemical and structural plant traits

    Science.gov (United States)

    Kattenborn, Teja; Schmidtlein, Sebastian

    2017-04-01

    Monitoring ecosystems is a key priority in order to understand vegetation patterns, underlying resource cycles and changes their off. Driven by biotic and abiotic factors, plant species within an ecosystem are likely to share similar structural, physiological or phenological traits and can therefore be grouped into plant functional types (PFT). It can be assumed that plants which share similar traits also share similar optical characteristics. Therefore optical remote sensing was identified as a valuable tool for differentiating PFT. Although several authors list structural and biochemical plant traits which are important for differentiating PFT using hyperspectral remote sensing, there is no quantitative or qualitative information on the relative importance of these traits. Thus, little is known about the explicit role of plant traits for an optical discrimination of PFT. One of the main reasons for this is that various optical traits affect the same wavelength regions and it is therefore difficult to isolate the discriminative power of a single trait. A way to determine the effect of single plant traits on the optical reflectance of plant canopies is given by radiative transfer models. The most established radiative transfer model is PROSAIL, which incorporates biochemical and structural plant traits, such as pigment contents or leaf area index. In the present study 25 grassland species of different PFT were cultivated and traits relevant for PROSAIL were measured for the entire vegetation season of 2016. The information content of each trait for differentiating PFTs was determined by applying a Multi-response Permutation Procedure on the actual traits, as well as on simulated canopy spectra derived from PROSAIL. According to our results some traits, especially biochemical traits, show a weaker separability of PFT on a spectral level than compared to the actual trait measurements. Overall structural traits (leaf angle and leaf area index) are more important for

  10. Quantitative trait loci mapping of calving and conformation traits on Bos taurus autosome 18 in the German Holstein population.

    Science.gov (United States)

    Brand, B; Baes, C; Mayer, M; Reinsch, N; Seidenspinner, T; Thaller, G; Kühn, Ch

    2010-03-01

    Linkage, linkage disequilibrium, and combined linkage and linkage disequilibrium analyses were performed to map quantitative trait loci (QTL) affecting calving and conformation traits on Bos taurus autosome 18 (BTA18) in the German Holstein population. Six paternal half-sib families consisting of a total of 1,054 animals were genotyped on 28 genetic markers in the telomeric region on BTA18 spanning approximately 30 Mb. Calving traits, body type traits, and udder type traits were investigated. Using univariately estimated breeding values, maternal and direct effects on calving ease and stillbirth were analyzed separately for first- and further-parity calvings. The QTL initially identified by separate linkage and linkage disequilibrium analyses could be confirmed by a combined linkage and linkage disequilibrium analysis for udder composite index, udder depth, fore udder attachment, front teat placement, body depth, rump angle, and direct effects on calving ease and stillbirth. Concurrence of QTL peaks and a similar shape of restricted log-likelihood ratio profiles were observed between udder type traits and for body depth and calving traits, respectively. Association analyses were performed for markers flanking the most likely QTL positions by applying a mixed model including a fixed allele effect of the maternally inherited allele and a random polygenic effect. Results indicated that microsatellite marker DIK4234 (located at 53.3 Mb) is associated with maternal effects on stillbirth, direct effects on calving ease, and body depth. A comparison of effects for maternally inherited DIK4234 alleles indicated a favorable, positive correlation of maternal and direct effects on calving. Additionally, the association of maternally inherited DIK4234 marker alleles with body depth implied that conformation traits might provide the functional background of the QTL for calving traits. For udder type traits, the strong coincidence of QTL peaks and the position of the QTL in a

  11. Large-scale in silico mapping of complex quantitative traits in inbred mice.

    Directory of Open Access Journals (Sweden)

    Pengyuan Liu

    2007-07-01

    Full Text Available Understanding the genetic basis of common disease and disease-related quantitative traits will aid in the development of diagnostics and therapeutics. The processs of gene discovery can be sped up by rapid and effective integration of well-defined mouse genome and phenome data resources. We describe here an in silico gene-discovery strategy through genome-wide association (GWA scans in inbred mice with a wide range of genetic variation. We identified 937 quantitative trait loci (QTLs from a survey of 173 mouse phenotypes, which include models of human disease (atherosclerosis, cardiovascular disease, cancer and obesity as well as behavioral, hematological, immunological, metabolic, and neurological traits. 67% of QTLs were refined into genomic regions <0.5 Mb with approximately 40-fold increase in mapping precision as compared with classical linkage analysis. This makes for more efficient identification of the genes that underlie disease. We have identified two QTL genes, Adam12 and Cdh2, as causal genetic variants for atherogenic diet-induced obesity. Our findings demonstrate that GWA analysis in mice has the potential to resolve multiple tightly linked QTLs and achieve single-gene resolution. These high-resolution QTL data can serve as a primary resource for positional cloning and gene identification in the research community.

  12. Replication of linkage to quantitative trait loci: variation in location and magnitude of the lod score.

    Science.gov (United States)

    Hsueh, W C; Göring, H H; Blangero, J; Mitchell, B D

    2001-01-01

    Replication of linkage signals from independent samples is considered an important step toward verifying the significance of linkage signals in studies of complex traits. The purpose of this empirical investigation was to examine the variability in the precision of localizing a quantitative trait locus (QTL) by analyzing multiple replicates of a simulated data set with the use of variance components-based methods. Specifically, we evaluated across replicates the variation in both the magnitude and the location of the peak lod scores. We analyzed QTLs whose effects accounted for 10-37% of the phenotypic variance in the quantitative traits. Our analyses revealed that the precision of QTL localization was directly related to the magnitude of the QTL effect. For a QTL with effect accounting for > 20% of total phenotypic variation, > 90% of the linkage peaks fall within 10 cM from the true gene location. We found no evidence that, for a given magnitude of the lod score, the presence of interaction influenced the precision of QTL localization.

  13. Quantitative trait loci analysis of individual and total isoflavone ...

    Indian Academy of Sciences (India)

    2014-08-19

    Aug 19, 2014 ... 2Seed Management Station of Jilin Province, Changchun 130062, Jilin, ... daidzein (DC), genistein (GeC), glycitein (GlC) and total isoflavone contents (TIC) in ..... ing and height) and quality (oil and protein content) traits.

  14. Identification of quantitative trait loci for carcass composition and meat quality traits in a commercial finishing cross

    NARCIS (Netherlands)

    Wijk, van H.J.; Dibbits, B.W.; Baron, E.E.; Brings, A.D.; Harlizius, B.; Groenen, M.A.M.; Knol, E.F.; Bovenhuis, H.

    2006-01-01

    A QTL study for carcass composition and meat quality traits was conducted on finisher pigs of a cross between a synthetic Pie¿train/Large White boar line and a commercial sow cross. The mapping population comprised 715 individuals evaluated for a total of 30 traits related to growth and fatness (4

  15. Comprehensive Comparison of Self-Administered Questionnaires for Measuring Quantitative Autistic Traits in Adults

    Science.gov (United States)

    Nishiyama, Takeshi; Suzuki, Masako; Adachi, Katsunori; Sumi, Satoshi; Okada, Kensuke; Kishino, Hirohisa; Sakai, Saeko; Kamio, Yoko; Kojima, Masayo; Suzuki, Sadao; Kanne, Stephen M.

    2014-01-01

    We comprehensively compared all available questionnaires for measuring quantitative autistic traits (QATs) in terms of reliability and construct validity in 3,147 non-clinical and 60 clinical subjects with normal intelligence. We examined four full-length forms, the Subthreshold Autism Trait Questionnaire (SATQ), the Broader Autism Phenotype…

  16. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations

    NARCIS (Netherlands)

    Santure, Anna W.; Poissant, Jocelyn; Cauwer, De Isabelle; Oers, Van Kees; Robinson, Matthew R.; Quinn, John L.; Groenen, M.A.M.; Visser, M.E.; Sheldon, Ben C.; Slate, Jon

    2015-01-01

    Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar

  17. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations

    NARCIS (Netherlands)

    Santure, Anna W; Poissant, Jocelyn; De Cauwer, Isabelle; van Oers, Kees; Robinson, Matthew R; Quinn, John L; Groenen, Martien A M; Visser, Marcel E; Sheldon, Ben C; Slate, Jon

    2015-01-01

    Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic

  18. Protein quantitative trait locus study in obesity during weight-loss identifies a leptin regulator

    DEFF Research Database (Denmark)

    Carayol, Jérôme; Chabert, Christian; Di Cara, Alessandro

    2017-01-01

    of an organism. Proteome analysis especially can provide new insights into the molecular mechanisms of complex traits like obesity. The role of genetic variation in determining protein level variation has not been assessed in obesity. To address this, we design a large-scale protein quantitative trait locus (p...

  19. Identification of quantitative trait loci for cadmium tolerance and accumulation in wheat

    DEFF Research Database (Denmark)

    Ci, Dunwei; Jiang, Dong; Li, Sishen

    2012-01-01

    Quantitative trait loci (QTL) for Cadmium (Cd) tolerance and accumulation in wheat (Triticum aestivum L.) were identified, using 103 recombinant inbred lines (RILs) derived from a cross of Ch×Sh at germination and seedling stages. The traits of germination, growth and physiology were measured. Cd...

  20. RAS1, a quantitative trait locus for salt tolerance and ABA sensitivity in Arabidopsis

    KAUST Repository

    Ren, Zhonghai; Zheng, Zhimin; Chinnusamy, Viswanathan; Zhu, Jianhua; Cui, Xinping; Iida, Kei; Zhu, Jian-Kang

    2010-01-01

    Soil salinity limits agricultural production and is a major obstacle for feeding the growing world population. We used natural genetic variation in salt tolerance among different Arabidopsis accessions to map a major quantitative trait locus (QTL

  1. Quantitative genetic methods depending on the nature of the phenotypic trait.

    Science.gov (United States)

    de Villemereuil, Pierre

    2018-01-24

    A consequence of the assumptions of the infinitesimal model, one of the most important theoretical foundations of quantitative genetics, is that phenotypic traits are predicted to be most often normally distributed (so-called Gaussian traits). But phenotypic traits, especially those interesting for evolutionary biology, might be shaped according to very diverse distributions. Here, I show how quantitative genetics tools have been extended to account for a wider diversity of phenotypic traits using first the threshold model and then more recently using generalized linear mixed models. I explore the assumptions behind these models and how they can be used to study the genetics of non-Gaussian complex traits. I also comment on three recent methodological advances in quantitative genetics that widen our ability to study new kinds of traits: the use of "modular" hierarchical modeling (e.g., to study survival in the context of capture-recapture approaches for wild populations); the use of aster models to study a set of traits with conditional relationships (e.g., life-history traits); and, finally, the study of high-dimensional traits, such as gene expression. © 2018 New York Academy of Sciences.

  2. Joint analysis of binary and quantitative traits with data sharing and outcome-dependent sampling.

    Science.gov (United States)

    Zheng, Gang; Wu, Colin O; Kwak, Minjung; Jiang, Wenhua; Joo, Jungnam; Lima, Joao A C

    2012-04-01

    We study the analysis of a joint association between a genetic marker with both binary (case-control) and quantitative (continuous) traits, where the quantitative trait values are only available for the cases due to data sharing and outcome-dependent sampling. Data sharing becomes common in genetic association studies, and the outcome-dependent sampling is the consequence of data sharing, under which a phenotype of interest is not measured for some subgroup. The trend test (or Pearson's test) and F-test are often, respectively, used to analyze the binary and quantitative traits. Because of the outcome-dependent sampling, the usual F-test can be applied using the subgroup with the observed quantitative traits. We propose a modified F-test by also incorporating the genotype frequencies of the subgroup whose traits are not observed. Further, a combination of this modified F-test and Pearson's test is proposed by Fisher's combination of their P-values as a joint analysis. Because of the correlation of the two analyses, we propose to use a Gamma (scaled chi-squared) distribution to fit the asymptotic null distribution for the joint analysis. The proposed modified F-test and the joint analysis can also be applied to test single trait association (either binary or quantitative trait). Through simulations, we identify the situations under which the proposed tests are more powerful than the existing ones. Application to a real dataset of rheumatoid arthritis is presented. © 2012 Wiley Periodicals, Inc.

  3. Gene Set Analyses of Genome-Wide Association Studies on 49 Quantitative Traits Measured in a Single Genetic Epidemiology Dataset

    Directory of Open Access Journals (Sweden)

    Jihye Kim

    2013-09-01

    Full Text Available Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait (pcorr < 0.05. Pairwise comparison of the traits in terms of the semantic similarity in their GO sets revealed surprising cases where phenotypically uncorrelated traits showed high similarity in terms of biological pathways. For example, the pH level was related to 7 other traits that showed low phenotypic correlations with it. A literature survey implies that these traits may be regulated partly by common pathways that involve neuronal or nerve systems.

  4. Identification of Quantitative Trait Loci for Resistance to RSIVD in Red Sea Bream (Pagrus major).

    Science.gov (United States)

    Sawayama, Eitaro; Tanizawa, Shiho; Kitamura, Shin-Ichi; Nakayama, Kei; Ohta, Kohei; Ozaki, Akiyuki; Takagi, Motohiro

    2017-12-01

    Red sea bream iridoviral disease (RSIVD) is a major viral disease in red sea bream farming in Japan. Previously, we identified one candidate male individual of red sea bream that was significantly associated with convalescent individuals after RSIVD. The purpose of this study is to identify the quantitative trait loci (QTL) linked to the RSIVD-resistant trait for future marker-assisted selection (MAS). Two test families were developed using the candidate male in 2014 (Fam-2014) and 2015 (Fam-2015). These test families were challenged with RSIV, and phenotypes were evaluated. Then, de novo genome sequences of red sea bream were obtained through next-generation sequencing, and microsatellite markers were searched and selected for linkage map construction. One immune-related gene, MHC class IIβ, was also used for linkage map construction. Of the microsatellite markers searched, 148 and 197 were mapped on 23 and 27 linkage groups in the female and male linkage maps, respectively, covering approximately 65% of genomes in both sexes. One QTL linked to an RSIVD-resistant trait was found in linkage group 2 of the candidate male in Fam-2014, and the phenotypic variance of the QTL was 31.1%. The QTL was closely linked to MHC class IIβ. Moreover, the QTL observed in Fam-2014 was also significantly linked to an RSIVD-resistant trait in the candidate male of Fam-2015. Our results suggest that the RSIVD-resistant trait in the candidate male was controlled by one major QTL closely linked to the MHC class IIβ gene and could be useful for MAS of red sea bream.

  5. Plants with useful traits and related methods

    Science.gov (United States)

    Mackenzie, Sally Ann; De la Rosa Santamaria, Roberto

    2016-10-25

    The present invention provides methods for obtaining plants that exhibit useful traits by transient suppression of the MSH1 gene of the plants. Methods for identifying genetic loci that provide for useful traits in plants and plants produced with those loci are also provided. In addition, plants that exhibit the useful traits, parts of the plants including seeds, and products of the plants are provided as well as methods of using the plants.

  6. A Genome Scan for Quantitative Trait Loci Affecting Average Daily ...

    Indian Academy of Sciences (India)

    reviewer

    Sari, P.O. Box -578, Iran .... (2015) identified one SNP with genome wide significance effect within SYNE1 gene on ..... analysis of thirty one production, health, reproduction and body conformation traits in contemporary US Holstein cows. ... Problems involved in breeding for efficiency of food utilization. Proc .... 131, 210-216.

  7. Testing for biases in selection on avian reproductive traits and partitioning direct and indirect selection using quantitative genetic models.

    Science.gov (United States)

    Reed, Thomas E; Gienapp, Phillip; Visser, Marcel E

    2016-10-01

    Key life history traits such as breeding time and clutch size are frequently both heritable and under directional selection, yet many studies fail to document microevolutionary responses. One general explanation is that selection estimates are biased by the omission of correlated traits that have causal effects on fitness, but few valid tests of this exist. Here, we show, using a quantitative genetic framework and six decades of life-history data on two free-living populations of great tits Parus major, that selection estimates for egg-laying date and clutch size are relatively unbiased. Predicted responses to selection based on the Robertson-Price Identity were similar to those based on the multivariate breeder's equation (MVBE), indicating that unmeasured covarying traits were not missing from the analysis. Changing patterns of phenotypic selection on these traits (for laying date, linked to climate change) therefore reflect changing selection on breeding values, and genetic constraints appear not to limit their independent evolution. Quantitative genetic analysis of correlational data from pedigreed populations can be a valuable complement to experimental approaches to help identify whether apparent associations between traits and fitness are biased by missing traits, and to parse the roles of direct versus indirect selection across a range of environments. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  8. Effect of genetic architecture on the prediction accuracy of quantitative traits in samples of unrelated individuals.

    Science.gov (United States)

    Morgante, Fabio; Huang, Wen; Maltecca, Christian; Mackay, Trudy F C

    2018-06-01

    Predicting complex phenotypes from genomic data is a fundamental aim of animal and plant breeding, where we wish to predict genetic merits of selection candidates; and of human genetics, where we wish to predict disease risk. While genomic prediction models work well with populations of related individuals and high linkage disequilibrium (LD) (e.g., livestock), comparable models perform poorly for populations of unrelated individuals and low LD (e.g., humans). We hypothesized that low prediction accuracies in the latter situation may occur when the genetics architecture of the trait departs from the infinitesimal and additive architecture assumed by most prediction models. We used simulated data for 10,000 lines based on sequence data from a population of unrelated, inbred Drosophila melanogaster lines to evaluate this hypothesis. We show that, even in very simplified scenarios meant as a stress test of the commonly used Genomic Best Linear Unbiased Predictor (G-BLUP) method, using all common variants yields low prediction accuracy regardless of the trait genetic architecture. However, prediction accuracy increases when predictions are informed by the genetic architecture inferred from mapping the top variants affecting main effects and interactions in the training data, provided there is sufficient power for mapping. When the true genetic architecture is largely or partially due to epistatic interactions, the additive model may not perform well, while models that account explicitly for interactions generally increase prediction accuracy. Our results indicate that accounting for genetic architecture can improve prediction accuracy for quantitative traits.

  9. Dominant Epistasis Between Two Quantitative Trait Loci Governing Sporulation Efficiency in Yeast Saccharomyces cerevisiae

    Science.gov (United States)

    Bergman, Juraj; Mitrikeski, Petar T.

    2015-01-01

    Summary Sporulation efficiency in the yeast Saccharomyces cerevisiae is a well-established model for studying quantitative traits. A variety of genes and nucleotides causing different sporulation efficiencies in laboratory, as well as in wild strains, has already been extensively characterised (mainly by reciprocal hemizygosity analysis and nucleotide exchange methods). We applied a different strategy in order to analyze the variation in sporulation efficiency of laboratory yeast strains. Coupling classical quantitative genetic analysis with simulations of phenotypic distributions (a method we call phenotype modelling) enabled us to obtain a detailed picture of the quantitative trait loci (QTLs) relationships underlying the phenotypic variation of this trait. Using this approach, we were able to uncover a dominant epistatic inheritance of loci governing the phenotype. Moreover, a molecular analysis of known causative quantitative trait genes and nucleotides allowed for the detection of novel alleles, potentially responsible for the observed phenotypic variation. Based on the molecular data, we hypothesise that the observed dominant epistatic relationship could be caused by the interaction of multiple quantitative trait nucleotides distributed across a 60--kb QTL region located on chromosome XIV and the RME1 locus on chromosome VII. Furthermore, we propose a model of molecular pathways which possibly underlie the phenotypic variation of this trait. PMID:27904371

  10. Influence of obesity gene in quantitative traits of swine

    Directory of Open Access Journals (Sweden)

    Graciele Segantini do Nascimento Borges

    2002-01-01

    Full Text Available Genotype data of 477 animals of several swine races (Landrace - LD, Large White - LW, Pietrain - PI, LWXLDXPI, Piau, Monteiro, and unknown race were obtained to determine the allele frequency of the obesity gene. Genotype data of 174 crossbred swine (LWXLDXPI were also obtained, in order to assess its correlation with carcass evaluation data (lean meat percentage, backfat thickness at P2, loin eye area, adjacent fat area, total fat and meat. Finally, genotype data of 96 pure swine (Landrace, Large White and Pietrain were collected, to establish its relation with meat quality (drip loss, meat color, texture analysis and intramuscular fat and carcass evaluation data (lean meat percentage; ham, loin, shoulder and belly weights; and backfat thickness at P2. This work also aimed associating EPDs (expected progeny differences for litter size, daily weight gain and backfat thickness with genotype data of 49 Large White males and 54 Landrace females. Genotyping was done on animal blood by PCR-RFLP, based on Stratil et al. (1997. Statistical analysis was done by using SAS software for variance analysis between genotypes and data for each cited class. For purebred animals, a mixed model was used, with sire within race as random effect. The allelic frequencies of alleles T and C were, respectively: 0.8142; 0.1857 (Landrace; 0.9125; 0.0875 (Large White; 0.9433; 0.0566 (Pietrain; 0.8333; 0.1666 (LWXLDXPI; 0.2500; 0.7500 (Piau; 0.8750; 0.1250 (Monteiro, and 0.8870; 0.1130 (unknown race. Since the highest allele C frequency occurred in Piau, we suggest that this allele could be associated with fat accumulation. In the Landrace race, a study was done separating the frequencies of 2 generations (great-grandfather and grandfather, and the differences confirmed by a Chi-square test, a higher frequency of allele C having been found in the grandparental generation. This suggests that this allele could be eliminated by selection from the great

  11. Adrenal cortex expression quantitative trait loci in a German Holstein × Charolais cross.

    Science.gov (United States)

    Brand, Bodo; Scheinhardt, Markus O; Friedrich, Juliane; Zimmer, Daisy; Reinsch, Norbert; Ponsuksili, Siriluck; Schwerin, Manfred; Ziegler, Andreas

    2016-10-06

    The importance of the adrenal gland in regard to lactation and reproduction in cattle has been recognized early. Caused by interest in animal welfare and the impact of stress on economically important traits in farm animals the adrenal gland and its function within the stress response is of increasing interest. However, the molecular mechanisms and pathways involved in stress-related effects on economically important traits in farm animals are not fully understood. Gene expression is an important mechanism underlying complex traits, and genetic variants affecting the transcript abundance are thought to influence the manifestation of an expressed phenotype. We therefore investigated the genetic background of adrenocortical gene expression by applying an adaptive linear rank test to identify genome-wide expression quantitative trait loci (eQTL) for adrenal cortex transcripts in cattle. A total of 10,986 adrenal cortex transcripts and 37,204 single nucleotide polymorphisms (SNPs) were analysed in 145 F2 cows of a Charolais × German Holstein cross. We identified 505 SNPs that were associated with the abundance of 129 transcripts, comprising 482 cis effects and 17 trans effects. These SNPs were located on all chromosomes but X, 16, 24 and 28. Associated genes are mainly involved in molecular and cellular functions comprising free radical scavenging, cellular compromise, cell morphology and lipid metabolism, including genes such as CYP27A1 and LHCGR that have been shown to affect economically important traits in cattle. In this study we showed that adrenocortical eQTL affect the expression of genes known to contribute to the phenotypic manifestation in cattle. Furthermore, some of the identified genes and related molecular pathways were previously shown to contribute to the phenotypic variation of behaviour, temperament and growth at the onset of puberty in the same population investigated here. We conclude that eQTL analysis appears to be a useful approach providing

  12. Genetic analysis of relative traits for a drought-sensitive mutant

    International Nuclear Information System (INIS)

    Gao Kangning; Wang Huaqi

    2009-01-01

    A drought-sensitive mutant (M616), selected from Handao 616 (HD616) by 60 Co γ-irradiation at 200Gy, was used. Some morphological and yield related traits of M166 and HD616 related to drought resistance were investigated. We further developed F 1 and F 2 reciprocal hybrid combinations derived from the crosses between M616 and HD616, between M616 and IRAT109, respectively, and genetic analysis of 3 traits including plant height, culm width of main stem and seed setting rate on main panicle were camed out. The results showed that M616 showed obviously sensitive to drought stress. Analysis of variance for three traits in upland and paddy between F 1 reciprocal hybrid combinations showed that each trait had no significant difference, and indicated that there were no differences of cytoplasmic hereditary effect. In addition, 3 traits of F 2 populations, were found that the frequency distributions of culm width showed normal distribution, indicating that culm width was polygenic trait, and the frequency distribution of plant height and seed setting rate did not show normal distribution, indicating that the two traits were qualitative-quantitative traits. Genetic analysis of relative traits for a drought-sensitive mutant of upland rice was a basic work for the gene location and cloning. (authors)

  13. Stereotypes about sex related personality traits

    Directory of Open Access Journals (Sweden)

    Andreja Avsec

    2002-05-01

    Full Text Available In present research, stereotypes about sex differences in personality traits were examined. They were compared to traits, included in two masculinity and femininity questionnaires and to big five factors. Results indicate the presence of gender stereotypes and their similarity to stereotypes, discovered in other studies. The majority of attributes that comprise stereotypes about average man pertain to assertive and controlling tendency, but in stereotypes about average woman caring and nurturant qualities predominate.

  14. Pleiotropy analysis of quantitative traits at gene level by multivariate functional linear models.

    Science.gov (United States)

    Wang, Yifan; Liu, Aiyi; Mills, James L; Boehnke, Michael; Wilson, Alexander F; Bailey-Wilson, Joan E; Xiong, Momiao; Wu, Colin O; Fan, Ruzong

    2015-05-01

    In genetics, pleiotropy describes the genetic effect of a single gene on multiple phenotypic traits. A common approach is to analyze the phenotypic traits separately using univariate analyses and combine the test results through multiple comparisons. This approach may lead to low power. Multivariate functional linear models are developed to connect genetic variant data to multiple quantitative traits adjusting for covariates for a unified analysis. Three types of approximate F-distribution tests based on Pillai-Bartlett trace, Hotelling-Lawley trace, and Wilks's Lambda are introduced to test for association between multiple quantitative traits and multiple genetic variants in one genetic region. The approximate F-distribution tests provide much more significant results than those of F-tests of univariate analysis and optimal sequence kernel association test (SKAT-O). Extensive simulations were performed to evaluate the false positive rates and power performance of the proposed models and tests. We show that the approximate F-distribution tests control the type I error rates very well. Overall, simultaneous analysis of multiple traits can increase power performance compared to an individual test of each trait. The proposed methods were applied to analyze (1) four lipid traits in eight European cohorts, and (2) three biochemical traits in the Trinity Students Study. The approximate F-distribution tests provide much more significant results than those of F-tests of univariate analysis and SKAT-O for the three biochemical traits. The approximate F-distribution tests of the proposed functional linear models are more sensitive than those of the traditional multivariate linear models that in turn are more sensitive than SKAT-O in the univariate case. The analysis of the four lipid traits and the three biochemical traits detects more association than SKAT-O in the univariate case. © 2015 WILEY PERIODICALS, INC.

  15. Quantitative trait loci and the relevance of phased haplotypes

    DEFF Research Database (Denmark)

    Gregersen, Vivi Raundahl

    Genetic control of different production traits and diseases within livestock has been of great interest since domenstication. SNPs have greatly facilitated the use of QTL studies in the search of genomic regions affecting different phenotypes. The studies have been conducted to identify regions...... underlying gentic control both as traditional linkage studies relying on genetic maps and as GWAS where an approach of phasing haplotypes within the QTL have been conducted to validate the regions. Overall, regions of interest have been identified for chronic pleuritis and osteochondrosis in addition to meat...... quality and boar taint in pigs, and for improved chees production within cows...

  16. Validation and dissection of quantitative trait loci for leaf traits in ...

    Indian Academy of Sciences (India)

    Validation and dissection of a QTL region for leaf traits in rice which has been reported in a number of independent studies were conducted. Three sets of near isogenic lines (NILs) were originated from a residual heterozygous line derived the indica cross Zhenshan 97B/Milyang 46. They were overlapping and totally ...

  17. Using Extreme Phenotype Sampling to Identify the Rare Causal Variants of Quantitative Traits in Association Studies

    OpenAIRE

    Li, Dalin; Lewinger, Juan Pablo; Gauderman, William J.; Murcray, Cassandra Elizabeth; Conti, David

    2011-01-01

    Variants identified in recent genome-wide association studies based on the common-disease common-variant hypothesis are far from fully explaining the hereditability of complex traits. Rare variants may, in part, explain some of the missing hereditability. Here, we explored the advantage of the extreme phenotype sampling in rare-variant analysis and refined this design framework for future large-scale association studies on quantitative traits. We first proposed a power calculation approach fo...

  18. Quantitative magnetic resonance imaging traits as endophenotypes for genetic mapping in epilepsy

    Directory of Open Access Journals (Sweden)

    Saud Alhusaini

    2016-01-01

    Full Text Available Over the last decade, the field of imaging genomics has combined high-throughput genotype data with quantitative magnetic resonance imaging (QMRI measures to identify genes associated with brain structure, cognition, and several brain-related disorders. Despite its successful application in different psychiatric and neurological disorders, the field has yet to be advanced in epilepsy. In this article we examine the relevance of imaging genomics for future genetic studies in epilepsy from three perspectives. First, we discuss prior genome-wide genetic mapping efforts in epilepsy, considering the possibility that some studies may have been constrained by inherent theoretical and methodological limitations of the genome-wide association study (GWAS method. Second, we offer a brief overview of the imaging genomics paradigm, from its original inception, to its role in the discovery of important risk genes in a number of brain-related disorders, and its successful application in large-scale multinational research networks. Third, we provide a comprehensive review of past studies that have explored the eligibility of brain QMRI traits as endophenotypes for epilepsy. While the breadth of studies exploring QMRI-derived endophenotypes in epilepsy remains narrow, robust syndrome-specific neuroanatomical QMRI traits have the potential to serve as accessible and relevant intermediate phenotypes for future genetic mapping efforts in epilepsy.

  19. Fine mapping of quantitative trait loci for mastitis resistance on bovine chromosome 11

    DEFF Research Database (Denmark)

    Schulman, N F; Sahana, G; Iso-Touru, T

    2009-01-01

    Quantitative trait loci (QTL) affecting clinical mastitis (CM) and somatic cell score (SCS) were mapped on bovine chromosome 11. The mapping population consisted of 14 grandsire families belonging to three Nordic red cattle breeds: Finnish Ayrshire (FA), Swedish Red and White (SRB) and Danish Red......, each affecting one trait; or one QTL affecting a single trait. A QTL affecting CM was fine-mapped. In FA, a haplotype having a strong association with a high negative effect on mastitis resistance was identified. The mapping precision of an earlier detected SCS-QTL was not improved by the LDLA analysis...

  20. A generalized estimating equations approach to quantitative trait locus detection of non-normal traits

    Directory of Open Access Journals (Sweden)

    Thomson Peter C

    2003-05-01

    Full Text Available Abstract To date, most statistical developments in QTL detection methodology have been directed at continuous traits with an underlying normal distribution. This paper presents a method for QTL analysis of non-normal traits using a generalized linear mixed model approach. Development of this method has been motivated by a backcross experiment involving two inbred lines of mice that was conducted in order to locate a QTL for litter size. A Poisson regression form is used to model litter size, with allowances made for under- as well as over-dispersion, as suggested by the experimental data. In addition to fixed parity effects, random animal effects have also been included in the model. However, the method is not fully parametric as the model is specified only in terms of means, variances and covariances, and not as a full probability model. Consequently, a generalized estimating equations (GEE approach is used to fit the model. For statistical inferences, permutation tests and bootstrap procedures are used. This method is illustrated with simulated as well as experimental mouse data. Overall, the method is found to be quite reliable, and with modification, can be used for QTL detection for a range of other non-normally distributed traits.

  1. Mapping quantitative trait loci (QTL in sheep. IV. Analysis of lactation persistency and extended lactation traits in sheep

    Directory of Open Access Journals (Sweden)

    Lam Mary K

    2011-06-01

    Full Text Available Abstract Background In sheep dairy production, total lactation performance, and length of lactation of lactation are of economic significance. A more persistent lactation has been associated with improved udder health. An extended lactation is defined by a longer period of milkability. This study is the first investigation to examine the presence of quantitative trait loci (QTL for extended lactation and lactation persistency in sheep. Methods An (Awassi × Merino × Merino single-sire backcross family with 172 ewes was used to map QTL for lactation persistency and extended lactation traits on a framework map of 189 loci across all autosomes. The Wood model was fitted to data from multiple lactations to estimate parameters of ovine lactation curves, and these estimates were used to derive measures of lactation persistency and extended lactation traits of milk, protein, fat, lactose, useful yield, and somatic cell score. These derived traits were subjected to QTL analyses using maximum likelihood estimation and regression analysis. Results Overall, one highly significant (LOD > 3.0, four significant (2.0 Conclusion This study identified ten novel QTL for lactation persistency and extended lactation in sheep, but results suggest that lactation persistency and extended lactation do not have a major gene in common. These results provide a basis for further validation in extended families and other breeds as well as targeting regions for genome-wide association mapping using high-density SNP arrays.

  2. Estimation of genetic parameters and detection of quantitative trait loci for metabolites in Danish Holstein milk

    DEFF Research Database (Denmark)

    Buitenhuis, Albert Johannes; Sundekilde, Ulrik; Poulsen, Nina Aagaard

    2013-01-01

    Small components and metabolites in milk are significant for the utilization of milk, not only in dairy food production but also as disease predictors in dairy cattle. This study focused on estimation of genetic parameters and detection of quantitative trait loci for metabolites in bovine milk. F...... for lactic acid to >0.8 for orotic acid and β-hydroxybutyrate. A single SNP association analysis revealed 7 genome-wide significant quantitative trait loci [malonate: Bos taurus autosome (BTA)2 and BTA7; galactose-1-phosphate: BTA2; cis-aconitate: BTA11; urea: BTA12; carnitine: BTA25...

  3. The Relations of Motivational Traits with Workplace Deviance

    Science.gov (United States)

    Diefendorff, James M.; Mehta, Kajal

    2007-01-01

    The authors developed and tested new theoretical relations between approach and avoidance motivational traits and deviant work behaviors. Approach motivation was divided into 3 traits: personal mastery (i.e., desire to achieve), competitive excellence (i.e., desire to perform better than others), and behavioral activation system (BAS) sensitivity…

  4. A PP2C-1 Allele Underlying a Quantitative Trait Locus Enhances Soybean 100-Seed Weight

    Institute of Scientific and Technical Information of China (English)

    Xiang Lu; Yong-Cai Lai; Wei-Guang Du; Wei-Qun Man; Shou-Yi Chen; Jin-Song Zhang; Qing Xiong; Tong Cheng; Qing-Tian Li; Xin-Lei Liu; Ying-Dong Bi; Wei Li; Wan-Ke Zhang; Biao Ma

    2017-01-01

    Cultivated soybeans may lose some useful genetic loci during domestication.Introgression of genes from wild soybeans could broaden the genetic background and improve soybean agronomic traits.In this study,through whole-genome sequencing of a recombinant inbred line population derived from a cross between a wild soybean ZYD7 and a cultivated soybean HN44,and mapping of quantitative trait loci for seed weight,we discovered that a phosphatase 2C-1 (PP2C-1) allele from wild soybean ZYD7 contributes to the increase in seed weight/size.PP2C-1 may achieve this function by enhancing cell size of integument and activating a subset of seed trait-related genes.We found that PP2C-1 is associated with GmBZR1,a soybean ortholog of Arabidopsis BZR1,one of key transcription factors in brassinosteroid (BR) signaling,and facilitate accumulation of dephosphorylated GmBZR1.In contrast,the PP2C-2 allele with variations of a few amino acids at the N-terminus did not exhibit this function.Moreover,we showed that GmBZR1 could promote seed weight/size in transgenic plants.Through analysis of cultivated soybean accessions,we found that 40% of the examined accessions do not have the PP2C-1 allele,suggesting that these accessions can be improved by introduction of this allele.Taken together,our study identifies an elite allele PP2C-1,which can enhance seed weight and/or size in soybean,and pinpoints that manipulation of this allele by molecular-assisted breeding may increase production in soybean and other legumes/crops.

  5. An Investigation of Personality Traits in Relation to Job Performance of Online Instructors

    Science.gov (United States)

    Holmes, Charles; Kirwan, Jeral R.; Bova, Mark; Belcher, Trevor

    2015-01-01

    This quantitative study examined the relationship between the Big 5 personality traits and how they relate to online teacher effectiveness. The primary method of data collection for this study was through the use of surveys primarily building upon the Personality Style Inventory (PSI) (Lounsbury & Gibson, 2010), a work-based personality…

  6. Response Monitoring and Adjustment: Differential Relations with Psychopathic Traits

    Science.gov (United States)

    Bresin, Konrad; Finy, M. Sima; Sprague, Jenessa; Verona, Edelyn

    2014-01-01

    Studies on the relation between psychopathy and cognitive functioning often show mixed results, partially because different factors of psychopathy have not been considered fully. Based on previous research, we predicted divergent results based on a two-factor model of psychopathy (interpersonal-affective traits and impulsive-antisocial traits). Specifically, we predicted that the unique variance of interpersonal-affective traits would be related to increased monitoring (i.e., error-related negativity) and adjusting to errors (i.e., post-error slowing), whereas impulsive-antisocial traits would be related to reductions in these processes. Three studies using a diverse selection of assessment tools, samples, and methods are presented to identify response monitoring correlates of the two main factors of psychopathy. In Studies 1 (undergraduates), 2 (adolescents), and 3 (offenders), interpersonal-affective traits were related to increased adjustment following errors and, in Study 3, to enhanced monitoring of errors. Impulsive-antisocial traits were not consistently related to error adjustment across the studies, although these traits were related to a deficient monitoring of errors in Study 3. The results may help explain previous mixed findings and advance implications for etiological models of psychopathy. PMID:24933282

  7. Lack of association between PKLR rs3020781 and NOS1AP rs7538490 and type 2 diabetes, overweight, obesity and related metabolic phenotypes in a Danish large-scale study: case-control studies and analyses of quantitative traits

    Directory of Open Access Journals (Sweden)

    Almind Katrine

    2008-12-01

    Full Text Available Abstract Background Several studies in multiple ethnicities have reported linkage to type 2 diabetes on chromosome 1q21-25. Both PKLR encoding the liver pyruvate kinase and NOS1AP encoding the nitric oxide synthase 1 (neuronal adaptor protein (CAPON are positioned within this chromosomal region and are thus positional candidates for the observed linkage peak. The C-allele of PKLR rs3020781 and the T-allele of NOS1AP rs7538490 are reported to strongly associate with type 2 diabetes in various European-descent populations comprising a total of 2,198 individuals with a combined odds ratio (OR of 1.33 [1.16–1.54] and 1.53 [1.28–1.81], respectively. Our aim was to validate these findings by investigating the impact of the two variants on type 2 diabetes and related quantitative metabolic phenotypes in a large study sample of Danes. Further, we intended to expand the analyses by examining the effect of the variants in relation to overweight and obesity. Methods PKLR rs3020781 and NOS1AP rs7538490 were genotyped, using TaqMan allelic discrimination, in a combined study sample comprising a total of 16,801 and 16,913 individuals, respectively. The participants were ascertained from four different study groups; the population-based Inter99 cohort (nPKLR = 5,962, nNOS1AP = 6,008, a type 2 diabetic patient group (nPKLR = 1,873, nNOS1AP = 1,874 from Steno Diabetes Center, a population-based study sample (nPKLR = 599, nNOS1AP = 596 from Steno Diabetes Center and the ADDITION Denmark screening study cohort (nPKLR = 8,367, nNOS1AP = 8,435. Results In case-control studies we evaluated the potential association between rs3020781 and rs7538490 and type 2 diabetes and obesity. No significant associations were observed for type 2 diabetes (rs3020781: pAF = 0.49, OR = 1.02 [0.96–1.10]; rs7538490: pAF = 0.84, OR = 0.99 [0.93–1.06]. Neither did we show association with overweight or obesity. Additionally, the PKLR and the NOS1AP genotypes were demonstrated not

  8. Exercise and diet affect quantitative trait loci for body weight and composition traits in an advanced intercross population of mice

    Science.gov (United States)

    Kelly, Scott A.; Hua, Kunjie; Pomp, Daniel

    2012-01-01

    Driven by the recent obesity epidemic, interest in understanding the complex genetic and environmental basis of body weight and composition is great. We investigated this by searching for quantitative trait loci (QTLs) affecting a number of weight and adiposity traits in a G10 advanced intercross population produced from crosses of mice in inbred strain C57BL/6J with those in a strain selected for high voluntary wheel running. The mice in this population were fed either a high-fat or a control diet throughout the study and also measured for four exercise traits prior to death, allowing us to test for pre- and postexercise QTLs as well as QTL-by-diet and QTL-by-exercise interactions. Our genome scan uncovered a number of QTLs, of which 40% replicated QTLs previously found for similar traits in an earlier (G4) generation. For those replicated QTLs, the confidence intervals were reduced from an average of 19 Mb in the G4 to 8 Mb in the G10. Four QTLs on chromosomes 3, 8, 13, and 18 were especially prominent in affecting the percentage of fat in the mice. About of all QTLs showed interactions with diet, exercise, or both, their genotypic effects on the traits showing a variety of patterns depending on the diet or level of exercise. It was concluded that the indirect effects of these QTLs provide an underlying genetic basis for the considerable variability in weight or fat loss typically found among individuals on the same diet and/or exercise regimen. PMID:23048196

  9. A method to prioritize quantitative traits and individuals for sequencing in family-based studies.

    Directory of Open Access Journals (Sweden)

    Kaanan P Shah

    Full Text Available Owing to recent advances in DNA sequencing, it is now technically feasible to evaluate the contribution of rare variation to complex traits and diseases. However, it is still cost prohibitive to sequence the whole genome (or exome of all individuals in each study. For quantitative traits, one strategy to reduce cost is to sequence individuals in the tails of the trait distribution. However, the next challenge becomes how to prioritize traits and individuals for sequencing since individuals are often characterized for dozens of medically relevant traits. In this article, we describe a new method, the Rare Variant Kinship Test (RVKT, which leverages relationship information in family-based studies to identify quantitative traits that are likely influenced by rare variants. Conditional on nuclear families and extended pedigrees, we evaluate the power of the RVKT via simulation. Not unexpectedly, the power of our method depends strongly on effect size, and to a lesser extent, on the frequency of the rare variant and the number and type of relationships in the sample. As an illustration, we also apply our method to data from two genetic studies in the Old Order Amish, a founder population with extensive genealogical records. Remarkably, we implicate the presence of a rare variant that lowers fasting triglyceride levels in the Heredity and Phenotype Intervention (HAPI Heart study (p = 0.044, consistent with the presence of a previously identified null mutation in the APOC3 gene that lowers fasting triglyceride levels in HAPI Heart study participants.

  10. Detecting Genetic Interactions for Quantitative Traits Using m-Spacing Entropy Measure

    Directory of Open Access Journals (Sweden)

    Jaeyong Yee

    2015-01-01

    Full Text Available A number of statistical methods for detecting gene-gene interactions have been developed in genetic association studies with binary traits. However, many phenotype measures are intrinsically quantitative and categorizing continuous traits may not always be straightforward and meaningful. Association of gene-gene interactions with an observed distribution of such phenotypes needs to be investigated directly without categorization. Information gain based on entropy measure has previously been successful in identifying genetic associations with binary traits. We extend the usefulness of this information gain by proposing a nonparametric evaluation method of conditional entropy of a quantitative phenotype associated with a given genotype. Hence, the information gain can be obtained for any phenotype distribution. Because any functional form, such as Gaussian, is not assumed for the entire distribution of a trait or a given genotype, this method is expected to be robust enough to be applied to any phenotypic association data. Here, we show its use to successfully identify the main effect, as well as the genetic interactions, associated with a quantitative trait.

  11. High Resolution of Quantitative Traits Into Multiple Loci via Interval Mapping

    OpenAIRE

    Jansen, Ritsert C.; Stam, Piet

    1994-01-01

    A very general method is described for multiple linear regression of a quantitative phenotype on genotype [putative quantitative trait loci (QTLs) and markers] in segregating generations obtained from line crosses. The method exploits two features, (a) the use of additional parental and F1 data, which fixes the joint QTL effects and the environmental error, and (b) the use of markers as cofactors, which reduces the genetic background noise. As a result, a significant increase of QTL detection...

  12. Quantitative trait locus affecting birth weight on bovine chromosome 5 in a F2 Gyr x Holstein population

    Directory of Open Access Journals (Sweden)

    Gustavo Gasparin

    2005-12-01

    Full Text Available Segregation between a genetic marker and a locus influencing a quantitative trait in a well delineated population is the basis for success in mapping quantitative trait loci (QTL. To detect bovine chromosome 5 (BTA5 birth weight QTL we genotyped 294 F2 Gyr (Bos indicus x Holstein (Bos taurus crossbreed cattle for five microsatellite markers. A linkage map was constructed for the markers and an interval analysis for the presence of QTL was performed. The linkage map indicated differences in the order of two markers relative to the reference map (http://www.marc.usda.gov. Interval analysis detected a QTL controlling birth weight (p < 0.01 at 69 centimorgans (cM from the most centromeric marker with an effect of 0.32 phenotypic standard-error. These results support other studies with crossbred Bos taurus x Bos indicus populations.

  13. Genomic Prediction and Association Mapping of Curd-Related Traits in Gene Bank Accessions of Cauliflower.

    Science.gov (United States)

    Thorwarth, Patrick; Yousef, Eltohamy A A; Schmid, Karl J

    2018-02-02

    Genetic resources are an important source of genetic variation for plant breeding. Genome-wide association studies (GWAS) and genomic prediction greatly facilitate the analysis and utilization of useful genetic diversity for improving complex phenotypic traits in crop plants. We explored the potential of GWAS and genomic prediction for improving curd-related traits in cauliflower ( Brassica oleracea var. botrytis ) by combining 174 randomly selected cauliflower gene bank accessions from two different gene banks. The collection was genotyped with genotyping-by-sequencing (GBS) and phenotyped for six curd-related traits at two locations and three growing seasons. A GWAS analysis based on 120,693 single-nucleotide polymorphisms identified a total of 24 significant associations for curd-related traits. The potential for genomic prediction was assessed with a genomic best linear unbiased prediction model and BayesB. Prediction abilities ranged from 0.10 to 0.66 for different traits and did not differ between prediction methods. Imputation of missing genotypes only slightly improved prediction ability. Our results demonstrate that GWAS and genomic prediction in combination with GBS and phenotyping of highly heritable traits can be used to identify useful quantitative trait loci and genotypes among genetically diverse gene bank material for subsequent utilization as genetic resources in cauliflower breeding. Copyright © 2018 Thorwarth et al.

  14. Genomic Prediction and Association Mapping of Curd-Related Traits in Gene Bank Accessions of Cauliflower

    Directory of Open Access Journals (Sweden)

    Patrick Thorwarth

    2018-02-01

    Full Text Available Genetic resources are an important source of genetic variation for plant breeding. Genome-wide association studies (GWAS and genomic prediction greatly facilitate the analysis and utilization of useful genetic diversity for improving complex phenotypic traits in crop plants. We explored the potential of GWAS and genomic prediction for improving curd-related traits in cauliflower (Brassica oleracea var. botrytis by combining 174 randomly selected cauliflower gene bank accessions from two different gene banks. The collection was genotyped with genotyping-by-sequencing (GBS and phenotyped for six curd-related traits at two locations and three growing seasons. A GWAS analysis based on 120,693 single-nucleotide polymorphisms identified a total of 24 significant associations for curd-related traits. The potential for genomic prediction was assessed with a genomic best linear unbiased prediction model and BayesB. Prediction abilities ranged from 0.10 to 0.66 for different traits and did not differ between prediction methods. Imputation of missing genotypes only slightly improved prediction ability. Our results demonstrate that GWAS and genomic prediction in combination with GBS and phenotyping of highly heritable traits can be used to identify useful quantitative trait loci and genotypes among genetically diverse gene bank material for subsequent utilization as genetic resources in cauliflower breeding.

  15. The relations of motivational traits with workplace deviance.

    Science.gov (United States)

    Diefendorff, James M; Mehta, Kajal

    2007-07-01

    The authors developed and tested new theoretical relations between approach and avoidance motivational traits and deviant work behaviors. Approach motivation was divided into 3 traits: personal mastery (i.e., desire to achieve), competitive excellence (i.e., desire to perform better than others), and behavioral activation system (BAS) sensitivity (i.e., responsiveness to rewards). Avoidance motivation, which reflects one's sensitivity to negative stimuli and the desire to escape such stimuli, was conceptualized as a unitary construct. Using structural equation modeling, the authors examined the relations of these 4 motivational traits with interpersonal and organizational deviance in a sample of primarily part-time employees. For the approach motivation traits, results showed that personal mastery was negatively related to interpersonal and organizational deviance, BAS sensitivity was positively related to interpersonal and organizational deviance, and competitive excellence was unrelated to both types of workplace deviance. Finally, avoidance motivation was positively related to organizational deviance and interacted with organizational constraints to predict interpersonal deviance.

  16. Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction

    DEFF Research Database (Denmark)

    Brøndum, Rasmus Froberg; Su, Guosheng; Janss, Luc

    2015-01-01

    This study investigated the effect on the reliability of genomic prediction when a small number of significant variants from single marker analysis based on whole genome sequence data were added to the regular 54k single nucleotide polymorphism (SNP) array data. The extra markers were selected...... with the aim of augmenting the custom low-density Illumina BovineLD SNP chip (San Diego, CA) used in the Nordic countries. The single-marker analysis was done breed-wise on all 16 index traits included in the breeding goals for Nordic Holstein, Danish Jersey, and Nordic Red cattle plus the total merit index...... itself. Depending on the trait’s economic weight, 15, 10, or 5 quantitative trait loci (QTL) were selected per trait per breed and 3 to 5 markers were selected to tag each QTL. After removing duplicate markers (same marker selected for more than one trait or breed) and filtering for high pairwise linkage...

  17. Quantitative trait loci associated with the tocochromanol (vitamin E) pathway in barley

    Science.gov (United States)

    In this study, the Genome-Wide Association Studies approach was used to detect Quantitative Trait Loci associated with tocochromanol concentrations using a panel of 1,466 barley accessions. All major tocochromanol types- alpha-, beta-, delta-, gamma-tocopherol and tocotrienol- were assayed. We found...

  18. Mapping quantitative trait loci in a selectively genotyped outbred population using a mixture model approach

    NARCIS (Netherlands)

    Johnson, David L.; Jansen, Ritsert C.; Arendonk, Johan A.M. van

    1999-01-01

    A mixture model approach is employed for the mapping of quantitative trait loci (QTL) for the situation where individuals, in an outbred population, are selectively genotyped. Maximum likelihood estimation of model parameters is obtained from an Expectation-Maximization (EM) algorithm facilitated by

  19. CBCL Pediatric Bipolar Disorder Profile and ADHD: Comorbidity and Quantitative Trait Loci Analysis

    Science.gov (United States)

    McGough, James J.; Loo, Sandra K.; McCracken, James T.; Dang, Jeffery; Clark, Shaunna; Nelson, Stanley F.; Smalley, Susan L.

    2008-01-01

    The pediatric bipolar disorder profile of the Child Behavior checklist is used to differentiate patterns of comorbidity and to search for quantitative trait loci in multiple affected ADHD sibling pairs. The CBCL-PBD profiling identified 8 percent of individuals with severe psychopathology and increased rates of oppositional defiant, conduct and…

  20. Meta-Analysis of Results from Quantitative Trait Loci Mapping Studies on Pig Chromosome 4

    NARCIS (Netherlands)

    Moraes Silva, De K.M.; Bastiaansen, J.W.M.; Knol, E.F.; Merks, J.W.M.; Lopes, P.S.; Guimaraes, R.M.; Arendonk, van J.A.M.

    2011-01-01

    Meta-analysis of results from multiple studies could lead to more precise quantitative trait loci (QTL) position estimates compared to the individual experiments. As the raw data from many different studies are not readily available, the use of results from published articles may be helpful. In this

  1. Identification of quantitative trait loci influencing wood specific gravity in an outbred pedigree of loblolly pine

    Science.gov (United States)

    A. Groover; M. Devey; T. Fiddler; J. Lee; R. Megraw; T. Mitchel-Olds; B. Sherman; S. Vujcic; C. Williams; D. Neale

    1994-01-01

    We report the identification of quantitative trait loci (QTL) influencing wood specific gravity (WSG) in an outbred pedigree of loblolly pine (Pinus taeda L.) . QTL mapping in an outcrossing species is complicated by the presence of multiple alleles (>2) at QTL and marker loci. Multiple alleles at QTL allow the examination of interaction among...

  2. Basal host resistance of barley to powdery mildew: connecting quantitative trait loci and candidate genes

    NARCIS (Netherlands)

    Aghnoum, R.; Marcel, T.C.; Johrde, A.; Pecchioni, N.; Schweizer, P.; Niks, R.E.

    2010-01-01

    The basal resistance of barley to powdery mildew (Blumeria graminis f. sp. hordei) is a quantitatively inherited trait that is based on nonhypersensitive mechanisms of defense. A functional genomic approach indicates that many plant candidate genes are involved in the defense against formation of

  3. Complex pedigree analysis to detect quantitative trait loci in dairy cattle

    NARCIS (Netherlands)

    Bink, M.C.A.M.

    1998-01-01

    In dairy cattle, many quantitative traits of economic importance show phenotypic variation. For breeding purposes the analysis of this phenotypic variation and uncovering the contribution of genetic factors is very important. Usually, the individual gene effects contributing to the

  4. Association Mapping of Malting Quality Quantitative Trait Loci in Winter Barley: Positive Signals from Small Germplasm Arrays

    Directory of Open Access Journals (Sweden)

    Lucía Gutiérrez

    2011-11-01

    Full Text Available Malting quality comprises one of the most economically relevant set of traits in barley ( L.. It is a complex phenotype, expensive and difficult to measure, that would benefit from a marker-assisted selection strategy. Malting quality is a target of the U.S. Barley Coordinated Agricultural Project (CAP and development of winter habit malting barley varieties is a key objective of the U.S. barley research community. The objective of this work was to detect quantitative trait loci (QTL for malting quality traits in a winter breeding program that is a component of the U.S. Barley CAP. We studied the association between five malting quality traits and 3072 single nucleotide polymorphisms (SNPs from the barley oligonucleotide pool assay (BOPA 1 and 2, assayed in advanced inbred lines from the Oregon State University (OSU breeding program from three germplasm arrays (CAP I, CAP II, and CAP III. After comparing 16 models we selected a structured association model with posterior probabilities inferred from software STRUCTURE (QK approach to use on all germplasm arrays. Most of the marker-trait associations are germplasm- and environment-specific and close to previously mapped genes and QTL relevant for malt and beer quality. We found alleles fixed by random genetic drift, novel unmasked alleles, and genetic-background interaction. In a relatively small population size study we provide strong evidence for detecting true QTL.

  5. A population genetic interpretation of GWAS findings for human quantitative traits

    Science.gov (United States)

    Bullaughey, Kevin; Hudson, Richard R.; Sella, Guy

    2018-01-01

    Human genome-wide association studies (GWASs) are revealing the genetic architecture of anthropomorphic and biomedical traits, i.e., the frequencies and effect sizes of variants that contribute to heritable variation in a trait. To interpret these findings, we need to understand how genetic architecture is shaped by basic population genetics processes—notably, by mutation, natural selection, and genetic drift. Because many quantitative traits are subject to stabilizing selection and because genetic variation that affects one trait often affects many others, we model the genetic architecture of a focal trait that arises under stabilizing selection in a multidimensional trait space. We solve the model for the phenotypic distribution and allelic dynamics at steady state and derive robust, closed-form solutions for summary statistics of the genetic architecture. Our results provide a simple interpretation for missing heritability and why it varies among traits. They predict that the distribution of variances contributed by loci identified in GWASs is well approximated by a simple functional form that depends on a single parameter: the expected contribution to genetic variance of a strongly selected site affecting the trait. We test this prediction against the results of GWASs for height and body mass index (BMI) and find that it fits the data well, allowing us to make inferences about the degree of pleiotropy and mutational target size for these traits. Our findings help to explain why the GWAS for height explains more of the heritable variance than the similarly sized GWAS for BMI and to predict the increase in explained heritability with study sample size. Considering the demographic history of European populations, in which these GWASs were performed, we further find that most of the associations they identified likely involve mutations that arose shortly before or during the Out-of-Africa bottleneck at sites with selection coefficients around s = 10−3. PMID

  6. Genome-wide Association Study to Identify Quantitative Trait Loci for Meat and Carcass Quality Traits in Berkshire

    Science.gov (United States)

    Iqbal, Asif; Kim, You-Sam; Kang, Jun-Mo; Lee, Yun-Mi; Rai, Rajani; Jung, Jong-Hyun; Oh, Dong-Yup; Nam, Ki-Chang; Lee, Hak-Kyo; Kim, Jong-Joo

    2015-01-01

    Meat and carcass quality attributes are of crucial importance influencing consumer preference and profitability in the pork industry. A set of 400 Berkshire pigs were collected from Dasan breeding farm, Namwon, Chonbuk province, Korea that were born between 2012 and 2013. To perform genome wide association studies (GWAS), eleven meat and carcass quality traits were considered, including carcass weight, backfat thickness, pH value after 24 hours (pH24), Commission Internationale de l’Eclairage lightness in meat color (CIE L), redness in meat color (CIE a), yellowness in meat color (CIE b), filtering, drip loss, heat loss, shear force and marbling score. All of the 400 animals were genotyped with the Porcine 62K SNP BeadChips (Illumina Inc., USA). A SAS general linear model procedure (SAS version 9.2) was used to pre-adjust the animal phenotypes before GWAS with sire and sex effects as fixed effects and slaughter age as a covariate. After fitting the fixed and covariate factors in the model, the residuals of the phenotype regressed on additive effects of each single nucleotide polymorphism (SNP) under a linear regression model (PLINK version 1.07). The significant SNPs after permutation testing at a chromosome-wise level were subjected to stepwise regression analysis to determine the best set of SNP markers. A total of 55 significant (p<0.05) SNPs or quantitative trait loci (QTL) were detected on various chromosomes. The QTLs explained from 5.06% to 8.28% of the total phenotypic variation of the traits. Some QTLs with pleiotropic effect were also identified. A pair of significant QTL for pH24 was also found to affect both CIE L and drip loss percentage. The significant QTL after characterization of the functional candidate genes on the QTL or around the QTL region may be effectively and efficiently used in marker assisted selection to achieve enhanced genetic improvement of the trait considered. PMID:26580276

  7. Genome-wide Association Study to Identify Quantitative Trait Loci for Meat and Carcass Quality Traits in Berkshire

    Directory of Open Access Journals (Sweden)

    Asif Iqbal

    2015-11-01

    Full Text Available Meat and carcass quality attributes are of crucial importance influencing consumer preference and profitability in the pork industry. A set of 400 Berkshire pigs were collected from Dasan breeding farm, Namwon, Chonbuk province, Korea that were born between 2012 and 2013. To perform genome wide association studies (GWAS, eleven meat and carcass quality traits were considered, including carcass weight, backfat thickness, pH value after 24 hours (pH24, Commission Internationale de l’Eclairage lightness in meat color (CIE L, redness in meat color (CIE a, yellowness in meat color (CIE b, filtering, drip loss, heat loss, shear force and marbling score. All of the 400 animals were genotyped with the Porcine 62K SNP BeadChips (Illumina Inc., USA. A SAS general linear model procedure (SAS version 9.2 was used to pre-adjust the animal phenotypes before GWAS with sire and sex effects as fixed effects and slaughter age as a covariate. After fitting the fixed and covariate factors in the model, the residuals of the phenotype regressed on additive effects of each single nucleotide polymorphism (SNP under a linear regression model (PLINK version 1.07. The significant SNPs after permutation testing at a chromosome-wise level were subjected to stepwise regression analysis to determine the best set of SNP markers. A total of 55 significant (p<0.05 SNPs or quantitative trait loci (QTL were detected on various chromosomes. The QTLs explained from 5.06% to 8.28% of the total phenotypic variation of the traits. Some QTLs with pleiotropic effect were also identified. A pair of significant QTL for pH24 was also found to affect both CIE L and drip loss percentage. The significant QTL after characterization of the functional candidate genes on the QTL or around the QTL region may be effectively and efficiently used in marker assisted selection to achieve enhanced genetic improvement of the trait considered.

  8. Nonparametric modeling of longitudinal covariance structure in functional mapping of quantitative trait loci.

    Science.gov (United States)

    Yap, John Stephen; Fan, Jianqing; Wu, Rongling

    2009-12-01

    Estimation of the covariance structure of longitudinal processes is a fundamental prerequisite for the practical deployment of functional mapping designed to study the genetic regulation and network of quantitative variation in dynamic complex traits. We present a nonparametric approach for estimating the covariance structure of a quantitative trait measured repeatedly at a series of time points. Specifically, we adopt Huang et al.'s (2006, Biometrika 93, 85-98) approach of invoking the modified Cholesky decomposition and converting the problem into modeling a sequence of regressions of responses. A regularized covariance estimator is obtained using a normal penalized likelihood with an L(2) penalty. This approach, embedded within a mixture likelihood framework, leads to enhanced accuracy, precision, and flexibility of functional mapping while preserving its biological relevance. Simulation studies are performed to reveal the statistical properties and advantages of the proposed method. A real example from a mouse genome project is analyzed to illustrate the utilization of the methodology. The new method will provide a useful tool for genome-wide scanning for the existence and distribution of quantitative trait loci underlying a dynamic trait important to agriculture, biology, and health sciences.

  9. Quantitative trait loci for magnitude of the plasma cortisol response to confinement in rainbow trout.

    Science.gov (United States)

    Quillet, E; Krieg, F; Dechamp, N; Hervet, C; Bérard, A; Le Roy, P; Guyomard, R; Prunet, P; Pottinger, T G

    2014-04-01

    Better understanding of the mechanisms underlying interindividual variation in stress responses and their links with production traits is a key issue for sustainable animal breeding. In this study, we searched for quantitative trait loci (QTL) controlling the magnitude of the plasma cortisol stress response and compared them to body size traits in five F2 full-sib families issued from two rainbow trout lines divergently selected for high or low post-confinement plasma cortisol level. Approximately 1000 F2 individuals were individually tagged and exposed to two successive acute confinement challenges (1 month interval). Post-stress plasma cortisol concentrations were determined for each fish. A medium density genome scan was carried out (268 markers, overall marker spacing less than 10 cM). QTL detection was performed using qtlmap software, based on an interval mapping method (http://www.inra.fr/qtlmap). Overall, QTL of medium individual effects on cortisol responsiveness (confinement stressor are distinct traits sharing only part of their genetic control. Chromosomal location of the steroidogenic acute regulatory protein (STAR) makes it a good potential candidate gene for one of the QTL. Finally, comparison of body size traits QTL (weight, length and body conformation) with cortisol-associated QTL did not support evidence for negative genetic relationships between the two types of traits. © 2014 Stichting International Foundation for Animal Genetics.

  10. Identification of quantitative trait loci controlling root and shoot traits associated with drought tolerance in a lentil (Lens culinaris Medik. recombinant inbred line population

    Directory of Open Access Journals (Sweden)

    Omar Idrissi

    2016-08-01

    Full Text Available Drought is one of the major abiotic stresses limiting lentil productivity in rainfed production systems. Specific rooting patterns can be associated with drought avoidance mechanisms that can be used in lentil breeding programs. In all, 252 co-dominant and dominant markers were used for Quantitative Trait Loci (QTL analysis on 132 lentil recombinant inbred lines based on greenhouse experiments for root and shoot traits during two seasons under progressive drought-stressed conditions. Eighteen QTLs controlling a total of 14 root and shoot traits were identified. A QTL-hotspot genomic region related to a number of root and shoot characteristics associated with drought tolerance such as dry root biomass, root surface area, lateral root number, dry shoot biomass and shoot length was identified. Interestingly, a QTL related to root-shoot ratio, an important trait for drought avoidance, explaining the highest phenotypic variance of 27.6 % and 28.9 % for the two consecutive seasons, respectively, was detected. This QTL was closed to the co-dominant SNP marker TP6337 and also flanked by the two SNP TP518 and TP1280. An important QTL related to lateral root number was found close to TP3371 and flanked by TP5093 and TP6072 SNP markers. Also, a QTL associated with specific root length was identified close to TP1873 and flanked by F7XEM6b SRAP marker and TP1035 SNP marker. These two QTLs were detected in both seasons. Our results could be used for marker-assisted selection in lentil breeding programs targeting root and shoot characteristics conferring drought avoidance as an efficient alternative to slow and labour-intensive conventional breeding methods.

  11. GWAPower: a statistical power calculation software for genome-wide association studies with quantitative traits.

    Science.gov (United States)

    Feng, Sheng; Wang, Shengchu; Chen, Chia-Cheng; Lan, Lan

    2011-01-21

    In designing genome-wide association (GWA) studies it is important to calculate statistical power. General statistical power calculation procedures for quantitative measures often require information concerning summary statistics of distributions such as mean and variance. However, with genetic studies, the effect size of quantitative traits is traditionally expressed as heritability, a quantity defined as the amount of phenotypic variation in the population that can be ascribed to the genetic variants among individuals. Heritability is hard to transform into summary statistics. Therefore, general power calculation procedures cannot be used directly in GWA studies. The development of appropriate statistical methods and a user-friendly software package to address this problem would be welcomed. This paper presents GWAPower, a statistical software package of power calculation designed for GWA studies with quantitative traits, where genetic effect is defined as heritability. Based on several popular one-degree-of-freedom genetic models, this method avoids the need to specify the non-centrality parameter of the F-distribution under the alternative hypothesis. Therefore, it can use heritability information directly without approximation. In GWAPower, the power calculation can be easily adjusted for adding covariates and linkage disequilibrium information. An example is provided to illustrate GWAPower, followed by discussions. GWAPower is a user-friendly free software package for calculating statistical power based on heritability in GWA studies with quantitative traits. The software is freely available at: http://dl.dropbox.com/u/10502931/GWAPower.zip.

  12. Genetic divergence in quercus suber L. based on qualitative and quantitative traits

    International Nuclear Information System (INIS)

    Akbar, F.; Shinwari, Z.K.; Khan, S.J.

    2011-01-01

    Sesame (Sesamum indicum L.) is one of the world's oldest oil crops and has been cultivated in Asia since ancient times. The breeding potential of the germplasm accessions held in PGRP gene-bank has hardly been exploited to date. This study was carried out to evaluate the phenotypic variability in the local sesame genotypes using 16 qualitative and quantitative traits. A total of 105 sesame accessions collected from diverse ecologies of Pakistan were used. A considerable level of variation was recorded for a number of morphologic and agronomic traits, while limited diversity for observed among the accessions for characters like stem hairiness, flower color (white with purple shading), seed color and to some extent phyllody disease. The correlation coefficient analysis indicated that plant height, capsules plant/sup -1/, capsule length and 1000-seed weight had the significant positive effect on seed yield. The characters related to maturity, days to flower initiation an d days to 50% flowering showed negative correlation with seed yield. Multivariate analysis was performed in order to establish similarity and dissimilarity patterns. Principal component (PC) analysis revealed that first three PC axes explained 54.21% of the total multivariate variation, while the first four PC axes explaining 63.64%. Plant height, days to maturity, capsules plant/sup -1/ and seed yield plant/sup -1/ were the major determinants of the genetic diversity in the collection. Cluster analysis places all the accessions into seven groups. Clustering was not associated with the geographical distribution instead accessions were mainly grouped due to their morphological differences. Elite sesame germplasm has been selected on the basis of best agro-morphological performance from 105 sesame collections. These results have an important suggestion for sesame germplasm agro-morphological assessment, enhancement, categorization and conservation in Pakistan. (author)

  13. Ascertainment correction for Markov chain Monte Carlo segregation and linkage analysis of a quantitative trait.

    Science.gov (United States)

    Ma, Jianzhong; Amos, Christopher I; Warwick Daw, E

    2007-09-01

    Although extended pedigrees are often sampled through probands with extreme levels of a quantitative trait, Markov chain Monte Carlo (MCMC) methods for segregation and linkage analysis have not been able to perform ascertainment corrections. Further, the extent to which ascertainment of pedigrees leads to biases in the estimation of segregation and linkage parameters has not been previously studied for MCMC procedures. In this paper, we studied these issues with a Bayesian MCMC approach for joint segregation and linkage analysis, as implemented in the package Loki. We first simulated pedigrees ascertained through individuals with extreme values of a quantitative trait in spirit of the sequential sampling theory of Cannings and Thompson [Cannings and Thompson [1977] Clin. Genet. 12:208-212]. Using our simulated data, we detected no bias in estimates of the trait locus location. However, in addition to allele frequencies, when the ascertainment threshold was higher than or close to the true value of the highest genotypic mean, bias was also found in the estimation of this parameter. When there were multiple trait loci, this bias destroyed the additivity of the effects of the trait loci, and caused biases in the estimation all genotypic means when a purely additive model was used for analyzing the data. To account for pedigree ascertainment with sequential sampling, we developed a Bayesian ascertainment approach and implemented Metropolis-Hastings updates in the MCMC samplers used in Loki. Ascertainment correction greatly reduced biases in parameter estimates. Our method is designed for multiple, but a fixed number of trait loci. Copyright (c) 2007 Wiley-Liss, Inc.

  14. Prioritizing quantitative trait loci for root system architecture in tetraploid wheat.

    Science.gov (United States)

    Maccaferri, Marco; El-Feki, Walid; Nazemi, Ghasemali; Salvi, Silvio; Canè, Maria Angela; Colalongo, Maria Chiara; Stefanelli, Sandra; Tuberosa, Roberto

    2016-02-01

    Optimization of root system architecture (RSA) traits is an important objective for modern wheat breeding. Linkage and association mapping for RSA in two recombinant inbred line populations and one association mapping panel of 183 elite durum wheat (Triticum turgidum L. var. durum Desf.) accessions evaluated as seedlings grown on filter paper/polycarbonate screening plates revealed 20 clusters of quantitative trait loci (QTLs) for root length and number, as well as 30 QTLs for root growth angle (RGA). Divergent RGA phenotypes observed by seminal root screening were validated by root phenotyping of field-grown adult plants. QTLs were mapped on a high-density tetraploid consensus map based on transcript-associated Illumina 90K single nucleotide polymorphisms (SNPs) developed for bread and durum wheat, thus allowing for an accurate cross-referencing of RSA QTLs between durum and bread wheat. Among the main QTL clusters for root length and number highlighted in this study, 15 overlapped with QTLs for multiple RSA traits reported in bread wheat, while out of 30 QTLs for RGA, only six showed co-location with previously reported QTLs in wheat. Based on their relative additive effects/significance, allelic distribution in the association mapping panel, and co-location with QTLs for grain weight and grain yield, the RSA QTLs have been prioritized in terms of breeding value. Three major QTL clusters for root length and number (RSA_QTL_cluster_5#, RSA_QTL_cluster_6#, and RSA_QTL_cluster_12#) and nine RGA QTL clusters (QRGA.ubo-2A.1, QRGA.ubo-2A.3, QRGA.ubo-2B.2/2B.3, QRGA.ubo-4B.4, QRGA.ubo-6A.1, QRGA.ubo-6A.2, QRGA.ubo-7A.1, QRGA.ubo-7A.2, and QRGA.ubo-7B) appear particularly valuable for further characterization towards a possible implementation of breeding applications in marker-assisted selection and/or cloning of the causal genes underlying the QTLs. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  15. DISSECTING QUANTITATIVE TRAIT LOCI FOR AGRONOMIC TRAITS RESPONDING TO IRON DEFICEINCY IN MUNGBEAN [Vigna radiata (L. Wilczek

    Directory of Open Access Journals (Sweden)

    Prakit Somta

    2014-06-01

    Full Text Available Calcareous soil is prevalent in many areas of the world agricultural land causing substantial yield loss of crops. We previously identified two quantitative trait locus (QTL qIDC3.1 and qIDC2.1 controlling leaf chlorosis in mungbean grown in calcareous soil in two years (2010 and 2011 using visual score and SPAD measurement in a RIL population derived from KPS2 (susceptible and NM10-12-1 (resistant. The two QTLs together accounted for 50% of the total leaf chlorosis variation and only qIDC3.1 was confirmed, although heritability estimated for the traits was as high as 91.96%. In this study, we detected QTLs associated with days to flowering , plant height, number of pods per plants, number of seeds per pods, and seed yield per plants in the same population grown under the same environment with the aim to identify additional QTLs controlling resistance to calcareous soil in mungbean. Single marker analysis revealed 18 simple sequence repeat markers, while composite interval mapping identified 33 QTLs on six linkage groups (1A, 2, 3, 4, 5 and 9 controlling the five agronomic traits. QTL cluster on LG 3 coincided with the position of qIDC3.1, while QTL cluster on LG 2 was not far from qIDC2.1. The results confirmed the importance of qIDC3.1 and qIDC2.1 and revealed four new QTLs for the resistance to calcareous soil.

  16. Quantitative Trait Loci Mapping Problem: An Extinction-Based Multi-Objective Evolutionary Algorithm Approach

    Directory of Open Access Journals (Sweden)

    Nicholas S. Flann

    2013-09-01

    Full Text Available The Quantitative Trait Loci (QTL mapping problem aims to identify regions in the genome that are linked to phenotypic features of the developed organism that vary in degree. It is a principle step in determining targets for further genetic analysis and is key in decoding the role of specific genes that control quantitative traits within species. Applications include identifying genetic causes of disease, optimization of cross-breeding for desired traits and understanding trait diversity in populations. In this paper a new multi-objective evolutionary algorithm (MOEA method is introduced and is shown to increase the accuracy of QTL mapping identification for both independent and epistatic loci interactions. The MOEA method optimizes over the space of possible partial least squares (PLS regression QTL models and considers the conflicting objectives of model simplicity versus model accuracy. By optimizing for minimal model complexity, MOEA has the advantage of solving the over-fitting problem of conventional PLS models. The effectiveness of the method is confirmed by comparing the new method with Bayesian Interval Mapping approaches over a series of test cases where the optimal solutions are known. This approach can be applied to many problems that arise in analysis of genomic data sets where the number of features far exceeds the number of observations and where features can be highly correlated.

  17. Cassava traits and end-user preference: Relating traits to consumer liking, sensory perception, and genetics.

    Science.gov (United States)

    Bechoff, Aurélie; Tomlins, Keith; Fliedel, Geneviève; Becerra Lopez-Lavalle, Luis Augusto; Westby, Andrew; Hershey, Clair; Dufour, Dominique

    2018-03-04

    Breeding efforts have focused on improving agronomic traits of the cassava plant however little research has been done to enhance the crop palatability. This review investigates the links between cassava traits and end-user preference in relation with sensory characteristics. The main trait is starch and its composition related to the textural properties of the food. Pectin degradation during cooking resulted in increased mealiness. Nutritional components such as carotenoids made the cassava yellow but also altered sweetness and softness; however, yellow cassava was more appreciated by consumers than traditional (white) varieties. Components formed during processing such as organic acids gave fermented cassava products an acidic taste that was appreciated but the fermented smell was not always liked. Anti-nutritional compounds such as cyanogenic glucosides were mostly related to bitter taste. Post-harvest Physiological Deterioration (PPD) affected the overall sensory characteristics and acceptability. Genes responsible for some of these traits were also investigated. Diversity in cassava food products can provide a challenge to identifying acceptance criteria. Socio-economic factors such as gender may also be critical. This review leads to questions in relation to the adaptation of cassava breeding to meet consumer needs and preference in order to maximize income, health and food security.

  18. A simple linear regression method for quantitative trait loci linkage analysis with censored observations.

    Science.gov (United States)

    Anderson, Carl A; McRae, Allan F; Visscher, Peter M

    2006-07-01

    Standard quantitative trait loci (QTL) mapping techniques commonly assume that the trait is both fully observed and normally distributed. When considering survival or age-at-onset traits these assumptions are often incorrect. Methods have been developed to map QTL for survival traits; however, they are both computationally intensive and not available in standard genome analysis software packages. We propose a grouped linear regression method for the analysis of continuous survival data. Using simulation we compare this method to both the Cox and Weibull proportional hazards models and a standard linear regression method that ignores censoring. The grouped linear regression method is of equivalent power to both the Cox and Weibull proportional hazards methods and is significantly better than the standard linear regression method when censored observations are present. The method is also robust to the proportion of censored individuals and the underlying distribution of the trait. On the basis of linear regression methodology, the grouped linear regression model is computationally simple and fast and can be implemented readily in freely available statistical software.

  19. Two developmentally temporal quantitative trait loci underlie convergent evolution of increased branchial bone length in sticklebacks

    Science.gov (United States)

    Erickson, Priscilla A.; Glazer, Andrew M.; Cleves, Phillip A.; Smith, Alyson S.; Miller, Craig T.

    2014-01-01

    In convergent evolution, similar phenotypes evolve repeatedly in independent populations, often reflecting adaptation to similar environments. Understanding whether convergent evolution proceeds via similar or different genetic and developmental mechanisms offers insight towards the repeatability and predictability of evolution. Oceanic populations of threespine stickleback fish, Gasterosteus aculeatus, have repeatedly colonized countless freshwater lakes and streams, where new diets lead to morphological adaptations related to feeding. Here, we show that heritable increases in branchial bone length have convergently evolved in two independently derived freshwater stickleback populations. In both populations, an increased bone growth rate in juveniles underlies the convergent adult phenotype, and one population also has a longer cartilage template. Using F2 crosses from these two freshwater populations, we show that two quantitative trait loci (QTL) control branchial bone length at distinct points in development. In both populations, a QTL on chromosome 21 controls bone length throughout juvenile development, and a QTL on chromosome 4 controls bone length only in adults. In addition to these similar developmental profiles, these QTL show similar chromosomal locations in both populations. Our results suggest that sticklebacks have convergently evolved longer branchial bones using similar genetic and developmental programmes in two independently derived populations. PMID:24966315

  20. Modularization and epistatic hierarchy determine homeostatic actions of multiple blood pressure quantitative trait loci.

    Science.gov (United States)

    Chauvet, Cristina; Crespo, Kimberley; Ménard, Annie; Roy, Julie; Deng, Alan Y

    2013-11-15

    Hypertension, the most frequently diagnosed clinical condition world-wide, predisposes individuals to morbidity and mortality, yet its underlying pathological etiologies are poorly understood. So far, a large number of quantitative trait loci (QTLs) have been identified in both humans and animal models, but how they function together in determining overall blood pressure (BP) in physiological settings is unknown. Here, we systematically and comprehensively performed pair-wise comparisons of individual QTLs to create a global picture of their functionality in an inbred rat model. Rather than each of numerous QTLs contributing to infinitesimal BP increments, a modularized pattern arises: two epistatic 'blocks' constitute basic functional 'units' for nearly all QTLs, designated as epistatic module 1 (EM1) and EM2. This modularization dictates the magnitude and scope of BP effects. Any EM1 member can contribute to BP additively to that of EM2, but not to those of the same module. Members of each EM display epistatic hierarchy, which seems to reflect a related functional pathway. Rat homologues of 11 human BP QTLs belong to either EM1 or EM2. Unique insights emerge into the novel genetic mechanism and hierarchy determining BP in the Dahl salt-sensitive SS/Jr (DSS) rat model that implicate a portion of human QTLs. Elucidating the pathways underlying EM1 and EM2 may reveal the genetic regulation of BP.

  1. Increased pericarp cell length underlies a major quantitative trait locus for grain weight in hexaploid wheat.

    Science.gov (United States)

    Brinton, Jemima; Simmonds, James; Minter, Francesca; Leverington-Waite, Michelle; Snape, John; Uauy, Cristobal

    2017-08-01

    Crop yields must increase to address food insecurity. Grain weight, determined by grain length and width, is an important yield component, but our understanding of the underlying genes and mechanisms is limited. We used genetic mapping and near isogenic lines (NILs) to identify, validate and fine-map a major quantitative trait locus (QTL) on wheat chromosome 5A associated with grain weight. Detailed phenotypic characterisation of developing and mature grains from the NILs was performed. We identified a stable and robust QTL associated with a 6.9% increase in grain weight. The positive interval leads to 4.0% longer grains, with differences first visible 12 d after fertilization. This grain length effect was fine-mapped to a 4.3 cM interval. The locus also has a pleiotropic effect on grain width (1.5%) during late grain development that determines the relative magnitude of the grain weight increase. Positive NILs have increased maternal pericarp cell length, an effect which is independent of absolute grain length. These results provide direct genetic evidence that pericarp cell length affects final grain size and weight in polyploid wheat. We propose that combining genes that control distinct biological mechanisms, such as cell expansion and proliferation, will enhance crop yields. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  2. The quantitative LOD score: test statistic and sample size for exclusion and linkage of quantitative traits in human sibships.

    Science.gov (United States)

    Page, G P; Amos, C I; Boerwinkle, E

    1998-04-01

    We present a test statistic, the quantitative LOD (QLOD) score, for the testing of both linkage and exclusion of quantitative-trait loci in randomly selected human sibships. As with the traditional LOD score, the boundary values of 3, for linkage, and -2, for exclusion, can be used for the QLOD score. We investigated the sample sizes required for inferring exclusion and linkage, for various combinations of linked genetic variance, total heritability, recombination distance, and sibship size, using fixed-size sampling. The sample sizes required for both linkage and exclusion were not qualitatively different and depended on the percentage of variance being linked or excluded and on the total genetic variance. Information regarding linkage and exclusion in sibships larger than size 2 increased as approximately all possible pairs n(n-1)/2 up to sibships of size 6. Increasing the recombination (theta) distance between the marker and the trait loci reduced empirically the power for both linkage and exclusion, as a function of approximately (1-2theta)4.

  3. Quantitative trait loci and candidate genes underlying genotype by environment interaction in the response of Arabidopsis thaliana to drought

    NARCIS (Netherlands)

    El-Soda, M.; Kruijer, Willem; Malosetti, M.; Koornneef, M.; Aarts, M.G.M.

    2015-01-01

    Drought stress was imposed on two sets of Arabidopsis thaliana genotypes grown in sand under short-day conditions and analysed for several shoot and root growth traits. The response to drought was assessed for quantitative trait locus (QTL) mapping in a genetically diverse set of Arabidopsis

  4. A simple bias correction in linear regression for quantitative trait association under two-tail extreme selection.

    Science.gov (United States)

    Kwan, Johnny S H; Kung, Annie W C; Sham, Pak C

    2011-09-01

    Selective genotyping can increase power in quantitative trait association. One example of selective genotyping is two-tail extreme selection, but simple linear regression analysis gives a biased genetic effect estimate. Here, we present a simple correction for the bias.

  5. Effects of physical and chemical mutagens on various quantitative traits in chickpea (Cicer arietinum L.)

    International Nuclear Information System (INIS)

    Wani, Aijaz A.; Anis, Mohammad

    2004-01-01

    Seeds of two chickpea varieties viz., Pusa-212 and Pusa-372 were subjected to 15, 20, 30 and 40 Kr doses of gamma rays and 0.1, 0.2, 0.3 and 0.4 per cent EMS treatment. A set of seeds of both the varieties irradiated at 20 Kr and 30 Kr was also subjected to treatment with EMS at 0.2, and 0.3 per cent. Data on eight quantitative traits viz., days taken to flowering and maturity, plant height (em), number of primary branches plant -1 , number of pods plant -1 , number of seeds pod -1 , 100-seed weight (g) and total seed yield plant -1 (g) were recorded for all the mutagenic treatments. The lower dose treatments in general, showed stimulatory effect whereas, higher treatments showed inhibitory effects on the mean performance of all the polygenic traits. Increase in C.V. in the mutagen treated population indicated that significant spectrum of phenotypic variability was created in all the polygenic traits in both the varieties. A comparison of the pooled effect of different levels of a particular mutagen on the mean value of various traits revealed that combination treatments proved to be most effective followed by EMS and gamma rays in inducing the magnitude of variability. The Var. Pusa 372 was comparatively more sensitive than the Var. Pusa-212. (author)

  6. and maturity-related traits in white yam ( Dioscorea rotundata )

    African Journals Online (AJOL)

    ... tuber fresh weight (tuber yield), tuber number/plant, tuber parenchyma colour, tuber dry matter content and tuber dormancy period were assessed in eight accessions of D. rotundata (white Guinea yam) on the field in 2008 and 2009. Shoot dry weight and plant height were identified as the major tuber yield-related traits.

  7. Exploiting wild relatives of S. lycopersicum for quality traits

    NARCIS (Netherlands)

    Víquez Zamora, A.M.

    2015-01-01

    Exploiting wild relatives of S. lycopersicum for quality traits Ana Marcela Víquez Zamora Tomatoes are consumed worldwide and became a model for crop plant research. A part of the research aims at expanding genetic diversity in tomato; this can be done by incorporating

  8. Quantitative variation in water-use efficiency across water regimes and its relationship with circadian, vegetative, reproductive, and leaf gas-exchange traits.

    Science.gov (United States)

    Edwards, Christine E; Ewers, Brent E; McClung, C Robertson; Lou, Ping; Weinig, Cynthia

    2012-05-01

    Drought limits light harvesting, resulting in lower plant growth and reproduction. One trait important for plant drought response is water-use efficiency (WUE). We investigated (1) how the joint genetic architecture of WUE, reproductive characters, and vegetative traits changed across drought and well-watered conditions, (2) whether traits with distinct developmental bases (e.g. leaf gas exchange versus reproduction) differed in the environmental sensitivity of their genetic architecture, and (3) whether quantitative variation in circadian period was related to drought response in Brassica rapa. Overall, WUE increased in drought, primarily because stomatal conductance, and thus water loss, declined more than carbon fixation. Genotypes with the highest WUE in drought expressed the lowest WUE in well-watered conditions, and had the largest vegetative and floral organs in both treatments. Thus, large changes in WUE enabled some genotypes to approach vegetative and reproductive trait optima across environments. The genetic architecture differed for gas-exchange and vegetative traits across drought and well-watered conditions, but not for floral traits. Correlations between circadian and leaf gas-exchange traits were significant but did not vary across treatments, indicating that circadian period affects physiological function regardless of water availability. These results suggest that WUE is important for drought tolerance in Brassica rapa and that artificial selection for increased WUE in drought will not result in maladaptive expression of other traits that are correlated with WUE.

  9. Smoothing of the bivariate LOD score for non-normal quantitative traits.

    Science.gov (United States)

    Buil, Alfonso; Dyer, Thomas D; Almasy, Laura; Blangero, John

    2005-12-30

    Variance component analysis provides an efficient method for performing linkage analysis for quantitative traits. However, type I error of variance components-based likelihood ratio testing may be affected when phenotypic data are non-normally distributed (especially with high values of kurtosis). This results in inflated LOD scores when the normality assumption does not hold. Even though different solutions have been proposed to deal with this problem with univariate phenotypes, little work has been done in the multivariate case. We present an empirical approach to adjust the inflated LOD scores obtained from a bivariate phenotype that violates the assumption of normality. Using the Collaborative Study on the Genetics of Alcoholism data available for the Genetic Analysis Workshop 14, we show how bivariate linkage analysis with leptokurtotic traits gives an inflated type I error. We perform a novel correction that achieves acceptable levels of type I error.

  10. A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.)

    Science.gov (United States)

    2011-01-01

    Background A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS). Results Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in

  11. A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.

    Directory of Open Access Journals (Sweden)

    Schaffer Arthur

    2011-07-01

    Full Text Available Abstract Background A number of molecular marker linkage maps have been developed for melon (Cucumis melo L. over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS. Results Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org, an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability

  12. Nonparametric evaluation of quantitative traits in population-based association studies when the genetic model is unknown.

    Science.gov (United States)

    Konietschke, Frank; Libiger, Ondrej; Hothorn, Ludwig A

    2012-01-01

    Statistical association between a single nucleotide polymorphism (SNP) genotype and a quantitative trait in genome-wide association studies is usually assessed using a linear regression model, or, in the case of non-normally distributed trait values, using the Kruskal-Wallis test. While linear regression models assume an additive mode of inheritance via equi-distant genotype scores, Kruskal-Wallis test merely tests global differences in trait values associated with the three genotype groups. Both approaches thus exhibit suboptimal power when the underlying inheritance mode is dominant or recessive. Furthermore, these tests do not perform well in the common situations when only a few trait values are available in a rare genotype category (disbalance), or when the values associated with the three genotype categories exhibit unequal variance (variance heterogeneity). We propose a maximum test based on Marcus-type multiple contrast test for relative effect sizes. This test allows model-specific testing of either dominant, additive or recessive mode of inheritance, and it is robust against variance heterogeneity. We show how to obtain mode-specific simultaneous confidence intervals for the relative effect sizes to aid in interpreting the biological relevance of the results. Further, we discuss the use of a related all-pairwise comparisons contrast test with range preserving confidence intervals as an alternative to Kruskal-Wallis heterogeneity test. We applied the proposed maximum test to the Bogalusa Heart Study dataset, and gained a remarkable increase in the power to detect association, particularly for rare genotypes. Our simulation study also demonstrated that the proposed non-parametric tests control family-wise error rate in the presence of non-normality and variance heterogeneity contrary to the standard parametric approaches. We provide a publicly available R library nparcomp that can be used to estimate simultaneous confidence intervals or compatible

  13. Quantitative sexing (Q-Sexing) and relative quantitative sexing (RQ ...

    African Journals Online (AJOL)

    samer

    Key words: Polymerase chain reaction (PCR), quantitative real time polymerase chain reaction (qPCR), quantitative sexing, Siberian tiger. INTRODUCTION. Animal molecular sexing .... 43:3-12. Ellegren H (1996). First gene on the avian W chromosome (CHD) provides a tag for universal sexing of non-ratite birds. Proc.

  14. Genetic dissection of milk yield traits and mastitis resistance quantitative trait loci on chromosome 20 in dairy cattle.

    Science.gov (United States)

    Kadri, Naveen K; Guldbrandtsen, Bernt; Lund, Mogens S; Sahana, Goutam

    2015-12-01

    Intense selection to increase milk yield has had negative consequences for mastitis incidence in dairy cattle. Due to low heritability of mastitis resistance and an unfavorable genetic correlation with milk yield, a reduction in mastitis through traditional breeding has been difficult to achieve. Here, we examined quantitative trait loci (QTL) that segregate for clinical mastitis and milk yield on Bos taurus autosome 20 (BTA20) to determine whether both traits are affected by a single polymorphism (pleiotropy) or by multiple closely linked polymorphisms. In the latter but not the former situation, undesirable genetic correlation could potentially be broken by selecting animals that have favorable variants for both traits. First, we performed a within-breed association study using a haplotype-based method in Danish Holstein cattle (HOL). Next, we analyzed Nordic Red dairy cattle (RDC) and Danish Jersey cattle (JER) with the goal of determining whether these QTL identified in Holsteins were segregating across breeds. Genotypes for 12,566 animals (5,966 HOL, 5,458 RDC, and 1,142 JER) were determined by using the Illumina Bovine SNP50 BeadChip (50K; Illumina, San Diego, CA), which identifies 1,568 single nucleotide polymorphisms on BTA20. Data were combined, phased, and clustered into haplotype states, followed by within- and across-breed haplotype-based association analyses using a linear mixed model. Association signals for both clinical mastitis and milk yield peaked in the 26- to 40-Mb region on BTA20 in HOL. Single-variant association analyses were carried out in the QTL region using whole sequence level variants imputed from references of 2,036 HD genotypes (BovineHD BeadChip; Illumina) and 242 whole-genome sequences. The milk QTL were also segregating in RDC and JER on the BTA20-targeted region; however, an indication of differences in the causal factor(s) was observed across breeds. A previously reported F279Y mutation (rs385640152) within the growth hormone

  15. [The study of tomato fruit weight quantitative trait locus and its application in genetics teaching].

    Science.gov (United States)

    Wang, Hai-yan

    2015-08-01

    The classical research cases, which have greatly promoted the development of genetics in history, can be combined with the content of courses in genetics teaching to train students' ability of scientific thinking and genetic analysis. The localization and clone of gene controlling tomato fruit weight is a pioneer work in quantitative trait locus (QTL) studies and represents a complete process of QTL research in plants. Application of this integrated case in genetics teaching, which showed a wonderful process of scientific discovery and the fascination of genetic research, has inspired students' interest in genetics and achieved a good teaching effect.

  16. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.

    Directory of Open Access Journals (Sweden)

    Fagen Li

    Full Text Available Dense genetic maps, along with quantitative trait loci (QTLs detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR, expressed sequence tag (EST derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS, and diversity arrays technology (DArT markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age and wood density (56 months were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

  17. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus

    Science.gov (United States)

    Weng, Qijie; Li, Mei; Yu, Xiaoli; Guo, Yong; Wang, Yu; Zhang, Xiaohong; Gan, Siming

    2015-01-01

    Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10–56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa. PMID:26695430

  18. Quantitative trait loci associated with longevity of lettuce seeds under conventional and controlled deterioration storage conditions.

    Science.gov (United States)

    Schwember, Andrés R; Bradford, Kent J

    2010-10-01

    Lettuce (Lactuca sativa L.) seeds have poor shelf life and exhibit thermoinhibition (fail to germinate) above ∼25°C. Seed priming (controlled hydration followed by drying) alleviates thermoinhibition by increasing the maximum germination temperature, but reduces lettuce seed longevity. Controlled deterioration (CD) or accelerated ageing storage conditions (i.e. elevated temperature and relative humidity) are used to study seed longevity and to predict potential seed lifetimes under conventional storage conditions. Seeds produced in 2002 and 2006 of a recombinant inbred line (RIL) population derived from a cross between L. sativa cv. Salinas×L. serriola accession UC96US23 were utilized to identify quantitative trait loci (QTLs) associated with seed longevity under CD and conventional storage conditions. Multiple longevity-associated QTLs were identified under both conventional and CD storage conditions for control (non-primed) and primed seeds. However, seed longevity was poorly correlated between the two storage conditions, suggesting that deterioration processes under CD conditions are not predictive of ageing in conventional storage conditions. Additionally, the same QTLs were not identified when RIL populations were grown in different years, indicating that lettuce seed longevity is strongly affected by production environment. Nonetheless, a major QTL on chromosome 4 [Seed longevity 4.1 (Slg4.1)] was responsible for almost 23% of the phenotypic variation in viability of the conventionally stored control seeds of the 2006 RIL population, with improved longevity conferred by the Salinas allele. QTL analyses may enable identification of mechanisms responsible for the sensitivity of primed seeds to CD conditions and breeding for improved seed longevity.

  19. Mapping quantitative trait loci in plant breeding populations : Use of parental haplotype sharing

    NARCIS (Netherlands)

    Jansen, Ritsert C.; Jannink, Jean-Luc; Beavis, William D.

    2003-01-01

    Applied breeding programs evaluate large numbers of progeny derived from multiple related crosses for a wide range of agronomic traits and for tens to hundreds of molecular markers. This study was conducted to determine how these phenotypic and genetic data could be used for routinely mapping

  20. Identification of QTL controlling domestication-related traits in cowpea (Vigna unguiculata L. Walp).

    Science.gov (United States)

    Lo, Sassoum; Muñoz-Amatriaín, María; Boukar, Ousmane; Herniter, Ira; Cisse, Ndiaga; Guo, Yi-Ning; Roberts, Philip A; Xu, Shizhong; Fatokun, Christian; Close, Timothy J

    2018-04-19

    Cowpea (Vigna unguiculata L. Walp) is a warm-season legume with a genetically diverse gene-pool composed of wild and cultivated forms. Cowpea domestication involved considerable phenotypic changes from the wild progenitor, including reduction of pod shattering, increased organ size, and changes in flowering time. Little is known about the genetic basis underlying these changes. In this study, 215 recombinant inbred lines derived from a cross between a cultivated and a wild cowpea accession were used to evaluate nine domestication-related traits (pod shattering, peduncle length, flower color, days to flowering, 100-seed weight, pod length, leaf length, leaf width and seed number per pod). A high-density genetic map containing 17,739 single nucleotide polymorphisms was constructed and used to identify 16 quantitative trait loci (QTL) for these nine traits. Based on annotations of the cowpea reference genome, genes within these regions are reported. Four regions with clusters of QTL were identified, including one on chromosome 8 related to increased organ size. This study provides new knowledge of the genomic regions controlling domestication-related traits in cowpea as well as candidate genes underlying those QTL. This information can help to exploit wild relatives in cowpea breeding programs.

  1. Lack of association between PKLR rs3020781 and NOS1AP rs7538490 and type 2 diabetes, overweight, obesity and related metabolic phenotypes in a Danish large-scale study: case-control studies and analyses of quantitative traits

    DEFF Research Database (Denmark)

    Andreasen, Camilla Helene; Mogensen, Mette S.; Borch-Johnsen, Knut

    2008-01-01

    of the variants in relation to overweight and obesity. METHODS: PKLR rs3020781 and NOS1AP rs7538490 were genotyped, using TaqMan allelic discrimination, in a combined study sample comprising a total of 16,801 and 16,913 individuals, respectively. The participants were ascertained from four different study groups...

  2. Combining quantitative trait loci analysis with physiological models to predict genotype-specific transpiration rates.

    Science.gov (United States)

    Reuning, Gretchen A; Bauerle, William L; Mullen, Jack L; McKay, John K

    2015-04-01

    Transpiration is controlled by evaporative demand and stomatal conductance (gs ), and there can be substantial genetic variation in gs . A key parameter in empirical models of transpiration is minimum stomatal conductance (g0 ), a trait that can be measured and has a large effect on gs and transpiration. In Arabidopsis thaliana, g0 exhibits both environmental and genetic variation, and quantitative trait loci (QTL) have been mapped. We used this information to create a genetically parameterized empirical model to predict transpiration of genotypes. For the parental lines, this worked well. However, in a recombinant inbred population, the predictions proved less accurate. When based only upon their genotype at a single g0 QTL, genotypes were less distinct than our model predicted. Follow-up experiments indicated that both genotype by environment interaction and a polygenic inheritance complicate the application of genetic effects into physiological models. The use of ecophysiological or 'crop' models for predicting transpiration of novel genetic lines will benefit from incorporating further knowledge of the genetic control and degree of independence of core traits/parameters underlying gs variation. © 2014 John Wiley & Sons Ltd.

  3. Identification and Characterization of Quantitative Trait Loci for Shattering in Japonica Rice Landrace Jiucaiqing from Taihu Lake Valley, China

    Directory of Open Access Journals (Sweden)

    Jinping Cheng

    2016-11-01

    Full Text Available Easy shattering reduces yield from grain loss during rice ( L. harvest. We characterized a nonshattering rice landrace Jiucaiqing from Taihu Lake valley in China. The breaking tensile strength (BTS; grams force, gf of the grain pedicel was measured using a digital force gauge to evaluate the degree of shattering at 0, 7, 14, 21, 28, and 35 d after heading (DAH. The BTS of Jiucaiqing did not significantly decrease with increasing DAH, maintaining a level of 152.2 to 195.9 gf, while that of IR26 decreased greatly during 0 to 14 DAH and finally stabilized at ∼100 gf. Then the chromosome segment substitution lines (CSSLs and near isogenic lines (NILs of Jiucaiqing in IR26 background were developed for quantitative trait loci (QTL mapping. Four putative QTL (, , , and for shattering were detected, and the was confirmed on chromosome 1. We further mapped to a 98.4-kb region, which contains 14 genes. Os01g62920 was considered to be a strong candidate for , which colocated with . Further quantitative real-time polymerase chain reaction (PCR analyses confirmed that the QTL can significantly decrease the expression of shattering related genes (, , , , and especially at the middle development stage at 10 and 15 cm panicle length, which causes rice shattering decrease. The elite allele and the NIL with desirable agronomic traits identified in this study could be useful for rice breeding.

  4. Impulsivity-related traits and their relation to DSM-5 section II and III personality disorders.

    Science.gov (United States)

    Few, Lauren R; Lynam, Donald R; Miller, Joshua D

    2015-07-01

    Difficulties with impulse control are considered a core feature of personality disorders (PDs) as assessed by the Diagnostic and Statistical Manual of Mental Disorders (5th edition [DSM-5]; American Psychiatric Association, 2013). Despite this, there has been relatively little examination of the manner in which DSM-5 PDs are characterized by multidimensional models of impulsivity that parse this broad umbrella construct into smaller, more unidimensional constructs. Using the UPPS model and measure of impulsivity (Whiteside & Lynam, 2001), the relations between 4 impulsivity-related traits and interview-rated scores on both DSM-5 Section II and III PDs and PD traits were examined in a community sample of individuals currently receiving psychological or psychiatric care (N = 106). As expected, the UPPS traits manifested correlations with the new Section III trait model that were generally consistent with the assertion that this new DSM-5 trait model reflects a pathological variant of the Five-Factor Model (FFM; e.g., UPPS traits associated with FFM conscientiousness were most strongly related to DSM-5 disinhibition traits). Overall, the UPPS traits accounted best for variance in DSM-5 Section II and III Cluster B PDs, consistent with these PDs being characterized, in part, by emotionally and cognitively based forms of impulsivity. (c) 2015 APA, all rights reserved).

  5. Detection of quantitative trait loci in Danish Holstein cattle affecting clinical mastitis, somatic cell score, udder conformation traits, and assessment of associated effects on milk yield

    DEFF Research Database (Denmark)

    Lund, M S; Guldbrandtsen, B; Buitenhuis, A J

    2008-01-01

    The aim of this study was to 1) detect QTL across the cattle genome that influence the incidence of clinical mastitis and somatic cell score (SCS) in Danish Holsteins, and 2) characterize these QTL for pleiotropy versus multiple linked quantitative trait loci (QTL) when chromosomal regions...... affecting clinical mastitis were also affecting other traits in the Danish udder health index or milk production traits. The chromosomes were scanned using a granddaughter design where markers were typed for 19 to 34 grandsire families and 1,373 to 2,042 sons. A total of 356 microsatellites covering all 29...... autosomes were used in the scan. Among the across-family regression analyses, 16 showed chromosome-wide significance for the primary traits incidence of clinical mastitis in first (CM1), second (CM2), and third (CM3) lactations, and SCS. Regions of chromosomes 5, 6, 9, 11, 15, and 26 were found to affect CM...

  6. Alternative models for detection of quantitative trait loci (QTL) for growth and carcass traits in pigs chromosomes 4, 5 and 7

    NARCIS (Netherlands)

    Moraes Gonçalves, de T.; Nunes de Oliveira, H.; Bovenhuis, H.; Bink, M.C.A.M.; Arendonk, van J.A.M.

    2005-01-01

    Genome scans can be used to identify chromosomal regions and eventually genes that control quantitative traits (QTL) of economic importance. In an experimental cross between Meishan (male) and Dutch Large White and Landrace lines (female), 298 F1 and 831 F2 animals were evaluated for intramuscular

  7. Quantitative trait loci for live animal and carcass composition traits in Jersey and Limousin back-cross cattle finished on pasture or feedlot.

    Science.gov (United States)

    Morris, C A; Pitchford, W S; Cullen, N G; Esmailizadeh, A K; Hickey, S M; Hyndman, D; Dodds, K G; Afolayan, R A; Crawford, A M; Bottema, C D K

    2009-10-01

    A quantitative trait locus (QTL) study was carried out in two countries, recording live animal and carcass composition traits. Back-cross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin breed backgrounds. The New Zealand cattle were reared on pasture to carcass weights averaging 229 kg, whilst the Australian cattle were reared on grass and finished on grain (for at least 180 days) to carcass weights averaging 335 kg. From 11 live animal traits and 31 carcass composition traits respectively, 5 and 22 QTL were detected in combined-sire analyses, which were significant (P < 0.05) on a genome-wise basis. Fourteen significant traits for carcass composition QTL were on chromosome 2 and these were traits associated with muscling and fatness. This chromosome carried a variant myostatin allele (F94L), segregating from the Limousin ancestry. Despite very different cattle management systems between the two countries, the two populations had a large number of QTL in common. Of the 18 traits which were common to both countries, and which had significant QTL at the genome-wise level, eight were significant in both countries.

  8. Estimating Body Related Soft Biometric Traits in Video Frames

    Directory of Open Access Journals (Sweden)

    Olasimbo Ayodeji Arigbabu

    2014-01-01

    Full Text Available Soft biometrics can be used as a prescreening filter, either by using single trait or by combining several traits to aid the performance of recognition systems in an unobtrusive way. In many practical visual surveillance scenarios, facial information becomes difficult to be effectively constructed due to several varying challenges. However, from distance the visual appearance of an object can be efficiently inferred, thereby providing the possibility of estimating body related information. This paper presents an approach for estimating body related soft biometrics; specifically we propose a new approach based on body measurement and artificial neural network for predicting body weight of subjects and incorporate the existing technique on single view metrology for height estimation in videos with low frame rate. Our evaluation on 1120 frame sets of 80 subjects from a newly compiled dataset shows that the mentioned soft biometric information of human subjects can be adequately predicted from set of frames.

  9. Little effect of HSP90 inhibition on the quantitative wing traits variation in Drosophila melanogaster.

    Science.gov (United States)

    Takahashi, Kazuo H

    2017-02-01

    Drosophila wings have been a model system to study the effect of HSP90 on quantitative trait variation. The effect of HSP90 inhibition on environmental buffering of wing morphology varies among studies while the genetic buffering effect of it was examined in only one study and was not detected. Variable results so far might show that the genetic background influences the environmental and genetic buffering effect of HSP90. In the previous studies, the number of the genetic backgrounds used is limited. To examine the effect of HSP90 inhibition with a larger number of genetic backgrounds than the previous studies, 20 wild-type strains of Drosophila melanogaster were used in this study. Here I investigated the effect of HSP90 inhibition on the environmental buffering of wing shape and size by assessing within-individual and among-individual variations, and as a result, I found little or very weak effects on environmental and genetic buffering. The current results suggest that the role of HSP90 as a global regulator of environmental and genetic buffering is limited at least in quantitative traits.

  10. Identifying the genes underlying quantitative traits: a rationale for the QTN programme.

    Science.gov (United States)

    Lee, Young Wha; Gould, Billie A; Stinchcombe, John R

    2014-01-01

    The goal of identifying the genes or even nucleotides underlying quantitative and adaptive traits has been characterized as the 'QTN programme' and has recently come under severe criticism. Part of the reason for this criticism is that much of the QTN programme has asserted that finding the genes and nucleotides for adaptive and quantitative traits is a fundamental goal, without explaining why it is such a hallowed goal. Here we outline motivations for the QTN programme that offer general insight, regardless of whether QTNs are of large or small effect, and that aid our understanding of the mechanistic dynamics of adaptive evolution. We focus on five areas: (i) vertical integration of insight across different levels of biological organization, (ii) genetic parallelism and the role of pleiotropy in shaping evolutionary dynamics, (iii) understanding the forces maintaining genetic variation in populations, (iv) distinguishing between adaptation from standing variation and new mutation, and (v) the role of genomic architecture in facilitating adaptation. We argue that rather than abandoning the QTN programme, we should refocus our efforts on topics where molecular data will be the most effective for testing hypotheses about phenotypic evolution.

  11. Identifying the genes underlying quantitative traits: a rationale for the QTN programme

    Science.gov (United States)

    Lee, Young Wha; Gould, Billie A.; Stinchcombe, John R.

    2014-01-01

    The goal of identifying the genes or even nucleotides underlying quantitative and adaptive traits has been characterized as the ‘QTN programme’ and has recently come under severe criticism. Part of the reason for this criticism is that much of the QTN programme has asserted that finding the genes and nucleotides for adaptive and quantitative traits is a fundamental goal, without explaining why it is such a hallowed goal. Here we outline motivations for the QTN programme that offer general insight, regardless of whether QTNs are of large or small effect, and that aid our understanding of the mechanistic dynamics of adaptive evolution. We focus on five areas: (i) vertical integration of insight across different levels of biological organization, (ii) genetic parallelism and the role of pleiotropy in shaping evolutionary dynamics, (iii) understanding the forces maintaining genetic variation in populations, (iv) distinguishing between adaptation from standing variation and new mutation, and (v) the role of genomic architecture in facilitating adaptation. We argue that rather than abandoning the QTN programme, we should refocus our efforts on topics where molecular data will be the most effective for testing hypotheses about phenotypic evolution. PMID:24790125

  12. Identification of QTLs for grain yield and grain-related traits of maize (Zea mays L.) using an AFLP-map, different testers, and cofactor analysis

    NARCIS (Netherlands)

    Ajimone Marsan, P.; Gorni, C.; Chitto, A.; Redaelli, R.; Vijk, van R.; Stam, P.; Motto, M.

    2001-01-01

    Abstract We exploited the AFLP?1(AFLP? is a registered trademark of Keygene, N.V.) technique to map and characterise quantitative trait loci (QTLs) for grain yield and two grain-related traits of a maize segregating population. Two maize elite inbred lines were crossed to produce 229 F2 individuals

  13. Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding

    Science.gov (United States)

    Fu, Yong-Bi; Yang, Mo-Hua; Zeng, Fangqin; Biligetu, Bill

    2017-01-01

    Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST) SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding. PMID:28729875

  14. Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding

    Directory of Open Access Journals (Sweden)

    Yong-Bi Fu

    2017-07-01

    Full Text Available Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding.

  15. Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding.

    Science.gov (United States)

    Fu, Yong-Bi; Yang, Mo-Hua; Zeng, Fangqin; Biligetu, Bill

    2017-01-01

    Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST) SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding.

  16. QTL Analysis of Kernel-Related Traits in Maize Using an Immortalized F2 Population

    Science.gov (United States)

    Hu, Yanmin; Li, Weihua; Fu, Zhiyuan; Ding, Dong; Li, Haochuan; Qiao, Mengmeng; Tang, Jihua

    2014-01-01

    Kernel size and weight are important determinants of grain yield in maize. In this study, multivariate conditional and unconditional quantitative trait loci (QTL), and digenic epistatic analyses were utilized in order to elucidate the genetic basis for these kernel-related traits. Five kernel-related traits, including kernel weight (KW), volume (KV), length (KL), thickness (KT), and width (KWI), were collected from an immortalized F2 (IF2) maize population comprising of 243 crosses performed at two separate locations over a span of two years. A total of 54 unconditional main QTL for these five kernel-related traits were identified, many of which were clustered in chromosomal bins 6.04–6.06, 7.02–7.03, and 10.06–10.07. In addition, qKL3, qKWI6, qKV10a, qKV10b, qKW10a, and qKW7a were detected across multiple environments. Sixteen main QTL were identified for KW conditioned on the other four kernel traits (KL, KWI, KT, and KV). Thirteen main QTL were identified for KV conditioned on three kernel-shape traits. Conditional mapping analysis revealed that KWI and KV had the strongest influence on KW at the individual QTL level, followed by KT, and then KL; KV was mostly strongly influenced by KT, followed by KWI, and was least impacted by KL. Digenic epistatic analysis identified 18 digenic interactions involving 34 loci over the entire genome. However, only a small proportion of them were identical to the main QTL we detected. Additionally, conditional digenic epistatic analysis revealed that the digenic epistasis for KW and KV were entirely determined by their constituent traits. The main QTL identified in this study for determining kernel-related traits with high broad-sense heritability may play important roles during kernel development. Furthermore, digenic interactions were shown to exert relatively large effects on KL (the highest AA and DD effects were 4.6% and 6.7%, respectively) and KT (the highest AA effects were 4.3%). PMID:24586932

  17. Characterization of variation and quantitative trait loci related to ...

    Indian Academy of Sciences (India)

    2012-04-13

    Apr 13, 2012 ... heterologous organisms for increasing the yield of .... to be genetically distant by morphological, biochemical and molecular analyses ... some modifications was used for the extraction of alkaloids from the dry samples of ...

  18. Maternal and pregnancy related predictors of cardiometabolic traits in newborns.

    Directory of Open Access Journals (Sweden)

    Katherine M Morrison

    Full Text Available BACKGROUND: The influence of multiple maternal and pregnancy characteristics on offspring cardiometabolic traits at birth is not well understood and was evaluated in this study. METHODS AND FINDINGS: The Family Atherosclerosis Monitoring In earLY life (FAMILY Study prospectively evaluated 11 cardiometabolic traits in 901 babies born to 857 mothers. The influence of maternal age, health (pre-pregnancy weight, blood pressure, glycemic status, lipids, health behaviors (diet, activity, smoking and pregnancy characteristics (gestational age at birth, gestational weight gain and placental-fetal ratio were examined. Greater gestational age influenced multiple newborn cardiometabolic traits including cord blood lipids, glucose and insulin, body fat and blood pressure. In a subset of 442 singleton mother/infant pairs, principal component analysis grouped 11 newborn cardiometabolic traits into 5 components (anthropometry/insulin, 2 lipid components, blood pressure and glycemia, accounting for 74% of the variance of the 11 outcome variables. Determinants of these components, corrected for sex and gestational age, were examined. Baby anthropometry/insulin was independently predicted by higher maternal pre-pregnancy weight (standardized estimate 0.30 and gestational weight gain (0.30; both p<0.0001 and was inversely related to smoking during pregnancy (-0.144; p = 0.01 and maternal polyunsaturated to saturated fat intake (-0.135;p = 0.01. Component 2 (HDL-C/Apo Apolipoprotein1 was inversely associated with maternal age. Component 3 (blood pressure was not clustered with any other newborn cardiometabolic trait and no associations with maternal pregnancy characteristics were identified. Component 4 (triglycerides was positively associated with maternal hypertension and triglycerides, and inversely associated with maternal HDL and age. Component 5 (glycemia was inversely associated with placental/fetal ratio (-0.141; p = 0.005. LDL-C was a bridging

  19. Impulsivity traits and addiction-related behaviors in youth

    DEFF Research Database (Denmark)

    Rømer Thomsen, Kristine; Callesen, Mette Buhl; Hesse, Morten

    2018-01-01

    problems to achieve a broad distribution of involvement in addiction-related behaviors. Participants completed the UPPS-P Questionnaire and standardized questionnaires assessing problematic use of substances (alcohol, cannabis, and other drugs) and non-substances (Internet gaming, pornography, and food...... eating and lack of perseverance was associated with problematic use of pornography. Discussion and conclusions We emphasize the role of trait impulsivity across multiple addiction-related behaviors. Our findings in at-risk youth highlight urgency and lack of perseverance as potential predictors...

  20. The sensitivity of murine spermiogenesis to miglustat is a quantitative trait: a pharmacogenetic study

    Directory of Open Access Journals (Sweden)

    Boomkamp Stephanie

    2007-01-01

    parental strains. Conclusion The effects of miglustat on spermatogenesis in mice are strain-dependent, while in rabbits the drug is ineffective. Evaluation of interstrain hybrid mice indicated that the sensitivity of spermatogenesis to miglustat is a quantitative trait. These studies pave the way for identifying the genetic factors underlying the strain/species differences in the effect of miglustat.

  1. Are quantitative trait-dependent sampling designs cost-effective for analysis of rare and common variants?

    Science.gov (United States)

    Yilmaz, Yildiz E; Bull, Shelley B

    2011-11-29

    Use of trait-dependent sampling designs in whole-genome association studies of sequence data can reduce total sequencing costs with modest losses of statistical efficiency. In a quantitative trait (QT) analysis of data from the Genetic Analysis Workshop 17 mini-exome for unrelated individuals in the Asian subpopulation, we investigate alternative designs that sequence only 50% of the entire cohort. In addition to a simple random sampling design, we consider extreme-phenotype designs that are of increasing interest in genetic association analysis of QTs, especially in studies concerned with the detection of rare genetic variants. We also evaluate a novel sampling design in which all individuals have a nonzero probability of being selected into the sample but in which individuals with extreme phenotypes have a proportionately larger probability. We take differential sampling of individuals with informative trait values into account by inverse probability weighting using standard survey methods which thus generalizes to the source population. In replicate 1 data, we applied the designs in association analysis of Q1 with both rare and common variants in the FLT1 gene, based on knowledge of the generating model. Using all 200 replicate data sets, we similarly analyzed Q1 and Q4 (which is known to be free of association with FLT1) to evaluate relative efficiency, type I error, and power. Simulation study results suggest that the QT-dependent selection designs generally yield greater than 50% relative efficiency compared to using the entire cohort, implying cost-effectiveness of 50% sample selection and worthwhile reduction of sequencing costs.

  2. Discovery of quantitative trait loci for crossability from a synthetic wheat genotype

    Institute of Scientific and Technical Information of China (English)

    Li Zhang; Jin Wang; Ronghua Zhou; Jizeng Jia

    2011-01-01

    Crossability between wheat and rye is an important trait for wheat improvement.No quantitative trait loci (QTLs) were detected from wheat ancestors previously.The objectives of this study were to dissect the QTLs for crossability using 111 introgression lines (ILs) derived from synthetic hexaploid wheat.A total of 1275 SSR markers were screened for polymorphism between the two parents,and 552 markers of them displayed polymorphism,of which 64 were selected for genotyping the 111 BC5F6 ILs.Field trials were performed in a Latinized α-lattice design in Luoyang and Jiaozuo of Henan Province of China in 2007-2008 and 2008-2009 cropping seasons.One-way ANOVA and interval mapping (IM) analysis were used to detect QTL for crossability between wheat and rye.A total of 13 putative QTLs were detected.Five of them,QCa.caas.1A,QCa.caas.2D,QCa.caas.4B,QCa.caas.5B and QCa.caas.6A,were detected in both trials and three of them,QCa.caas.2D,QCa.caas.4B and QCa.caas.6A,were novel.The positive effect allele of the four QTLs came from the donor parent Am3 except QCa.caas.6A that came from the recurrent parent Laizhou953.ILs with both higher positive effect alleles and favorable agronomic traits developed in present study are elite germplasm for wide crossing in wheat.Results from the current study suggest that wheat ancestors can be rich in new sources of crossability genes.

  3. Trait aggression and trait impulsivity are not related to frontal cortex 5-HT2A receptor binding in healthy individuals

    DEFF Research Database (Denmark)

    da Cunha-Bang, Sophie; Stenbæk, Dea Siggaard; Holst, Klaus

    2013-01-01

    age 47.0±18.7, range 23-86) to determine if trait aggression and trait impulsivity were related to frontal cortex 5-HT2A receptor binding (5-HT2AR) as measured with [(18)F]-altanserin PET imaging. Trait aggression and trait impulsivity were assessed with the Buss-Perry Aggression Questionnaire (AQ...... and the AQ or BIS-11 total scores. Also, there was no significant interaction between gender and frontal cortex 5-HT2AR in predicting trait aggression and trait impulsivity. This is the first study to examine how 5-HT2AR relates to trait aggression and trait impulsivity in a large sample of healthy......Numerous studies indicate that the serotonergic (5-HT) transmitter system is involved in the regulation of impulsive aggression and there is from post-mortem, in vivo imaging and genetic studies evidence that the 5-HT2A receptor may be involved. We investigated 94 healthy individuals (60 men, mean...

  4. Quantitative Trait Loci Analysis of Seed Quality Characteristics in Lentil using Single Nucleotide Polymorphism Markers

    Directory of Open Access Journals (Sweden)

    Michael J. Fedoruk

    2013-11-01

    Full Text Available Seed shape, color, and pattern of lentil ( Medik. subsp. are important quality traits as they determine market class and possible end uses. A recombinant inbred line population was phenotyped for seed dimensions over multiple site–years and classified according to cotyledon and seed coat color and pattern. The objectives were to determine the heritability of seed dimensions, identify genomic regions controlling these dimensions, and map seed coat and cotyledon color genes. A genetic linkage map consisting of 563 single nucleotide polymorphisms, 10 simple sequence repeats, and four seed color loci was developed for quantitative trait loci (QTL analysis. Loci for seed coat color and pattern mapped to linkage groups 2 (, 3 (, and 6 ( while the cotyledon color locus ( mapped to linkage group 1. The broad sense heritability estimates were high for seed diameter (broad-sense heritability [] = 0.92 and seed plumpness ( = 0.94 while seed thickness ( = 0.60 and days to flowering ( = 0.45 were more moderate. There were significant seed dimension QTL on six of the seven linkage groups. The most significant QTL for diameter and plumpness was found at the cotyledon color locus (. The markers identified in this study can be used to help enrich breeding populations for desired seed quality characteristics, thereby increasing efficiency in the lentil breeding program.

  5. Targeted introgression of cotton fibre quality quantitative trait loci using molecular markers

    International Nuclear Information System (INIS)

    Lacape, J.M.; Trung-Bieu Nguyen; Hau, B.; Giband, M.

    2007-01-01

    Within the framework of a cotton breeding programme, molecular markers are used to improve the efficiency of the introgression of fibre quality traits of Gossypium barbadense into G. hirsutum. A saturated genetic map was developed based on genotyping data obtained from the BC 1 (75 plants) and BC 2 (200 plants) generations. Phenotypic measurements conducted over three generations (BC 1 , BC 2 and BC 2 S 1 ) allowed 80 quantitative trait loci (QTL) to be detected for fibre length, uniformity, strength, elongation, fineness and colour. Positive QTL, i.e. those for which favourable alleles came from the G. barbadense parent, were harboured by 19 QTL-rich regions on 15 'carrier' chromosomes. In subsequent generations (BC 3 and BC 4 ), markers framing the QTL-rich regions were used to select about 10 percent of over 400 plants analysed in each generation. Although BC plants selected through the marker-assisted selection (MAS) process show promising fibre quality, only their full field evaluation will allow validation of the procedure. (author)

  6. Quantitative traits for the tail suspension test: automation, optimization, and BXD RI mapping.

    Science.gov (United States)

    Lad, Heena V; Liu, Lin; Payá-Cano, José L; Fernandes, Cathy; Schalkwyk, Leonard C

    2007-07-01

    Immobility in the tail suspension test (TST) is considered a model of despair in a stressful situation, and acute treatment with antidepressants reduces immobility. Inbred strains of mouse exhibit widely differing baseline levels of immobility in the TST and several quantitative trait loci (QTLs) have been nominated. The labor of manual scoring and various scoring criteria make obtaining robust data and comparisons across different laboratories problematic. Several studies have validated strain gauge and video analysis methods by comparison with manual scoring. We set out to find objective criteria for automated scoring parameters that maximize the biological information obtained, using a video tracking system on tapes of tail suspension tests of 24 lines of the BXD recombinant inbred panel and the progenitor strains C57BL/6J and DBA/2J. The maximum genetic effect size is captured using the highest time resolution and a low mobility threshold. Dissecting the trait further by comparing genetic association of multiple measures reveals good evidence for loci involved in immobility on chromosomes 4 and 15. These are best seen when using a high threshold for immobility, despite the overall better heritability at the lower threshold. A second trial of the test has greater duration of immobility and a completely different genetic profile. Frequency of mobility is also an independent phenotype, with a distal chromosome 1 locus.

  7. Generation mean analysis for quantitative traits in sesame (Sesamum indicum L. crosses

    Directory of Open Access Journals (Sweden)

    Vijayarajan Sharmila

    2007-01-01

    Full Text Available To study the nature and magnitude of gene effects for yield and its components in sesame (Sesamum indicum L. we carried out generation mean analysis using the following four crosses of different sesame cultivars: VS 9510 x Co1; NIC 7907 x TMV 3; Cianno 13/10x VRI 1; and Si 1115/1 x TMV 3. The P1, P2, F1, F2, BC1 and BC2 of these generations were studied for seven quantitative traits. The analysis showed the presence of additive, dominance and epistatic gene interactions. The additive dominance model was adequate for plant height in the NIC 7907 x TMV3 and Si 1115/1x TMV 3 crosses and for capsule length in the VS 9510 x Co1, NIC 7907 x TMV 3 and Si 1115/1 x TMV 3 crosses. An epistatic digenic model was assumed for the remaining crosses. Duplicate-type epistasis played a greater role than complementary epistasis. The study revealed the importance of both additive and non-additive types of gene action for all the traits studied.

  8. Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice.

    Science.gov (United States)

    Lou, Qiaojun; Chen, Liang; Mei, Hanwei; Wei, Haibin; Feng, Fangjun; Wang, Pei; Xia, Hui; Li, Tiemei; Luo, Lijun

    2015-08-01

    Deep rooting is a very important trait for plants' drought avoidance, and it is usually represented by the ratio of deep rooting (RDR). Three sets of rice populations were used to determine the genetic base for RDR. A linkage mapping population with 180 recombinant inbred lines and an association mapping population containing 237 rice varieties were used to identify genes linked to RDR. Six quantitative trait loci (QTLs) of RDR were identified as being located on chromosomes 1, 2, 4, 7, and 10. Using 1 019 883 single-nucleotide polymorphisms (SNPs), a genome-wide association study of the RDR was performed. Forty-eight significant SNPs of the RDR were identified and formed a clear peak on the short arm of chromosome 1 in a Manhattan plot. Compared with the shallow-rooting group and the whole collection, the deep-rooting group had selective sweep regions on chromosomes 1 and 2, especially in the major QTL region on chromosome 2. Seven of the nine candidate SNPs identified by association mapping were verified in two RDR extreme groups. The findings from this study will be beneficial to rice drought-resistance research and breeding. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  9. Six quantitative trait loci influence task thresholds for hygienic behaviour in honeybees (Apis mellifera).

    Science.gov (United States)

    Oxley, Peter R; Spivak, Marla; Oldroyd, Benjamin P

    2010-04-01

    Honeybee hygienic behaviour provides colonies with protection from many pathogens and is an important model system of the genetics of a complex behaviour. It is a textbook example of complex behaviour under simple genetic control: hygienic behaviour consists of two components--uncapping a diseased brood cell, followed by removal of the contents--each of which are thought to be modulated independently by a few loci of medium to large effect. A worker's genetic propensity to engage in hygienic tasks affects the intensity of the stimulus required before she initiates the behaviour. Genetic diversity within colonies leads to task specialization among workers, with a minority of workers performing the majority of nest-cleaning tasks. We identify three quantitative trait loci that influence the likelihood that workers will engage in hygienic behaviour and account for up to 30% of the phenotypic variability in hygienic behaviour in our population. Furthermore, we identify two loci that influence the likelihood that a worker will perform uncapping behaviour only, and one locus that influences removal behaviour. We report the first candidate genes associated with engaging in hygienic behaviour, including four genes involved in olfaction, learning and social behaviour, and one gene involved in circadian locomotion. These candidates will allow molecular characterization of this distinctive behavioural mode of disease resistance, as well as providing the opportunity for marker-assisted selection for this commercially significant trait.

  10. Limits to behavioral evolution: the quantitative genetics of a complex trait under directional selection.

    Science.gov (United States)

    Careau, Vincent; Wolak, Matthew E; Carter, Patrick A; Garland, Theodore

    2013-11-01

    Replicated selection experiments provide a powerful way to study how "multiple adaptive solutions" may lead to differences in the quantitative-genetic architecture of selected traits and whether this may translate into differences in the timing at which evolutionary limits are reached. We analyze data from 31 generations (n=17,988) of selection on voluntary wheel running in house mice. The rate of initial response, timing of selection limit, and height of the plateau varied significantly between sexes and among the four selected lines. Analyses of litter size and realized selection differentials seem to rule out counterposing natural selection as a cause of the selection limits. Animal-model analyses showed that although the additive genetic variance was significantly lower in selected than control lines, both before and after the limits, the decrease was not sufficient to explain the limits. Moreover, directional selection promoted a negative covariance between additive and maternal genetic variance over the first 10 generations. These results stress the importance of replication in selection studies of higher-level traits and highlight the fact that long-term predictions of response to selection are not necessarily expected to be linear because of the variable effects of selection on additive genetic variance and maternal effects. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  11. Mapping of imprinted quantitative trait loci using immortalized F2 populations.

    Directory of Open Access Journals (Sweden)

    Yongxian Wen

    Full Text Available Mapping of imprinted quantitative trait loci (iQTLs is helpful for understanding the effects of genomic imprinting on complex traits in animals and plants. At present, the experimental designs and corresponding statistical methods having been proposed for iQTL mapping are all based on temporary populations including F2 and BC1, which can be used only once and suffer some other shortcomings respectively. In this paper, we propose a framework for iQTL mapping, including methods of interval mapping (IM and composite interval mapping (CIM based on conventional low-density genetic maps and point mapping (PM and composite point mapping (CPM based on ultrahigh-density genetic maps, using an immortalized F2 (imF2 population generated by random crosses between recombinant inbred lines or doubled haploid lines. We demonstrate by simulations that imF2 populations are very desirable and the proposed statistical methods (especially CIM and CPM are very powerful for iQTL mapping, with which the imprinting effects as well as the additive and dominance effects of iQTLs can be unbiasedly estimated.

  12. SplicePlot: a utility for visualizing splicing quantitative trait loci.

    Science.gov (United States)

    Wu, Eric; Nance, Tracy; Montgomery, Stephen B

    2014-04-01

    RNA sequencing has provided unprecedented resolution of alternative splicing and splicing quantitative trait loci (sQTL). However, there are few tools available for visualizing the genotype-dependent effects of splicing at a population level. SplicePlot is a simple command line utility that produces intuitive visualization of sQTLs and their effects. SplicePlot takes mapped RNA sequencing reads in BAM format and genotype data in VCF format as input and outputs publication-quality Sashimi plots, hive plots and structure plots, enabling better investigation and understanding of the role of genetics on alternative splicing and transcript structure. Source code and detailed documentation are available at http://montgomerylab.stanford.edu/spliceplot/index.html under Resources and at Github. SplicePlot is implemented in Python and is supported on Linux and Mac OS. A VirtualBox virtual machine running Ubuntu with SplicePlot already installed is also available.

  13. Linkage of DNA Methylation Quantitative Trait Loci to Human Cancer Risk

    Directory of Open Access Journals (Sweden)

    Holger Heyn

    2014-04-01

    Full Text Available Epigenetic regulation and, in particular, DNA methylation have been linked to the underlying genetic sequence. DNA methylation quantitative trait loci (meQTL have been identified through significant associations between the genetic and epigenetic codes in physiological and pathological contexts. We propose that interrogating the interplay between polymorphic alleles and DNA methylation is a powerful method for improving our interpretation of risk alleles identified in genome-wide association studies that otherwise lack mechanistic explanation. We integrated patient cancer risk genotype data and genome-scale DNA methylation profiles of 3,649 primary human tumors, representing 13 solid cancer types. We provide a comprehensive meQTL catalog containing DNA methylation associations for 21% of interrogated cancer risk polymorphisms. Differentially methylated loci harbor previously reported and as-yet-unidentified cancer genes. We suggest that such regulation at the DNA level can provide a considerable amount of new information about the biology of cancer-risk alleles.

  14. Fine mapping quantitative trait loci under selective phenotyping strategies based on linkage and linkage disequilibrium criteria

    DEFF Research Database (Denmark)

    Ansari-Mahyari, S; Berg, P; Lund, M S

    2009-01-01

    disequilibrium-based sampling criteria (LDC) for selecting individuals to phenotype are compared to random phenotyping in a quantitative trait loci (QTL) verification experiment using stochastic simulation. Several strategies based on LAC and LDC for selecting the most informative 30%, 40% or 50% of individuals...... for phenotyping to extract maximum power and precision in a QTL fine mapping experiment were developed and assessed. Linkage analyses for the mapping was performed for individuals sampled on LAC within families and combined linkage disequilibrium and linkage analyses was performed for individuals sampled across...... the whole population based on LDC. The results showed that selecting individuals with similar haplotypes to the paternal haplotypes (minimum recombination criterion) using LAC compared to random phenotyping gave at least the same power to detect a QTL but decreased the accuracy of the QTL position. However...

  15. A quantitative trait locus mixture model that avoids spurious LOD score peaks.

    Science.gov (United States)

    Feenstra, Bjarke; Skovgaard, Ib M

    2004-06-01

    In standard interval mapping of quantitative trait loci (QTL), the QTL effect is described by a normal mixture model. At any given location in the genome, the evidence of a putative QTL is measured by the likelihood ratio of the mixture model compared to a single normal distribution (the LOD score). This approach can occasionally produce spurious LOD score peaks in regions of low genotype information (e.g., widely spaced markers), especially if the phenotype distribution deviates markedly from a normal distribution. Such peaks are not indicative of a QTL effect; rather, they are caused by the fact that a mixture of normals always produces a better fit than a single normal distribution. In this study, a mixture model for QTL mapping that avoids the problems of such spurious LOD score peaks is presented.

  16. On coding genotypes for genetic markers with multiple alleles in genetic association study of quantitative traits

    Directory of Open Access Journals (Sweden)

    Wang Tao

    2011-09-01

    Full Text Available Abstract Background In genetic association study of quantitative traits using F∞ models, how to code the marker genotypes and interpret the model parameters appropriately is important for constructing hypothesis tests and making statistical inferences. Currently, the coding of marker genotypes in building F∞ models has mainly focused on the biallelic case. A thorough work on the coding of marker genotypes and interpretation of model parameters for F∞ models is needed especially for genetic markers with multiple alleles. Results In this study, we will formulate F∞ genetic models under various regression model frameworks and introduce three genotype coding schemes for genetic markers with multiple alleles. Starting from an allele-based modeling strategy, we first describe a regression framework to model the expected genotypic values at given markers. Then, as extension from the biallelic case, we introduce three coding schemes for constructing fully parameterized one-locus F∞ models and discuss the relationships between the model parameters and the expected genotypic values. Next, under a simplified modeling framework for the expected genotypic values, we consider several reduced one-locus F∞ models from the three coding schemes on the estimability and interpretation of their model parameters. Finally, we explore some extensions of the one-locus F∞ models to two loci. Several fully parameterized as well as reduced two-locus F∞ models are addressed. Conclusions The genotype coding schemes provide different ways to construct F∞ models for association testing of multi-allele genetic markers with quantitative traits. Which coding scheme should be applied depends on how convenient it can provide the statistical inferences on the parameters of our research interests. Based on these F∞ models, the standard regression model fitting tools can be used to estimate and test for various genetic effects through statistical contrasts with the

  17. Joint analysis of quantitative trait loci and major-effect causative mutations affecting meat quality and carcass composition traits in pigs.

    Science.gov (United States)

    Cherel, Pierre; Pires, José; Glénisson, Jérôme; Milan, Denis; Iannuccelli, Nathalie; Hérault, Frédéric; Damon, Marie; Le Roy, Pascale

    2011-08-29

    Detection of quantitative trait loci (QTLs) affecting meat quality traits in pigs is crucial for the design of efficient marker-assisted selection programs and to initiate efforts toward the identification of underlying polymorphisms. The RYR1 and PRKAG3 causative mutations, originally identified from major effects on meat characteristics, can be used both as controls for an overall QTL detection strategy for diversely affected traits and as a scale for detected QTL effects. We report on a microsatellite-based QTL detection scan including all autosomes for pig meat quality and carcass composition traits in an F2 population of 1,000 females and barrows resulting from an intercross between a Pietrain and a Large White-Hampshire-Duroc synthetic sire line. Our QTL detection design allowed side-by-side comparison of the RYR1 and PRKAG3 mutation effects seen as QTLs when segregating at low frequencies (0.03-0.08), with independent QTL effects detected from most of the same population, excluding any carrier of these mutations. Large QTL effects were detected in the absence of the RYR1 and PRKGA3 mutations, accounting for 12.7% of phenotypic variation in loin colour redness CIE-a* on SSC6 and 15% of phenotypic variation in glycolytic potential on SSC1. We detected 8 significant QTLs with effects on meat quality traits and 20 significant QTLs for carcass composition and growth traits under these conditions. In control analyses including mutation carriers, RYR1 and PRKAG3 mutations were detected as QTLs, from highly significant to suggestive, and explained 53% to 5% of the phenotypic variance according to the trait. Our results suggest that part of muscle development and backfat thickness effects commonly attributed to the RYR1 mutation may be a consequence of linkage with independent QTLs affecting those traits. The proportion of variation explained by the most significant QTLs detected in this work is close to the influence of major-effect mutations on the least affected

  18. Joint analysis of quantitative trait loci and major-effect causative mutations affecting meat quality and carcass composition traits in pigs

    Directory of Open Access Journals (Sweden)

    Iannuccelli Nathalie

    2011-08-01

    Full Text Available Abstract Background Detection of quantitative trait loci (QTLs affecting meat quality traits in pigs is crucial for the design of efficient marker-assisted selection programs and to initiate efforts toward the identification of underlying polymorphisms. The RYR1 and PRKAG3 causative mutations, originally identified from major effects on meat characteristics, can be used both as controls for an overall QTL detection strategy for diversely affected traits and as a scale for detected QTL effects. We report on a microsatellite-based QTL detection scan including all autosomes for pig meat quality and carcass composition traits in an F2 population of 1,000 females and barrows resulting from an intercross between a Pietrain and a Large White-Hampshire-Duroc synthetic sire line. Our QTL detection design allowed side-by-side comparison of the RYR1 and PRKAG3 mutation effects seen as QTLs when segregating at low frequencies (0.03-0.08, with independent QTL effects detected from most of the same population, excluding any carrier of these mutations. Results Large QTL effects were detected in the absence of the RYR1 and PRKGA3 mutations, accounting for 12.7% of phenotypic variation in loin colour redness CIE-a* on SSC6 and 15% of phenotypic variation in glycolytic potential on SSC1. We detected 8 significant QTLs with effects on meat quality traits and 20 significant QTLs for carcass composition and growth traits under these conditions. In control analyses including mutation carriers, RYR1 and PRKAG3 mutations were detected as QTLs, from highly significant to suggestive, and explained 53% to 5% of the phenotypic variance according to the trait. Conclusions Our results suggest that part of muscle development and backfat thickness effects commonly attributed to the RYR1 mutation may be a consequence of linkage with independent QTLs affecting those traits. The proportion of variation explained by the most significant QTLs detected in this work is close to the

  19. QTL variations for growth-related traits in eight distinct families of common carp (Cyprinus carpio).

    Science.gov (United States)

    Lv, Weihua; Zheng, Xianhu; Kuang, Youyi; Cao, Dingchen; Yan, Yunqin; Sun, Xiaowen

    2016-05-05

    affecting body growth. Discovery of these common QTLs between families and growth-related traits represents an important step towards understanding of quantitative genetic variation in common carp.

  20. Quantitative Trait Loci Mapping in Brassica rapa Revealed the Structural and Functional Conservation of Genetic Loci Governing Morphological and Yield Component Traits in the A, B, and C Subgenomes of Brassica Species

    Science.gov (United States)

    Li, Xiaonan; Ramchiary, Nirala; Dhandapani, Vignesh; Choi, Su Ryun; Hur, Yoonkang; Nou, Ill-Sup; Yoon, Moo Kyoung; Lim, Yong Pyo

    2013-01-01

    Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species. PMID:23223793

  1. Mapping and validation of major quantitative trait loci for kernel length in wild barley (Hordeum vulgare ssp. spontaneum).

    Science.gov (United States)

    Zhou, Hong; Liu, Shihang; Liu, Yujiao; Liu, Yaxi; You, Jing; Deng, Mei; Ma, Jian; Chen, Guangdeng; Wei, Yuming; Liu, Chunji; Zheng, Youliang

    2016-09-13

    Kernel length is an important target trait in barley (Hordeum vulgare L.) breeding programs. However, the number of known quantitative trait loci (QTLs) controlling kernel length is limited. In the present study, we aimed to identify major QTLs for kernel length, as well as putative candidate genes that might influence kernel length in wild barley. A recombinant inbred line (RIL) population derived from the barley cultivar Baudin (H. vulgare ssp. vulgare) and the long-kernel wild barley genotype Awcs276 (H.vulgare ssp. spontaneum) was evaluated at one location over three years. A high-density genetic linkage map was constructed using 1,832 genome-wide diversity array technology (DArT) markers, spanning a total of 927.07 cM with an average interval of approximately 0.49 cM. Two major QTLs for kernel length, LEN-3H and LEN-4H, were detected across environments and further validated in a second RIL population derived from Fleet (H. vulgare ssp. vulgare) and Awcs276. In addition, a systematic search of public databases identified four candidate genes and four categories of proteins related to LEN-3H and LEN-4H. This study establishes a fundamental research platform for genomic studies and marker-assisted selection, since LEN-3H and LEN-4H could be used for accelerating progress in barley breeding programs that aim to improve kernel length.

  2. Fabp7 Maps to a Quantitative Trait Locus for a Schizophrenia Endophenotype

    Science.gov (United States)

    Watanabe, Akiko; Toyota, Tomoko; Owada, Yuji; Hayashi, Takeshi; Iwayama, Yoshimi; Matsumata, Miho; Ishitsuka, Yuichi; Nakaya, Akihiro; Maekawa, Motoko; Ohnishi, Tetsuo; Arai, Ryoichi; Sakurai, Katsuyasu; Yamada, Kazuo; Kondo, Hisatake; Hashimoto, Kenji; Osumi, Noriko; Yoshikawa, Takeo

    2007-01-01

    Deficits in prepulse inhibition (PPI) are a biological marker for schizophrenia. To unravel the mechanisms that control PPI, we performed quantitative trait loci (QTL) analysis on 1,010 F2 mice derived by crossing C57BL/6 (B6) animals that show high PPI with C3H/He (C3) animals that show low PPI. We detected six major loci for PPI, six for the acoustic startle response, and four for latency to response peak, some of which were sex-dependent. A promising candidate on the Chromosome 10-QTL was Fabp7 (fatty acid binding protein 7, brain), a gene with functional links to the N-methyl-D-aspartic acid (NMDA) receptor and expression in astrocytes. Fabp7-deficient mice showed decreased PPI and a shortened startle response latency, typical of the QTL's proposed effects. A quantitative complementation test supported Fabp7 as a potential PPI-QTL gene, particularly in male mice. Disruption of Fabp7 attenuated neurogenesis in vivo. Human FABP7 showed altered expression in schizophrenic brains and genetic association with schizophrenia, which were both evident in males when samples were divided by sex. These results suggest that FABP7 plays a novel and crucial role, linking the NMDA, neurodevelopmental, and glial theories of schizophrenia pathology and the PPI endophenotype, with larger or overt effects in males. We also discuss the results from the perspective of fetal programming. PMID:18001149

  3. Fabp7 maps to a quantitative trait locus for a schizophrenia endophenotype.

    Directory of Open Access Journals (Sweden)

    Akiko Watanabe

    2007-11-01

    Full Text Available Deficits in prepulse inhibition (PPI are a biological marker for schizophrenia. To unravel the mechanisms that control PPI, we performed quantitative trait loci (QTL analysis on 1,010 F2 mice derived by crossing C57BL/6 (B6 animals that show high PPI with C3H/He (C3 animals that show low PPI. We detected six major loci for PPI, six for the acoustic startle response, and four for latency to response peak, some of which were sex-dependent. A promising candidate on the Chromosome 10-QTL was Fabp7 (fatty acid binding protein 7, brain, a gene with functional links to the N-methyl-D-aspartic acid (NMDA receptor and expression in astrocytes. Fabp7-deficient mice showed decreased PPI and a shortened startle response latency, typical of the QTL's proposed effects. A quantitative complementation test supported Fabp7 as a potential PPI-QTL gene, particularly in male mice. Disruption of Fabp7 attenuated neurogenesis in vivo. Human FABP7 showed altered expression in schizophrenic brains and genetic association with schizophrenia, which were both evident in males when samples were divided by sex. These results suggest that FABP7 plays a novel and crucial role, linking the NMDA, neurodevelopmental, and glial theories of schizophrenia pathology and the PPI endophenotype, with larger or overt effects in males. We also discuss the results from the perspective of fetal programming.

  4. Borderline personality disorder and related traits in forensic psychiatry.

    Science.gov (United States)

    Reid, William H

    2009-05-01

    Persons with borderline personality disorder (BPD) and related traits appear in many forensic psychiatry settings. Their clinical hallmarks affecting judgment, insight, impulsivity, motivations, and regulation of emotions, as well as their frequently chaotic lives (internal and external), inaccurate perceptions, rationalizations, and comorbid syndromes can have a marked effect on many civil, criminal, and institutional (eg, corrections) issues. Individuals with BPD are overrepresented in civil, criminal, and child custody forensic situations. The character psychopathology of these individuals is substantial, but is often not obvious to laypersons, including lawyers, judges, and jurors. The presence of BPD rarely affects basic responsibility for the person's actions, nor does it usually compromise most forms of competency. Function, not diagnosis, is the key arbiter of forensic relevance. BPD is associated with an increase in the likelihood of doctor-patient problems, including patient complaints and lawsuits that may not be deserved. Forensic professionals evaluating persons with BPD and related traits should be aware of personal and professional bias, particularly that associated with true countertransference.

  5. Sense of Coherence and Personality Traits Related to Depressive State

    Directory of Open Access Journals (Sweden)

    Yoko Kikuchi

    2014-01-01

    Full Text Available Aims. The current study aims to examine the influence of job stress, SOC, and personality traits on depressive state. Methods. A self-reported survey was conducted among 347 female nurses in a general hospital. Job stress was measured using the Japanese version of the Brief-Job Stress Questionnaire scale. Depressive state was assessed by the K6 scale. We used 13-item SOC scale. Personality traits were assessed by the Japanese version of Ten-Item Personality Inventory. Multiple liner regression analyses were conducted to examine predictors that significantly affect depressive state. Results. Job and life satisfaction and SOC negatively related to the depressive state (β=-0.76,  P<0.01;  β=-0.18,  P<0.001, resp. while neuroticism was positively correlated (β=0.49,  P<0.001. Also, intrinsic rewards tended to negatively relate (β=-0.80,  P<0.1. Conclusions. From a practical perspective, the possible influence of SOC and neurotic personality on depressive state should be considered for health care professionals.

  6. Effects of body-size variation on flight-related traits in latitudinal ...

    Indian Academy of Sciences (India)

    2014-04-21

    Apr 21, 2014 ... quantitative traits (Endler 1977; Coyne and Beecham 1987;. Imasheva et al ... Journal of Genetics, Vol. 93, No. 1, April ... ple regression analysis as a function of average tempera- ture(Tave) and ...... Financial assistance (F 41-.

  7. A Simple and Computationally Efficient Approach to Multifactor Dimensionality Reduction Analysis of Gene-Gene Interactions for Quantitative Traits

    OpenAIRE

    Gui, Jiang; Moore, Jason H.; Williams, Scott M.; Andrews, Peter; Hillege, Hans L.; van der Harst, Pim; Navis, Gerjan; Van Gilst, Wiek H.; Asselbergs, Folkert W.; Gilbert-Diamond, Diane

    2013-01-01

    We present an extension of the two-class multifactor dimensionality reduction (MDR) algorithm that enables detection and characterization of epistatic SNP-SNP interactions in the context of a quantitative trait. The proposed Quantitative MDR (QMDR) method handles continuous data by modifying MDR's constructive induction algorithm to use a T-test. QMDR replaces the balanced accuracy metric with a T-test statistic as the score to determine the best interaction model. We used a simulation to ide...

  8. Studies of CTNNBL1 and FDFT1 variants and measures of obesity: analyses of quantitative traits and case-control studies in 18,014 Danes

    DEFF Research Database (Denmark)

    Andreasen, Camilla Helene; Mogensen, Mette Sloth; Borch-Johnsen, Knut

    2009-01-01

    of obesity-related quantitative traits, and case-control studies in large study samples of Danes. METHODS: The FDFT1 rs7001819, CTNNBL1 rs6013029 and rs6020846 were genotyped, using TaqMan allelic discrimination, in a combined study sample comprising 18,014 participants ascertained from; the population...... and a previous study. FDFT1 rs7001819 showed no association with obesity, neither when analysing quantitative traits nor when performing case-control studies of obesity.......). The most significantly associating variants within CTNNBL1 including rs6013029 and rs6020846 were additionally confirmed to associate with morbid obesity in a French Caucasian case-control sample. The aim of this study was to investigate the impact of these three variants on obesity, through analyses...

  9. Effects of Bos taurus autosome 9-located quantitative trait loci haplotypes on enzymatic mastitis indicators of milk from dairy cows experimentally inoculated with Escherichia coli

    DEFF Research Database (Denmark)

    Sørensen, Lars Peter; Engberg, Ricarda Greuel; Løvendahl, Peter

    2015-01-01

    The aim of this study was to investigate the effect of a quantitative trait locus associated with mastitis caused by Escherichia coli, with one haplotype being more susceptible (HH) and another being more resistant (HL) to E. coli mastitis, on the activity of 4 inflammatory related milk enzymes....... In particular, we investigated the suitability of β-glucuronidase (GLU) as an early indicator of E. coli mastitis. Besides GLU, the enzymes l-lactate dehydrogenase (LDH), N-acetyl-β-d-glucosaminidase (NAGase), and alkaline phosphatase were included. The study was conducted in an experimental setup with 31...... Holstein cows divided into 4 groups representing repeated experiments and, within group, divided according to quantitative trait locus haplotype. All cows were inoculated with viable E. coli, and milk samples were collected 27 times from −6 to 396 h post-E. coli inoculation (PI). Activity of the 4 enzymes...

  10. Genetic susceptibility to obesity and related traits in childhood and adolescence

    DEFF Research Database (Denmark)

    den Hoed, Marcel; Ekelund, Ulf; Brage, Søren

    2010-01-01

    Large-scale genome-wide association (GWA) studies have thus far identified 16 loci incontrovertibly associated with obesity-related traits in adults. We examined associations of variants in these loci with anthropometric traits in children and adolescents.......Large-scale genome-wide association (GWA) studies have thus far identified 16 loci incontrovertibly associated with obesity-related traits in adults. We examined associations of variants in these loci with anthropometric traits in children and adolescents....

  11. Genetic and Quantitative Trait Locus Analysis for Bio-Oil Compounds after Fast Pyrolysis in Maize Cobs.

    Directory of Open Access Journals (Sweden)

    Brandon Jeffrey

    Full Text Available Fast pyrolysis has been identified as one of the biorenewable conversion platforms that could be a part of an alternative energy future, but it has not yet received the same attention as cellulosic ethanol in the analysis of genetic inheritance within potential feedstocks such as maize. Ten bio-oil compounds were measured via pyrolysis/gas chromatography-mass spectrometry (Py/GC-MS in maize cobs. 184 recombinant inbred lines (RILs of the intermated B73 x Mo17 (IBM Syn4 population were analyzed in two environments, using 1339 markers, for quantitative trait locus (QTL mapping. QTL mapping was performed using composite interval mapping with significance thresholds established by 1000 permutations at α = 0.05. 50 QTL were found in total across those ten traits with R2 values ranging from 1.7 to 5.8%, indicating a complex quantitative inheritance of these traits.

  12. A simple bias correction in linear regression for quantitative trait association under two-tail extreme selection

    OpenAIRE

    Kwan, Johnny S. H.; Kung, Annie W. C.; Sham, Pak C.

    2011-01-01

    Selective genotyping can increase power in quantitative trait association. One example of selective genotyping is two-tail extreme selection, but simple linear regression analysis gives a biased genetic effect estimate. Here, we present a simple correction for the bias. © The Author(s) 2011.

  13. Mapping of quantitative trait loci for resistance to fall armyworm and southwestern corn borer leaf-feeding damage in maize.

    Science.gov (United States)

    Fall armyworm (FAW), Spodoptera frugiperda (J. E. Smith), and southwestern corn borer (SWCB), Diatraea grandiosella Dyar are damaging insect pests of maize resulting in significant yield and economic losses. A previous study identified quantitative trait loci (QTL) that contribute to reduced leaf-fe...

  14. Quantitative trait loci affecting phenotypic variation in the vacuolated lens mouse mutant, a multigenic mouse model of neural tube defects

    NARCIS (Netherlands)

    Korstanje, Ron; Desai, Jigar; Lazar, Gloria; King, Benjamin; Rollins, Jarod; Spurr, Melissa; Joseph, Jamie; Kadambi, Sindhuja; Li, Yang; Cherry, Allison; Matteson, Paul G.; Paigen, Beverly; Millonig, James H.

    Korstanje R, Desai J, Lazar G, King B, Rollins J, Spurr M, Joseph J, Kadambi S, Li Y, Cherry A, Matteson PG, Paigen B, Millonig JH. Quantitative trait loci affecting phenotypic variation in the vacuolated lens mouse mutant, a multigenic mouse model of neural tube defects. Physiol Genomics 35:

  15. Varied definitions of risk related to sensation seeking trait

    International Nuclear Information System (INIS)

    Daastoel, P.Oe.U.; Drottz-Sjoeberg, B.M.

    1999-01-01

    This pilot study is based on the assumption and the knowledge that previous results show that the normal use of the word risk varies across subjects. The risk definitions the subjects use have also been shown to be related to various educational interests. A related field of research has developed measures for Sensation Seeking personality trait, with four facets. Three independent groups of first year psychology students reported their normal definition of the word risk using one of three measurement formats. The results showed, e.g. that the typical open-ended response to the personal definition of risk was danger. Subjects who defined risk as the combination of probability and consequences tended to score higher on the total Sensation Seeking Scale, as compared to those defining risk as the probability of an event

  16. Varied definitions of risk related to sensation seeking trait

    Energy Technology Data Exchange (ETDEWEB)

    Daastoel, P.Oe.U.; Drottz-Sjoeberg, B.M. [Norwegian Univ. of Science and Technology, Trondheim (Norway). Dept. of Psychology

    1999-12-01

    This pilot study is based on the assumption and the knowledge that previous results show that the normal use of the word risk varies across subjects. The risk definitions the subjects use have also been shown to be related to various educational interests. A related field of research has developed measures for Sensation Seeking personality trait, with four facets. Three independent groups of first year psychology students reported their normal definition of the word risk using one of three measurement formats. The results showed, e.g. that the typical open-ended response to the personal definition of risk was danger. Subjects who defined risk as the combination of probability and consequences tended to score higher on the total Sensation Seeking Scale, as compared to those defining risk as the probability of an event.

  17. Localization of quantitative trait loci associated with radiation induced pulmonary fibrosis in the mouse

    International Nuclear Information System (INIS)

    Oas, L.G.; Haston, C.K.; Travis, E.L.

    1997-01-01

    Purpose/Objective: Pulmonary fibrosis is often a limiting factor in the planning of radiotherapy for thoracic neoplasms. Differences in the propensity to develop radiation induced pulmonary fibrosis have been noted between C3Hf/Kam (resistant) and C57BL/6J (susceptible) mouse strains. Bleomycin and radiation induced pulmonary fibrosis have been shown to be heritable traits in mice with significant linkage to the major histocompatibility complex on chromosome 17. The heritability of radiation induced damage was estimated to be 38%±11% with 1-2 genetic factors influencing expression. Only 6.6% of the phenotypic variance could be attributed to chromosome 17. A search of the genome was undertaken to identify loci which may be responsible for the remaining phenotypic variance. Materials and Methods: C3Hf/Kam and C57BL/6J mice were crosbred to yield F1 and F2 (F1 intercross) generations. Two hundred sixty eight males and females of the F2 generation were treated with orthovoltage radiation, 14 or 16 Gy, to the whole thorax. The mice were sacrificed after development of respiratory distress or at 33 weeks. Histologic sections were assessed with quantified image analysis to determine the percentage of fibrosis in both lungs. Genotyping was done on the pooled DNA of the mice who developed respiratory distress with 44 32 P labeled microsatellite markers having an average spacing of 24.5 cM. Correlation of the quantitative trait loci (QTLs) with the highest quartile of fibrosis revealed 10 out of 44 regions showing possible linkage. Individual DNA from 54 mice with the least fibrosis and 40 with the most fibrosis were probed using these markers. PCR and gel electrophoresis were performed and the results analysed. Results: Of the 10 markers analysed, one locus on chromosome 1 meets the criterion of suggestion of linkage. Conclusion: These findings point to regions on the mouse genome for which further investigation of fibrosis associated loci may be warranted

  18. Network-based group variable selection for detecting expression quantitative trait loci (eQTL

    Directory of Open Access Journals (Sweden)

    Zhang Xuegong

    2011-06-01

    Full Text Available Abstract Background Analysis of expression quantitative trait loci (eQTL aims to identify the genetic loci associated with the expression level of genes. Penalized regression with a proper penalty is suitable for the high-dimensional biological data. Its performance should be enhanced when we incorporate biological knowledge of gene expression network and linkage disequilibrium (LD structure between loci in high-noise background. Results We propose a network-based group variable selection (NGVS method for QTL detection. Our method simultaneously maps highly correlated expression traits sharing the same biological function to marker sets formed by LD. By grouping markers, complex joint activity of multiple SNPs can be considered and the dimensionality of eQTL problem is reduced dramatically. In order to demonstrate the power and flexibility of our method, we used it to analyze two simulations and a mouse obesity and diabetes dataset. We considered the gene co-expression network, grouped markers into marker sets and treated the additive and dominant effect of each locus as a group: as a consequence, we were able to replicate results previously obtained on the mouse linkage dataset. Furthermore, we observed several possible sex-dependent loci and interactions of multiple SNPs. Conclusions The proposed NGVS method is appropriate for problems with high-dimensional data and high-noise background. On eQTL problem it outperforms the classical Lasso method, which does not consider biological knowledge. Introduction of proper gene expression and loci correlation information makes detecting causal markers more accurate. With reasonable model settings, NGVS can lead to novel biological findings.

  19. Multiple Linkage Disequilibrium Mapping Methods to Validate Additive Quantitative Trait Loci in Korean Native Cattle (Hanwoo

    Directory of Open Access Journals (Sweden)

    Yi Li

    2015-07-01

    Full Text Available The efficiency of genome-wide association analysis (GWAS depends on power of detection for quantitative trait loci (QTL and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM, a combined linkage and linkage disequilibrium analysis (LDLA and a BayesCπ approach. The phenotypes of 486 steers were collected for weaning weight (WWT, yearling weight (YWT, carcass weight (CWT, backfat thickness (BFT, longissimus dorsi muscle area, and marbling score (Marb. Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX] may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.

  20. Mapping quantitative trait loci (QTLs for fatty acid composition in an interspecific cross of oil palm

    Directory of Open Access Journals (Sweden)

    Sharma Mukesh

    2009-08-01

    Full Text Available Abstract Background Marker Assisted Selection (MAS is well suited to a perennial crop like oil palm, in which the economic products are not produced until several years after planting. The use of DNA markers for selection in such crops can greatly reduce the number of breeding cycles needed. With the use of DNA markers, informed decisions can be made at the nursery stage, regarding which individuals should be retained as breeding stock, which are satisfactory for agricultural production, and which should be culled. The trait associated with oil quality, measured in terms of its fatty acid composition, is an important agronomic trait that can eventually be tracked using molecular markers. This will speed up the production of new and improved oil palm planting materials. Results A map was constructed using AFLP, RFLP and SSR markers for an interspecific cross involving a Colombian Elaeis oleifera (UP1026 and a Nigerian E. guinneensis (T128. A framework map was generated for the male parent, T128, using Joinmap ver. 4.0. In the paternal (E. guineensis map, 252 markers (199 AFLP, 38 RFLP and 15 SSR could be ordered in 21 linkage groups (1815 cM. Interval mapping and multiple-QTL model (MQM mapping (also known as composite interval mapping, CIM were used to detect quantitative trait loci (QTLs controlling oil quality (measured in terms of iodine value and fatty acid composition. At a 5% genome-wide significance threshold level, QTLs associated with iodine value (IV, myristic acid (C14:0, palmitic acid (C16:0, palmitoleic acid (C16:1, stearic acid (C18:0, oleic acid (C18:1 and linoleic acid (C18:2 content were detected. One genomic region on Group 1 appears to be influencing IV, C14:0, C16:0, C18:0 and C18:1 content. Significant QTL for C14:0, C16:1, C18:0 and C18:1 content was detected around the same locus on Group 15, thus revealing another major locus influencing fatty acid composition in oil palm. Additional QTL for C18:0 was detected on Group 3

  1. Quantitative trait loci associated with the immune response to a bovine respiratory syncytial virus vaccine.

    Directory of Open Access Journals (Sweden)

    Richard J Leach

    Full Text Available Infectious disease is an important problem for animal breeders, farmers and governments worldwide. One approach to reducing disease is to breed for resistance. This linkage study used a Charolais-Holstein F2 cattle cross population (n = 501 which was genotyped for 165 microsatellite markers (covering all autosomes to search for associations with phenotypes for Bovine Respiratory Syncytial Virus (BRSV specific total-IgG, IgG1 and IgG2 concentrations at several time-points pre- and post-BRSV vaccination. Regions of the bovine genome which influenced the immune response induced by BRSV vaccination were identified, as well as regions associated with the clearance of maternally derived BRSV specific antibodies. Significant positive correlations were detected within traits across time, with negative correlations between the pre- and post-vaccination time points. The whole genome scan identified 27 Quantitative Trait Loci (QTL on 13 autosomes. Many QTL were associated with the Thymus Helper 1 linked IgG2 response, especially at week 2 following vaccination. However the most significant QTL, which reached 5% genome-wide significance, was on BTA 17 for IgG1, also 2 weeks following vaccination. All animals had declining maternally derived BRSV specific antibodies prior to vaccination and the levels of BRSV specific antibody prior to vaccination were found to be under polygenic control with several QTL detected.Heifers from the same population (n = 195 were subsequently immunised with a 40-mer Foot-and-Mouth Disease Virus peptide (FMDV in a previous publication. Several of these QTL associated with the FMDV traits had overlapping peak positions with QTL in the current study, including the QTL on BTA23 which included the bovine Major Histocompatibility Complex (BoLA, and QTL on BTA9 and BTA24, suggesting that the genes underlying these QTL may control responses to multiple antigens. These results lay the groundwork for future investigations to identify the

  2. Genome-Wide Search for Quantitative Trait Loci Controlling Important Plant and Flower Traits in Petunia Using an Interspecific Recombinant Inbred Population of Petunia axillaris and Petunia exserta.

    Science.gov (United States)

    Cao, Zhe; Guo, Yufang; Yang, Qian; He, Yanhong; Fetouh, Mohammed; Warner, Ryan M; Deng, Zhanao

    2018-05-15

    A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve important horticultural traits in garden petunia. An F 7 recombinant inbred population derived between Petunia axillaris and P. exserta was phenotyped for plant height, plant spread, plant size, flower counts, flower diameter, flower length, and days to anthesis, in Florida in two consecutive years. Transgressive segregation was observed for all seven traits in both years. The broad-sense heritability estimates for the traits ranged from 0.20 (days to anthesis) to 0.62 (flower length). A genome-wide genetic linkage map consisting 368 single nucleotide polymorphism bins and extending over 277 cM was searched to identify QTL for these traits. Nineteen QTL were identified and localized to five linkage groups. Eleven of the loci were identified consistently in both years; several loci explained up to 34.0% and 24.1% of the phenotypic variance for flower length and flower diameter, respectively. Multiple loci controlling different traits are co-localized in four intervals in four linkage groups. These intervals contain desirable alleles that can be introgressed into commercial petunia germplasm to expand the genetic base and improve plant performance and flower characteristics in petunia. Copyright © 2018, G3: Genes, Genomes, Genetics.

  3. Dissecting genetic architecture of grape proanthocyanidin composition through quantitative trait locus mapping

    Directory of Open Access Journals (Sweden)

    Huang Yung-Fen

    2012-02-01

    Full Text Available Abstract Background Proanthocyanidins (PAs, or condensed tannins, are flavonoid polymers, widespread throughout the plant kingdom, which provide protection against herbivores while conferring organoleptic and nutritive values to plant-derived foods, such as wine. However, the genetic basis of qualitative and quantitative PA composition variation is still poorly understood. To elucidate the genetic architecture of the complex grape PA composition, we first carried out quantitative trait locus (QTL analysis on a 191-individual pseudo-F1 progeny. Three categories of PA variables were assessed: total content, percentages of constitutive subunits and composite ratio variables. For nine functional candidate genes, among which eight co-located with QTLs, we performed association analyses using a diversity panel of 141 grapevine cultivars in order to identify causal SNPs. Results Multiple QTL analysis revealed a total of 103 and 43 QTLs, respectively for seed and skin PA variables. Loci were mainly of additive effect while some loci were primarily of dominant effect. Results also showed a large involvement of pairwise epistatic interactions in shaping PA composition. QTLs for PA variables in skin and seeds differed in number, position, involvement of epistatic interaction and allelic effect, thus revealing different genetic determinisms for grape PA composition in seeds and skin. Association results were consistent with QTL analyses in most cases: four out of nine tested candidate genes (VvLAR1, VvMYBPA2, VvCHI1, VvMYBPA1 showed at least one significant association with PA variables, especially VvLAR1 revealed as of great interest for further functional investigation. Some SNP-phenotype associations were observed only in the diversity panel. Conclusions This study presents the first QTL analysis on grape berry PA composition with a comparison between skin and seeds, together with an association study. Our results suggest a complex genetic control for PA

  4. Broad and Narrow Personality Traits of Women's College Students in Relation to Early Departure from College

    Science.gov (United States)

    Taylor, Sarah E.; Scepansky, James A.; Lounsbury, John W.; Gibson, Lucy W.

    2010-01-01

    Personality traits of coeducational students have been shown to correlate with early withdrawal intention from college (Lounsbury, Saudargas, & Gibson, 2004). The current study investigated the relationship between the Big Five personality traits as well as seven narrow personality traits in relation to withdrawal intention among 103 female…

  5. Mapping quantitative trait loci (QTL in sheep. II. Meta-assembly and identification of novel QTL for milk production traits in sheep

    Directory of Open Access Journals (Sweden)

    Lam Mary K

    2009-10-01

    Full Text Available Abstract An (Awassi × Merino × Merino backcross family of 172 ewes was used to map quantitative trait loci (QTL for different milk production traits on a framework map of 200 loci across all autosomes. From five previously proposed mathematical models describing lactation curves, the Wood model was considered the most appropriate due to its simplicity and its ability to determine ovine lactation curve characteristics. Derived milk traits for milk, fat, protein and lactose yield, as well as percentage composition and somatic cell score were used for single and two-QTL approaches using maximum likelihood estimation and regression analysis. A total of 15 significant (P P http://crcidp.vetsci.usyd.edu.au/cgi-bin/gbrowse/oaries_genome/. Many of the QTL for milk production traits have been reported on chromosomes 1, 3, 6, 16 and 20. Those on chromosomes 3 and 20 are in strong agreement with the results reported here. In addition, novel QTL were found on chromosomes 7, 8, 9, 14, 22 and 24. In a cross-species comparison, we extended the meta-assembly by comparing QTL regions of sheep and cattle, which provided strong evidence for synteny conservation of QTL regions for milk, fat, protein and somatic cell score data between cattle and sheep.

  6. Are Youth Psychopathic Traits Related to Bullying? Meta-analyses on Callous-Unemotional Traits, Narcissism, and Impulsivity.

    Science.gov (United States)

    van Geel, Mitch; Toprak, Fatih; Goemans, Anouk; Zwaanswijk, Wendy; Vedder, Paul

    2017-10-01

    In the current manuscript meta-analyses are performed to analyze the relations between three aspects of psychopathy in youth, Callous-Unemotional (CU) traits, Narcissism, and Impulsivity, and bullying behaviors. The databases PsycINFO, MEDLINE, ERIC, Web of Science and Proquest were searched for relevant articles on bullying and CU traits, Narcissism, or Impulsivity in youth under 20 years of age. Two authors each independently screened 842 studies that were found in the literature search. Two authors independently coded ten studies on bullying and CU (N = 4115) traits, six studies on bullying and Narcissism (N = 3376) and 14 studies on bullying and Impulsivity (N = 33,574) that met the inclusion criteria. Significant correlations were found between bullying and CU traits, Narcissism, and Impulsivity. These results were not affected by publication bias. Anti-bullying interventions could potentially benefit from including elements that have been found effective in the treatment of youth psychopathy.

  7. QTL mapping of flag leaf-related traits in wheat (Triticum aestivum L.).

    Science.gov (United States)

    Liu, Kaiye; Xu, Hao; Liu, Gang; Guan, Panfeng; Zhou, Xueyao; Peng, Huiru; Yao, Yingyin; Ni, Zhongfu; Sun, Qixin; Du, Jinkun

    2018-04-01

    QTL controlling flag leaf length, flag leaf width, flag leaf area and flag leaf angle were mapped in wheat. This study aimed to advance our understanding of the genetic mechanisms underlying morphological traits of the flag leaves of wheat (Triticum aestivum L.). A recombinant inbred line (RIL) population derived from ND3331 and the Tibetan semi-wild wheat Zang1817 was used to identify quantitative trait loci (QTLs) controlling flag leaf length (FLL), flag leaf width (FLW), flag leaf area (FLA), and flag leaf angle (FLANG). Using an available simple sequence repeat genetic linkage map, 23 putative QTLs for FLL, FLW, FLA, and FLANG were detected on chromosomes 1B, 2B, 3A, 3D, 4B, 5A, 6B, 7B, and 7D. Individual QTL explained 4.3-68.52% of the phenotypic variance in different environments. Four QTLs for FLL, two for FLW, four for FLA, and five for FLANG were detected in at least two environments. Positive alleles of 17 QTLs for flag leaf-related traits originated from ND3331 and 6 originated from Zang1817. QTLs with pleiotropic effects or multiple linked QTL were also identified on chromosomes 1B, 4B, and 5A; these are potential target regions for fine-mapping and marker-assisted selection in wheat breeding programs.

  8. Association of the Single Nucleotide Polymorphisms in , , and with Blood Related Traits in Pigs

    Directory of Open Access Journals (Sweden)

    Jae-Bong Lee

    2016-12-01

    Full Text Available The aim of this study was to detect positional candidate genes located within the support interval (SI regions based on the results of red blood cell, mean corpuscular volume (MCV, and mean corpuscular hemoglobin quantitative trait locus (QTL in Sus scrofa chromosome 13, and to verify the correlation between specific single-nucleotide polymorphisms (SNPs located in the exonic region of the positional candidate gene and the three genetic traits. The flanking markers of the three QTL SI regions are SW38 and S0215. Within the QTL SI regions, 44 genes were located, and runt-related transcription factor 1, dual-specificity tyrosine-(Y-phosphorylation regulated kinase 1A (DYRK1A, and potassium inwardly-rectifying channel, subfamily J, member 15 KCNJ15–which are reported to be related to the hematological traits and clinical features of Down syndrome–were selected as positional candidate genes. The ten SNPs located in the exonic region of the three genes were detected by next generation sequencing. A total of 1,232 pigs of an F2 resource population between Landrace and Korean native pigs were genotyped. To investigate the effects of the three genes on each genotype, a mixed-effect model which is the considering family structure model was used to evaluate the associations between the SNPs and three genetic traits in the F2 intercross population. Among them, the MCV level was highly significant (nominal p = 9.8×10−9 in association with the DYRK1A-SNP1 (c.2989 G

  9. The adaptation rate of a quantitative trait in an environmental gradient.

    Science.gov (United States)

    Hermsen, R

    2016-11-30

    The spatial range of a species habitat is generally determined by the ability of the species to cope with biotic and abiotic variables that vary in space. Therefore, the species range is itself an evolvable property. Indeed, environmental gradients permit a mode of evolution in which range expansion and adaptation go hand in hand. This process can contribute to rapid evolution of drug resistant bacteria and viruses, because drug concentrations in humans and livestock treated with antibiotics are far from uniform. Here, we use a minimal stochastic model of discrete, interacting organisms evolving in continuous space to study how the rate of adaptation of a quantitative trait depends on the steepness of the gradient and various population parameters. We discuss analytical results for the mean-field limit as well as extensive stochastic simulations. These simulations were performed using an exact, event-driven simulation scheme that can deal with continuous time-, density- and coordinate-dependent reaction rates and could be used for a wide variety of stochastic systems. The results reveal two qualitative regimes. If the gradient is shallow, the rate of adaptation is limited by dispersion and increases linearly with the gradient slope. If the gradient is steep, the adaptation rate is limited by mutation. In this regime, the mean-field result is highly misleading: it predicts that the adaptation rate continues to increase with the gradient slope, whereas stochastic simulations show that it in fact decreases with the square root of the slope. This discrepancy underscores the importance of discreteness and stochasticity even at high population densities; mean-field results, including those routinely used in quantitative genetics, should be interpreted with care.

  10. The adaptation rate of a quantitative trait in an environmental gradient

    Science.gov (United States)

    Hermsen, R.

    2016-12-01

    The spatial range of a species habitat is generally determined by the ability of the species to cope with biotic and abiotic variables that vary in space. Therefore, the species range is itself an evolvable property. Indeed, environmental gradients permit a mode of evolution in which range expansion and adaptation go hand in hand. This process can contribute to rapid evolution of drug resistant bacteria and viruses, because drug concentrations in humans and livestock treated with antibiotics are far from uniform. Here, we use a minimal stochastic model of discrete, interacting organisms evolving in continuous space to study how the rate of adaptation of a quantitative trait depends on the steepness of the gradient and various population parameters. We discuss analytical results for the mean-field limit as well as extensive stochastic simulations. These simulations were performed using an exact, event-driven simulation scheme that can deal with continuous time-, density- and coordinate-dependent reaction rates and could be used for a wide variety of stochastic systems. The results reveal two qualitative regimes. If the gradient is shallow, the rate of adaptation is limited by dispersion and increases linearly with the gradient slope. If the gradient is steep, the adaptation rate is limited by mutation. In this regime, the mean-field result is highly misleading: it predicts that the adaptation rate continues to increase with the gradient slope, whereas stochastic simulations show that it in fact decreases with the square root of the slope. This discrepancy underscores the importance of discreteness and stochasticity even at high population densities; mean-field results, including those routinely used in quantitative genetics, should be interpreted with care.

  11. A computational approach for functional mapping of quantitative trait loci that regulate thermal performance curves.

    Directory of Open Access Journals (Sweden)

    John Stephen Yap

    2007-06-01

    Full Text Available Whether and how thermal reaction norm is under genetic control is fundamental to understand the mechanistic basis of adaptation to novel thermal environments. However, the genetic study of thermal reaction norm is difficult because it is often expressed as a continuous function or curve. Here we derive a statistical model for dissecting thermal performance curves into individual quantitative trait loci (QTL with the aid of a genetic linkage map. The model is constructed within the maximum likelihood context and implemented with the EM algorithm. It integrates the biological principle of responses to temperature into a framework for genetic mapping through rigorous mathematical functions established to describe the pattern and shape of thermal reaction norms. The biological advantages of the model lie in the decomposition of the genetic causes for thermal reaction norm into its biologically interpretable modes, such as hotter-colder, faster-slower and generalist-specialist, as well as the formulation of a series of hypotheses at the interface between genetic actions/interactions and temperature-dependent sensitivity. The model is also meritorious in statistics because the precision of parameter estimation and power of QTLdetection can be increased by modeling the mean-covariance structure with a small set of parameters. The results from simulation studies suggest that the model displays favorable statistical properties and can be robust in practical genetic applications. The model provides a conceptual platform for testing many ecologically relevant hypotheses regarding organismic adaptation within the Eco-Devo paradigm.

  12. Well posedness and maximum entropy approximation for the dynamics of quantitative traits

    KAUST Repository

    Boďová , Katarí na; Haskovec, Jan; Markowich, Peter A.

    2017-01-01

    We study the Fokker–Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker–Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain’s boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker–Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one.

  13. RAS1, a quantitative trait locus for salt tolerance and ABA sensitivity in Arabidopsis

    KAUST Repository

    Ren, Zhonghai

    2010-03-08

    Soil salinity limits agricultural production and is a major obstacle for feeding the growing world population. We used natural genetic variation in salt tolerance among different Arabidopsis accessions to map a major quantitative trait locus (QTL) for salt tolerance and abscisic acid (ABA) sensitivity during seed germination and early seedling growth. A recombinant inbred population derived from Landsberg erecta (Ler; salt and ABA sensitive) x Shakdara (Sha; salt and ABA resistant) was used for QTL mapping. High-resolution mapping and cloning of this QTL, Response to ABA and Salt 1 (RAS1), revealed that it is an ABA- and salt stress-inducible gene and encodes a previously undescribed plant-specific protein. A premature stop codon results in a truncated RAS1 protein in Sha. Reducing the expression of RAS1 by transfer-DNA insertion in Col or RNA interference in Ler leads to decreased salt and ABA sensitivity, whereas overexpression of the Ler allele but not the Sha allele causes increased salt and ABA sensitivity. Our results suggest that RAS1 functions as a negative regulator of salt tolerance during seed germination and early seedling growth by enhancing ABA sensitivity and that its loss of function contributes to the increased salt tolerance of Sha.

  14. Quantitative trait loci for a neurocranium deformity, lack of operculum, in gilthead seabream (Sparus aurata L.).

    Science.gov (United States)

    Negrín-Báez, D; Navarro, A; Afonso, J M; Toro, M A; Zamorano, M J

    2016-04-01

    Lack of operculum, a neurocranial deformity, is the most common external abnormality to be found among industrially produced gilthead seabream (Sparus aurata L.), and this entails significant financial losses. This study conducts, for the first time in this species, a quantitative trait loci (QTL) analysis of the lack of operculum. A total of 142 individuals from a paternal half-sibling family (six full-sibling families) were selected for QTL mapping. They had previously shown a highly significant association with the prevalence of lack of operculum in a segregation analysis. All the fish were genotyped for 106 microsatellite markers using a set of multiplex PCRs (ReMsa1-ReMsa13). A linear regression methodology was used for the QTL analysis. Four QTL were detected for this deformity, two of which (QTLOP1 and QTLOP2) were significant. They were located at LG (linkage group) nine and LG10 respectively. Both QTL showed a large effect (about 27%), and furthermore, the association between lack of operculum and sire allelic segregation observed was statistically significant in the QTLOP1 analysis. These results represent a significant step towards including marker-assisted selection for this deformity in genetic breeding programmes to reduce the incidence of the deformity in the species. © 2016 Stichting International Foundation for Animal Genetics.

  15. Quantitative Trait Locus Analysis of Mating Behavior and Male Sex Pheromones in Nasonia Wasps

    Directory of Open Access Journals (Sweden)

    Wenwen Diao

    2016-06-01

    Full Text Available A major focus in speciation genetics is to identify the chromosomal regions and genes that reduce hybridization and gene flow. We investigated the genetic architecture of mating behavior in the parasitoid wasp species pair Nasonia giraulti and Nasonia oneida that exhibit strong prezygotic isolation. Behavioral analysis showed that N. oneida females had consistently higher latency times, and broke off the mating sequence more often in the mounting stage when confronted with N. giraulti males compared with males of their own species. N. oneida males produce a lower quantity of the long-range male sex pheromone (4R,5S-5-hydroxy-4-decanolide (RS-HDL. Crosses between the two species yielded hybrid males with various pheromone quantities, and these males were used in mating trials with females of either species to measure female mate discrimination rates. A quantitative trait locus (QTL analysis involving 475 recombinant hybrid males (F2, 2148 reciprocally backcrossed females (F3, and a linkage map of 52 equally spaced neutral single nucleotide polymorphism (SNP markers plus SNPs in 40 candidate mating behavior genes revealed four QTL for male pheromone amount, depending on partner species. Our results demonstrate that the RS-HDL pheromone plays a role in the mating system of N. giraulti and N. oneida, but also that additional communication cues are involved in mate choice. No QTL were found for female mate discrimination, which points at a polygenic architecture of female choice with strong environmental influences.

  16. Fine Mapping of QUICK ROOTING 1 and 2, Quantitative Trait Loci Increasing Root Length in Rice.

    Science.gov (United States)

    Kitomi, Yuka; Nakao, Emari; Kawai, Sawako; Kanno, Noriko; Ando, Tsuyu; Fukuoka, Shuichi; Irie, Kenji; Uga, Yusaku

    2018-02-02

    The volume that the root system can occupy is associated with the efficiency of water and nutrient uptake from soil. Genetic improvement of root length, which is a limiting factor for root distribution, is necessary for increasing crop production. In this report, we describe identification of two quantitative trait loci (QTLs) for maximal root length, QUICK ROOTING 1 ( QRO1 ) on chromosome 2 and QRO2 on chromosome 6, in cultivated rice ( Oryza sativa L.). We measured the maximal root length in 26 lines carrying chromosome segments from the long-rooted upland rice cultivar Kinandang Patong in the genetic background of the short-rooted lowland cultivar IR64. Five lines had longer roots than IR64. By rough mapping of the target regions in BC 4 F 2 populations, we detected putative QTLs for maximal root length on chromosomes 2, 6, and 8. To fine-map these QTLs, we used BC 4 F 3 recombinant homozygous lines. QRO1 was mapped between markers RM5651 and RM6107, which delimit a 1.7-Mb interval on chromosome 2, and QRO2 was mapped between markers RM20495 and RM3430-1, which delimit an 884-kb interval on chromosome 6. Both QTLs may be promising gene resources for improving root system architecture in rice. Copyright © 2018 Kitomi et al.

  17. A two-locus model of spatially varying stabilizing or directional selection on a quantitative trait.

    Science.gov (United States)

    Geroldinger, Ludwig; Bürger, Reinhard

    2014-06-01

    The consequences of spatially varying, stabilizing or directional selection on a quantitative trait in a subdivided population are studied. A deterministic two-locus two-deme model is employed to explore the effects of migration, the degree of divergent selection, and the genetic architecture, i.e., the recombination rate and ratio of locus effects, on the maintenance of genetic variation. The possible equilibrium configurations are determined as functions of the migration rate. They depend crucially on the strength of divergent selection and the genetic architecture. The maximum migration rates are investigated below which a stable fully polymorphic equilibrium or a stable single-locus polymorphism can exist. Under stabilizing selection, but with different optima in the demes, strong recombination may facilitate the maintenance of polymorphism. However usually, and in particular with directional selection in opposite direction, the critical migration rates are maximized by a concentrated genetic architecture, i.e., by a major locus and a tightly linked minor one. Thus, complementing previous work on the evolution of genetic architectures in subdivided populations subject to diversifying selection, it is shown that concentrated architectures may aid the maintenance of polymorphism. Conditions are obtained when this is the case. Finally, the dependence of the phenotypic variance, linkage disequilibrium, and various measures of local adaptation and differentiation on the parameters is elaborated. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  18. Well posedness and maximum entropy approximation for the dynamics of quantitative traits

    KAUST Repository

    Boďová, Katarína

    2017-11-06

    We study the Fokker–Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker–Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain’s boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker–Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one.

  19. Fine Mapping of QUICK ROOTING 1 and 2, Quantitative Trait Loci Increasing Root Length in Rice

    Directory of Open Access Journals (Sweden)

    Yuka Kitomi

    2018-02-01

    Full Text Available The volume that the root system can occupy is associated with the efficiency of water and nutrient uptake from soil. Genetic improvement of root length, which is a limiting factor for root distribution, is necessary for increasing crop production. In this report, we describe identification of two quantitative trait loci (QTLs for maximal root length, QUICK ROOTING 1 (QRO1 on chromosome 2 and QRO2 on chromosome 6, in cultivated rice (Oryza sativa L.. We measured the maximal root length in 26 lines carrying chromosome segments from the long-rooted upland rice cultivar Kinandang Patong in the genetic background of the short-rooted lowland cultivar IR64. Five lines had longer roots than IR64. By rough mapping of the target regions in BC4F2 populations, we detected putative QTLs for maximal root length on chromosomes 2, 6, and 8. To fine-map these QTLs, we used BC4F3 recombinant homozygous lines. QRO1 was mapped between markers RM5651 and RM6107, which delimit a 1.7-Mb interval on chromosome 2, and QRO2 was mapped between markers RM20495 and RM3430-1, which delimit an 884-kb interval on chromosome 6. Both QTLs may be promising gene resources for improving root system architecture in rice.

  20. Genome-wide quantitative trait loci mapping of the human cerebrospinal fluid proteome.

    Science.gov (United States)

    Sasayama, Daimei; Hattori, Kotaro; Ogawa, Shintaro; Yokota, Yuuki; Matsumura, Ryo; Teraishi, Toshiya; Hori, Hiroaki; Ota, Miho; Yoshida, Sumiko; Kunugi, Hiroshi

    2017-01-01

    Cerebrospinal fluid (CSF) is virtually the only one accessible source of proteins derived from the central nervous system (CNS) of living humans and possibly reflects the pathophysiology of a variety of neuropsychiatric diseases. However, little is known regarding the genetic basis of variation in protein levels of human CSF. We examined CSF levels of 1,126 proteins in 133 subjects and performed a genome-wide association analysis of 514,227 single nucleotide polymorphisms (SNPs) to detect protein quantitative trait loci (pQTLs). To be conservative, Spearman's correlation was used to identify an association between genotypes of SNPs and protein levels. A total of 421 cis and 25 trans SNP-protein pairs were significantly correlated at a false discovery rate (FDR) of less than 0.01 (nominal P genome-wide association studies. The present findings suggest that genetic variations play an important role in the regulation of protein expression in the CNS. The obtained database may serve as a valuable resource to understand the genetic bases for CNS protein expression pattern in humans. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  1. Mapping a Quantitative Trait Locus (QTL conferring pyrethroid resistance in the African malaria vector Anopheles funestus

    Directory of Open Access Journals (Sweden)

    Hunt Richard H

    2007-01-01

    Full Text Available Abstract Background Pyrethroid resistance in Anopheles funestus populations has led to an increase in malaria transmission in southern Africa. Resistance has been attributed to elevated activities of cytochrome P450s but the molecular basis underlying this metabolic resistance is unknown. Microsatellite and SNP markers were used to construct a linkage map and to detect a quantitative trait locus (QTL associated with pyrethroid resistance in the FUMOZ-R strain of An. funestus from Mozambique. Results By genotyping 349 F2 individuals from 11 independent families, a single major QTL, rp1, at the telomeric end of chromosome 2R was identified. The rp1 QTL appears to present a major effect since it accounts for more than 60% of the variance in susceptibility to permethrin. This QTL has a strong additive genetic effect with respect to susceptibility. Candidate genes associated with pyrethroid resistance in other species were physically mapped to An. funestus polytene chromosomes. This showed that rp1 is genetically linked to a cluster of CYP6 cytochrome P450 genes located on division 9 of chromosome 2R and confirmed earlier reports that pyrethroid resistance in this strain is not associated with target site mutations (knockdown resistance. Conclusion We hypothesize that one or more of these CYP6 P450s clustered on chromosome 2R confers pyrethroid resistance in the FUMOZ-R strain of An. funestus.

  2. Chromosomal mapping of quantitative trait loci controlling elastin content in rat aorta.

    Science.gov (United States)

    Gauguier, Dominique; Behmoaras, Jacques; Argoud, Karène; Wilder, Steven P; Pradines, Christelle; Bihoreau, Marie Thérèse; Osborne-Pellegrin, Mary; Jacob, Marie Paule

    2005-03-01

    Extracellular matrix molecules such as elastin and collagens provide mechanical support to the vessel wall. In addition to its structural role, elastin is a regulator that maintains homeostasis through biologic signaling. Genetically determined minor modifications in elastin and collagen in the aorta could influence the onset and evolution of arterial pathology, such as hypertension and its complications. We previously demonstrated that the inbred Brown Norway (BN) rat shows an aortic elastin deficit in both abdominal and thoracic segments, partly because of a decrease in tropoelastin synthesis when compared with the LOU rat, that elastin gene polymorphisms in these strains do not significantly account for. After a genome-wide search for quantitative trait loci (QTL) influencing the aortic elastin, collagen, and cell protein contents in an F2 population derived from BN and LOU rats, we identified on chromosomes 2 and 14, 3 QTL specifically controlling elastin levels, and a further highly significant QTL on chromosome 17 linked to the level of cell proteins. We also mapped 3 highly significant QTL linked to body weight (on chromosomes 1 and 3) and heart weight (on chromosome 1) in the cross. This study demonstrates the polygenic control of the content of key components of the arterial wall. Such information represents a first step in understanding possible mechanisms involved in dysregulation of these parameters in arterial pathology.

  3. Virulence attributes and hyphal growth of C. neoformans are quantitative traits and the MATalpha allele enhances filamentation.

    Directory of Open Access Journals (Sweden)

    Xiaorong Lin

    2006-11-01

    Full Text Available Cryptococcus neoformans is a fungal human pathogen with a bipolar mating system. It undergoes a dimorphic transition from a unicellular yeast to hyphal filamentous growth during mating and monokaryotic fruiting. The traditional sexual cycle that leads to the production of infectious basidiospores involves cells of both alpha and a mating type. Monokaryotic fruiting is a modified form of sexual reproduction that involves cells of the same mating type, most commonly alpha, which is the predominant mating type in both the environment and clinical isolates. However, some a isolates can also undergo monokaryotic fruiting. To determine whether mating type and other genetic loci contribute to the differences in fruiting observed between alpha and a cells, we applied quantitative trait loci (QTL mapping to an inbred population of F2 progeny. We discovered that variation in hyphal length produced during fruiting is a quantitative trait resulting from the combined effects of multiple genetic loci, including the mating type (MAT locus. Importantly, the alpha allele of the MAT locus enhanced hyphal growth compared with the a allele. Other virulence traits, including melanization and growth at 39 degrees C, also are quantitative traits that share a common QTL with hyphal growth. The Mac1 transcription factor, encoded in this common QTL, regulates copper homeostasis. MAC1 allelic differences contribute to phenotypic variation, and mac1Delta mutants exhibit defects in filamentation, melanin production, and high temperature growth. Further characterization of these QTL regions will reveal additional quantitative trait genes controlling biological processes central to fungal development and pathogenicity.

  4. Genomic prediction of traits related to canine hip dysplasia

    Directory of Open Access Journals (Sweden)

    Enrique eSanchez-Molano

    2015-03-01

    Full Text Available Increased concern for the welfare of pedigree dogs has led to development of selection programs against inherited diseases. An example is canine hip dysplasia (CHD, which has a moderate heritability and a high prevalence in some large-sized breeds. To date, selection using phenotypes has led to only modest improvement, and alternative strategies such as genomic selection may prove more effective. The primary aims of this study were to compare the performance of pedigree- and genomic-based breeding against CHD in the UK Labrador retriever population and to evaluate the performance of different genomic selection methods. A sample of 1179 Labrador Retrievers evaluated for CHD according to the UK scoring method (hip score, HS was genotyped with the Illumina CanineHD BeadChip. Twelve functions of HS and its component traits were analyzed using different statistical methods (GBLUP, Bayes C and Single-Step methods, and results were compared with a pedigree-based approach (BLUP using cross-validation. Genomic methods resulted in similar or higher accuracies than pedigree-based methods with training sets of 944 individuals for all but the untransformed HS, suggesting that genomic selection is an effective strategy. GBLUP and Bayes C gave similar prediction accuracies for HS and related traits, indicating a polygenic architecture. This conclusion was also supported by the low accuracies obtained in additional GBLUP analyses performed using only the SNPs with highest test statistics, also indicating that marker-assisted selection would not be as effective as genomic selection. A Single-Step method that combines genomic and pedigree information also showed higher accuracy than GBLUP and Bayes C for the log-transformed HS, which is currently used for pedigree based evaluations in UK. In conclusion, genomic selection is a promising alternative to pedigree-based selection against CHD, requiring more phenotypes with genomic data to improve further the accuracy

  5. QTLs for seed vigor-related traits identified in maize seeds germinated under artificial aging conditions.

    Science.gov (United States)

    Han, Zanping; Ku, Lixia; Zhang, Zhenzhen; Zhang, Jun; Guo, Shulei; Liu, Haiying; Zhao, Ruifang; Ren, Zhenzhen; Zhang, Liangkun; Su, Huihui; Dong, Lei; Chen, Yanhui

    2014-01-01

    High seed vigor is important for agricultural production due to the associated potential for increased growth and productivity. However, a better understanding of the underlying molecular mechanisms is required because the genetic basis for seed vigor remains unknown. We used single-nucleotide polymorphism (SNP) markers to map quantitative trait loci (QTLs) for four seed vigor traits in two connected recombinant inbred line (RIL) maize populations under four treatment conditions during seed germination. Sixty-five QTLs distributed between the two populations were identified and a meta-analysis was used to integrate genetic maps. Sixty-one initially identified QTLs were integrated into 18 meta-QTLs (mQTLs). Initial QTLs with contribution to phenotypic variation values of R(2)>10% were integrated into mQTLs. Twenty-three candidate genes for association with seed vigor traits coincided with 13 mQTLs. The candidate genes had functions in the glycolytic pathway and in protein metabolism. QTLs with major effects (R(2)>10%) were identified under at least one treatment condition for mQTL2, mQTL3-2, and mQTL3-4. Candidate genes included a calcium-dependent protein kinase gene (302810918) involved in signal transduction that mapped in the mQTL3-2 interval associated with germination energy (GE) and germination percentage (GP), and an hsp20/alpha crystallin family protein gene (At5g51440) that mapped in the mQTL3-4 interval associated with GE and GP. Two initial QTLs with a major effect under at least two treatment conditions were identified for mQTL5-2. A cucumisin-like Ser protease gene (At5g67360) mapped in the mQTL5-2 interval associated with GP. The chromosome regions for mQTL2, mQTL3-2, mQTL3-4, and mQTL5-2 may be hot spots for QTLs related to seed vigor traits. The mQTLs and candidate genes identified in this study provide valuable information for the identification of additional quantitative trait genes.

  6. QTLs for seed vigor-related traits identified in maize seeds germinated under artificial aging conditions.

    Directory of Open Access Journals (Sweden)

    Zanping Han

    Full Text Available High seed vigor is important for agricultural production due to the associated potential for increased growth and productivity. However, a better understanding of the underlying molecular mechanisms is required because the genetic basis for seed vigor remains unknown. We used single-nucleotide polymorphism (SNP markers to map quantitative trait loci (QTLs for four seed vigor traits in two connected recombinant inbred line (RIL maize populations under four treatment conditions during seed germination. Sixty-five QTLs distributed between the two populations were identified and a meta-analysis was used to integrate genetic maps. Sixty-one initially identified QTLs were integrated into 18 meta-QTLs (mQTLs. Initial QTLs with contribution to phenotypic variation values of R(2>10% were integrated into mQTLs. Twenty-three candidate genes for association with seed vigor traits coincided with 13 mQTLs. The candidate genes had functions in the glycolytic pathway and in protein metabolism. QTLs with major effects (R(2>10% were identified under at least one treatment condition for mQTL2, mQTL3-2, and mQTL3-4. Candidate genes included a calcium-dependent protein kinase gene (302810918 involved in signal transduction that mapped in the mQTL3-2 interval associated with germination energy (GE and germination percentage (GP, and an hsp20/alpha crystallin family protein gene (At5g51440 that mapped in the mQTL3-4 interval associated with GE and GP. Two initial QTLs with a major effect under at least two treatment conditions were identified for mQTL5-2. A cucumisin-like Ser protease gene (At5g67360 mapped in the mQTL5-2 interval associated with GP. The chromosome regions for mQTL2, mQTL3-2, mQTL3-4, and mQTL5-2 may be hot spots for QTLs related to seed vigor traits. The mQTLs and candidate genes identified in this study provide valuable information for the identification of additional quantitative trait genes.

  7. High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping.

    Science.gov (United States)

    Esteras, Cristina; Gómez, Pedro; Monforte, Antonio J; Blanca, José; Vicente-Dólera, Nelly; Roig, Cristina; Nuez, Fernando; Picó, Belén

    2012-02-22

    Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species.The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL). We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo) × Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations. Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research, especially considering that most of these markers are located in

  8. Genetic control of environmental variation of two quantitative traits of Drosophila melanogaster revealed by whole-genome sequencing

    DEFF Research Database (Denmark)

    Sørensen, Peter; de los Campos, Gustavo; Morgante, Fabio

    2015-01-01

    and others more volatile performance. Understanding the mechanisms responsible for environmental variability not only informs medical questions but is relevant in evolution and in agricultural science. In this work fully sequenced inbred lines of Drosophila melanogaster were analyzed to study the nature...... of genetic control of environmental variance for two quantitative traits: starvation resistance (SR) and startle response (SL). The evidence for genetic control of environmental variance is compelling for both traits. Sequence information is incorporated in random regression models to study the underlying...... genetic signals, which are shown to be different in the two traits. Genomic variance in sexual dimorphism was found for SR but not for SL. Indeed, the proportion of variance captured by sequence information and the contribution to this variance from four chromosome segments differ between sexes in SR...

  9. Relationships between nutrient-related plant traits and combinations of soil N and P fertility measures.

    Science.gov (United States)

    Fujita, Yuki; van Bodegom, Peter M; Witte, Jan-Philip M

    2013-01-01

    Soil fertility and nutrient-related plant functional traits are in general only moderately related, hindering the progress in trait-based prediction models of vegetation patterns. Although the relationships may have been obscured by suboptimal choices in how soil fertility is expressed, there has never been a systematic investigation into the suitability of fertility measures. This study, therefore, examined the effect of different soil fertility measures on the strength of fertility-trait relationships in 134 natural plant communities. In particular, for eight plot-mean traits we examined (1) whether different elements (N or P) have contrasting or shared influences, (2) which timescale of fertility measures (e.g. mineralization rates for one or five years) has better predictive power, and (3) if integrated fertility measures explain trait variation better than individual fertility measures. Soil N and P had large mutual effects on leaf nutrient concentrations, whereas they had element-specific effects on traits related to species composition (e.g. Grime's CSR strategy). The timescale of fertility measures only had a minor impact on fertility-trait relationships. Two integrated fertility measures (one reflecting overall fertility, another relative availability of soil N and P) were related significantly to most plant traits, but were not better in explaining trait variation than individual fertility measures. Using all fertility measures together, between-site variations of plant traits were explained only moderately for some traits (e.g. 33% for leaf N concentrations) but largely for others (e.g. 66% for whole-canopy P concentration). The moderate relationships were probably due to complex regulation mechanisms of fertility on traits, rather than to a wrong choice of fertility measures. We identified both mutual (i.e. shared) and divergent (i.e. element-specific and stoichiometric) effects of soil N and P on traits, implying the importance of explicitly

  10. Quantitative Trait Locus Mapping of Salt Tolerance and Identification of Salt-Tolerant Genes in Brassica napus L

    Directory of Open Access Journals (Sweden)

    Lina Lang

    2017-06-01

    Full Text Available Salinity stress is one of typical abiotic stresses that seriously limit crop production. In this study, a genetic linkage map based on 532 molecular markers covering 1341.1 cM was constructed to identify the loci associated with salt tolerance in Brassica napus. Up to 45 quantitative trait loci (QTLs for 10 indicators were identified in the F2:3 populations. These QTLs can account for 4.80–51.14% of the phenotypic variation. A major QTL, qSPAD5 on LG5 associated with chlorophyll can be detected in three replicates. Two intron polymorphic (IP markers in this QTL region were developed successfully to narrow down the QTL location to a region of 390 kb. A salt tolerance related gene Bra003640 was primary identified as the candidate gene in this region. The full length of the candidate gene was 1,063 bp containing three exons and two introns in B. napus L. The open reading frame (ORF is 867 bp and encodes 287 amino acids. Three amino acid differences (34, 54, and 83 in the conserved domain (B-box were identified. RT-qPCR analysis showed that the gene expression had significant difference between the two parents. The study laid great foundation for salt tolerance related gene mapping and cloning in B. napus L.

  11. Personality Traits Related to Binge Drinking: A Systematic Review

    Directory of Open Access Journals (Sweden)

    Ana Adan

    2017-07-01

    Full Text Available The pattern of alcohol consumption in the form of binge drinking (BD or heavy episodic drinking has increased notably worldwide in recent years, especially among adolescent and young people, being currently recognized as a global health problem. Although only a minority of binge drinkers will develop a substance use disorder, BD may have negative personal and social consequences in the short and medium term. The objective of this article is to review the findings on personality traits related to binge drinkers and to emphasize the aspects that should be examined in order to make progress in this area. The main characteristics of personality related to the practice of BD, regardless of the theoretical model used, are high Impulsivity and high Sensation seeking, as well as Anxiety sensitivity, Neuroticism (Hopelessness, Extraversion and low Conscientiousness. The data obtained may have theoretical implications to elucidate the endophenotype of BD, but they are especially useful for their preventive applications. Integration into prevention programs of emotional self-control skills, decision-making, social skills, and strategies to manage negative emotions will minimize the risk factors or consequences of BD associated with personality and will improve their effectiveness. In the future, it is necessary to harmonize a common measurement instrument for the assessment of personality, develop longitudinal studies with large samples that also integrate biological and neurocognitive measurements, and determine the reciprocal relationship between personality and BD together with its modulating variables, as well as the possible cultural differences.

  12. Predicting personality traits related to consumer behavior using SNS analysis

    Science.gov (United States)

    Baik, Jongbum; Lee, Kangbok; Lee, Soowon; Kim, Yongbum; Choi, Jayoung

    2016-07-01

    Modeling a user profile is one of the important factors for devising a personalized recommendation. The traditional approach for modeling a user profile in computer science is to collect and generalize the user's buying behavior or preference history, generated from the user's interactions with recommender systems. According to consumer behavior research, however, internal factors such as personality traits influence a consumer's buying behavior. Existing studies have tried to adapt the Big 5 personality traits to personalized recommendations. However, although studies have shown that these traits can be useful to some extent for personalized recommendation, the causal relationship between the Big 5 personality traits and the buying behaviors of actual consumers has not been validated. In this paper, we propose a novel method for predicting the four personality traits-Extroversion, Public Self-consciousness, Desire for Uniqueness, and Self-esteem-that correlate with buying behaviors. The proposed method automatically constructs a user-personality-traits prediction model for each user by analyzing the user behavior on a social networking service. The experimental results from an analysis of the collected Facebook data show that the proposed method can predict user-personality traits with greater precision than methods that use the variables proposed in previous studies.

  13. Analysis of genetic effects of nuclear-cytoplasmic interaction on quantitative traits: genetic model for diploid plants.

    Science.gov (United States)

    Han, Lide; Yang, Jian; Zhu, Jun

    2007-06-01

    A genetic model was proposed for simultaneously analyzing genetic effects of nuclear, cytoplasm, and nuclear-cytoplasmic interaction (NCI) as well as their genotype by environment (GE) interaction for quantitative traits of diploid plants. In the model, the NCI effects were further partitioned into additive and dominance nuclear-cytoplasmic interaction components. Mixed linear model approaches were used for statistical analysis. On the basis of diallel cross designs, Monte Carlo simulations showed that the genetic model was robust for estimating variance components under several situations without specific effects. Random genetic effects were predicted by an adjusted unbiased prediction (AUP) method. Data on four quantitative traits (boll number, lint percentage, fiber length, and micronaire) in Upland cotton (Gossypium hirsutum L.) were analyzed as a worked example to show the effectiveness of the model.

  14. Quantitative trait loci controlling sulfur containing amino acids, methionine and cysteine, in soybean seeds.

    Science.gov (United States)

    Panthee, D R; Pantalone, V R; Sams, C E; Saxton, A M; West, D R; Orf, J H; Killam, A S

    2006-02-01

    Soybean [Glycine max (L.) Merr.] is the single largest source of protein in animal feed. However, a major limitation of soy proteins is their deficiency in sulfur-containing amino acids, methionine (Met) and cysteine (Cys). The objective of this study was to identify quantitative trait loci (QTL) associated with Met and Cys concentration in soybean seed. To achieve this objective, 101 F(6)-derived recombinant inbred lines (RIL) from a population developed from a cross of N87-984-16 x TN93-99 were used. Ground soybean seed samples were analyzed for Met and Cys concentration using a near infrared spectroscopy instrument. Data were analyzed using SAS software and QTL Cartographer. RIL differed (Pseed dry weight) for Cys and 4.4-8.8 (g kg(-1) seed dry weight) for Met. Heritability estimates on an entry mean basis were 0.14 and 0.57 for Cys and Met, respectively. A total of 94 polymorphic simple sequence repeat molecular genetic markers were screened in the RIL. Single factor ANOVA was used to identify candidate QTL, which were confirmed by composite interval mapping using QTL Cartographer. Four QTL linked to molecular markers Satt235, Satt252, Satt427 and Satt436 distributed on three molecular linkage groups (MLG) D1a, F and G were associated with Cys and three QTL linked to molecular markers Satt252, Satt564 and Satt590 distributed on MLG F, G and M were associated with Met concentration in soybean seed. QTL associated with Met and Cys in soybean seed will provide important information to breeders targeting improvements in the nutritional quality of soybean.

  15. Mapping Quantitative Trait Loci (QTL for Resistance to Late Blight in Tomato

    Directory of Open Access Journals (Sweden)

    Dilip R. Panthee

    2017-07-01

    Full Text Available Late blight caused by Phytophthora infestans (Montagne, Bary is a devastating disease of tomato worldwide. There are three known major genes, Ph-1, Ph-2, and Ph-3, conferring resistance to late blight. In addition to these three genes, it is also believed that there are additional factors or quantitative trait loci (QTL conferring resistance to late blight. Precise molecular mapping of all those major genes and potential QTL is important in the development of suitable molecular markers and hence, marker-assisted selection (MAS. The objective of the present study was to map the genes and QTL associated with late blight resistance in a tomato population derived from intra-specific crosses. To achieve this objective, a population, derived from the crossings of NC 1CELBR × Fla. 7775, consisting of 250 individuals at F2 and F2-derived families, were evaluated in replicated trials. These were conducted at Mountain Horticultural Crops Reseach & Extension Center (MHCREC at Mills River, NC, and Mountain Research Staion (MRS at Waynesville, NC in 2011, 2014, and 2015. There were two major QTL associated with late blight resistance located on chromosomes 9 and 10 with likelihood of odd (LOD scores of more than 42 and 6, explaining 67% and 14% of the total phenotypic variation, respectively. The major QTLs are probably caused by the Ph-2 and Ph-3 genes. Furthermore, there was a minor QTL on chromosomes 12, which has not been reported before. This minor QTL may be novel and may be worth investigating further. Source of resistance to Ph-2, Ph-3, and this minor QTL traces back to line L3707, or Richter’s Wild Tomato. The combination of major genes and minor QTL may provide a durable resistance to late blight in tomato.

  16. Expression quantitative trait loci for PAX8 contributes to the prognosis of hepatocellular carcinoma.

    Directory of Open Access Journals (Sweden)

    Shijie Ma

    Full Text Available Paired-box family member PAX8 encodes a transcription factor that has a role in cell differentiation and cell growth and may participate in the prognosis of hepatocellular carcinoma (HCC. By bioinformatics analysis, we identified several single nucleotide polymorphisms (SNPs within a newly identified long non-coding RNA (lncRNA AC016683.6 as expression quantitative trait loci (eQTLs for PAX8. Hence, we hypothesized that PAX8eQTLs in lncRNA AC016683.6 may influence the HCC prognosis. We then performed a case-only study to assess the association between the two SNPs as well as the prognosis of HCC in 331 HBV-positive HCC patients without surgical treatment. Cox proportional hazard models were used for survival analysis with adjustments for the age, gender, smoking status, drinking status, Barcelona-Clinic Liver Cancer (BCLC stage, and chemotherapy or TACE (transcatheter hepatic arterial chemoembolization status. We found that the G allele of rs1110839 and the T allele of rs4848320 in PAX8was significantly associated with a better prognosis compared with the T allele of rs1110839 and the C allele of rs4848320 (adjusted HR = 0.74, 95% CI = 0.61-0.91, P = 0.004 for rs1110839 and adjusted HR = 0.71, 95% CI = 0.54-0.94, P = 0.015 for rs4848320 in the additive model. Furthermore, the combined effect of the variant genotypes for these two SNPs was more prominent in patients with the BCLC-C stage orpatients with chemotherapy or TACE. Although the exact biological function remains to be explored, our findings suggest a possible association of PAX8eQTLs in lncRNA AC016683.6 with the HCC prognosis inthe Chinese population. Further large and functional studies are needed to confirm our findings.

  17. Genome-wide haplotype analysis of cis expression quantitative trait loci in monocytes.

    Directory of Open Access Journals (Sweden)

    Sophie Garnier

    Full Text Available In order to assess whether gene expression variability could be influenced by several SNPs acting in cis, either through additive or more complex haplotype effects, a systematic genome-wide search for cis haplotype expression quantitative trait loci (eQTL was conducted in a sample of 758 individuals, part of the Cardiogenics Transcriptomic Study, for which genome-wide monocyte expression and GWAS data were available. 19,805 RNA probes were assessed for cis haplotypic regulation through investigation of ~2,1 × 10(9 haplotypic combinations. 2,650 probes demonstrated haplotypic p-values >10(4-fold smaller than the best single SNP p-value. Replication of significant haplotype effects were tested for 412 probes for which SNPs (or proxies that defined the detected haplotypes were available in the Gutenberg Health Study composed of 1,374 individuals. At the Bonferroni correction level of 1.2 × 10(-4 (~0.05/412, 193 haplotypic signals replicated. 1000 G imputation was then conducted, and 105 haplotypic signals still remained more informative than imputed SNPs. In-depth analysis of these 105 cis eQTL revealed that at 76 loci genetic associations were compatible with additive effects of several SNPs, while for the 29 remaining regions data could be compatible with a more complex haplotypic pattern. As 24 of the 105 cis eQTL have previously been reported to be disease-associated loci, this work highlights the need for conducting haplotype-based and 1000 G imputed cis eQTL analysis before commencing functional studies at disease-associated loci.

  18. Gene-based testing of interactions in association studies of quantitative traits.

    Directory of Open Access Journals (Sweden)

    Li Ma

    Full Text Available Various methods have been developed for identifying gene-gene interactions in genome-wide association studies (GWAS. However, most methods focus on individual markers as the testing unit, and the large number of such tests drastically erodes statistical power. In this study, we propose novel interaction tests of quantitative traits that are gene-based and that confer advantage in both statistical power and biological interpretation. The framework of gene-based gene-gene interaction (GGG tests combine marker-based interaction tests between all pairs of markers in two genes to produce a gene-level test for interaction between the two. The tests are based on an analytical formula we derive for the correlation between marker-based interaction tests due to linkage disequilibrium. We propose four GGG tests that extend the following P value combining methods: minimum P value, extended Simes procedure, truncated tail strength, and truncated P value product. Extensive simulations point to correct type I error rates of all tests and show that the two truncated tests are more powerful than the other tests in cases of markers involved in the underlying interaction not being directly genotyped and in cases of multiple underlying interactions. We applied our tests to pairs of genes that exhibit a protein-protein interaction to test for gene-level interactions underlying lipid levels using genotype data from the Atherosclerosis Risk in Communities study. We identified five novel interactions that are not evident from marker-based interaction testing and successfully replicated one of these interactions, between SMAD3 and NEDD9, in an independent sample from the Multi-Ethnic Study of Atherosclerosis. We conclude that our GGG tests show improved power to identify gene-level interactions in existing, as well as emerging, association studies.

  19. A narrow quantitative trait locus in C. elegans coordinately affects longevity, thermotolerance, and resistance to paraquat

    Directory of Open Access Journals (Sweden)

    Anthony eVertino

    2011-09-01

    Full Text Available By linkage mapping of quantitative trait loci, we previously identified at least 11 natural genetic variants that significantly modulate C. elegans lifespan, many of which would have eluded discovery by knockdown or mutation screens. A region on chromosome IV between markers stP13 and stP35 had striking effects on longevity in three interstrain crosses (each P < 1E–9. In order to define the limits of that interval, we have now constructed two independent lines by marker-based selection during 20 backcross generations, isolating the stP13–stP35 interval from strain Bergerac-BO in a CL2a background. These congenic lines differed significantly from CL2a in lifespan, assayed in two environments (each P<0.001. We then screened for exchange of flanking markers to isolate recombinants that partition this region, because fine mapping the boundaries for overlapping heteroallelic spans can greatly narrow the implicated interval. Recombinants carrying the CL2a allele at stP35 were consistently long-lived compared to those retaining the Bergerac-BO allele (P<0.001, and more resistant to temperature elevation and paraquat (each ~1.7-fold, P<0.0001, but gained little protection from ultraviolet or peroxide stresses. Two rounds of recombinant screening, followed by fine-mapping of break-points and survival testing, narrowed the interval to 0.18 Mb (13.35–13.53 Mb containing 26 putative genes and 6 small-nuclear RNAs – a manageable number of targets for functional assessment.

  20. Quantitative trait loci for broomrape (Orobanche cumana Wallr.) resistance in sunflower.

    Science.gov (United States)

    Pérez-Vich, B; Akhtouch, B; Knapp, S J; Leon, A J; Velasco, L; Fernández-Martínez, J M; Berry, S T

    2004-06-01

    Broomrape (Orobanche cumana Wallr.) is a root parasite of sunflower that is regarded as one of the most important constraints of sunflower production in the Mediterranean region. Breeding for resistance is the most effective method of control. P-96 is a sunflower line which shows dominant resistance to broomrape race E and recessive resistance to the very new race F. The objective of this study was to map and characterize quantitative trait loci (QTL) for resistance to race E and to race F of broomrape in P-96. A population from a cross between P-96 and the susceptible line P-21 was phenotyped for broomrape resistance in four experiments, two for race E and two for race F, by measuring different resistance parameters (resistance or susceptibility, number of broomrape per plant, and proportion of resistant plants per F(3) family). This population was also genotyped with microsatellite and RFLP markers. A linkage map comprising 103 marker loci distributed on 17 linkage groups was developed, and composite interval mapping analyses were performed. In total, five QTL ( or1.1, or3.1, or7.1 or13.1 and or13.2) for resistance to race E and six QTL ( or1.1, or4.1, or5.1, or13.1, or13.2 and or16.1) for resistance to race F of broomrape were detected on 7 of the 17 linkage groups. Phenotypic variance for race E resistance was mainly explained by the major QTL or3.1 associated to the resistance or susceptibility character ( R(2)=59%), while race F resistance was explained by QTL with a small to moderate effect ( R(2) from 15.0% to 38.7%), mainly associated with the number of broomrape per plant. Or3.1 was race E-specific, while or1.1, or13.1 and or13.2 of were non-race specific. Or13.1, and or13.2 were stable across the four experiments. Or3.1, and or7.1 were stable over the two race E experiments and or1.1 and or5.1 over the two race F experiments. The results from this study suggest that resistance to broomrape in sunflower is controlled by a combination of qualitative, race

  1. Identification of Quantitative Trait Loci (QTL) and Candidate Genes for Cadmium Tolerance in Populus

    Energy Technology Data Exchange (ETDEWEB)

    Induri, Brahma R [West Virginia University; Ellis, Danielle R [West Virginia University; Slavov, Gancho [West Virginia University; Yin, Tongming [ORNL; Muchero, Wellington [ORNL; Tuskan, Gerald A [ORNL; DiFazio, Stephen P [West Virginia University

    2012-01-01

    Knowledge of genetic variation in response of Populus to heavy metals like cadmium (Cd) is an important step in understanding the underlying mechanisms of tolerance. In this study, a pseudo-backcross pedigree of Populus trichocarpa and Populus deltoides was characterized for Cd exposure. The pedigree showed significant variation for Cd tolerance thus enabling the identification of relatively tolerant and susceptible genotypes for intensive characterization. A total of 16 QTLs at logarithm of odds (LOD) ratio > 2.5, were found to be associated with total dry weight, its components, and root volume. Four major QTLs for total dry weight were mapped to different linkage groups in control (LG III) and Cd conditions (LG XVI) and had opposite allelic effects on Cd tolerance, suggesting that these genomic regions were differentially controlled. The phenotypic variation explained by Cd QTL for all traits under study varied from 5.9% to 11.6% and averaged 8.2% across all QTL. Leaf Cd contents also showed significant variation suggesting the phytoextraction potential of Populus genotypes, though heritability of this trait was low (0.22). A whole-genome microarray study was conducted by using two genotypes with extreme responses for Cd tolerance in the above study and differentially expressed genes were identified. Candidate genes including CAD2 (CADMIUM SENSITIVE 2), HMA5 (HEAVY METAL ATPase5), ATGTST1 (Arabidopsis thaliana Glutathione S-Transferase1), ATGPX6 (Glutathione peroxidase 6), and ATMRP 14 (Arabidopsis thaliana Multidrug Resistance associated Protein 14) were identified from QTL intervals and microarray study. Functional characterization of these candidate genes could enhance phytoremediation capabilities of Populus.

  2. The Impact of Psychological Traits on Judgments Related to Ethics

    OpenAIRE

    Agarwalla, Sobhesh Kumar; Desai, Naman; Tripathy, Arindam

    2015-01-01

    This paper examines how two contradictory psychological traits, self-deception (SD) and professional skepticism (PS), affect managers and auditors assessments of the ethicality of various earnings management choices. Whereas, self-deception allows individuals to reduce cognitive dissonance (Festinger 1957) arising from their self-serving behavior which could be unethical (Audi 1988; Sanford 1988), professional skepticism or trait skepticism (Hurtt 2010) would force individuals to question suc...

  3. Comparative mapping of quantitative trait loci for tassel-related traits ...

    Indian Academy of Sciences (India)

    cultivated area and yield in the country (United Nations Food and Agriculture Organization, FAO, .... Gene action was judged according to the criteria of Stuber et al. (1987) ..... of tassel branch number in maize and its implications for a selection.

  4. Quantitative trait loci for rice yield-related traits using recombinant ...

    Indian Academy of Sciences (India)

    2011-08-19

    Aug 19, 2011 ... lated by map-based cloning strategy (Ashikari et al. 2005). ... 2000; Kojima et al. 2002; Doi et al. 2004). ... and PH but also on rice yield (Xue et al. 2008; Yan et al. ..... Cho Y. C., Suh J. P., Choi I. S., Hong H. C., Baek M. K., Kang K. H. et al. .... Yan C. J., Liang G. H., Chen F., Li X., Tang S. Z., Yi C. D. et al.

  5. Effects of Bos taurus autosome 9-located quantitative trait loci haplotypes on the disease phenotypes of dairy cows with experimentally induced Escherichia coli mastitis

    DEFF Research Database (Denmark)

    Khatun, Momena; Sørensen, Peter; Jørgensen, Hanne Birgitte Hede

    2013-01-01

    Several quantitative trait loci (QTL) affecting mastitis incidence and mastitis-related traits such as somatic cell score exist in dairy cows. Previously, QTL haplotypes associated with susceptibility to Escherichia coli mastitis in Nordic Holstein-Friesian (HF) cows were identified on Bos taurus...... autosome 9. In the present study, we induced experimental E. coli mastitis in Danish HF cows to investigate the effect of 2 E. coli mastitis-associated QTL haplotypes on the cows' disease phenotypes and recovery in early lactation. Thirty-two cows were divided in 2 groups bearing haplotypes with either low...... the HH group did. However, we also found interactions between the effects of haplotype and biopsy for body temperature, heart rate, and PMNL. In conclusion, when challenged with E. coli mastitis, HF cows with the specific Bos taurus autosome 9-located QTL haplotypes were associated with differences...

  6. Identification and validation of quantitative trait loci (QTL for canine hip dysplasia (CHD in German Shepherd Dogs.

    Directory of Open Access Journals (Sweden)

    Lena Fels

    Full Text Available Canine hip dysplasia (CHD is the most common hereditary skeletal disorder in dogs. To identify common alleles associated with CHD, we genotyped 96 German Shepherd Dogs affected by mild, moderate and severe CHD and 96 breed, sex, age and birth year matched controls using the Affymetrix canine high density SNP chip. A mixed linear model analysis identified five SNPs associated with CHD scores on dog chromosomes (CFA 19, 24, 26 and 34. These five SNPs were validated in a by sex, age, birth year and coancestry stratified sample of 843 German Shepherd Dogs including 277 unaffected dogs and 566 CHD-affected dogs. Mean coancestry coefficients among and within cases and controls were <0.1%. Genotype effects of these SNPs explained 20-32% of the phenotypic variance of CHD in German Shepherd Dogs employed for validation. Genome-wide significance in the validation data set could be shown for each one CHD-associated SNP on CFA24, 26 and 34. These SNPs are located within or in close proximity of genes involved in bone formation and related through a joint network. The present study validated positional candidate genes within two previously known quantitative trait loci (QTL and a novel QTL for CHD in German Shepherd Dogs.

  7. Evaluation and Exploration of Favorable QTL Alleles for Salt Stress Related Traits in Cotton Cultivars (G. hirsutum L.)

    Science.gov (United States)

    Du, Lei; Cai, Caiping; Wu, Shuang; Zhang, Fang; Hou, Sen; Guo, Wangzhen

    2016-01-01

    Soil salinization is one of the major problems in global agricultural production. Cotton is a pioneer crop with regard to salt stress tolerance, and can be used for saline-alkali land improvement. The large-scale detection of salt tolerance traits in cotton accessions, and the identification of elite quantitative trait loci (QTLs)/genes for salt-tolerance have been very important in salt tolerance breeding. Here, 43 advanced salt-tolerant and 31 highly salt-sensitive cultivars were detected by analyzing ten salt tolerance related traits in 304 upland cotton cultivars. Among them, 11 advanced salt-tolerance and eight highly salt-sensitive cultivars were consistent with previously reported results. Association analysis of ten salt-tolerance related traits and 145 SSRs was performed, and a total of 95 significant associations were detected; 17, 41, and 37 of which were associated with germinative index, seedling stage physiological index, and four seedling stage biochemical indexes, respectively. Of these associations, 20 SSR loci were simultaneously associated with two or more traits. Furthermore, we detected 117 elite alleles associated with salt-tolerance traits, 4 of which were reported previously. Among these loci, 44 (37.60%) were rare alleles with a frequency of less than 5%, 6 only existed in advanced salt-tolerant cultivars, and 2 only in highly salt-sensitive cultivars. As a result, 13 advanced salt-tolerant cultivars were selected to assemble the optimal cross combinations by computer simulation for the development of salt-tolerant accessions. This study lays solid foundations for further improvements in cotton salt-tolerance by referencing elite germplasms, alleles associated with salt-tolerance traits, and optimal crosses. PMID:26943816

  8. Accuracy and Training Population Design for Genomic Selection on Quantitative Traits in Elite North American Oats

    Directory of Open Access Journals (Sweden)

    Franco G. Asoro

    2011-07-01

    Full Text Available Genomic selection (GS is a method to estimate the breeding values of individuals by using markers throughout the genome. We evaluated the accuracies of GS using data from five traits on 446 oat ( L. lines genotyped with 1005 Diversity Array Technology (DArT markers and two GS methods (ridge regression–best linear unbiased prediction [RR-BLUP] and BayesCπ under various training designs. Our objectives were to (i determine accuracy under increasing marker density and training population size, (ii assess accuracies when data is divided over time, and (iii examine accuracy in the presence of population structure. Accuracy increased as the number of markers and training size become larger. Including older lines in the training population increased or maintained accuracy, indicating that older generations retained information useful for predicting validation populations. The presence of population structure affected accuracy: when training and validation subpopulations were closely related accuracy was greater than when they were distantly related, implying that linkage disequilibrium (LD relationships changed across subpopulations. Across many scenarios involving large training populations, the accuracy of BayesCπ and RR-BLUP did not differ. This empirical study provided evidence regarding the application of GS to hasten the delivery of cultivars through the use of inexpensive and abundant molecular markers available to the public sector.

  9. Effect of Cadmium and Lead on Quantitative and Essential Oil Traits of Peppermint (Mentha piperita L.

    Directory of Open Access Journals (Sweden)

    SH Amirmoradi

    2017-09-01

    Full Text Available **Introduction Industrialization has been the cause of environmental pollution and one of significant pollutant is that of heavy metals. These hazardous elements can cause to water and soil pollution. These metals can accumulate in the food chain and create damages for human and livestock. Researchers revealed that increasing Cd, Pb, Cu, Mn and Zn concentrations caused to decreasing of shoot fresh weight and essential oil yield. Scavroni et al (2005 indicated that peppermint was able to accumulate the heavy metals in shoot tissues but did not enter into essential oil. Therefore study the effect of heavy metals on morphological and quantitative traits of medicinal plants is essential. Material and Method The experiment was done in the research greenhouse of the Agricultural Faculty of Ferdowsi University of Mashhad in 2011.The treatments were arranged basis on a randomized block design with three replications. Treatments were included T1:0, T2:10 ppm cd , T3:20 ppm cd,T4:40 ppm cd,T5:60 ppm cd,T6:80 ppm cd cd,T7:100 ppm cd,T8:100ppm pb, T9:300 ppm pb, T10: 600 ppm pb, T11: 900 ppm pb, T12: 1200 ppm pb and T13: 1500 ppm pb. Peppermint was cultivated with uniform weight rhizomes harvested from the research farm of Ferdowsi University of Mashhad. Every rhizome had two buds and six rhizomes were planted in pots of dimensions 30×50×35 cm. Treatments were irrigated with cdcl2 and pbcl2 with the administered doses and control was irrigated with distilled water. Plants were harvested two times at the first stages of flowering. The essential oil percentage was measured with 30 grams of dried leaves by Clevenger device. Result and Discussion Increasing cadmium and lead concentrations caused a decline of fresh and dry weight, main stem height, leaf area per plant, leaf number per plant, number of nodes per plant and essential oil percentage compared to the control. At the first harvest, increasing doses of Cd caused a decrease of fresh weight. This

  10. Economic values of pork production related traits in Finland

    Directory of Open Access Journals (Sweden)

    T. SERENIUS

    2008-12-01

    Full Text Available The objective of the present study was to estimate economic values for sow efficiency and meat production traits in the Finnish pork production system including the consideration for subsidies. Economic values were estimated by developing a bio-economic model that describes the Finnish production system. Genetic improvement estimates for meat production traits were also developed in order to evaluate how much genetic gain is reduced due to selection for meat quality. Results showed that the highest economic values, when expressed in genetic standard deviations, were obtained for total number of piglets born (€2.07 per piglet, feed conversion ratio (€2.07 per feed unit per kg, and lean meat percentage (€1.69 per %. Economic values for litter size, piglet mortality, sows length of productive life, and lean meat percentage increased when subsidies were not accounted for in the bio-economic model. Results show further that meat quality should have 15–20 percent weight in the Finnish production trait index in order to prevent its deterioration. When the selection weights are 15–20% for meat quality, the expected loss in genetic gain is approximately 3 percent for other production traits when compared to selection indices where meat quality traits are not included.;

  11. Fine-mapping diabetes-related traits, including insulin resistance, in heterogeneous stock rats

    Science.gov (United States)

    Holl, Katie L.; Oreper, Daniel; Xie, Yuying; Tsaih, Shirng-Wern; Valdar, William

    2012-01-01

    Type 2 diabetes (T2D) is a disease of relative insulin deficiency resulting from both insulin resistance and beta cell failure. We have previously used heterogeneous stock (HS) rats to fine-map a locus for glucose tolerance. We show here that glucose intolerance in the founder strains of the HS colony is mediated by different mechanisms: insulin resistance in WKY and an insulin secretion defect in ACI, and we demonstrate a high degree of variability for measures of insulin resistance and insulin secretion in HS rats. As such, our goal was to use HS rats to fine-map several diabetes-related traits within a region on rat chromosome 1. We measured blood glucose and plasma insulin levels after a glucose tolerance test in 782 male HS rats. Using 97 SSLP markers, we genotyped a 68 Mb region on rat chromosome 1 previously implicated in glucose and insulin regulation. We used linkage disequilibrium mapping by mixed model regression with inferred descent to identify a region from 198.85 to 205.9 that contains one or more quantitative trait loci (QTL) for fasting insulin and a measure of insulin resistance, the quantitative insulin sensitivity check index. This region also encompasses loci identified for fasting glucose and Insulin_AUC (area under the curve). A separate <3 Mb QTL was identified for body weight. Using a novel penalized regression method we then estimated effects of alternative haplotype pairings under each locus. These studies highlight the utility of HS rats for fine-mapping genetic loci involved in the underlying causes of T2D. PMID:22947656

  12. Achievement Is a Relation, Not a Trait: The Gravity of the Situation

    Science.gov (United States)

    Corrado, Gail

    2012-01-01

    Ability and achievement are not traits: they are relations. Mistaking traits for relations has a history even in science (our understanding of gravity). This mistake is possibly responsible for the lackluster performance of the results of our educational research when we have tried to use it to inform policy. It is particularly troublesome for…

  13. Mapping of quantitative trait loci for oil content in cottonseed kernel

    Indian Academy of Sciences (India)

    (next to fiber) which serves as raw material for oil extraction or animal feed production ... systems that control the performance of these traits could facilitate the application of this information for cottonseed improvement that will help ensure ...

  14. Genetic Diversity of Upland Rice Germplasm in Malaysia Based on Quantitative Traits

    Directory of Open Access Journals (Sweden)

    M. Sohrabi

    2012-01-01

    Full Text Available Genetic diversity is prerequisite for any crop improvement program as it helps in the development of superior recombinants. Fifty Malaysian upland rice accessions were evaluated for 12 growth traits, yield and yield components. All of the traits were significant and highly significant among the accessions. The higher magnitudes of genotypic and phenotypic coefficients of variation were recorded for flag leaf length-to-width ratio, spikelet fertility, and days to flowering. High heritability along with high genetic advance was registered for yield of plant, days to flowering, and flag leaf length-to-width ratio suggesting preponderance of additive gene action in the gene expression of these characters. Plant height showed highly significant positive correlation with most of the traits. According to UPGMA cluster analysis all accessions were clustered into six groups. Twelve morphological traits provided around 77% of total variation among the accessions.

  15. Qualitative and quantitative dermatoglyphic traits in patients with breast cancer: a prospective clinical study

    Directory of Open Access Journals (Sweden)

    Tuteja Amita

    2007-03-01

    Full Text Available Abstract Background Breast cancer is one of the most extensively studied cancers and its genetic basis is well established. Dermatoglyphic traits are formed under genetic control early in development but may be affected by environmental factors during first trimester of pregnancy. They however do not change significantly thereafter, thus maintaining stability not greatly affected by age. These patterns may represent the genetic make up of an individual and therefore his/her predisposition to certain diseases. Patterns of dermatoglyphics have been studied in various congenital disorders like Down's syndrome and Kleinfelter syndrome. The prints can thus represent a non-invasive anatomical marker of breast cancer risk and thus facilitate early detection and treatment. Methods The study was conducted on 60 histo-pathologically confirmed breast cancer patients and their digital dermatoglyphic patterns were studied to assess their association with the type and onset of breast cancer. Simultaneously 60 age-matched controls were also selected that had no self or familial history of a diagnosed breast cancer and the observations were recorded. The differences of qualitative (dermatoglyphic patterns data were tested for their significance using the chi-square test, and for quantitative (ridge counts and pattern intensity index data using the t- test. Results It was observed that six or more whorls in the finger print pattern were statistically significant among the cancer patients as compared to controls. It was also seen that whorls in the right ring finger and right little finger were found increased among the cases as compared to controls. The differences between mean pattern intensity index of cases and controls were found to be statistically significant. Conclusion The dermatoglyphic patterns may be utilized effectively to study the genetic basis of breast cancer and may also serve as a screening tool in the high-risk population. In a developing

  16. A genome-wide association study identifies protein quantitative trait loci (pQTLs.

    Directory of Open Access Journals (Sweden)

    David Melzer

    2008-05-01

    locations. The identification of protein quantitative trait loci (pQTLs may be a powerful complementary method of improving our understanding of disease pathways.

  17. Incorporation of causative quantitative trait nucleotides in single-step GBLUP.

    Science.gov (United States)

    Fragomeni, Breno O; Lourenco, Daniela A L; Masuda, Yutaka; Legarra, Andres; Misztal, Ignacy

    2017-07-26

    Much effort is put into identifying causative quantitative trait nucleotides (QTN) in animal breeding, empowered by the availability of dense single nucleotide polymorphism (SNP) information. Genomic selection using traditional SNP information is easily implemented for any number of genotyped individuals using single-step genomic best linear unbiased predictor (ssGBLUP) with the algorithm for proven and young (APY). Our aim was to investigate whether ssGBLUP is useful for genomic prediction when some or all QTN are known. Simulations included 180,000 animals across 11 generations. Phenotypes were available for all animals in generations 6 to 10. Genotypes for 60,000 SNPs across 10 chromosomes were available for 29,000 individuals. The genetic variance was fully accounted for by 100 or 1000 biallelic QTN. Raw genomic relationship matrices (GRM) were computed from (a) unweighted SNPs, (b) unweighted SNPs and causative QTN, (c) SNPs and causative QTN weighted with results obtained with genome-wide association studies, (d) unweighted SNPs and causative QTN with simulated weights, (e) only unweighted causative QTN, (f-h) as in (b-d) but using only the top 10% causative QTN, and (i) using only causative QTN with simulated weight. Predictions were computed by pedigree-based BLUP (PBLUP) and ssGBLUP. Raw GRM were blended with 1 or 5% of the numerator relationship matrix, or 1% of the identity matrix. Inverses of GRM were obtained directly or with APY. Accuracy of breeding values for 5000 genotyped animals in the last generation with PBLUP was 0.32, and for ssGBLUP it increased to 0.49 with an unweighted GRM, 0.53 after adding unweighted QTN, 0.63 when QTN weights were estimated, and 0.89 when QTN weights were based on true effects known from the simulation. When the GRM was constructed from causative QTN only, accuracy was 0.95 and 0.99 with blending at 5 and 1%, respectively. Accuracies simulating 1000 QTN were generally lower, with a similar trend. Accuracies using the

  18. Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers.

    Science.gov (United States)

    Crossa, José; Campos, Gustavo de Los; Pérez, Paulino; Gianola, Daniel; Burgueño, Juan; Araus, José Luis; Makumbi, Dan; Singh, Ravi P; Dreisigacker, Susanne; Yan, Jianbing; Arief, Vivi; Banziger, Marianne; Braun, Hans-Joachim

    2010-10-01

    The availability of dense molecular markers has made possible the use of genomic selection (GS) for plant breeding. However, the evaluation of models for GS in real plant populations is very limited. This article evaluates the performance of parametric and semiparametric models for GS using wheat (Triticum aestivum L.) and maize (Zea mays) data in which different traits were measured in several environmental conditions. The findings, based on extensive cross-validations, indicate that models including marker information had higher predictive ability than pedigree-based models. In the wheat data set, and relative to a pedigree model, gains in predictive ability due to inclusion of markers ranged from 7.7 to 35.7%. Correlation between observed and predictive values in the maize data set achieved values up to 0.79. Estimates of marker effects were different across environmental conditions, indicating that genotype × environment interaction is an important component of genetic variability. These results indicate that GS in plant breeding can be an effective strategy for selecting among lines whose phenotypes have yet to be observed.

  19. Are personality traits of juvenile myoclonic epilepsy related to frontal lobe dysfunctions? A proton MRS study.

    Science.gov (United States)

    de Araújo Filho, Gerardo Maria; Lin, Katia; Lin, Jaime; Peruchi, Mirella M; Caboclo, Luís Otávio S F; Guaranha, Mirian S B; Guilhoto, Laura M F F; Carrete, Henrique; Yacubian, Elza Márcia T

    2009-05-01

    Personality traits characterized by emotional instability and immaturity, unsteadiness, lack of discipline, hedonism, frequent and rapid mood changes, and indifference toward one's disease have been associated with patients who have juvenile myoclonic epilepsy (JME). Literature data demonstrate worse seizure control and more psychosocial dysfunctions among patients with JME who have those traits. In this controlled study we performed a correlation analysis of psychiatric scores with magnetic resonance spectroscopy (MRS) values across JME patients, aiming to verify the existence of a possible relation between frontal lobe dysfunction and the prevalence of personality disorders (PDs) in JME. Sixteen JME patients with cluster B PDs, 41 JME patients without any psychiatric disorder, and 30 healthy controls were submitted to a psychiatric evaluation and to a quantitative multivoxel MRS of thalamus; insula; cingulate gyrus; striatum; and frontal, parietal, and occipital lobes. Groups were homogeneous according to age, gender, and manual dominance. Psychiatric evaluation was performed through the Scheduled Clinical Interview for DSM-IV, Axis I and II (SCID I and II, respectively). A significant reduction of N-acetyl-aspartate over creatinine (NAA/Cr) ratio was observed mainly in the left frontal lobe in the JME and PD group. In addition, a significant increase in the glutamate-glutamine over creatinine GLX/Cr ratio was also observed in this referred region in the same group. These data support the hypothesis that PDs in JME could represent neuronal dysfunction and possibly a more severe form of this epileptic syndrome.

  20. An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus)

    Science.gov (United States)

    2014-01-01

    Background Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Results Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. Conclusions The integrated map described herein enhances the utility of genomic tools over

  1. An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus).

    Science.gov (United States)

    Ren, Yi; McGregor, Cecilia; Zhang, Yan; Gong, Guoyi; Zhang, Haiying; Guo, Shaogui; Sun, Honghe; Cai, Wantao; Zhang, Jie; Xu, Yong

    2014-01-20

    Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. The integrated map described herein enhances the utility of genomic tools over previous watermelon genetic maps. A

  2. Comparison of gene-based rare variant association mapping methods for quantitative traits in a bovine population with complex familial relationships

    NARCIS (Netherlands)

    Zhang, Qianqian; Guldbrandtsen, Bernt; Calus, Mario P.L.; Lund, Mogens Sandø; Sahana, Goutam

    2016-01-01

    Background: There is growing interest in the role of rare variants in the variation of complex traits due to increasing evidence that rare variants are associated with quantitative traits. However, association methods that are commonly used for mapping common variants are not effective to map

  3. Heritability estimates for yield and related traits in bread wheat

    International Nuclear Information System (INIS)

    Din, R.; Jehan, S.; Ibraullah, A.

    2009-01-01

    A set of 22 experimental wheat lines along with four check cultivars were evaluated in in-irrigated and unirrgated environments with objectives to determine genetic and phenotypic variation and heritability estimates for yield and its traits- The two environments were statistically at par for physiological maturity, plant height, spikes m/sub -2/. spike lets spike/sup -1/ and 1000-grain weight. Highly significant genetic variability existed among wheat lines (P < 0.0 I) in the combined analysis across two test environments for traits except 1000- grain weight. Genotypes x environment interactions were non-significant for traits indicating consistent performance of lines in two test environments. However lines and check cultivars were two to five days early in maturity under unirrigated environment. Plant height, spikes m/sup -2/ and 1000-grain weight also reduced under unirrigated environments. Genetic variances were greater than Environmental variances for most of traits- Heritability estimates were of higher magnitude (0.74 to 0.96) for plant height, medium (0.31 to 0.56) for physiological maturity. spikelets spike/sup -1/ (unirrigated) and 1000-grain weight, and low for spikes m/sup -2/. (author)

  4. How are personality trait and profile agreement related?

    Czech Academy of Sciences Publication Activity Database

    Allik, J.; Borkenau, P.; Hřebíčková, Martina; Kuppens, P.; Realo, A.

    2015-01-01

    Roč. 6, č. 6 (2015), s. 785 ISSN 1664-1078 Institutional support: RVO:68081740 Keywords : self-other agreement * trait-centered approach * varable-cenetered approach Subject RIV: AN - Psychology Impact factor: 2.463, year: 2015 http://journal.frontiersin.org/article/10.3389/fpsyg.2015.00785/abstract

  5. Mapping of quantitative trait loci for grain yield and its components in a US popular winter wheat TAM 111 using 90K SNPs.

    Directory of Open Access Journals (Sweden)

    Silvano O Assanga

    Full Text Available Stable quantitative trait loci (QTL are important for deployment in marker assisted selection in wheat (Triticum aestivum L. and other crops. We reported QTL discovery in wheat using a population of 217 recombinant inbred lines and multiple statistical approach including multi-environment, multi-trait and epistatic interactions analysis. We detected nine consistent QTL linked to different traits on chromosomes 1A, 2A, 2B, 5A, 5B, 6A, 6B and 7A. Grain yield QTL were detected on chromosomes 2B.1 and 5B across three or four models of GenStat, MapQTL, and QTLNetwork while the QTL on chromosomes 5A.1, 6A.2, and 7A.1 were only significant with yield from one or two models. The phenotypic variation explained (PVE by the QTL on 2B.1 ranged from 3.3-25.1% based on single and multi-environment models in GenStat and was pleiotropic or co-located with maturity (days to heading and yield related traits (test weight, thousand kernel weight, harvest index. The QTL on 5B at 211 cM had PVE range of 1.8-9.3% and had no significant pleiotropic effects. Other consistent QTL detected in this study were linked to yield related traits and agronomic traits. The QTL on 1A was consistent for the number of spikes m-2 across environments and all the four analysis models with a PVE range of 5.8-8.6%. QTL for kernels spike-1 were found in chromosomes 1A, 2A.1, 2B.1, 6A.2, and 7A.1 with PVE ranged from 5.6-12.8% while QTL for thousand kernel weight were located on chromosomes 1A, 2B.1, 5A.1, 6A.2, 6B.1 and 7A.1 with PVEranged from 2.7-19.5%. Among the consistent QTL, five QTL had significant epistatic interactions (additive × additive at least for one trait and none revealed significant additive × additive × environment interactions. Comparative analysis revealed that the region within the confidence interval of the QTL on 5B from 211.4-244.2 cM is also linked to genes for aspartate-semialdehyde dehydrogenase, splicing regulatory glutamine/lysine-rich protein 1 isoform X1

  6. Remembering and knowing personality traits: figure/ground asymmetries in person-related retrieval experience.

    Science.gov (United States)

    Wehr, Thomas

    2008-01-01

    In two experiments, the effect of category salience on retrieval experience was investigated. In Experiment 1, participants rated typicality or concreteness of personality traits that differed in stereotype reference (i.e., consistent, inconsistent, and neutral in relation to the age stereotype). More remember judgments were given for consistent and inconsistent traits in contrast to neutral traits, thereby indicating a figure/ground asymmetry. In Experiment 2, neutral traits were excluded and a classical figure/ground phenomenon was demonstrated for the retrieval experience of traits (i.e., reversibility of an ambiguous figure after typicality and untypicality ratings). Altogether, the results suggest that metacognitive trait representations depend on principles of figure/ground asymmetries rather than on functional principles of social information processing.

  7. Comparative sequence analyses of the major quantitative trait locus phosphorus uptake 1 (Pup1) reveal a complex genetic structure.

    Science.gov (United States)

    Heuer, Sigrid; Lu, Xiaochun; Chin, Joong Hyoun; Tanaka, Juan Pariasca; Kanamori, Hiroyuki; Matsumoto, Takashi; De Leon, Teresa; Ulat, Victor Jun; Ismail, Abdelbagi M; Yano, Masahiro; Wissuwa, Matthias

    2009-06-01

    The phosphorus uptake 1 (Pup1) locus was identified as a major quantitative trait locus (QTL) for tolerance of phosphorus deficiency in rice. Near-isogenic lines with the Pup1 region from tolerant donor parent Kasalath typically show threefold higher phosphorus uptake and grain yield in phosphorus-deficient field trials than the intolerant parent Nipponbare. In this study, we report the fine mapping of the Pup1 locus to the long arm of chromosome 12 (15.31-15.47 Mb). Genes in the region were initially identified on the basis of the Nipponbare reference genome, but did not reveal any obvious candidate genes related to phosphorus uptake. Kasalath BAC clones were therefore sequenced and revealed a 278-kbp sequence significantly different from the syntenic regions in Nipponbare (145 kb) and in the indica reference genome of 93-11 (742 kbp). Size differences are caused by large insertions or deletions (INDELs), and an exceptionally large number of retrotransposon and transposon-related elements (TEs) present in all three sequences (45%-54%). About 46 kb of the Kasalath sequence did not align with the entire Nipponbare genome, and only three Nipponbare genes (fatty acid alpha-dioxygenase, dirigent protein and aspartic proteinase) are highly conserved in Kasalath. Two Nipponbare genes (expressed proteins) might have evolved by at least three TE integrations in an ancestor gene that is still present in Kasalath. Several predicted Kasalath genes are novel or unknown genes that are mainly located within INDEL regions. Our results highlight the importance of sequencing QTL regions in the respective donor parent, as important genes might not be present in the current reference genomes.

  8. Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs

    DEFF Research Database (Denmark)

    Drag, Markus; Hansen, Mathias B.; Kadarmideen, Haja N.

    2018-01-01

    Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed...... to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS) were slaughtered at similar to 100 kg. Gene...... monitoring of other overlapping QTL traits should be performed to avoid any negative consequences of selection....

  9. Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs

    DEFF Research Database (Denmark)

    Drag, Markus; Hansen, Mathias B.; Kadarmideen, Haja N.

    2018-01-01

    Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed...... to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS) were slaughtered at similar to 100 kg. Gene...... and SSC14. Functional characterisation of eQTLs revealed functions within regulation of androgen and the intracellular steroid hormone receptor signalling pathway and of xenobiotic metabolism by cytochrome P450 system and cellular response to oestradiol. A QTL enrichment test revealed 89 QTL traits...

  10. An Examination of Authentic Leadership Traits and Their Relation to Student Achievement Scores

    Science.gov (United States)

    Hunter, Robin C.

    2017-01-01

    The purpose of this quantitative, single case study was to examine principal perceptions of their own leadership traits which may impact student achievement. Principals in one Florida district were invited to participate in an open ended interview, providing their own perceptions of their personal leadership behaviors. By examining the data…

  11. Dissecting quantitative trait loci for boron efficiency across multiple environments in Brassica napus.

    Directory of Open Access Journals (Sweden)

    Zunkang Zhao

    Full Text Available High yield is the most important goal in crop breeding, and boron (B is an essential micronutrient for plants. However, B deficiency, leading to yield decreases, is an agricultural problem worldwide. Brassica napus is one of the most sensitive crops to B deficiency, and considerable genotypic variation exists among different cultivars in response to B deficiency. To dissect the genetic basis of tolerance to B deficiency in B. napus, we carried out QTL analysis for seed yield and yield-related traits under low and normal B conditions using the double haploid population (TNDH by two-year and the BQDH population by three-year field trials. In total, 80 putative QTLs and 42 epistatic interactions for seed yield, plant height, branch number, pod number, seed number, seed weight and B efficiency coefficient (BEC were identified under low and normal B conditions, singly explaining 4.15-23.16% and 0.53-14.38% of the phenotypic variation. An additive effect of putative QTLs was a more important controlling factor than the additive-additive effect of epistatic interactions. Four QTL-by-environment interactions and 7 interactions between epistatic interactions and the environment contributed to 1.27-4.95% and 1.17-3.68% of the phenotypic variation, respectively. The chromosome region on A2 of SYLB-A2 for seed yield under low B condition and BEC-A2 for BEC in the two populations was equivalent to the region of a reported major QTL, BE1. The B. napus homologous genes of Bra020592 and Bra020595 mapped to the A2 region and were speculated to be candidate genes for B efficiency. These findings reveal the complex genetic basis of B efficiency in B. napus. They provide a basis for the fine mapping and cloning of the B efficiency genes and for breeding B-efficient cultivars by marker-assisted selection (MAS.

  12. Genetic Evidence for Causal Relationships Between Maternal Obesity-Related Traits and Birth Weight

    DEFF Research Database (Denmark)

    Tyrrell, Jessica; Richmond, Rebecca C; Palmer, Tom M

    2016-01-01

    IMPORTANCE: Neonates born to overweight or obese women are larger and at higher risk of birth complications. Many maternal obesity-related traits are observationally associated with birth weight, but the causal nature of these associations is uncertain. OBJECTIVE: To test for genetic evidence...... of causal associations of maternal body mass index (BMI) and related traits with birth weight. DESIGN, SETTING, AND PARTICIPANTS: Mendelian randomization to test whether maternal BMI and obesity-related traits are potentially causally related to offspring birth weight. Data from 30,487 women in 18 studies...

  13. Enhanced fire-related traits may contribute to the invasiveness of Downy Brome (Bromus tectorum)

    Science.gov (United States)

    Although several invasive species have induced changes to the fire regime of invaded ecosystems, potential intraspecific shifts in fire-related traits that might enhance their invasion success, have never been addressed. We assumed that traits conferring persistence and competitiveness in post-fire ...

  14. Supplementary data: Table 1. QTL for tassel related traits of F2:3 ...

    Indian Academy of Sciences (India)

    User

    Supplementary data: Table 1. QTL for tassel related traits of F2:3 population across and RIL population through single-environment analysis (SEA). Trait. Population. Environment. QTL. Binlocusa. Flanking marker. Peak position. (cM). Range. (cM)b. Ac. Dd. Gene actione. R2(%)f. Subtotal R2. (%)g. F(0.05)h type. TTL. F2:3.

  15. Are Autistic Traits in the General Population Related to Global and Regional Brain Differences?

    Science.gov (United States)

    Koolschijn, P. Cédric M. P.; Geurts, Hilde M.; van der Leij, Andries R.; Scholte, H. Steven

    2015-01-01

    There is accumulating evidence that autistic-related traits in the general population lie on a continuum, with autism spectrum disorders representing the extreme end of this distribution. Here, we tested the hypothesis of a possible relationship between autistic traits and brain morphometry in the general population. Participants completed the…

  16. How Are Traits Related to Problem Behavior in Preschoolers? Similarities and Contrasts between Temperament and Personality

    Science.gov (United States)

    De Pauw, Sarah S. W.; Mervielde, Ivan; Van Leeuwen, Karla G.

    2009-01-01

    The lack of empirical research relating temperament models and personality hinders conceptual integration and holds back research linking childhood traits to problem behavior or maladjustment. This study evaluates, within a sample of 443 preschoolers, the relationships between children's maladaptation and traits measured by three temperament…

  17. Estrus Traits Derived from Activity Measurements are Heritable and Closely Related to Conventional

    DEFF Research Database (Denmark)

    Ismael, Ahmed Ismael Sayed; Kargo, Morten; Fogh, Anders

    This study was aimed at assessing the genetic parameters for fertility-related traits, comparing the interval from calving to first insemination (ICF) to physical activity traits, especially days from calving to first high activity, DFHA. Data from commercial Holstein herds included insemination ...

  18. Relation between observed locomotion traits and locomotion score in dairy cows

    NARCIS (Netherlands)

    Schlageter Tello, A.A.; Bokkers, E.A.M.; Groot Koerkamp, P.W.G.; Hertem, van T.; Viazzi, S.; Lokhorst, Kees

    2015-01-01

    Lameness is still an important problem in modern dairy farming. Human observation of locomotion, by looking at different traits in one go, is used in practice to assess locomotion. The objectives of this article were to determine which individual locomotion traits are most related to locomotion

  19. Regression Association Analysis of Yield-Related Traits with RAPD Molecular Markers in Pistachio (Pistacia vera L.

    Directory of Open Access Journals (Sweden)

    Saeid Mirzaei

    2017-10-01

    Full Text Available Introduction: The pistachio (Pistacia vera, a member of the cashew family, is a small tree originating from Central Asia and the Middle East. The tree produces seeds that are widely consumed as food. Pistacia vera often is confused with other species in the genus Pistacia that are also known as pistachio. These other species can be distinguished by their geographic distributions and their seeds which are much smaller and have a soft shell. Continual advances in crop improvement through plant breeding are driven by the available genetic diversity. Therefore, the recognition and measurement of such diversity is crucial to breeding programs. In the past 20 years, the major effort in plant breeding has changed from quantitative to molecular genetics with emphasis on quantitative trait loci (QTL identification and marker assisted selection (MAS. The germplasm-regression-combined association studies not only allow mapping of genes/QTLs with higher level of confidence, but also allow detection of genes/QTLs, which will otherwise escape detection in linkage-based QTL studies based on the planned populations. The development of the marker-based technology offers a fast, reliable, and easy way to perform multiple regression analysis and comprise an alternative approach to breeding in diverse species of plants. The availability of many makers and morphological traits can help to regression analysis between these markers and morphological traits. Materials and Methods: In this study, 20 genotypes of Pistachio were studied and yield related traits were measured. Young well-expanded leaves were collected for DNA extraction and total genomic DNA was extracted. Genotyping was performed using 15 RAPD primers and PCR amplification products were visualized by gel electrophoresis. The reproducible RAPD fragments were scored on the basis of present (1 or absent (0 bands and a binary matrix constructed using each molecular marker. Association analysis between

  20. Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta).

    Science.gov (United States)

    Xu, Yan; Huang, Long; Ji, Dehua; Chen, Changsheng; Zheng, Hongkun; Xie, Chaotian

    2015-09-21

    Pyropia haitanensis is one of the most economically important mariculture crops in China. A high-density genetic map has not been published yet and quantitative trait locus (QTL) mapping has not been undertaken for P. haitanensis because of a lack of sufficient molecular markers. Specific length amplified fragment sequencing (SLAF-seq) was developed recently for large-scale, high resolution de novo marker discovery and genotyping. In this study, SLAF-seq was used to obtain mass length polymorphic markers to construct a high-density genetic map for P. haitanensis. In total, 120.33 Gb of data containing 75.21 M pair-end reads was obtained after sequencing. The average coverage for each SLAF marker was 75.50-fold in the male parent, 74.02-fold in the female parent, and 6.14-fold average in each double haploid individual. In total, 188,982 SLAFs were detected, of which 6731 were length polymorphic SLAFs that could be used to construct a genetic map. The final map included 4550 length polymorphic markers that were combined into 740 bins on five linkage groups, with a length of 874.33 cM and an average distance of 1.18 cM between adjacent bins. This map was used for QTL mapping to identify chromosomal regions associated with six economically important traits: frond length, width, thickness, fresh weight, growth rates of frond length and growth rates of fresh weight. Fifteen QTLs were identified for these traits. The value of phenotypic variance explained by an individual QTL ranged from 9.59 to 16.61 %, and the confidence interval of each QTL ranged from 0.97 cM to 16.51 cM. The first high-density genetic linkage map for P. haitanensis was constructed, and fifteen QTLs associated with six economically important traits were identified. The results of this study not only provide a platform for gene and QTL fine mapping, map-based gene isolation, and molecular breeding for P. haitanensis, but will also serve as a reference for positioning sequence scaffolds on a physical

  1. Genetic and Physiological Characterization of Two Clusters of Quantitative Trait Loci Associated With Seed Dormancy and Plant Height in Rice

    OpenAIRE

    Ye, Heng; Beighley, Donn H.; Feng, Jiuhuan; Gu, Xing-You

    2013-01-01

    Seed dormancy and plant height have been well-studied in plant genetics, but their relatedness and shared regulatory mechanisms in natural variants remain unclear. The introgression of chromosomal segments from weedy into cultivated rice (Oryza sativa) prompted the detection of two clusters (qSD1-2/qPH1 and qSD7-2/qPH7) of quantitative trait loci both associated with seed dormancy and plant height. Together, these two clusters accounted for >96% of the variances for plant height and ~71% of t...

  2. Detection of parent-of-origin effects for quantitative traits using ...

    Indian Academy of Sciences (India)

    RESEARCH ARTICLE ... ever, these methods can only be applied to deal with nuclear families and thus are not suitable for ... For qualitative traits and nuclear families, the parental- .... across parents within each mating type, i.e. P(F=f, M=m).

  3. Simulating the yield impacts of organ-level quantitative trait loci associated with drought response in maize: a "gene-to-phenotype" modeling approach.

    Science.gov (United States)

    Chenu, Karine; Chapman, Scott C; Tardieu, François; McLean, Greg; Welcker, Claude; Hammer, Graeme L

    2009-12-01

    Under drought, substantial genotype-environment (G x E) interactions impede breeding progress for yield. Identifying genetic controls associated with yield response is confounded by poor genetic correlations across testing environments. Part of this problem is related to our inability to account for the interplay of genetic controls, physiological traits, and environmental conditions throughout the crop cycle. We propose a modeling approach to bridge this "gene-to-phenotype" gap. For maize under drought, we simulated the impact of quantitative trait loci (QTL) controlling two key processes (leaf and silk elongation) that influence crop growth, water use, and grain yield. Substantial G x E interaction for yield was simulated for hypothetical recombinant inbred lines (RILs) across different seasonal patterns of drought. QTL that accelerated leaf elongation caused an increase in crop leaf area and yield in well-watered or preflowering water deficit conditions, but a reduction in yield under terminal stresses (as such "leafy" genotypes prematurely exhausted the water supply). The QTL impact on yield was substantially enhanced by including pleiotropic effects of these QTL on silk elongation and on consequent grain set. The simulations obtained illustrated the difficulty of interpreting the genetic control of yield for genotypes influenced only by the additive effects of QTL associated with leaf and silk growth. The results highlight the potential of integrative simulation modeling for gene-to-phenotype prediction and for exploiting G x E interactions for complex traits such as drought tolerance.

  4. Relation between flower head traits and florivory in Asteraceae: a phylogenetically controlled approach.

    Science.gov (United States)

    Oguro, Michio; Sakai, Satoki

    2015-03-01

    • While much research has examined the relation between leaf traits and herbivory, very little is known about the interaction between floral traits, particularly biochemical traits, and florivory. We investigated patterns between floral traits and florivory across multiple species using phylogenetic comparative approaches to enhance our understanding of the evolution of plant-florivore interactions.• The relation between the intensity of florivory and five biochemical traits (concentrations of carbon, nitrogen, phosphorus, water, and total phenolics) and two morphological traits (diameter and number of flower heads) were investigated in wild individuals of 18 native species of Asteraceae. The phylogenetic signals in the morphological traits and intensity of florivory were also tested.• We found that species with higher nitrogen, water, and total phenolics and lower phosphorus concentrations in the flower heads and species with a large number and diameter of flower heads tended to be attacked by florivores. In addition, we found significant phylogenetic signals in florivory and morphological traits.• Our results clearly show that biochemical traits also play important roles in plant-florivore interactions, as previously shown in plant-leaf herbivore interactions. The positive relationship between florivory and total phenolics implies that phenolic compounds in flower heads may not act as a defense in the species. In addition, the observed pattern of signals in florivory might not be solely explained by the signals of the measured traits and other plant traits may also play significant roles in plant-florivore interaction in these species. © 2015 Botanical Society of America, Inc.

  5. Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits.

    Directory of Open Access Journals (Sweden)

    Noah Zaitlen

    2013-05-01

    Full Text Available Important knowledge about the determinants of complex human phenotypes can be obtained from the estimation of heritability, the fraction of phenotypic variation in a population that is determined by genetic factors. Here, we make use of extensive phenotype data in Iceland, long-range phased genotypes, and a population-wide genealogical database to examine the heritability of 11 quantitative and 12 dichotomous phenotypes in a sample of 38,167 individuals. Most previous estimates of heritability are derived from family-based approaches such as twin studies, which may be biased upwards by epistatic interactions or shared environment. Our estimates of heritability, based on both closely and distantly related pairs of individuals, are significantly lower than those from previous studies. We examine phenotypic correlations across a range of relationships, from siblings to first cousins, and find that the excess phenotypic correlation in these related individuals is predominantly due to shared environment as opposed to dominance or epistasis. We also develop a new method to jointly estimate narrow-sense heritability and the heritability explained by genotyped SNPs. Unlike existing methods, this approach permits the use of information from both closely and distantly related pairs of individuals, thereby reducing the variance of estimates of heritability explained by genotyped SNPs while preventing upward bias. Our results show that common SNPs explain a larger proportion of the heritability than previously thought, with SNPs present on Illumina 300K genotyping arrays explaining more than half of the heritability for the 23 phenotypes examined in this study. Much of the remaining heritability is likely to be due to rare alleles that are not captured by standard genotyping arrays.

  6. Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits.

    Science.gov (United States)

    Zaitlen, Noah; Kraft, Peter; Patterson, Nick; Pasaniuc, Bogdan; Bhatia, Gaurav; Pollack, Samuela; Price, Alkes L

    2013-05-01

    Important knowledge about the determinants of complex human phenotypes can be obtained from the estimation of heritability, the fraction of phenotypic variation in a population that is determined by genetic factors. Here, we make use of extensive phenotype data in Iceland, long-range phased genotypes, and a population-wide genealogical database to examine the heritability of 11 quantitative and 12 dichotomous phenotypes in a sample of 38,167 individuals. Most previous estimates of heritability are derived from family-based approaches such as twin studies, which may be biased upwards by epistatic interactions or shared environment. Our estimates of heritability, based on both closely and distantly related pairs of individuals, are significantly lower than those from previous studies. We examine phenotypic correlations across a range of relationships, from siblings to first cousins, and find that the excess phenotypic correlation in these related individuals is predominantly due to shared environment as opposed to dominance or epistasis. We also develop a new method to jointly estimate narrow-sense heritability and the heritability explained by genotyped SNPs. Unlike existing methods, this approach permits the use of information from both closely and distantly related pairs of individuals, thereby reducing the variance of estimates of heritability explained by genotyped SNPs while preventing upward bias. Our results show that common SNPs explain a larger proportion of the heritability than previously thought, with SNPs present on Illumina 300K genotyping arrays explaining more than half of the heritability for the 23 phenotypes examined in this study. Much of the remaining heritability is likely to be due to rare alleles that are not captured by standard genotyping arrays.

  7. Relationships among quantitative traits in F3, F4 and F5 wheat hybrids obtained by pedigree and bulk selection

    Directory of Open Access Journals (Sweden)

    Janković Snežana

    2010-01-01

    Full Text Available Relationships among quantitative traits of wheat were analyzed in parents and their F3, F4 and F5 hybrids. Three female parents (Briscard, Carifen 12 and Rescler were crossed with two male parents (Francuska and PKB-Prelivka. Same crosses were repeated 4 years, from 1996 to 1999. Hybrids were obtained via pedigree and bulk selection. In year 2000 the field experiments were set up with all parental and hybrid material, at the Institute 'PKB INI Agroekonomik', in Padinska Skela, near Belgrade. Six traits were measured: plant height, spike length, number of spikelets per spike, number of grains per spike, 1000 grain weight and grain weight per spike. In parental genotypes, it was found grain mass per spike was in significant and positive correlation with 1000 grain mass and number of grains per spike. As in parents, correlation between grain mass per spike and 1000 grain weight was almost functional in F3, F4 and F5 hybrids. However, correlation between grain mass per spike and number of grains per spike was negative or slight positive in hybrid descendents, what is surprising because it is oppositely to the parents. Similar values of correlation coefficients were found in both applied methods of selection. This fact shows correlations change between generations. Grain mass per spike depends on a 1000 grain mass in both, parental and hybrid generations. Stable relationship between traits could be use for selection of high yielding genotypes.

  8. Identification of elite pure-lines from local lentil germplasm using diversity index based on quantitative traits

    International Nuclear Information System (INIS)

    Sultana, T.; Nadeem, S.; Fatima, Z.

    2010-01-01

    Three hundred and seventeen accessions of lentil collected from all over the country were evaluated for six quantitative traits to investigate inter and intra-accession diversity in association with geographic pattern. Variation indicated that areas with high geographic diversity that is supposed to present high biological diversity are yet to be explored. Classification of germplasm gave rise to some elite lines for specific characters and the accessions for days to flowering (45), days to maturity (7), plant height (12), pods per cluster (17) and seed weight (27) have been selected and suggested for exploitation in breeding programme. Twelve clusters were observed with varying degrees of intercluster dissimilarity that suggested the selection of diverse superior parents for hybridization. Some of the characters associated with origin as high seed weight of germplasm collected from Baluchistan is needed to exploit for specific trait/s. Germplasm distribution revealed that Punjab and Sindh represented a high collections along with high diversity, whereas other areas are yet to be explored. Similarly zone 3a, 6, 7, 9 and 10 along with high mountains lack complete representation that indicated the importance for future collection mission to these areas. (author)

  9. Arms race between selfishness and policing: two-trait quantitative genetic model for caste fate conflict in eusocial Hymenoptera.

    Science.gov (United States)

    Dobata, Shigeto

    2012-12-01

    Policing against selfishness is now regarded as the main force maintaining cooperation, by reducing costly conflict in complex social systems. Although policing has been studied extensively in social insect colonies, its coevolution against selfishness has not been fully captured by previous theories. In this study, I developed a two-trait quantitative genetic model of the conflict between selfish immature females (usually larvae) and policing workers in eusocial Hymenoptera over the immatures' propensity to develop into new queens. This model allows for the analysis of coevolution between genomes expressed in immatures and workers that collectively determine the immatures' queen caste fate. The main prediction of the model is that a higher level of polyandry leads to a smaller fraction of queens produced among new females through caste fate policing. The other main prediction of the present model is that, as a result of arms race, caste fate policing by workers coevolves with exaggerated selfishness of the immatures achieving maximum potential to develop into queens. Moreover, the model can incorporate genetic correlation between traits, which has been largely unexplored in social evolution theory. This study highlights the importance of understanding social traits as influenced by the coevolution of conflicting genomes. © 2012 The Author. Evolution© 2012 The Society for the Study of Evolution.

  10. Software Application Profile: RVPedigree: a suite of family-based rare variant association tests for normally and non-normally distributed quantitative traits.

    Science.gov (United States)

    Oualkacha, Karim; Lakhal-Chaieb, Lajmi; Greenwood, Celia Mt

    2016-04-01

    RVPedigree (Rare Variant association tests in Pedigrees) implements a suite of programs facilitating genome-wide analysis of association between a quantitative trait and autosomal region-based genetic variation. The main features here are the ability to appropriately test for association of rare variants with non-normally distributed quantitative traits, and also to appropriately adjust for related individuals, either from families or from population structure and cryptic relatedness. RVPedigree is available as an R package. The package includes calculation of kinship matrices, various options for coping with non-normality, three different ways of estimating statistical significance incorporating triaging to enable efficient use of the most computationally-intensive calculations, and a parallelization option for genome-wide analysis. The software is available from the Comprehensive R Archive Network [CRAN.R-project.org] under the name 'RVPedigree' and at [https://github.com/GreenwoodLab]. It has been published under General Public License (GPL) version 3 or newer. © The Author 2016; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association.

  11. Imputation-based analysis of association studies: candidate regions and quantitative traits.

    Directory of Open Access Journals (Sweden)

    Bertrand Servin

    2007-07-01

    Full Text Available We introduce a new framework for the analysis of association studies, designed to allow untyped variants to be more effectively and directly tested for association with a phenotype. The idea is to combine knowledge on patterns of correlation among SNPs (e.g., from the International HapMap project or resequencing data in a candidate region of interest with genotype data at tag SNPs collected on a phenotyped study sample, to estimate ("impute" unmeasured genotypes, and then assess association between the phenotype and these estimated genotypes. Compared with standard single-SNP tests, this approach results in increased power to detect association, even in cases in which the causal variant is typed, with the greatest gain occurring when multiple causal variants are present. It also provides more interpretable explanations for observed associations, including assessing, for each SNP, the strength of the evidence that it (rather than another correlated SNP is causal. Although we focus on association studies with quantitative phenotype and a relatively restricted region (e.g., a candidate gene, the framework is applicable and computationally practical for whole genome association studies. Methods described here are implemented in a software package, Bim-Bam, available from the Stephens Lab website http://stephenslab.uchicago.edu/software.html.

  12. Hybrid vigour and gene action for two quantitative traits of castor ...

    African Journals Online (AJOL)

    Five homozygous lines of castor plant, namely RS1-Om, RN1-Om, RTl-2m, RSl- Owm, and RNl- Omb, were crossed to raise F1, F2, BC1, and BC2 generations. The hybrids were tested for hybrid vigour for two metric traits, viz; number of pods per plant and seed yield per plant. Highly significant hybrid vigour was detected ...

  13. Bovine Mastitis Resistance: Novel Quantitative Trait Loci and the Role of Bovine Mammary Epithelial Cells

    OpenAIRE

    Kurz, Jacqueline P.

    2018-01-01

    Bovine mastitis, or inflammation of the mammary gland, has substantial economic and animal welfare implications. A genetic basis for mastitis resistance traits is recognized and can be used to guide selective breeding programs. The discovery of regions of the genome associated with mastitis resistance, and knowledge of the underlying molecular mechanisms responsible, can facilitate development of efficient mastitis control and therapeutic strategies. The objectives of this dissertation resear...

  14. Whole-genome modeling accurately predicts quantitative traits, as revealed in plants.

    OpenAIRE

    Tatarinova, Tatiana; Shin, Min-Gyoung; Marjoram, Paul; Nuzhdin, Sergey; Triska, Martin; Rickauer, Martina; Nikolsky, Yuri; Mazurier, Melanie; Gentzbittel, Laurent; Ben, Cecile

    2016-01-01

    Many adaptive events in natural populations, as well as response to artificial selection, are caused by polygenic action. Under selective pressure, the adaptive traits can quickly respond via small allele frequency shifts spread across numerous loci. We hypothesize that a large proportion of current phenotypic variation between individuals may be best explained by population admixture. We thus consider the complete, genome-wide universe of genetic variability, spread across several ancestral ...

  15. Genetic mapping of quantitative trait loci for aseasonal reproduction in sheep.

    Science.gov (United States)

    Mateescu, R G; Thonney, M L

    2010-10-01

    The productivity and economic prosperity of sheep farming could benefit greatly from more effective methods of selection for year-round lambing. Identification of QTL for aseasonal reproduction in sheep could lead to more accurate selection and faster genetic improvement. One hundred and twenty microsatellite markers were genotyped on 159 backcross ewes from a Dorset × East Friesian crossbred pedigree. Interval mapping was undertaken to map the QTL underlying several traits describing aseasonal reproduction including the number of oestrous cycles, maximum level of progesterone prior to breeding, pregnancy status determined by progesterone level, pregnancy status determined by ultrasound, lambing status and number of lambs born. Seven chromosomes (1, 3, 12, 17, 19, 20 and 24) were identified to harbour putative QTL for one or more component traits used to describe aseasonal reproduction. Ovine chromosomes 12, 17, 19 and 24 harbour QTL significant at the 5% chromosome-wide level, chromosomes 3 and 20 harbour QTL that exceeded the threshold at the 1% chromosome-wide level, while the QTL identified on chromosome 1 exceeded the 1% experiment-wide significance level. These results are a first step towards understanding the genetic mechanism of this complex trait and show that variation in aseasonal reproduction is associated with multiple chromosomal regions. © 2010 The Authors, Animal Genetics © 2010 Stichting International Foundation for Animal Genetics.

  16. Quantitative trait loci mapping of heat tolerance in broccoli (Brassica oleracea var. italica) using genotyping-by-sequencing.

    Science.gov (United States)

    Branham, Sandra E; Stansell, Zachary J; Couillard, David M; Farnham, Mark W

    2017-03-01

    Five quantitative trait loci and one epistatic interaction were associated with heat tolerance in a doubled haploid population of broccoli evaluated in three summer field trials. Predicted rising global temperatures due to climate change have generated a demand for crops that are resistant to yield and quality losses from heat stress. Broccoli (Brassica oleracea var. italica) is a cool weather crop with high temperatures during production decreasing both head quality and yield. Breeding for heat tolerance in broccoli has potential to both expand viable production areas and extend the growing season but breeding efficiency is constrained by limited genetic information. A doubled haploid (DH) broccoli population segregating for heat tolerance was evaluated for head quality in three summer fields in Charleston, SC, USA. Multiple quantitative trait loci (QTL) mapping of 1,423 single nucleotide polymorphisms developed through genotyping-by-sequencing identified five QTL and one positive epistatic interaction that explained 62.1% of variation in heat tolerance. The QTL identified here can be used to develop markers for marker-assisted selection and to increase our understanding of the molecular mechanisms underlying plant response to heat stress.

  17. "Are we there yet?": Deciding when one has demonstrated specific genetic causation in complex diseases and quantitative traits.

    Science.gov (United States)

    Page, Grier P; George, Varghese; Go, Rodney C; Page, Patricia Z; Allison, David B

    2003-10-01

    Although mathematical relationships can be proven by deductive logic, biological relationships can only be inferred from empirical observations. This is a distinct disadvantage for those of us who strive to identify the genes involved in complex diseases and quantitative traits. If causation cannot be proven, however, what does constitute sufficient evidence for causation? The philosopher Karl Popper said, "Our belief in a hypothesis can have no stronger basis than our repeated unsuccessful critical attempts to refute it." We believe that to establish causation, as scientists, we must make a serious attempt to refute our own hypotheses and to eliminate all known sources of bias before association becomes causation. In addition, we suggest that investigators must provide sufficient data and evidence of their unsuccessful efforts to find any confounding biases. In this editorial, we discuss what "causation" means in the context of complex diseases and quantitative traits, and we suggest guidelines for steps that may be taken to address possible confounders of association before polymorphisms may be called "causative."

  18. Statistical correction of the Winner's Curse explains replication variability in quantitative trait genome-wide association studies.

    Directory of Open Access Journals (Sweden)

    Cameron Palmer

    2017-07-01

    Full Text Available Genome-wide association studies (GWAS have identified hundreds of SNPs responsible for variation in human quantitative traits. However, genome-wide-significant associations often fail to replicate across independent cohorts, in apparent inconsistency with their apparent strong effects in discovery cohorts. This limited success of replication raises pervasive questions about the utility of the GWAS field. We identify all 332 studies of quantitative traits from the NHGRI-EBI GWAS Database with attempted replication. We find that the majority of studies provide insufficient data to evaluate replication rates. The remaining papers replicate significantly worse than expected (p < 10-14, even when adjusting for regression-to-the-mean of effect size between discovery- and replication-cohorts termed the Winner's Curse (p < 10-16. We show this is due in part to misreporting replication cohort-size as a maximum number, rather than per-locus one. In 39 studies accurately reporting per-locus cohort-size for attempted replication of 707 loci in samples with similar ancestry, replication rate matched expectation (predicted 458, observed 457, p = 0.94. In contrast, ancestry differences between replication and discovery (13 studies, 385 loci cause the most highly-powered decile of loci to replicate worse than expected, due to difference in linkage disequilibrium.

  19. Quantitative trait loci (QTL study identifies novel genomic regions associated to Chiari-like malformation in Griffon Bruxellois dogs.

    Directory of Open Access Journals (Sweden)

    Philippe Lemay

    Full Text Available Chiari-like malformation (CM is a developmental abnormality of the craniocervical junction that is common in the Griffon Bruxellois (GB breed with an estimated prevalence of 65%. This disease is characterized by overcrowding of the neural parenchyma at the craniocervical junction and disturbance of cerebrospinal fluid (CSF flow. The most common clinical sign is pain either as a direct consequence of CM or neuropathic pain as a consequence of secondary syringomyelia. The etiology of CM remains unknown but genetic factors play an important role. To investigate the genetic complexity of the disease, a quantitative trait locus (QTL approach was adopted. A total of 14 quantitative skull and atlas measurements were taken and were tested for association to CM. Six traits were found to be associated to CM and were subjected to a whole-genome association study using the Illumina canine high density bead chip in 74 GB dogs (50 affected and 24 controls. Linear and mixed regression analyses identified associated single nucleotide polymorphisms (SNPs on 5 Canis Familiaris Autosomes (CFAs: CFA2, CFA9, CFA12, CFA14 and CFA24. A reconstructed haplotype of 0.53 Mb on CFA2 strongly associated to the height of the cranial fossa (diameter F and an haplotype of 2.5 Mb on CFA14 associated to both the height of the rostral part of the caudal cranial fossa (AE and the height of the brain (FG were significantly associated to CM after 10 000 permutations strengthening their candidacy for this disease (P = 0.0421, P = 0.0094 respectively. The CFA2 QTL harbours the Sall-1 gene which is an excellent candidate since its orthologue in humans is mutated in Townes-Brocks syndrome which has previously been associated to Chiari malformation I. Our study demonstrates the implication of multiple traits in the etiology of CM and has successfully identified two new QTL associated to CM and a potential candidate gene.

  20. Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries).

    Science.gov (United States)

    Beraldi, Dario; McRae, Allan F; Gratten, Jacob; Pilkington, Jill G; Slate, Jon; Visscher, Peter M; Pemberton, Josephine M

    2007-01-01

    A genome-wide scan was performed to detect quantitative trait loci (QTL) for resistance to gastrointestinal parasites and ectoparasitic keds segregating in the free-living Soay sheep population on St. Kilda (UK). The mapping panel consisted of a single pedigree of 882 individuals of which 588 were genotyped. The Soay linkage map used for the scans comprised 251 markers covering the whole genome at average spacing of 15cM. The traits here investigated were the strongyle faecal egg count (FEC), the coccidia faecal oocyst count (FOC) and a count of keds (Melophagus ovinus). QTL mapping was performed by means of variance component analysis so that the genetic parameters of the study traits were also estimated and compared with previous studies in Soay and domestic sheep. Strongyle FEC and coccidia FOC showed moderate heritability (h(2)=0.26 and 0.22, respectively) in lambs but low heritability in adults (h(2)<0.10). Ked count appeared to have very low h(2) in both lambs and adults. Genome scans were performed for the traits with moderate heritability and two genomic regions reached the level of suggestive linkage for coccidia FOC in lambs (logarithm of the odds=2.68 and 2.21 on chromosomes 3 and X, respectively). We believe this is the first study to report a QTL search for parasite resistance in a free-living animal population and therefore may represent a useful reference for similar studies aimed at understanding the genetics of host-parasite co-evolution in the wild.

  1. A study on the qualitative and quantitative traits of barley (Hordeum ...

    African Journals Online (AJOL)

    user

    Key words: Qualitative and quantitative, barley, narbon vetch, weed, dry land. ... and biomass production (Baishya and Sharma, 1990; ..... pakistan. Digitalverlag gmbh, germany. 157: 1-5. Pisulewska E, Hanczowski P, Pisulewski P (2003).

  2. Plant traits related to nitrogen uptake influence plant-microbe competition.

    Science.gov (United States)

    Moreau, Delphine; Pivato, Barbara; Bru, David; Busset, Hugues; Deau, Florence; Faivre, Céline; Matejicek, Annick; Strbik, Florence; Philippot, Laurent; Mougel, Christophe

    2015-08-01

    Plant species are important drivers of soil microbial communities. However, how plant functional traits are shaping these communities has received less attention though linking plant and microbial traits is crucial for better understanding plant-microbe interactions. Our objective was to determine how plant-microbe interactions were affected by plant traits. Specifically we analyzed how interactions between plant species and microbes involved in nitrogen cycling were affected by plant traits related to 'nitrogen nutrition in interaction with soil nitrogen availability. Eleven plant species, selected along an oligotrophic-nitrophilic gradient, were grown individually in a nitrogen-poor soil with two levels of nitrate availability. Plant traits for both carbon and nitrogen nutrition were measured and the genetic structure and abundance of rhizosphere. microbial communities, in particular the ammonia oxidizer and nitrate reducer guilds, were analyzed. The structure of the bacterial community in the rhizosphere differed significantly between plant species and these differences depended on nitrogen availability. The results suggest that the rate of nitrogen uptake per unit of root biomass and per day is a key plant trait, explaining why the effect of nitrogen availability on the structure of the bacterial community depends on the plant species. We also showed that the abundance of nitrate reducing bacteria always decreased with increasing nitrogen uptake per unit of root biomass per day, indicating that there was competition for nitrate between plants and nitrate reducing bacteria. This study demonstrates that nitrate-reducing microorganisms may be adversely affected by plants with a high nitrogen uptake rate. Our work puts forward the role of traits related to nitrogen in plant-microbe interactions, whereas carbon is commonly considered as the main driver. It also suggests that plant traits related to ecophysiological processes, such as nitrogen uptake rates, are more

  3. Genetic Parameters and Combining Ability Effects of Parents for Seed Yield and other Quantitative Traits in Black Gram [Vigna mungo (L. Hepper

    Directory of Open Access Journals (Sweden)

    Supriyo CHAKRABORTY

    2010-06-01

    Full Text Available Line x tester analysis was carried out in black gram [Vigna mungo (L. Hepper], an edible legume, to estimate the gca (general combining ability effects of parents (3 lines and 3 testers and the SCA (specific combining ability effects of 9 crosses for seed yield and other eleven quantitative traits. Though additive and nonadditive gene actions governed the expression of quantitative traits, the magnitude of nonadditive gene action was higher than that of additive gene action for each quantitative trait. Two parents viz. �UG157� and �DPU915� were good general combiners. Two crosses namely �PDB 88-31�/�DPU 915� and �PLU 277�/�KAU7� had high per se performance along with positive significant SCA effect for seed yield/plant. The degree of dominance revealed overdominance for all the traits except clusters/plant with partial dominance. The predictability ratio also revealed the predominant role of nonadditive gene action in the genetic control of quantitative traits. Narrow sense heritability was also low for each trait. Recurrent selection or biparental mating followed by selection which can exploit both additive and nonadditive gene actions would be of interest for yield improvement in black gram. Due to presence of high magnitude of nonadditive gene action, heterosis breeding could also be attempted to develop low cost hybrid variety using genetic male sterility system in black gram.

  4. Genetic Parameters and Combining Ability Effects of Parents for Seed Yield and other Quantitative Traits in Black Gram [Vigna mungo (L. Hepper

    Directory of Open Access Journals (Sweden)

    Supriyo CHAKRABORTY

    2010-06-01

    Full Text Available Line x tester analysis was carried out in black gram [Vigna mungo (L. Hepper], an edible legume, to estimate the gca (general combining ability effects of parents (3 lines and 3 testers and the SCA (specific combining ability effects of 9 crosses for seed yield and other eleven quantitative traits. Though additive and nonadditive gene actions governed the expression of quantitative traits, the magnitude of nonadditive gene action was higher than that of additive gene action for each quantitative trait. Two parents viz. UG157 and DPU915 were good general combiners. Two crosses namely PDB 88-31/DPU 915 and PLU 277/KAU7 had high per se performance along with positive significant SCA effect for seed yield/plant. The degree of dominance revealed overdominance for all the traits except clusters/plant with partial dominance. The predictability ratio also revealed the predominant role of nonadditive gene action in the genetic control of quantitative traits. Narrow sense heritability was also low for each trait. Recurrent selection or biparental mating followed by selection which can exploit both additive and nonadditive gene actions would be of interest for yield improvement in black gram. Due to presence of high magnitude of nonadditive gene action, heterosis breeding could also be attempted to develop low cost hybrid variety using genetic male sterility system in black gram.

  5. Effect of Regulated Deficit Irrigation (RDI and Partial Root zone Drying (PRD on Quantitative and Qualitative Traits of Strawberry

    Directory of Open Access Journals (Sweden)

    A. Shahnazari

    2016-02-01

    Full Text Available Introduction: Deficit irrigation (DI is a suitable solution to gain acceptable and economic performance by using minimum amount of water. The partial root zone drying (PRD method introduced in Australia for the first time and its goal was controlling the vine’s excessive growth. This goal gained by alternative drying the rootzone. Basically the theory of PRD method, is expanding the plant’s roots by applying alternative stress on different sides of the roots. So the plants with PRD irrigation method can have different root system in comparison with other irrigation methods. At this method the plant’s condition would be OK by uptaking water from wet side, and the roots at the dry side can release abscisic acid hormone which decrease the stomatal conductance and consequently the water use efficiency would be increase.There had been studies on the effect of water tension on strawberry. The previous studies on strawberry indicated that the water stress can increase the plant’s brix concentration and some of plant acids.The awareness of the impact of water deficit stress on strawberry plant quantity and quality is essential for irrigation and product management, and at the current study, effect of different deficit irrigation methods on quantitative and qualitative traits of strawberry have been evaluated. The focus at the current study was on the qualitative traits. Materials and Methods: The present study was conducted in one of strawberry farms of Babolsar city in 2012 to evaluate the effects of deficit irrigation and partial root zone drying on quantitative and qualitative traits of strawberry plants. Three Irrigation treatments were studied: Full Irrigation (FI, Regulated Deficit Irrigation (RDI75% at 75% level of plants water requirementand Partial Root zone Drying (PRD75% at 75% level of plants water requirement. The study was conducted in a randomized complete block design with three replications. Irrigation was continued until the

  6. Quantitative Trait Locus (QTL meta-analysis and comparative genomics for candidate gene prediction in perennial ryegrass (Lolium perenne L.

    Directory of Open Access Journals (Sweden)

    Shinozuka Hiroshi

    2012-11-01

    Full Text Available Abstract Background In crop species, QTL analysis is commonly used for identification of factors contributing to variation of agronomically important traits. As an important pasture species, a large number of QTLs have been reported for perennial ryegrass based on analysis of biparental mapping populations. Further characterisation of those QTLs is, however, essential for utilisation in varietal improvement programs. Results A bibliographic survey of perennial ryegrass trait-dissection studies identified a total of 560 QTLs from previously published papers, of which 189, 270 and 101 were classified as morphology-, physiology- and resistance/tolerance-related loci, respectively. The collected dataset permitted a subsequent meta-QTL study and implementation of a cross-species candidate gene identification approach. A meta-QTL analysis based on use of the BioMercator software was performed to identify two consensus regions for pathogen resistance traits. Genes that are candidates for causal polymorphism underpinning perennial ryegrass QTLs were identified through in silico comparative mapping using rice databases, and 7 genes were assigned to the p150/112 reference map. Markers linked to the LpDGL1, LpPh1 and LpPIPK1 genes were located close to plant size, leaf extension time and heading date-related QTLs, respectively, suggesting that these genes may be functionally associated with important agronomic traits in perennial ryegrass. Conclusions Functional markers are valuable for QTL meta-analysis and comparative genomics. Enrichment of such genetic markers may permit further detailed characterisation of QTLs. The outcomes of QTL meta-analysis and comparative genomics studies may be useful for accelerated development of novel perennial ryegrass cultivars with desirable traits.

  7. The roles of genetic drift and natural selection in quantitative trait divergence along an altitudinal gradient in Arabidopsis thaliana.

    Science.gov (United States)

    Luo, Y; Widmer, A; Karrenberg, S

    2015-02-01

    Understanding how natural selection and genetic drift shape biological variation is a central topic in biology, yet our understanding of the agents of natural selection and their target traits is limited. We investigated to what extent selection along an altitudinal gradient or genetic drift contributed to variation in ecologically relevant traits in Arabidopsis thaliana. We collected seeds from 8 to 14 individuals from each of 14 A. thaliana populations originating from sites between 800 and 2700 m above sea level in the Swiss Alps. Seed families were grown with and without vernalization, corresponding to winter-annual and summer-annual life histories, respectively. We analyzed putatively neutral genetic divergence between these populations using 24 simple sequence repeat markers. We measured seven traits related to growth, phenology and leaf morphology that are rarely reported in A. thaliana and performed analyses of altitudinal clines, as well as overall QST-FST comparisons and correlation analyses among pair-wise QST, FST and altitude of origin differences. Multivariate analyses suggested adaptive differentiation along altitude in the entire suite of traits, particularly when expressed in the summer-annual life history. Of the individual traits, a decrease in rosette leaf number in the vegetative state and an increase in leaf succulence with increasing altitude could be attributed to adaptive divergence. Interestingly, these patterns relate well to common within- and between-species trends of smaller plant size and thicker leaves at high altitude. Our results thus offer exciting possibilities to unravel the underlying mechanisms for these conspicuous trends using the model species A. thaliana.

  8. Evaluation of pea varieties based on correlation of quantitative traits and indices

    Directory of Open Access Journals (Sweden)

    О. І. Присяжнюк

    2016-12-01

    Full Text Available Purpose. To evaluate pea plants productivity and determine the degree of correlation among the main agronomic characters in pea varieties. Methods. Structural and statistical analysis. Results. Evaluation of pea samples in terms of indices of plant productivity elements level based on correlation analysis and single-factor indices appliance provided insight into the ratio of one trait share per unit of another one. It was defined that some correlations among the elements of productivity was not only moderate and weak, but they also changed their sign that could be the evidence of growth conditions influence on structural relationships bet­ween some traits and, consequently, redistribution of their contributions to the formation of variety productivity. Positive and very close relationship of many traits was revealed, particularly between plant height and the height of the plant up to the first bean, the number of nodes and the number of sterile nodes (r = 0,95–0,97. Methodological aspects of the variety model creation were considered, that may be useful not only in pea breeding but also for improving the techno­logy of its cultivation. Conclusions. Correlation relationships were established between the number of beans and the number of fruiting nodes and the number of carpophores containing 2 beans (r = 0,86–0,88, seed mass and plant mass (r = 0,81, the number of seeds per plant and plant mass and seed mass per plant (r = 0,78–0,81, the number of certified seeds and the number of seeds per plant (r = 0,84, the average number of beans per fertile node and the number of carpophores containing 2 beans (r = 0,74 that makes it possible to use them in assessing the productivity of plants.

  9. Pattern of quantitative inheritance of yield and component traits in opium poppy (Papaver somniferum L.

    Directory of Open Access Journals (Sweden)

    Maurya Krishna Nand

    2014-01-01

    Full Text Available Generation mean analysis of cross NB-5x58/1 and its reciprocal cross was carried out to understand the nature of gene action in opium poppy. The significance of A, B, C and D scaling tests indicated presence of non-allelic interaction in the inheritance of traits except capsule size and husk yield/plant for reciprocal cross. Additive as well as dominance components of gene action were found in both the crosses. Most of the traits had greater non fixable dominance ‘h’ and dominance x dominance effects ‘l’ than fixable additive (d and additive x additive effects (i except leaves/plant, branches/plant, capsules/plant, stem diameter, capsule weight/plant, husk yield/plant, opium yield/plant, codeine and narcotine content which showed greater importance of additive (d and additive x additive effects (i effects. Inter-mating of the best parents, diallel selective mating or biparental mating in early segregating generations followed by recurrent selections were suggested for genetic improvement of opium poppy.

  10. Evaluation of Quantitative and Qualitative Traits of Some Apricot Cultivars Grown in Zanjan Region

    Directory of Open Access Journals (Sweden)

    sanaz molaie

    2017-02-01

    Full Text Available Introduction Apricot (Prunus armeniaca L. has special position in Iran fruit culture industry. In terms of cultivation and producing, Iran is one of the major countries in the world but in terms of export Iran is ranked 23. For this reason, research on necessities of fruit culture industries and access to new cultivars by breeding project is required. Obviously, paying attention to quality and quantity of products and using of local germplasm that known completely, played a significant role in this project. Apricot with genomic feature 2n=16, has extensive diversity due to sexual propagation and cultivation in different areas. Central Asia and Caucasian groups of apricot that involving Iranian and Turkish cultivars, have greatest phenotypic variations, while European group including cultivars that cultivated in North America, Australia and South Africa have the lowest diversity. Climate adaptation, increasing of fruits quality, self-compatibility and resistance to diseases are the most important goals of apricot breeding. Of course, the quality of fruits depends on sugar and acid balance and special aroma. One of the important targets of apricot breeding is introduce and develop of cultivars that can be cultivated in extensive areas. Target of recent study is primary evaluating of morphological and pomological traits of some cultivar and genotypes of apricot grown in Zanjan province. In order to introduce the cultivars that produces fruit with high quality and complete scientific researches to selection of ideal cultivars in this region for future. Method and material: This research carried out on four cultivars (Badami, Daneshkadeh, Shekarpareh, Shahroodi and two genotypes (C and D and was conducted in a completely randomize design with three replications. Evaluating of tree, branch, leaf, flower and some fruit traits performed based on existing descriptor. For determining some important pomological traits, fruits harvested in commercial time

  11. Quantitative analysis of production traits in saltwater crocodiles (Crocodylus porosus): II. age at slaughter.

    Science.gov (United States)

    Isberg, S R; Thomson, P C; Nicholas, F W; Barker, S G; Moran, C

    2005-12-01

    Crocodile morphometric (head, snout-vent and total length) measurements were recorded at three stages during the production chain: hatching, inventory [average age (+/-SE) is 265.1 +/- 0.4 days] and slaughter (average age is 1037.8 +/- 0.4 days). Crocodile skins are used for the manufacture of exclusive leather products, with the most common-sized skin sold having 35-45 cm in belly width. One of the breeding objectives for inclusion into a multitrait genetic improvement programme for saltwater crocodiles is the time taken for a juvenile to reach this size or age at slaughter. A multivariate restricted maximum likelihood analysis provided (co)variance components for estimating the first published genetic parameter estimates for these traits. Heritability (+/-SE) estimates for the traits hatchling snout-vent length, inventory head length and age at slaughter were 0.60 (0.15), 0.59 (0.12) and 0.40 (0.10) respectively. There were strong negative genetic (-0.81 +/- 0.08) and phenotypic (-0.82 +/- 0.02) correlations between age at slaughter and inventory head length.

  12. Dissociable relations between amygdala subregional networks and psychopathy trait dimensions in conduct-disordered juvenile offenders.

    Science.gov (United States)

    Aghajani, Moji; Colins, Olivier F; Klapwijk, Eduard T; Veer, Ilya M; Andershed, Henrik; Popma, Arne; van der Wee, Nic J; Vermeiren, Robert R J M

    2016-11-01

    Psychopathy is a serious psychiatric phenomenon characterized by a pathological constellation of affective (e.g., callous, unemotional), interpersonal (e.g., manipulative, egocentric), and behavioral (e.g., impulsive, irresponsible) personality traits. Though amygdala subregional defects are suggested in psychopathy, the functionality and connectivity of different amygdala subnuclei is typically disregarded in neurocircuit-level analyses of psychopathic personality. Hence, little is known of how amygdala subregional networks may contribute to psychopathy and its underlying trait assemblies in severely antisocial people. We addressed this important issue by uniquely examining the intrinsic functional connectivity of basolateral (BLA) and centromedial (CMA) amygdala networks in relation to affective, interpersonal, and behavioral traits of psychopathy, in conduct-disordered juveniles with a history of serious delinquency (N = 50, mean age = 16.83 ± 1.32). As predicted, amygdalar connectivity profiles exhibited dissociable relations with different traits of psychopathy. Interpersonal psychopathic traits not only related to increased connectivity of BLA and CMA with a corticostriatal network formation accommodating reward processing, but also predicted stronger CMA connectivity with a network of cortical midline structures supporting sociocognitive processes. In contrast, affective psychopathic traits related to diminished CMA connectivity with a frontolimbic network serving salience processing and affective responding. Finally, behavioral psychopathic traits related to heightened BLA connectivity with a frontoparietal cluster implicated in regulatory executive functioning. We suggest that these trait-specific shifts in amygdalar connectivity could be particularly relevant to the psychopathic phenotype, as they may fuel a self-centered, emotionally cold, and behaviorally disinhibited profile. Hum Brain Mapp 37:4017-4033, 2016. © 2016 The Authors Human

  13. Impulsivity-related traits distinguish women with co-occurring bulimia nervosa in a psychiatric sample.

    Science.gov (United States)

    Reas, Deborah L; Pedersen, Geir; Rø, Øyvind

    2016-12-01

    This study investigated impulsivity-related personality traits using the Revised NEO Personality Inventory (NEO PI-R) in women diagnosed with co-occurring bulmia nervosa and borderline personality disorder (BN-BPD), borderline personality disorder (BPD no-BN), or major depressive disorder (MDD-only). The sample included 672 adult female admissions to a psychiatric day hospital treatment program. The NEO PI-R facets of impulsiveness (N5), excitement-seeking (E5), self-discipline (C5), and deliberation (C6) provided a proxy assessment of impulsivity-related traits tapping negative urgency, sensation-seeking, lack of perseverance, and lack of premeditation/planning. After adjusting for age, BN-BPD displayed significantly higher levels of negative urgency and lack of premeditation than BPD without co-occurring BN. Women with BN-BPD also had significantly higher levels of impulsivity traits than MDD across domains, except for lack of perseverance. Impulsivity-related traits of negative urgency and lack of premeditation significantly differentiated women with versus without co-occurring BN among women with borderline personality disorder. Lower levels of impulsivity-related traits in women with MDD indicated that effects were not simply attributable to any form of psychopathology. Of the impulsivity traits, negative urgency demonstrated the strongest effect, providing further evidence of the important relationship between negative urgency and the expression of bulimic symptomology. © 2016 Wiley Periodicals, Inc. (Int J Eat Disord 2016; 49:1093-1096). © 2016 Wiley Periodicals, Inc.

  14. Trait Emotional Intelligence Is Related to Risk Taking when Adolescents Make Deliberative Decisions

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    Angelo Panno

    2016-08-01

    Full Text Available Most forms of risky behavior reach their peak during adolescence. A prominent line of research is exploring the relationship between people’s emotional self-efficacy and risk taking, but little is known about this relationship in the cognitive-deliberative domain among adolescents. The main aim of the present study consists in investigating whether trait EI (Emotional Intelligence is positively related to risk taking under predominantly cognitive-deliberative conditions among adolescents. Ninety-four adolescents played the cold version of the Columbia Card Task one month following an assessment of their trait EI. Results showed that trait EI is associated with risk taking under cognitive-deliberative conditions among adolescents. Moreover, the present research showed that trait EI is related to risk taking through the decision makers’ self-motivation. These results provide novel insights into research investigating the connections between emotional intelligence, decision science and adolescence research.

  15. Similar traits, different genes? Examining convergent evolution in related weedy rice populations.

    Science.gov (United States)

    Thurber, Carrie S; Jia, Melissa H; Jia, Yulin; Caicedo, Ana L

    2013-02-01

    Convergent phenotypic evolution may or may not be associated with convergent genotypic evolution. Agricultural weeds have repeatedly been selected for weed-adaptive traits such as rapid growth, increased seed dispersal and dormancy, thus providing an ideal system for the study of convergent evolution. Here, we identify QTL underlying weedy traits and compare their genetic architecture to assess the potential for convergent genetic evolution in two distinct populations of weedy rice. F(2) offspring from crosses between an indica cultivar and two individuals from genetically differentiated U.S. weedy rice populations were used to map QTL for four quantitative (heading date, seed shattering, plant height and growth rate) and two qualitative traits. We identified QTL on nine of the twelve rice chromosomes, yet most QTL locations do not overlap between the two populations. Shared QTL among weed groups were only seen for heading date, a trait for which weedy groups have diverged from their cultivated ancestors and from each other. Sharing of some QTL with wild rice also suggests a possible role in weed evolution for genes under selection during domestication. The lack of overlapping QTL for the remaining traits suggests that, despite a close evolutionary relationship, weedy rice groups have adapted to the same agricultural environment through different genetic mechanisms. © 2012 Blackwell Publishing Ltd.

  16. Two alternative recessive quantitative trait loci influence resistance to spring black stem and leaf spot in Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Oliver Richard P

    2008-03-01

    Full Text Available Abstract Background Knowledge of the genetic basis of plant resistance to necrotrophic pathogens is incomplete and has been characterised in relatively few pathosystems. In this study, the cytology and genetics of resistance to spring black stem and leaf spot caused by Phoma medicaginis, an economically important necrotrophic pathogen of Medicago spp., was examined in the model legume M. truncatula. Results Macroscopically, the resistant response of accession SA27063 was characterised by small, hypersensitive-like spots following inoculation while the susceptible interaction with accessions A17 and SA3054 showed necrotic lesions and spreading chlorosis. No unique cytological differences were observed during early infection (2 populations segregating for resistance to spring black stem and leaf spot were established between SA27063 and the two susceptible accessions, A17 and SA3054. The cross between SA27063 and A17 represented a wider cross than between SA27063 and SA3054, as evidenced by higher genetic polymorphism, reduced fertility and aberrant phenotypes of F2 progeny. In the SA27063 × A17 F2 population a highly significant quantitative trait locus (QTL, LOD = 7.37; P Phoma medicaginis one (rnpm1 genetically mapped to the top arm of linkage group 4 (LG4. rnpm1 explained 33.6% of the phenotypic variance in the population's response to infection depicted on a 1–5 scale and was tightly linked to marker AW256637. A second highly significant QTL (LOD = 6.77; P rnpm2, was located on the lower arm of LG8 in the SA27063 × SA3054 map. rnpm2 explained 29.6% of the phenotypic variance and was fine mapped to a 0.8 cM interval between markers h2_16a6a and h2_21h11d. rnpm1 is tightly linked to a cluster of Toll/Interleukin1 receptor-nucleotide binding site-leucine-rich repeat (TIR-NBS-LRR genes and disease resistance protein-like genes, while no resistance gene analogues (RGAs are apparent in the genomic sequence of the reference accession A17 at the

  17. Study of multivariate analysis of quantitative traits in Iranian pumpkin lines

    Directory of Open Access Journals (Sweden)

    Yadegari Mehrab

    2017-01-01

    Full Text Available In this study, seed yield production and its different components fruit length, fruit diameter, fruit length/fruit diameter ratio (FL/FD, diameter of flesh, diameter of seed core, fruit weight, weight of 1000 seed from 24 lines of pumpkin grown in Iran was examined. Twenty-five characters in all plant lines were measured by Descriptor (UPOV and data were subjected to cluster analysis. Results showed that plants lines were divided in four groups. In all groups, regression comparisons were made for modeling the effect of different characters on seed yield, results also showed that fruit weight and fruit length in all groups had the most direct effect on seed yield. In conclusion, these traits are suggested as the best indirect selection criteria to improve the seed yield genetically in Cucurbita spp. genotypes especially in preliminary generation of breeding and selection programs.

  18. The Effect of Water Deficit Imposing Methods on Quantitative and Qualitative Traits of New Potato Cultivar

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    Kh Parvizi

    2016-02-01

    overlapping time for different irrigation regimes. The differences of flowering dateand its longevity between clones in different water treatments demonstrated that although flower longevity of potato is a qualitative trait related to cultivar inherit but it can be affected by environment condition like temperature, light intensity and soil moisture. In this research there have been remarkable changes in reducing sugar of tubers under different irrigation levels. Therefore we can conclude that by determining good strategy for water use management in potato, both water stresses and higher reduction of sugar can be avoided. This result was consistent with previous studies (12, 14 and 18 that evaluated the effect of water stress and water deficiency on qualitative characters of potato. Decreasing 20 percent water requirement of potato, resulted only 0.7 kg decrease of total yield per square meter. As a result, it can be save more than 40 million cubic meter of water only in Hamedan state every year. Moreover, if we apply some suitable cultivars same as Savalan and other promising clones that have more tolerance to water deficit, it can be more efficient. Conclusions Totally, the result of the this research showed that decreasing water requirement of potato until 20% not only did not impair the growth and performance of potato but also did not show adverse effects on qualify of harvested tuber. It is also found that Savalan and two clone had more advantage in comparison with others.

  19. "Lacking warmth": Alexithymia trait is related to warm-specific thermal somatosensory processing.

    Science.gov (United States)

    Borhani, Khatereh; Làdavas, Elisabetta; Fotopoulou, Aikaterini; Haggard, Patrick

    2017-09-01

    Alexithymia is a personality trait involving deficits in emotional processing. The personality construct has been extensively validated, but the underlying neural and physiological systems remain controversial. One theory suggests that low-level somatosensory mechanisms act as somatic markers of emotion, underpinning cognitive and affective impairments in alexithymia. In two separate samples (total N=100), we used an established Quantitative Sensory Testing (QST) battery to probe multiple neurophysiological submodalities of somatosensation, and investigated their associations with the widely-used Toronto Alexithymia Scale (TAS-20). Experiment one found reduced sensitivity to warmth in people with higher alexithymia scores, compared to individuals with lower scores, without deficits in other somatosensory submodalities. Experiment two replicated this result in a new group of participants using a full-sample correlation between threshold for warm detection and TAS-20 scores. We discuss the relations between low-level thermoceptive function and cognitive processing of emotion. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  20. Detection of quantitative trait loci causing abnormal spermatogenesis and reduced testis weight in the small testis (Smt) mutant mouse.

    Science.gov (United States)

    Bolor, Hasbaira; Wakasugi, Noboru; Zhao, Wei Dong; Ishikawa, Akira

    2006-04-01

    The small testis (Smt) mutant mouse is characterized by a small testis of one third to one half the size of a normal testis, and its spermatogenesis is mostly arrested at early stages of meiosis, although a small number of spermatocytes at the late prophase of meiosis and a few spermatids can sometimes be seen. We performed quantitative trait locus (QTL) analysis of these spermatogenic traits and testis weight using 221 F2 males obtained from a cross between Smt and MOM (Mus musculus molossinus) mice. At the genome-wide 5% level, we detected two QTLs affecting meiosis on chromosomes 4 and 13, and two QTLs for paired testis weight as a percentage of body weight on chromosomes 4 and X. In addition, we found several QTLs for degenerated germ cells and multinuclear giant cells on chromosomes 4, 7 and 13. Interestingly, for cell degeneration, the QTL on chromosome 13 interacted epistatically with the QTL on chromosome 4. These results reveal polygenic participation in the abnormal spermatogenesis and small testis size in the Smt mutant.

  1. Pathogen-specific effects of quantitative trait loci affecting clinical mastitis and somatic cell count in danish holstein cattle

    DEFF Research Database (Denmark)

    Sørensen, Lars Peter; Guldbrandtsen, Bernt; Thomasen, J.R.

    2008-01-01

    The aim of this study was to investigate whether quantitative trait loci (QTL) affecting the risk of clinical mastitis (CM) and QTL affecting somatic cell score (SCS) exhibit pathogen-specific effects on the incidence of mastitis. Bacteriological data on mastitis pathogens were used to investigate...... pathogen specificity of QTL affecting treatments of mastitis in first parity (CM1), second parity (CM2), and third parity (CM3), and QTL affecting SCS. The 5 most common mastitis pathogens in the Danish dairy population were analyzed: Streptococcus dysgalactiae, Escherichia coli, coagulase...... against coagulase-negative staphylococci and Strep. uberis. Our results show that particular mastitis QTL are highly likely to exhibit pathogen-specificity. However, the results should be interpreted carefully because the results are sensitive to the sampling method and method of analysis. Field data were...

  2. ffect of Nitrogen and Zinc Foliar Application on Quantitative Traits of Tea Rosslle (Hibiscus sabdariffa in Jiroft Zone

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    abdolreza raisi sarbijan

    2017-02-01

    increased with increasing amountof nitrogen up to N3 level. Theapplication of zinc fertilizer significantly increased the plant fresh weigh, plant dry weight, mucilage percentage and yield. The interactions of nitrogen and zinc improved the calycle, leaf dry weight, plant dry weight, and the highest calycle dry weight were achieved from N2Zn1 and N3Zn1 treatments. The results showed that any givenlevel of nitrogen fertilizer and zinc fertilizer increased growth, yieldand quantitative traits of Hibiscus tea, but the level of interaction between nitrogen and zinc fertilizer hada significant effect on growth traits of Hibiscus tea, and even reduced the growth and yield of quantitative traits. The nitrogen and the fertilizer mixture of nitrogen and zinc had a significant influence on Hibiscus tea quantitative traits. Nitrogen fertilizer with a higher level of performance and yield had the greatest effect on Hibiscus tea.The greatest impact of nitrogen fertilizer, zinc fertilizer and the fertilizer mixture of nitrogen and zinc on sepal fresh weight were215.481 gr, 209.935 gr and 216.893 gr respectively.The effect of nitrogen fertilizer, zinc fertilizer and fertilizer mixture of nitrogen and zinc on leaf fresh weight,leaf dry weight andsepals dry weight were 61.787 gr 13.378 gr and 19.482 gr respectively. Conclusion The results of this study showed thatin order to increase crop yield and quality,nitrogen fertilizer and spraying of manure on Hibiscus tea is recommended. Because of having useful properties in the treatment of diabetes, as well as the climate and soil conditions of Jiroft area, this plant is grown as a medicinal plant at a large scale. Since Jiroft region is a suitable place for growth of Hibiscus tea and due to the importance of medicinal plants, it recommend that this experiment should be repeated to evaluateplant characteristics.

  3. Boron toxicity in rice (Oryza sativa L.). I. Quantitative trait locus (QTL) analysis of tolerance to boron toxicity.

    Science.gov (United States)

    Ochiai, K; Uemura, S; Shimizu, A; Okumoto, Y; Matoh, T

    2008-06-01

    Boron toxicity tolerance of rice plants was studied. Modern japonica subspecies such as Koshihikari, Nipponbare, and Sasanishiki were tolerant, whereas indica subspecies such as Kasalath and IR36 were intolerant to excessive application of boron (B), even though their shoot B contents under B toxicity were not significantly different. Recombinant inbred lines (RILs) of japonica Nekken-1 and indica IR36 were used for quantitative trait locus (QTL) analysis to identify the gene responsible for B toxicity tolerance. A major QTL that could explain 45% of the phenotypic variation was detected in chromosome 4. The QTL was confirmed using a population derived from a recombinant inbred line which is heterogenic at the QTL region. The QTL was also confirmed in other chromosome segment substitution lines (CSSLs).

  4. Association Mapping of Quantitative Trait Loci for Mineral Element Contents in Whole Grain Rice (Oryza sativa L.).

    Science.gov (United States)

    Huang, Yan; Sun, Chengxiao; Min, Jie; Chen, Yaling; Tong, Chuan; Bao, Jinsong

    2015-12-23

    Mineral elements in brown rice grain play an important role in human health. In this study, variations in the content of iron (Fe), zinc (Zn), selenium (Se), cadmium (Cd), and lead (Pb) in 378 accessions of brown rice were investigated, and association mapping was used to detect the quantitative trait loci (QTLs) responsible for the variation. Among seven subpopulations, the mean values of Zn and Cd in the japonica group were significantly higher than in the indica groups. The population structure accounted for from 5.7% (Se) to 22.1% (Pb) of the total variation. Correlation analyses showed that Pb was positively correlated with the other minerals (P rice grain by marker-assisted selection (MAS).

  5. Discovery of Consistent QTLs of Wheat Spike-Related Traits under Nitrogen Treatment at Different Development Stages

    Directory of Open Access Journals (Sweden)

    Zhiying Deng

    2017-12-01

    Full Text Available Spike-related traits such as spike length (Sl, fertile spikelet number (Fsn, sterile spikelet number (Ssn, grain number per spike (Gns, and thousand-kernel weight (Tkw are important factors influencing wheat yield. However, reliably stable markers that can be used for molecular breeding in different environments have not yet been identified. In this study, a double haploid (DH population was used for quantitative trait locus (QTL mapping of five spike-related traits under four different nitrogen (N supply dates in two locations and years. Seventy additive QTLs with phenotypic variation ranging from 4.12 to 34.74% and 10 major epistatic QTLs were identified. Eight important chromosomal regions on five chromosomes (1B, 2B, 2D, 5D, and 6A were found. Sixteen stable QTLs were detected for which N application had little effect. Among those stable QTLs, QSl.sdau-2D-1, and QSl.sdau-2D-2, with phenotypic variation explained (PVE of 10.4 and 24.2%, respectively, were flanked by markers Xwmc112 and Xcfd53 in the same order. The QTLs QSsn.sdau-2B-1, QFsn.sdau-2B-1, and QGns.sdau-2B, with PVE ranging from 4.37 to 28.43%, collocated in the Xwmc179-Xbarc373 marker interval. The consistent kernel wheat QTL (QTkw.sdau-6A on the long arm of chromosome 6A, flanked by SSR markers Xbarc1055 and Xwmc553, showed PVE of 5.87–15.18%. Among these stable QTLs, the two flanking markers Xwmc112 and Xcfd53 have been validated using different varieties and populations for selecting Sl. Therefore, these results will be of great value for marker-assisted selection (MAS in breeding programs and will accelerate the understanding of the genetic relationships among spike-related traits at the molecular level.

  6. Discovery of Consistent QTLs of Wheat Spike-Related Traits under Nitrogen Treatment at Different Development Stages.

    Science.gov (United States)

    Deng, Zhiying; Cui, Yong; Han, Qingdian; Fang, Wenqi; Li, Jifa; Tian, Jichun

    2017-01-01

    Spike-related traits such as spike length (Sl), fertile spikelet number (Fsn), sterile spikelet number (Ssn), grain number per spike (Gns), and thousand-kernel weight (Tkw) are important factors influencing wheat yield. However, reliably stable markers that can be used for molecular breeding in different environments have not yet been identified. In this study, a double haploid (DH) population was used for quantitative trait locus (QTL) mapping of five spike-related traits under four different nitrogen (N) supply dates in two locations and years. Seventy additive QTLs with phenotypic variation ranging from 4.12 to 34.74% and 10 major epistatic QTLs were identified. Eight important chromosomal regions on five chromosomes (1B, 2B, 2D, 5D, and 6A) were found. Sixteen stable QTLs were detected for which N application had little effect. Among those stable QTLs, QSl.sdau-2D-1 , and QSl.sdau-2D-2 , with phenotypic variation explained (PVE) of 10.4 and 24.2%, respectively, were flanked by markers Xwmc112 and Xcfd53 in the same order. The QTLs QSsn.sdau-2B-1, QFsn.sdau-2B-1 , and QGns.sdau-2B , with PVE ranging from 4.37 to 28.43%, collocated in the Xwmc179 - Xbarc373 marker interval. The consistent kernel wheat QTL ( QTkw.sdau-6A ) on the long arm of chromosome 6A, flanked by SSR markers Xbarc1055 and Xwmc553 , showed PVE of 5.87-15.18%. Among these stable QTLs, the two flanking markers Xwmc112 and Xcfd53 have been validated using different varieties and populations for selecting Sl. Therefore, these results will be of great value for marker-assisted selection (MAS) in breeding programs and will accelerate the understanding of the genetic relationships among spike-related traits at the molecular level.

  7. Detection of expression quantitative trait Loci in complex mouse crosses: impact and alleviation of data quality and complex population substructure.

    Science.gov (United States)

    Iancu, Ovidiu D; Darakjian, Priscila; Kawane, Sunita; Bottomly, Daniel; Hitzemann, Robert; McWeeney, Shannon

    2012-01-01

    Complex Mus musculus crosses, e.g., heterogeneous stock (HS), provide increased resolution for quantitative trait loci detection. However, increased genetic complexity challenges detection methods, with discordant results due to low data quality or complex genetic architecture. We quantified the impact of theses factors across three mouse crosses and two different detection methods, identifying procedures that greatly improve detection quality. Importantly, HS populations have complex genetic architectures not fully captured by the whole genome kinship matrix, calling for incorporating chromosome specific relatedness information. We analyze three increasingly complex crosses, using gene expression levels as quantitative traits. The three crosses were an F(2) intercross, a HS formed by crossing four inbred strains (HS4), and a HS (HS-CC) derived from the eight lines found in the collaborative cross. Brain (striatum) gene expression and genotype data were obtained using the Illumina platform. We found large disparities between methods, with concordance varying as genetic complexity increased; this problem was more acute for probes with distant regulatory elements (trans). A suite of data filtering steps resulted in substantial increases in reproducibility. Genetic relatedness between samples generated overabundance of detected eQTLs; an adjustment procedure that includes the kinship matrix attenuates this problem. However, we find that relatedness between individuals is not evenly distributed across the genome; information from distinct chromosomes results in relatedness structure different from the whole genome kinship matrix. Shared polymorphisms from distinct chromosomes collectively affect expression levels, confounding eQTL detection. We suggest that considering chromosome specific relatedness can result in improved eQTL detection.

  8. Dissociable relations between amygdala subregional networks and psychopathy trait dimensions in conduct‐disordered juvenile offenders

    Science.gov (United States)

    Colins, Olivier F.; Klapwijk, Eduard T.; Veer, Ilya M.; Andershed, Henrik; Popma, Arne; van der Wee, Nic J.; Vermeiren, Robert R.J.M.

    2016-01-01

    Abstract Psychopathy is a serious psychiatric phenomenon characterized by a pathological constellation of affective (e.g., callous, unemotional), interpersonal (e.g., manipulative, egocentric), and behavioral (e.g., impulsive, irresponsible) personality traits. Though amygdala subregional defects are suggested in psychopathy, the functionality and connectivity of different amygdala subnuclei is typically disregarded in neurocircuit‐level analyses of psychopathic personality. Hence, little is known of how amygdala subregional networks may contribute to psychopathy and its underlying trait assemblies in severely antisocial people. We addressed this important issue by uniquely examining the intrinsic functional connectivity of basolateral (BLA) and centromedial (CMA) amygdala networks in relation to affective, interpersonal, and behavioral traits of psychopathy, in conduct‐disordered juveniles with a history of serious delinquency (N = 50, mean age = 16.83 ± 1.32). As predicted, amygdalar connectivity profiles exhibited dissociable relations with different traits of psychopathy. Interpersonal psychopathic traits not only related to increased connectivity of BLA and CMA with a corticostriatal network formation accommodating reward processing, but also predicted stronger CMA connectivity with a network of cortical midline structures supporting sociocognitive processes. In contrast, affective psychopathic traits related to diminished CMA connectivity with a frontolimbic network serving salience processing and affective responding. Finally, behavioral psychopathic traits related to heightened BLA connectivity with a frontoparietal cluster implicated in regulatory executive functioning. We suggest that these trait‐specific shifts in amygdalar connectivity could be particularly relevant to the psychopathic phenotype, as they may fuel a self‐centered, emotionally cold, and behaviorally disinhibited profile. Hum Brain Mapp 37:4017–4033, 2016. © 2016

  9. Quantitative trait loci for resistance to trichostrongylid infection in Spanish Churra sheep

    Directory of Open Access Journals (Sweden)

    Primitivo Fermin San

    2009-10-01

    Full Text Available Abstract Background For ruminants reared on grazing systems, gastrointestinal nematode (GIN parasite infections represent the class of diseases with the greatest impact on animal health and productivity. Among the many possible strategies for controlling GIN infection, the enhancement of host resistance through the selection of resistant animals has been suggested by many authors. Because of the difficulty of routinely collecting phenotypic indicators of parasite resistance, information derived from molecular markers may be used to improve the efficiency of classical genetic breeding. Methods A total of 181 microsatellite markers evenly distributed along the 26 sheep autosomes were used in a genome scan analysis performed in a commercial population of Spanish Churra sheep to detect chromosomal regions associated with parasite resistance. Following a daughter design, we analysed 322 ewes distributed in eight half-sib families. The phenotypes studied included two faecal egg counts (LFEC0 and LFEC1, anti-Teladorsagia circumcincta LIV IgA levels (IgA and serum pepsinogen levels (Peps. Results The regression analysis revealed one QTL at the 5% genome-wise significance level on chromosome 6 for LFEC1 within the marker interval BM4621-CSN3. This QTL was found to be segregating in three out of the eight families analysed. Four other QTL were identified at the 5% chromosome-wise level on chromosomes 1, 10 and 14. Three of these QTL influenced faecal egg count, and the other one had an effect on IgA levels. Conclusion This study has successfully identified segregating QTL for parasite resistance traits in a commercial population. For some of the QTL detected, we have identified interesting coincidences with QTL previously reported in sheep, although most of those studies have been focused on young animals. Some of these coincidences might indicate that some common underlying loci affect parasite resistance traits in different sheep breeds. The

  10. Correlações entre caracteres quantitativos em milho pipoca Correlation among quantitative traits in popcorn maize

    Directory of Open Access Journals (Sweden)

    Valéria Carpentieri-Pípolo

    2002-12-01

    Full Text Available Em um programa de melhoramento, o conhecimento da grandeza das associações entre caracteres de interesse, é de fundamental importância na obtenção de populações melhoradas. O presente trabalho teve como objetivo determinar as correlações genotípicas, fenotípicas e ambientais entre caracteres quantitativos em milho pipoca. Foram avaliados nove genótipos de milho pipoca dispostos no campo em delineamento em blocos casualizados com oito repetições. Os genótipos UEL ZP, UEL SI e UEL PAP revelaram maiores capacidades de expansão (27,50; 27,15 e 24,40 respectivamente e número de grãos por volume (244,75; 248,50 e 248,75 respectivamente. A capacidade de expansão revelou correlação fenotípica positiva com o tamanho da pipoca e com o número de grãos por volume, e correlação negativa com massa de grãos por planta. Os caracteres massa de grãos por planta e peso total da espiga revelaram correlações fenotípicas e genotípicas positivas entre si, o que possibilita a utilização de um ou outro na seleção, optando-se pelo que melhor convier aos propósitos do programa de melhoramento.Knowledge of the size of the association among traits of interest is of fundamental importance in a breeding program to allow genetic progress. The genotypic, phenotypic and environment correlation were studied among quantitative traits of popcorn maize. Nine popcorn maize genotypes were assessed. A randomized complete block design with eight replications was used. The UEL ZP, UEL SI and UEL PAP. genotypes which had greatest expansion capacity (27.50; 27.15 and 24.20, respectively, also had the greatest values for the number of grains per volume (244.75; 248.50 and 248.75, respectively. The expansion capacity correlated positively with the popcorn size and with number of grains per volume and negatively with plant yield. The traits plant yield, and total ear weight showed positive phenotypic and genotypic correlation that permits the choice of

  11. Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs.

    Directory of Open Access Journals (Sweden)

    Markus Drag

    Full Text Available Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed to identify expression quantitative trait loci (eQTLs with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS were slaughtered at ~100 kg. Gene expression profiles were obtained by RNA-Seq, and genotype data were obtained by an Illumina 60K Porcine SNP chip. Following quality control and filtering, 10,545 and 12,731 genes from liver and testis were included in the eQTL analysis, together with 20,827 SNP variants. A total of 205 and 109 single-tissue eQTLs associated with 102 and 58 unique genes were identified in liver and testis, respectively. By employing a multivariate Bayesian hierarchical model, 26 eQTLs were identified as significant multi-tissue eQTLs. The highest densities of eQTLs were found on pig chromosomes SSC12, SSC1, SSC13, SSC9 and SSC14. Functional characterisation of eQTLs revealed functions within regulation of androgen and the intracellular steroid hormone receptor signalling pathway and of xenobiotic metabolism by cytochrome P450 system and cellular response to oestradiol. A QTL enrichment test revealed 89 QTL traits curated by the Animal Genome PigQTL database to be significantly overlapped by the genomic coordinates of cis-acting eQTLs. Finally, a subset of 35 cis-acting eQTLs overlapped with known boar taint QTL traits. These eQTLs could be useful in the development of a DNA test for boar taint but careful monitoring of other overlapping QTL traits should be performed to avoid any negative consequences of selection.

  12. Quantitative trait loci identified for blood chemistry components of an advanced intercross line of chickens under heat stress.

    Science.gov (United States)

    Van Goor, Angelica; Ashwell, Christopher M; Persia, Michael E; Rothschild, Max F; Schmidt, Carl J; Lamont, Susan J

    2016-04-14

    Heat stress in poultry results in considerable economic losses and is a concern for both animal health and welfare. Physiological changes occur during periods of heat stress, including changes in blood chemistry components. A highly advanced intercross line, created from a broiler (heat susceptible) by Fayoumi (heat resistant) cross, was exposed to daily heat cycles for seven days starting at 22 days of age. Blood components measured pre-heat treatment and on the seventh day of heat treatment included pH, pCO2, pO2, base excess, HCO3, TCO2, K, Na, ionized Ca, hematocrit, hemoglobin, sO2, and glucose. A genome-wide association study (GWAS) for these traits and their calculated changes was conducted to identify quantitative trait loci (QTL) using a 600 K SNP panel. There were significant increases in pH, base excess, HCO3, TCO2, ionized Ca, hematocrit, hemoglobin, and sO2, and significant decreases in pCO2 and glucose after 7 days of heat treatment. Heritabilities ranged from 0.01-0.21 for pre-heat measurements, 0.01-0.23 for measurements taken during heat, and 0.00-0.10 for the calculated change due to heat treatment. All blood components were highly correlated within measurement days, but not correlated between measurement days. The GWAS revealed 61 QTL for all traits, located on GGA (Gallus gallus chromosome) 1, 3, 6, 9, 10, 12-14, 17, 18, 21-28, and Z. A functional analysis of the genes in these QTL regions identified the Angiopoietin pathway as significant. The QTL that co-localized for three or more traits were on GGA10, 22, 26, 28, and Z and revealed candidate genes for birds' response to heat stress. The results of this study contribute to our knowledge of levels and heritabilities of several blood components of chickens under thermoneutral and heat stress conditions. Most components responded to heat treatment. Mapped QTL may serve as markers for genomic selection to enhance heat tolerance in poultry. The Angiopoietin pathway is likely involved in the

  13. Genetic and Quantitative Trait Locus Analysis of Cell Wall Components and Forage Digestibility in the Zheng58 × HD568 Maize RIL Population at Anthesis Stage.

    Science.gov (United States)

    Li, Kun; Wang, Hongwu; Hu, Xiaojiao; Ma, Feiqian; Wu, Yujin; Wang, Qi; Liu, Zhifang; Huang, Changling

    2017-01-01

    The plant cell wall plays vital roles in various aspects of the plant life cycle. It provides a basic structure for cells and gives mechanical rigidity to the whole plant. Some complex cell wall components are involved in signal transduction during pathogenic infection and pest infestations. Moreover, the lignification level of cell walls strongly influences the digestibility of forage plants. To determine the genetic bases of cell wall components and digestibility, quantitative trait locus (QTL) analyses for six related traits were performed using a recombinant inbred line (RIL) population from a cross between Zheng58 and HD568. Eight QTL for in vitro neutral detergent fiber (NDF) digestibility were observed, out of which only two increasing alleles came from HD568. Three QTL out of ten with alleles increasing in vitro dry matter digestibility also originated from HD568. Five-ten QTL were detected for lignin, cellulose content, acid detergent fiber, and NDF content. Among these results, 29.8% (14/47) of QTL explained >10% of the phenotypic variation in the RIL population, whereas 70.2% (33/47) explained ≤10%. These results revealed that in maize stalks, a few large-effect QTL and a number of minor-effect QTL contributed to most of the genetic components involved in cell wall biosynthesis and digestibility.

  14. Mixed-methods quantitative-qualitative study of 29 nonagenarians and centenarians in rural Southern Italy: focus on positive psychological traits.

    Science.gov (United States)

    Scelzo, Anna; Di Somma, Salvatore; Antonini, Paola; Montross, Lori P; Schork, Nicholas; Brenner, David; Jeste, Dilip V

    2018-01-01

    This was a study of positive psychological traits in a group of rural Italians aged 90 to 101 years, and their children or other family members. Mixed-methods quantitative (standardized rating scales) and qualitative (semi-structured interviews) study. Study participants' homes in nine villages in the Cilento region of southern Italy. Twenty-nine nonagenarians and centenarians and 51 family members aged 51-75 years, selected by their general practitioners as a part of a larger study called CIAO (Cilento Initiative on Aging Outcomes). We used published rating scales of mental and physical well-being, resilience, optimism, anxiety, depression, and perceived stress. Qualitative interviews gathered personal narratives of the oldest-old individuals, including migrations, traumatic events, and beliefs. Family members described their impressions about the personality traits of their older relative. Participants age ≥90 years had worse physical health but better mental well-being than their younger family members. Mental well-being correlated negatively with levels of depression and anxiety in both the groups. The main themes that emerged from qualitative interviews included positivity (resilience and optimism), working hard, and bond with family and religion, as described in previously published studies of the oldest old, but also a need for control and love of the land, which appeared to be unique features of this rural population. Exceptional longevity was characterized by a balance between acceptance of and grit to overcome adversities along with a positive attitude and close ties to family, religion, and land, providing purpose in life.

  15. Prediction of genetic values of quantitative traits with epistatic effects in plant breeding populations.

    Science.gov (United States)

    Wang, D; Salah El-Basyoni, I; Stephen Baenziger, P; Crossa, J; Eskridge, K M; Dweikat, I

    2012-11-01

    Though epistasis has long been postulated to have a critical role in genetic regulation of important pathways as well as provide a major source of variation in the process of speciation, the importance of epistasis for genomic selection in the context of plant breeding is still being debated. In this paper, we report the results on the prediction of genetic values with epistatic effects for 280 accessions in the Nebraska Wheat Breeding Program using adaptive mixed least absolute shrinkage and selection operator (LASSO). The development of adaptive mixed LASSO, originally designed for association mapping, for the context of genomic selection is reported. The results show that adaptive mixed LASSO can be successfully applied to the prediction of genetic values while incorporating both marker main effects and epistatic effects. Especially, the prediction accuracy is substantially improved by the inclusion of two-locus epistatic effects (more than onefold in some cases as measured by cross-validation correlation coefficient), which is observed for multiple traits and planting locations. This points to significant potential in using non-additive genetic effects for genomic selection in crop breeding practices.

  16. Exploring single nucleotide polymorphisms previously related to obesity and metabolic traits in pediatric-onset type 2 diabetes.

    Science.gov (United States)

    Miranda-Lora, América Liliana; Cruz, Miguel; Aguirre-Hernández, Jesús; Molina-Díaz, Mario; Gutiérrez, Jorge; Flores-Huerta, Samuel; Klünder-Klünder, Miguel

    2017-07-01

    To evaluate the association of 64 obesity-related polymorphisms with pediatric-onset type 2 diabetes and other glucose- and insulin-related traits in Mexican children. Case-control and case-sibling designs were followed. We studied 99 patients with pediatric-onset type 2 diabetes, their siblings (n = 101) without diabetes, 83 unrelated pediatric controls and 137 adult controls. Genotypes were determined for 64 single nucleotide polymorphisms, and a possible association was examined between those genotypes and type 2 diabetes and other quantitative traits, after adjusting for age, sex and body mass index. In the case-pediatric control and case-adult control analyses, five polymorphisms were associated with increased likelihood of pediatric-onset type 2 diabetes; only one of these polymorphisms (CADM2/rs1307880) also showed a consistent effect in the case-sibling analysis. The associations in the combined analysis were as follows: ADORA1/rs903361 (OR 1.9, 95% CI 1.2; 3.0); CADM2/rs13078807 (OR 2.2, 95% CI 1.2; 4.0); GNPDA2/rs10938397 (OR 2.2, 95% CI 1.4; 3.7); VEGFA/rs6905288 (OR 1.4, 95% CI 1.1; 2.1) and FTO/rs9939609 (OR 1.8, 95% CI 1.0; 3.2). We also identified 16 polymorphisms nominally associated with quantitative traits in participants without diabetes. ADORA/rs903361, CADM2/rs13078807, GNPDA2/rs10938397, VEGFA/rs6905288 and FTO/rs9939609 are associated with an increased risk of pediatric-onset type 2 diabetes in the Mexican population.

  17. QTL Mapping of Kernel Number-Related Traits and Validation of One Major QTL for Ear Length in Maize.

    Science.gov (United States)

    Huo, Dongao; Ning, Qiang; Shen, Xiaomeng; Liu, Lei; Zhang, Zuxin

    2016-01-01

    The kernel number is a grain yield component and an important maize breeding goal. Ear length, kernel number per row and ear row number are highly correlated with the kernel number per ear, which eventually determines the ear weight and grain yield. In this study, two sets of F2:3 families developed from two bi-parental crosses sharing one inbred line were used to identify quantitative trait loci (QTL) for four kernel number-related traits: ear length, kernel number per row, ear row number and ear weight. A total of 39 QTLs for the four traits were identified in the two populations. The phenotypic variance explained by a single QTL ranged from 0.4% to 29.5%. Additionally, 14 overlapping QTLs formed 5 QTL clusters on chromosomes 1, 4, 5, 7, and 10. Intriguingly, six QTLs for ear length and kernel number per row overlapped in a region on chromosome 1. This region was designated qEL1.10 and was validated as being simultaneously responsible for ear length, kernel number per row and ear weight in a near isogenic line-derived population, suggesting that qEL1.10 was a pleiotropic QTL with large effects. Furthermore, the performance of hybrids generated by crossing 6 elite inbred lines with two near isogenic lines at qEL1.10 showed the breeding value of qEL1.10 for the improvement of the kernel number and grain yield of maize hybrids. This study provides a basis for further fine mapping, molecular marker-aided breeding and functional studies of kernel number-related traits in maize.

  18. Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean) Cattle.

    Science.gov (United States)

    Lim, Dajeong; Lee, Seung-Hwan; Kim, Nam-Kuk; Cho, Yong-Min; Chai, Han-Ha; Seong, Hwan-Hoo; Kim, Heebal

    2013-01-01

    Marbling (intramuscular fat) is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the 'marbling score' trait and systemically analyzed the network topology in Hanwoo (Korean cattle). As a result, we determined 3 modules (gene groups) that showed statistically significant results for marbling score. In particular, one module (denoted as red) has a statistically significant result for marbling score (p = 0.008) and intramuscular fat (p = 0.02) and water capacity (p = 0.006). From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA) have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.

  19. Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean Cattle

    Directory of Open Access Journals (Sweden)

    Dajeong Lim

    2013-01-01

    Full Text Available Marbling (intramuscular fat is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the ‘marbling score’ trait and systemically analyzed the network topology in Hanwoo (Korean cattle. As a result, we determined 3 modules (gene groups that showed statistically significant results for marbling score. In particular, one module (denoted as red has a statistically significant result for marbling score (p = 0.008 and intramuscular fat (p = 0.02 and water capacity (p = 0.006. From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.

  20. Evolution of cultural traits occurs at similar relative rates in different world regions.

    Science.gov (United States)

    Currie, Thomas E; Mace, Ruth

    2014-11-22

    A fundamental issue in understanding human diversity is whether or not there are regular patterns and processes involved in cultural change. Theoretical and mathematical models of cultural evolution have been developed and are increasingly being used and assessed in empirical analyses. Here, we test the hypothesis that the rates of change of features of human socio-cultural organization are governed by general rules. One prediction of this hypothesis is that different cultural traits will tend to evolve at similar relative rates in different world regions, despite the unique historical backgrounds of groups inhabiting these regions. We used phylogenetic comparative methods and systematic cross-cultural data to assess how different socio-cultural traits changed in (i) island southeast Asia and the Pacific, and (ii) sub-Saharan Africa. The relative rates of change in these two regions are significantly correlated. Furthermore, cultural traits that are more directly related to external environmental conditions evolve more slowly than traits related to social structures. This is consistent with the idea that a form of purifying selection is acting with greater strength on these more environmentally linked traits. These results suggest that despite contingent historical events and the role of humans as active agents in the historical process, culture does indeed evolve in ways that can be predicted from general principles.

  1. Trait self-esteem and neural activities related to self-evaluation and social feedback

    Science.gov (United States)

    Yang, Juan; Xu, Xiaofan; Chen, Yu; Shi, Zhenhao; Han, Shihui

    2016-01-01

    Self-esteem has been associated with neural responses to self-reflection and attitude toward social feedback but in different brain regions. The distinct associations might arise from different tasks or task-related attitudes in the previous studies. The current study aimed to clarify these by investigating the association between self-esteem and neural responses to evaluation of one’s own personality traits and of others’ opinion about one’s own personality traits. We scanned 25 college students using functional MRI during evaluation of oneself or evaluation of social feedback. Trait self-esteem was measured using the Rosenberg self-esteem scale after scanning. Whole-brain regression analyses revealed that trait self-esteem was associated with the bilateral orbitofrontal activity during evaluation of one’s own positive traits but with activities in the medial prefrontal cortex, posterior cingulate, and occipital cortices during evaluation of positive social feedback. Our findings suggest that trait self-esteem modulates the degree of both affective processes in the orbitofrontal cortex during self-reflection and cognitive processes in the medial prefrontal cortex during evaluation of social feedback. PMID:26842975

  2. Trait self-esteem and neural activities related to self-evaluation and social feedback.

    Science.gov (United States)

    Yang, Juan; Xu, Xiaofan; Chen, Yu; Shi, Zhenhao; Han, Shihui

    2016-02-04

    Self-esteem has been associated with neural responses to self-reflection and attitude toward social feedback but in different brain regions. The distinct associations might arise from different tasks or task-related attitudes in the previous studies. The current study aimed to clarify these by investigating the association between self-esteem and neural responses to evaluation of one's own personality traits and of others' opinion about one's own personality traits. We scanned 25 college students using functional MRI during evaluation of oneself or evaluation of social feedback. Trait self-esteem was measured using the Rosenberg self-esteem scale after scanning. Whole-brain regression analyses revealed that trait self-esteem was associated with the bilateral orbitofrontal activity during evaluation of one's own positive traits but with activities in the medial prefrontal cortex, posterior cingulate, and occipital cortices during evaluation of positive social feedback. Our findings suggest that trait self-esteem modulates the degree of both affective processes in the orbitofrontal cortex during self-reflection and cognitive processes in the medial prefrontal cortex during evaluation of social feedback.

  3. Assessing the relative importance of health and conformation traits in the cavalier king Charles spaniel.

    Science.gov (United States)

    Wijnrocx, Katrien; François, Liesbeth; Goos, Peter; Buys, Nadine; Janssens, Steven

    2018-01-01

    The selection of a future breeding dog is a complicated task, in which disease characteristics and different traits have to be combined and weighed against one another. Truncation selection, that is the exclusion of affected animals, may be very inefficient when selecting on a large number of traits, and may result in a reduction of the genetic diversity in a population or breed. Selection could be facilitated by the use of a selection index that combines multiple traits or breeding values into one score. This however requires a consideration of their relative value according to their economic weight, which is difficult to express in monetary units for health traits. The use of a choice experiment to derive non-market values might be a solution to this problem. This is a pilot study to assess the potential use of choice experiments to ascertain the public preference and relative importance attached to health- and conformation traits in the selection of a Cavalier King Charles spaniel. The focus was on two prevalent disorders, mitral valve disease and syringomyelia, and on several important conformation traits such as muzzle length and eye shape. Based on available prior information, a Bayesian D-optimal design approach was used to develop a choice experiment and the resulting choice sets. Every participant (breeder or owner) in the choice experiment was presented with a total of 17 choice sets, in which at most four traits could vary to reduce the cognitive burden. A total of 114 respondents participated in the choice experiment and results showed that respondents (breeders/owners) current attitudes were directed towards health (syringomyelia and mitral valve disease), followed by eye shape and level of inbreeding. This approach identifies the value breeders and owners attach to certain traits in the breeding objective. The resulting relative weights, represented as the logworths obtained from the choice experiment, could be an alternative to economic weights. They

  4. Genetic variability for different quantitative traits in M2 generations of opium poppy (Papaver somniferum L.)

    International Nuclear Information System (INIS)

    Chatterjee, A.; Shukla, S.; Singh, S.P.

    2004-01-01

    An experiment on induced mutation in two varieties of opium poppy was laid out to create new genetic variability for isolation of high yielding genotypes. Varieties NBRI-1 and NBRI-5 were subjected to irradiation for five doses of gamma rays and NBRI-5 was also treated with four doses of EMS and 20 mixed doses of EMS plus gamma rays. The data were recorded on 15 plants/treatment for 10 polygenic characters as pooled in M1 and M2 generations separately as well as in each dose-wise in M2 population. The results indicated that GCV, heritability and genetic advance were higher in M1 than M2 in both the varieties for all the traits except for opium and seed yield. The genetic advance was consistently high for opium yield, seed yield and capsule weight in all the doses for both the varieties with some exception. The dose level of kR10 and kR30 in NBRI-1 revealed high GCV, heritability and genetic advance for seed weight. These treatment levels also had high values of all these three genetic parameters for capsules per plant, capsule size and capsule weight. The values of these three parameters were also high for all the doses in M2 generations of both the varieties for opium yield, seed weight, capsule weight and capsule size in comparison to control. The GCV, heritability and genetic advance were consistently high for all the mixed doses in NBRI-5 for opium yield, seed weight and capsule weight, with some exception [it

  5. Dark personality traits and impulsivity among adolescents : Differential links to problem behaviors and family relations

    NARCIS (Netherlands)

    Dubas, Judith Semon; Baams, Laura; Doornwaard, Suzan M.; van Aken, Marcel A.G.

    2017-01-01

    Research on how dark personality traits develop and relate to risky behaviors and family relations during adolescence is scarce. This study used a person-oriented approach to examine (a) whether distinct groups of adolescents could be identified based on their developmental profiles of

  6. Bilaterally Asymmetric Effects of Quantitative Trait Loci (QTLs): QTLs That Affect Laxity in the Right Versus Left Coxofemoral (Hip) Joints of the Dog (Canis familiaris)

    OpenAIRE

    Chase, Kevin; Lawler, Dennis F.; Adler, Fred R.; Ostrander, Elaine A.; Lark, Karl G.

    2004-01-01

    In dogs hip joint laxity that can lead to degenerative joint disease (DJD) is frequent and heritable, providing a genetic model for some aspects of the human disease. We have used Portuguese water dogs (PWDs) to identify Quantitative trait loci (QTLs) that regulate laxity in the hip joint.A population of 286 PWDs, each characterized by ca. 500 molecular genetic markers, was analyzed for subluxation of the hip joint as measured by the Norberg angle, a quantitative radiographic measure of laxit...

  7. Traits related to species persistence and dispersal explain changes in plant communities subjected to habitat loss

    DEFF Research Database (Denmark)

    Marini, Lorenzo; Bruun, Hans Henrik; Heikkinen, Risto

    2012-01-01

    Aim Habitat fragmentation is a major driver of biodiversity loss but it is insufficiently known how much its effects vary among species with different life-history traits; especially in plant communities, the understanding of the role of traits related to species persistence and dispersal in dete...... rural landscapes in NW Europe, mitigating the spatial isolation of remaining grasslands should be accompanied by restoration measures aimed at improving habitat quality for low competitors, abiotically dispersed and perennial, clonal species.......Aim Habitat fragmentation is a major driver of biodiversity loss but it is insufficiently known how much its effects vary among species with different life-history traits; especially in plant communities, the understanding of the role of traits related to species persistence and dispersal...... in determining dynamics of species communities in fragmented landscapes is still limited. The primary aim of this study was to test how plant traits related to persistence and dispersal and their interactions modify plant species vulnerability to decreasing habitat area and increasing isolation. Location Five...

  8. Delayed effects of chlorpyrifos across metamorphosis on dispersal-related traits in a poleward moving damselfly.

    Science.gov (United States)

    Dinh, Khuong Van; Janssens, Lizanne; Therry, Lieven; Bervoets, Lieven; Bonte, Dries; Stoks, Robby

    2016-11-01

    How exposure to contaminants may interfere with the widespread poleward range expansions under global warming is largely unknown. Pesticide exposure may negatively affect traits shaping the speed of range expansion, including traits related to population growth rate and dispersal-related traits. Moreover, rapid evolution of growth rates during poleward range expansions may come at a cost of a reduced investment in detoxification and repair thereby increasing the vulnerability to contaminants at expanding range fronts. We tested effects of a sublethal concentration of the widespread pesticide chlorpyrifos on traits related to range expansion in replicated edge and core populations of the poleward moving damselfly Coenagrion scitulum reared at low and high food levels in a common garden experiment. Food limitation in the larval stage had strong negative effects both in the larval stage and across metamorphosis in the adult stage. Exposure to chlorpyrifos during the larval stage did not affect larval traits but caused delayed effects across metamorphosis by increasing the incidence of wing malformations during metamorphosis and by reducing a key component of the adult immune response. There was some support for an evolutionary trade-off scenario as the faster growing edge larvae suffered a higher mortality during metamorphosis. Instead, there was no clear support for the faster growing edge larvae being more vulnerable to chlorpyrifos. Our data indicate that sublethal delayed effects of pesticide exposure, partly in association with the rapid evolution of faster growth rates, may slow down range expansions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Plant functional traits in relation to fire in crown-fire ecosystems

    Science.gov (United States)

    Pausas, Juli G.; Bradstock, Ross A.; Keith, David A.; Keeley, Jon E.

    2004-01-01

    Disturbance is a dominant factor in many ecosystems, and the disturbance regime is likely to change over the next decades in response to land-use changes and global warming. We assume that predictions of vegetation dynamics can be made on the basis of a set of life-history traits that characterize the response of a species to disturbance. For crown-fire ecosystems, the main plant traits related to postfire persistence are the ability to resprout (persistence of individuals) and the ability to retain a persistent seed bank (persistence of populations). In this context, we asked (1) to what extent do different life-history traits co-occur with the ability to resprout and/or the ability to retain a persistent seed bank among differing ecosystems and (2) to what extent do combinations of fire-related traits (fire syndromes) change in a fire regime gradient? We explored these questions by reviewing the literature and analyzing databases compiled from different crown-fire ecosystems (mainly eastern Australia, California, and the Mediterranean basin). The review suggests that the pattern of correlation between the two basic postfire persistent traits and other plant traits varies between continents and ecosystems. From these results we predict, for instance, that not all resprouters respond in a similar way everywhere because the associated plant traits of resprouter species vary in different places. Thus, attempts to generalize predictions on the basis of the resprouting capacity may have limited power at a global scale. An example is presented for Australian heathlands. Considering the combination of persistence at individual (resprouting) and at population (seed bank) level, the predictive power at local scale was significantly increased.

  10. The effects of dominance, regular inbreeding and sampling design on Q(ST), an estimator of population differentiation for quantitative traits.

    Science.gov (United States)

    Goudet, Jérôme; Büchi, Lucie

    2006-02-01

    To test whether quantitative traits are under directional or homogenizing selection, it is common practice to compare population differentiation estimates at molecular markers (F(ST)) and quantitative traits (Q(ST)). If the trait is neutral and its determinism is additive, then theory predicts that Q(ST) = F(ST), while Q(ST) > F(ST) is predicted under directional selection for different local optima, and Q(ST) sampling designs and find that it is always best to sample many populations (>20) with few families (five) rather than few populations with many families. Provided that estimates of Q(ST) are derived from individuals originating from many populations, we conclude that the pattern Q(ST) > F(ST), and hence the inference of directional selection for different local optima, is robust to the effect of nonadditive gene actions.

  11. Genes and quantitative trait loci (QTL) controlling trace element concentrations in perennial grasses grown on phytotoxic soil contaminated with heavy metals

    Science.gov (United States)

    Perennial grasses cover diverse soils throughout the world, including sites contaminated with heavy metals, producing forages that must be safe for livestock and wildlife. Chromosome regions known as quantitative trait loci (QTLs) controlling forage mineral concentrations were mapped in a populatio...

  12. Detection of novel quantitative trait loci for cutaneous melanoma by genome-wide scan in the MeLiM swine model

    Czech Academy of Sciences Publication Activity Database

    Du, Z. Q.; Vincent-Naulleau, S.; Gilbert, H.; Vignoles, F.; Créchet, F.; Shimogiri, T.; Yasue, H.; Leplat, J. J.; Bouet, S.; Gruand, J.; Horák, Vratislav; Milan, D.; Le Roy, P.; Geffrotin, C.

    2006-01-01

    Roč. 120, - (2006), s. 303-320 ISSN 0020-7136 Institutional research plan: CEZ:AV0Z50450515 Keywords : swine melanoma * quantitative trait loci * MC1R Subject RIV: FD - Oncology ; Hematology Impact factor: 4.693, year: 2006

  13. A journey from a SSR-based low density map to a SNP-based high density map for identification of disease resistance quantitative trait loci in peanut

    Science.gov (United States)

    Mapping and identification of quantitative trait loci (QTLs) are important for efficient marker-assisted breeding. Diseases such as leaf spots and Tomato spotted wilt virus (TSWV) cause significant loses to peanut growers. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to...

  14. The relations between interpersonal self-support traits and emotion regulation strategies: a longitudinal study.

    Science.gov (United States)

    Xia, Ling-Xiang; Gao, Xin; Wang, Qian; Hollon, Steven D

    2014-08-01

    Although several cross-sectional surveys have shown that certain traits such as extraversion and neuroticism are related to emotion regulation, few studies have explored the nature of this relationship. The present study tried to explore the longitudinal relation between traits and emotion regulation strategies. The Interpersonal Self-Support Scale for Middle School Students (ISSS-MSS) and the Emotion Regulation Questionnaire (ERQ) were administrated to 374 middle school students two times across a 6-month interval. A path analysis via structural equation modeling of the five interpersonal self-support traits and the two emotion regulation strategies was tested. The results showed that interpersonal independence predicted expressive suppression and cognitive reappraisal, and that interpersonal initiative also predicted reappraisal, while reappraisal predicted interpersonal flexibility and interpersonal openness 6 month later. These results support the hypotheses that some personality traits influence certain emotion regulation strategies, while other traits may be influenced by specific emotion regulation strategies. Copyright © 2014 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

  15. Genetic analysis and hybrid vigor study of grain yield and other quantitative traits in auto tetraploid rice

    International Nuclear Information System (INIS)

    Shahid, M.Q.; Xiong, C.Z.; Juan, L.Y.; Ming, X.H.

    2011-01-01

    Genetic analysis and genotype-by-environment interaction for important traits of auto tetraploid rice were evaluated by additive, dominance and additive X additive model. It was show n that genetic effects had more influence on grain yield and other quantitative traits of auto tetraploid rice than genotypic environment interaction. Plant height, panicle length, seed set , grain yield, dry matter production and 1000-grain weight we re mainly regulated by dominance variance. Additive and additive X additive gene action constructed the main proportion of genetic variance for heading date (flowering), number of panicles, grains per panicle, grain length, however grain width was supposed to be affected by additive X additive and dominance variance. Flag leaf length and width, fresh weight, peduncle length, unfilled grains and awn length were greatly influenced by genotypic environment interaction. Heading date produced highly negative heterosis over mid parent (H pm) and better parent ( H pb), whereas H pm and H pb were detected to be highly positive and significant for grain yield, seed set, peduncle length, filled grains and 1000-grain weight in F/sub 1/ and F/sub 2/ generations. The results indicated that auto tetraploid hybrids 96025 X Jackson (indica/japonica), 96025 X Linglun (indica/indica) and Linglun X Jackson (indica/japonica) showed highly significant hybrid vigor with improved seed set percentage and grain yield. These results suggest that intra-specific auto tetraploid rice hybrids have more hybrid vigor as compared to intra-sub specific auto tetraploid rice hybrids and auto tetraploid rice has the potential to be used for further studies and commercial application. (author)

  16. Effect of genetic variants and traits related to glucose metabolism and their interaction with obesity on breast and colorectal cancer risk among postmenopausal women.

    Science.gov (United States)

    Jung, Su Yon; Sobel, Eric M; Papp, Jeanette C; Zhang, Zuo-Feng

    2017-04-26

    Impaired glucose metabolism-related genetic variants and traits likely interact with obesity and related lifestyle factors, influencing postmenopausal breast and colorectal cancer (CRC), but their interconnected pathways are not fully understood. By stratifying via obesity and lifestyles, we partitioned the total effect of glucose metabolism genetic variants on cancer risk into two putative mechanisms: 1) indirect (risk-associated glucose metabolism genetic variants mediated by glucose metabolism traits) and 2) direct (risk-associated glucose metabolism genetic variants through pathways other than glucose metabolism traits) effects. Using 16 single-nucleotide polymorphisms (SNPs) associated with glucose metabolism and data from 5379 postmenopausal women in the Women's Health Initiative Harmonized and Imputed Genome-Wide Association Studies, we retrospectively assessed the indirect and direct effects of glucose metabolism-traits (fasting glucose, insulin, and homeostatic model assessment-insulin resistance [HOMA-IR]) using two quantitative tests. Several SNPs were associated with breast cancer and CRC risk, and these SNP-cancer associations differed between non-obese and obese women. In both strata, the direct effect of cancer risk associated with the SNP accounted for the majority of the total effect for most SNPs, with roughly 10% of cancer risk due to the SNP that was from an indirect effect mediated by glucose metabolism traits. No apparent differences in the indirect (glucose metabolism-mediated) effects were seen between non-obese and obese women. It is notable that among obese women, 50% of cancer risk was mediated via glucose metabolism trait, owing to two SNPs: in breast cancer, in relation to GCKR through glucose, and in CRC, in relation to DGKB/TMEM195 through HOMA-IR. Our findings suggest that glucose metabolism genetic variants interact with obesity, resulting in altered cancer risk through pathways other than those mediated by glucose metabolism traits.

  17. A non-parametric mixture model for genome-enabled prediction of genetic value for a quantitative trait.

    Science.gov (United States)

    Gianola, Daniel; Wu, Xiao-Lin; Manfredi, Eduardo; Simianer, Henner

    2010-10-01

    A Bayesian nonparametric form of regression based on Dirichlet process priors is adapted to the analysis of quantitative traits possibly affected by cryptic forms of gene action, and to the context of SNP-assisted genomic selection, where the main objective is to predict a genomic signal on phenotype. The procedure clusters unknown genotypes into groups with distinct genetic values, but in a setting in which the number of clusters is unknown a priori, so that standard methods for finite mixture analysis do not work. The central assumption is that genetic effects follow an unknown distribution with some "baseline" family, which is a normal process in the cases considered here. A Bayesian analysis based on the Gibbs sampler produces estimates of the number of clusters, posterior means of genetic effects, a measure of credibility in the baseline distribution, as well as estimates of parameters of the latter. The procedure is illustrated with a simulation representing two populations. In the first one, there are 3 unknown QTL, with additive, dominance and epistatic effects; in the second, there are 10 QTL with additive, dominance and additive × additive epistatic effects. In the two populations, baseline parameters are inferred correctly. The Dirichlet process model infers the number of unique genetic values correctly in the first population, but it produces an understatement in the second one; here, the true number of clusters is over 900, and the model gives a posterior mean estimate of about 140, probably because more replication of genotypes is needed for correct inference. The impact on inferences of the prior distribution of a key parameter (M), and of the extent of replication, was examined via an analysis of mean body weight in 192 paternal half-sib families of broiler chickens, where each sire was genotyped for nearly 7,000 SNPs. In this small sample, it was found that inference about the number of clusters was affected by the prior distribution of M. For a

  18. Temperament and character traits in patients with conversion disorder and their relations with dissociation.

    Science.gov (United States)

    Sarisoy, Gökhan; Kaçar, Ö Mer Faruk; Öztürk, Arif; Yilman, Tuba; Mor, Sema; Özturan, Deniz Deniz; Yazici, Neslihan; Gümüş, Kübra

    2015-12-01

    The purpose of this study was to investigate temperament and character traits in patients with conversion disorder and the relation of these traits with dissociative symptoms. Sixty patients (60) diagnosed with conversion disorder according to DSM-IV-TR and 60 healthy volunteers were included in the study. All participants' temperament and character traits were determined using Cloninger's Temperament and Character Inventory (TCI). Patients with conversion disorder were divided into two subgroups using the Dissociative Experiences Scale (DES), dissociative (n=30, 50%) and non-dissociative (n=30, 50%). The two conversion disorder subgroups were compared with the control group in terms of temperament and character traits. Correlation analysis was also performed between TCI and DES scores in the entire conversion group. Novelty seeking (NS) scores were lower in both the dissociative and non-dissociative groups compared to the control group. Harm avoidance (HA) scores were higher in the dissociative group than in the control group. Reward dependence (RD) scores were lower in the dissociative group than in the non-dissociative and control group. Self-directedness (SD) scores were lower in the dissociative group than in the control group. Self-transcendence (ST) scores were higher in the dissociative group than in the non-dissociative group. DES scores were negatively correlated with RD and SD scores in the entire conversion group and positively correlated with ST scores. Low NS temperament traits may be associated with conversion disorder. High HA and low RD temperament traits and low SD and high ST character traits may be associated with pathological dissociation in patients with conversion disorder.

  19. Effects of Organic and Chemical Fertilizers on some Quantitative Traits and Anthocyanin of Roselle under Zabol conditions

    Directory of Open Access Journals (Sweden)

    rahman Ebrahimzadeh abdashti

    2017-02-01

    Full Text Available Introduction: Roselle (Hibiscus sabdariffa L. belongs to the Malvaceae family, and is an annual or biennial plant that cultivated in tropical and subtropical regions for its stem fibers, eatable calyces, leaves and grains. Roselle is resistant to relatively high temperatures throughout the growing and fruiting times. Continuous use of chemical fertilizers destroys the soil ecological balance, reduces soil fertility and groundwater pollution is caused. In contrast, organic fertilizers are very safe for human health and the environment. It is made by recycling organic material as plant and animals waste, and food scraps in a controlled process. Of the organic fertilizers can be noted to compost, vermicompost, cattle manure andhumic acid. The study was carried out in order to sustainable agriculture. The aim of this study was to investigate the effects of organic and chemical fertilizers on some quantitative traits and anthocyanin of roselle. Materials and Methods: The experiment was performed in complete randomized block design with ten treatments and four replications in research field of agricultural faculty, university of zabol. The treatments included T1: control, T2: NPK in a ratio of 2:1:1 (300 kg ha-1, T3: cattle manure (20 t ha-1, T4: compost (10 t ha-1, T5: vermicompost (5 t ha-1, T6: humic acid foliar in a ratio of 1.5 per thousands, T7: 50% of T2 and T6 , T8: 50% of T3 and T6, T9: 50% of T4 and T6 and T10: 50% of the T5 and T6. Five plants were chosen and an average of five plants was calculated as the single plant for measuring of variables that included the height, number of branches, stem diameter, shoot fresh weight, number of fruits per plant, fruit weight, number of seeds per plant, fresh and dry weights of sepals, inflorescence length, length and diameter of fruit. Method of Wagner has been used for the anthocyanin measurement. Results and Discussion: Results of this research showed that the application of different fertilizers

  20. Analysis of personality traits as a risk factor in crash related trauma.

    Science.gov (United States)

    Kumar, Vineet; Goyal, Rahul; Singh, Ajai; Sharma, Vineet; Srivastava, Rajeshwer Nath; Kumar, Santosh; Kumar, Ashish

    2016-09-01

    Due to increasing stress, individual personality traits are becoming a significant contributor to CRT (Crash Related Trauma). In the present study, we hypothesized that there will be no difference in personality characteristics of CRT patients and control subjects and there will be no association between trauma and personality characteristics of CRT patients. A total of 119 cases and 112 controls of age >18 years were selected as per criteria decided. After obtaining ethical clearance, patients presenting to the emergency orthopedic unit were included in the study. After primary management all enrolled subjects were assessed by ICD 10 module screening questionnaire and analyzed for nine personality traits, subject to written informed consent. Of all the cases enrolled 82.35% were males. Impulsive personality trait is found in 84.78% (39/46) cases. There were 46 motorcyclists out of 119 cases enrolled. Most of the personality traits showed a statistical significant association (p personality characteristics which accounted for 84.78% and 82.61% cases respectively. These traits showed a statistical significant association with CRT.

  1. Personality traits predict perceived health-related quality of life in persons with multiple sclerosis.

    Science.gov (United States)

    Zarbo, Ignazio Roberto; Minacapelli, Eleonora; Falautano, Monica; Demontis, Silvia; Carpentras, Giovanni; Pugliatti, Maura

    2016-04-01

    Personality traits can affect health-related quality of life (HRQoL) in different disorders. In multiple sclerosis (MS), personality traits can determine patients' willingness to take on more risky treatment options, predispose to neuropsychiatric symptoms and affect coping strategies. We investigated the role of personality traits as possible predictors of HRQoL in a large cohort of persons with MS (PwMS). In total, 253 consecutively recruited PwMS were screened for intellectual deficits with Raven Colour Progressive Matrices (RCPM), state anxiety with STAI-X1 and major depression on a clinical basis. PwMS' self-perceived mental and physical health status was measured with the 36-Item Short Form Health Survey (SF-36), and the personality profile with the Eysenck Personality Questionnaire (EPQ-R). The correlation between HRQoL and personality traits was investigated by means of analysis of variance, adjusting for possible confounders. Of the 253 MS patients, 195 (F:M=2.75), aged 41.7±10.2 years were included in the analysis. The variance of SF-36 mental and physical composite score was largely explained by extraversion and neuroticism. Our data confirm that PwMS' HRQoL is largely influenced by personality traits, which may therefore act as predictors of perceived quality of life and should be included in clinical and experimental settings focusing on HRQoL. © The Author(s), 2015.

  2. [The God image in relation to autistic traits and religious denomination].

    Science.gov (United States)

    Schaap-Jonker, H; van Schothorst-van Roekel, J; Sizoo, B

    2012-01-01

    Estimates of the prevalence of autism spectrum disorders (ASD) range from 0.6 to 1.0 per cent of the general population. Among the characteristic traits of ASD are qualitative impairments in social reciprocity and in abstract imagination. Not surprisingly, these traits can affect the personal religion of ASD patients, in the same manner as religious background does. To determine to what extent the religiousness of religious patients is associated with autistic traits and religious background. Dutch adults attending a Protestant mental healthcare institution as outpatients were asked to complete the 'Questionnaire God Image' (QGI) and the 'Autism Quotient' (AQNL). In this cross-sectional study various aspects of the God image were related to autistic traits and religious background. The more that respondents reported autistic traits, the greater was their fear of God and the less positive were their feelings. Respondents who were strict Calvinists experienced greater fear of God than did other respondents. Treatment of religious patients with asd needs to take into account these patients' greater fear of God and their less positive feelings. Those patients who had had a strict Calvinist upbringing had a more pronounced fear of God.

  3. Mapping of genes for flower-related traits and QTLs for flowering ...

    Indian Academy of Sciences (India)

    Mapping of genes for flower-related traits and QTLs for flowering time ... which would greatly enhance the use of G. darwinii-specific desirable genes in ... used to determine all linkage groups, the order of groups on the same ... age groups.

  4. Genetic evidence for causal relationships between maternal obesity-related traits and birth weight

    NARCIS (Netherlands)

    A.W.R. Tyrrell; R.C. Richmond (Rebecca C.); T.M. Palmer (Tom); B. Feenstra (Bjarke); J. Rangarajan (Janani); S. Metrustry (Sarah); A. Cavadino (Alana); L. Paternoster (Lavinia); L.L. Armstrong (Loren L.); N.M.G. De Silva (N. Maneka G.); A.R. Wood (Andrew); M. Horikoshi (Momoko); F. Geller (Frank); R. Myhre (Ronny); J.P. Bradfield (Jonathan); E. Kreiner-Møller (Eskil); I. Huikari (Ille); J.N. Painter (Jodie N.); J.J. Hottenga (Jouke Jan); C. Allard (Catherine); D. Berry (Diane); L. Bouchard (Luigi); S. Das (Shikta); D.M. Evans (David); H. Hakonarson (Hakon); M.G. Hayes (M. Geoffrey); J. Heikkinen (Jani); A. Hofman (Albert); B.A. Knight (Bridget); P.A. Lind (Penelope); M.I. McCarthy (Mark); G. Mcmahon (George); S.E. Medland (Sarah Elizabeth); M. Melbye (Mads); A.P. Morris (Andrew); M. Nodzenski (Michael); C. Reichetzeder (Christoph); S.M. Ring (Susan); S. Sebert (Sylvain); V. Sengpiel (Verena); T.I.A. Sørensen (Thorkild); G.A.H.M. Willemsen (Gonneke); E.J.C. de Geus (Eco); N.G. Martin (Nicholas); T.D. Spector (Timothy); C. Power (Christine); M.-R. Jarvelin (Marjo-Riitta); H. Bisgaard (Hans); S.F.A. Grant (Struan); C. Nohr (Christian); V.W.V. Jaddoe (Vincent); B. Jacobsson (Bo); J.C. Murray (Jeffrey C.); B. Hocher (Berthold); A.T. Hattersley (Andrew); D.M. Scholtens (Denise M.); G.D. Smith; M.-F. Hivert (Marie-France); J.F. Felix (Janine); E. Hypponen (Elina); W.L. Lowe Jr. (William); T.M. Frayling (Timothy); D.A. Lawlor (Debbie); R.M. Freathy (Rachel)

    2016-01-01

    textabstractIMPORTANCE Neonates born to overweight or obese women are larger and at higher risk of birth complications. Many maternal obesity-related traits are observationally associated with birth weight, but the causal nature of these associations is uncertain. OBJECTIVE To test for genetic

  5. Analysis of QTLs for yield-related traits in Yuanjiang common wild rice (Oryza rufipogon Griff.).

    Science.gov (United States)

    Fu, Qiang; Zhang, Peijiang; Tan, Lubin; Zhu, Zuofeng; Ma, Dan; Fu, Yongcai; Zhan, Xinchun; Cai, Hongwei; Sun, Chuanqing

    2010-02-01

    Using an accession of common wild rice (Oryza rufipogon Griff.) collected from Yuanjiang County, Yunnan Province, China, as the donor and an elite cultivar 93-11, widely used in two-line indica hybrid rice production in China, as the recurrent parent, an advanced backcross populations were developed. Through genotyping of 187 SSR markers and investigation of six yield-related traits of two generations (BC(4)F(2) and BC(4)F(4)), a total of 26 QTLs were detected by employing single point analysis and interval mapping in both generations. Of the 26 QTLs, the alleles of 10 (38.5%) QTLs originating from O. rufipogon had shown a beneficial effect for yield-related traits in the 93-11 genetic background. In addition, five QTLs controlling yield and its components were newly identified, indicating that there are potentially novel alleles in Yuanjiang common wild rice. Three regions underling significant QTLs for several yield-related traits were detected on chromosome 1, 7 and 12. The QTL clusters were founded and corresponding agronomic traits of those QTLs showed highly significant correlation, suggesting the pleiotropism or tight linkage. Fine-mapping and cloning of these yield-related QTLs from wild rice would be helpful to elucidating molecular mechanism of rice domestication and rice breeding in the future. Copyright 2010 Institute of Genetics and Developmental Biology and the Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

  6. Mapping of genes for flower-related traits and QTLs for flowering ...

    Indian Academy of Sciences (India)

    Mapping of genes for flower-related traits and QTLs for flowering time in an interspecific population of Gossypium hirsutum × G. darwinii. Shuwen Zhang, Qianqian Lan, Xiang Gao, Biao Yang, Caiping Cai, Tianzhen Zhang and Baoliang Zhou. J. Genet. 95, 197–201. Table 1. Loci composition and recombination distances of ...

  7. Identification of QTL for maize grain yield and kernel-related traits

    Indian Academy of Sciences (India)

    [Yang C., Zhang L., Jia A. and Rong T. 2016 Identification of QTL for maize grain yield and kernel-related traits. ... 2010; Zhang et al. ...... in the structure and evolution of genetic systems. ... 2013 Fine mapping a major QTL for kernel number per.

  8. Emotional processing and psychopathic traits in male college students: An event-related potential study.

    Science.gov (United States)

    Medina, Amy L; Kirilko, Elvira; Grose-Fifer, Jillian

    2016-08-01

    Emotional processing deficits are often considered a hallmark of psychopathy. However, there are relatively few studies that have investigated how the late positive potential (LPP) elicited by both positive and negative emotional stimuli is modulated by psychopathic traits, especially in undergraduates. Attentional deficits have also been posited to be associated with emotional blunting in psychopathy, consequently, results from previous studies may have been influenced by task demands. Therefore, we investigated the relationship between the neural correlates of emotional processing and psychopathic traits by measuring event-related potentials (ERPs) during a task with a relatively low cognitive load. A group of male undergraduates were classified as having either high or low levels of psychopathic traits according to their total scores on the Psychopathic Personality Inventory - Revised (PPI-R). A subgroup of these participants then passively viewed complex emotional and neutral images from the International Affective Picture System (IAPS) while their EEGs were recorded. As hypothesized, in general the late LPP elicited by emotional pictures was found to be significantly reduced for participants with high Total PPI-R scores relative to those with low scores, especially for pictures that were rated as less emotionally arousing. Our data suggest that male undergraduates with high, but subclinical levels of psychopathic traits did not maintain continued higher-order processing of affective information, especially when it was perceived to be less arousing in nature. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Schizotypal traits in painters: Relations with intelligence, creativity and creative productivity

    Directory of Open Access Journals (Sweden)

    Međedović Janko

    2017-01-01

    Full Text Available In the present research we explored the presence of schizotypal traits in painters. Furthermore, the relations of schizotypy and creativity-related variables (intelligence, creativity and creative productivity were analyzed. Study participants were divided into the criterion (132 students of art academy and art high school and control group (119 psychology students and members of grammar school. Two hypotheses were set: 1 schizotypal traits are more pronounced in painters than in control group; 2 schizotypy is more closely associated with the creativitylinked variables in the criterion than in control group. Schizotypy was operationalized by Disintegration construct and measured via DELTA 10 inventory. Intelligence was assessed by Advanced Progressive Matrices-18; creativity was measured by the same labeled scale from HEXACO-PI-R inventory and creative productivity was explored by a set of questions regarding the frequency of creative behavior. Results showed that Magical thinking, Enhanced awareness, Somatoform Dysregulation, Perceptual distortions and Social anhedonia were the schizotypal traits which were more pronounced in painters as compared to the control group. Factor analyses performed in each group separately revealed a latent component loaded both with schizotypal traits, creativity and creative productivity, but only in the group of painters: schizotypy and creativity were not so closely related in the control group. Thus, the study hypotheses were largely confirmed. Results provide a more detailed understanding of the relations between schizotypy and creativity.

  10. Relating adaptive genetic traits to climate for Sandberg bluegrass from the intermountain western United States

    Science.gov (United States)

    Richard C. Johnson; Matthew E. Horning; Erin Espeland; Ken Vance-Borland

    2015-01-01

    Genetic variation for potentially adaptive traits of the key restoration species Sandberg bluegrass (Poa secunda J. Presl) was assessed over the intermountain western United States in relation to source population climate. Common gardens were established at two intermountain west sites with progeny from two maternal parents from each of 130 wild populations. Data were...

  11. Psycholexical Value Factors in Spain and Their Relation with Personality Traits

    NARCIS (Netherlands)

    Morales-Vives, Fabia; De Raad, Boele; Vigil-Colet, Andreu

    2012-01-01

    The aim of the present study is to determine the structure of values in the Spanish population and its relation to the Big Five personality traits. Using a psycholexical approach, 566 words were identified as values and administered to a sample of participants who were instructed to rate the extent

  12. Identification of quantitative trait loci for fibrin clot phenotypes: the EuroCLOT study

    DEFF Research Database (Denmark)

    Williams, Frances M K; Carter, Angela M; Kato, Bernet

    2009-01-01

    OBJECTIVE: Fibrin makes up the structural basis of an occlusive arterial thrombus, and variability in fibrin phenotype relates to cardiovascular risk. The aims of the current study from the EU consortium EuroCLOT were to (1) determine the heritability of fibrin phenotypes and (2) identify QTLs as...

  13. Relations between female students' personality traits and reported handicaps to rhythmic gymnastics performance.

    Science.gov (United States)

    Ferrand, Claude; Champely, Stephane; Brunel, Philippe C

    2005-04-01

    The present study evaluated the relative contributions of Self-esteem, Trait anxiety, and Public Self-consciousness to self-handicapping on a sex-typed task, within a specific academic sport context. Prior to the competitive examination used to recruit French Physical Education Teachers, female sport students (N = 74) were asked to list and rate on a 7-point scale handicaps which could be disruptive to their Rhythmic Gymnastics performance. Self-esteem did not account for significant variance in any category of handicaps. Trait Anxiety was negatively related to handicaps related to Rhythmic Gymnastics and to Social and Work Commitments. Public Self-consciousness was significantly related to endorsement of Friends and Family Commitments handicaps. These results were discussed in relation to the literature.

  14. Wine yeast phenomics: A standardized fermentation method for assessing quantitative traits of Saccharomyces cerevisiae strains in enological conditions

    Science.gov (United States)

    Bernard, Margaux; Trujillo, Marine; Prodhomme, Duyên; Barbe, Jean-Christophe; Gibon, Yves; Marullo, Philippe

    2018-01-01

    This work describes the set up of a small scale fermentation methodology for measuring quantitative traits of hundreds of samples in an enological context. By using standardized screw cap vessels, the alcoholic fermentation kinetics of Saccharomyces cerevisiae strains were measured by following their weight loss over the time. This dispositive was coupled with robotized enzymatic assays for measuring metabolites of enological interest in natural grape juices. Despite the small volume used, kinetic parameters and fermentation end products measured are similar with those observed in larger scale vats. The vessel used also offers the possibility to assay 32 volatiles compounds using a headspace solid-phase micro-extraction coupled to gas chromatography and mass spectrometry. The vessel shaking applied strongly impacted most of the phenotypes investigated due to oxygen transfer occuring in the first hours of the alcoholic fermentation. The impact of grape must and micro-oxygenation was investigated illustrating some relevant genetic x environmental interactions. By phenotyping a wide panel of commercial wine starters in five grape juices, broad phenotypic correlations between kinetics and metabolic end products were evidentiated. Moreover, a multivariate analysis illustrates that some grape musts are more able than others to discriminate commercial strains since some are less robust to environmental changes. PMID:29351285

  15. Quantitative trait loci for maysin synthesis in maize (Zea mays L.) lines selected for high silk maysin content.

    Science.gov (United States)

    Meyer, J D F; Snook, M E; Houchins, K E; Rector, B G; Widstrom, N W; McMullen, M D

    2007-06-01

    Maysin is a naturally occurring C-glycosyl flavone found in maize (Zea mays L.) silk tissue that confers resistance to corn earworm (Helicoverpa zea, Boddie). Recently, two new maize populations were derived for high silk maysin. The two populations were named the exotic populations of maize (EPM) and the southern inbreds of maize (SIM). Quantitative trait locus (QTL) analysis was employed to determine which loci were responsible for elevated maysin levels in inbred lines derived from the EPM and SIM populations. The candidate genes consistent with QTL position included the p (pericarp color), c2 (colorless2), whp1 (white pollen1) and in1 (intensifier1) loci. The role of these loci in controlling high maysin levels in silks was tested by expression analysis and use of the loci as genetic markers onto the QTL populations. These studies support p, c2 and whp1, but not in1, as loci controlling maysin. Through this study, we determined that the p locus regulates whp1 transcription and that increased maysin in these inbred lines was primarily due to alleles at both structural and regulatory loci promoting increased flux through the flavone pathway by increasing chalcone synthase activity.

  16. Wine yeast phenomics: A standardized fermentation method for assessing quantitative traits of Saccharomyces cerevisiae strains in enological conditions.

    Science.gov (United States)

    Peltier, Emilien; Bernard, Margaux; Trujillo, Marine; Prodhomme, Duyên; Barbe, Jean-Christophe; Gibon, Yves; Marullo, Philippe

    2018-01-01

    This work describes the set up of a small scale fermentation methodology for measuring quantitative traits of hundreds of samples in an enological context. By using standardized screw cap vessels, the alcoholic fermentation kinetics of Saccharomyces cerevisiae strains were measured by following their weight loss over the time. This dispositive was coupled with robotized enzymatic assays for measuring metabolites of enological interest in natural grape juices. Despite the small volume used, kinetic parameters and fermentation end products measured are similar with those observed in larger scale vats. The vessel used also offers the possibility to assay 32 volatiles compounds using a headspace solid-phase micro-extraction coupled to gas chromatography and mass spectrometry. The vessel shaking applied strongly impacted most of the phenotypes investigated due to oxygen transfer occuring in the first hours of the alcoholic fermentation. The impact of grape must and micro-oxygenation was investigated illustrating some relevant genetic x environmental interactions. By phenotyping a wide panel of commercial wine starters in five grape juices, broad phenotypic correlations between kinetics and metabolic end products were evidentiated. Moreover, a multivariate analysis illustrates that some grape musts are more able than others to discriminate commercial strains since some are less robust to environmental changes.

  17. Relationship of the Interaction Between Two Quantitative Trait Loci with γ-Globin Expression in β-Thalassemia Intermedia Patients.

    Science.gov (United States)

    NickAria, Shiva; Haghpanah, Sezaneh; Ramzi, Mani; Karimi, Mehran

    2018-05-10

    Globin switching is a significant factor on blood hemoglobin (Hb) level but its molecular mechanisms have not yet been identified, however, several quantitative trait loci (QTL) and polymorphisms involved regions on chromosomes 2p, 6q, 8q and X account for variation in the γ-globin expression level. We studied the effect of interaction between a region on intron six of the TOX gene, chromosome 8q (chr8q) and XmnI locus on the γ-globin promoter, chr11p on γ-globin expression in 150 β-thalassemia intermedia (β-TI) patients, evaluated by statistical interaction analysis. Our results showed a significant interaction between one QTL on intron six of the TOX gene (rs9693712) and XmnI locus that effect γ-globin expression. Interchromosomal interaction mediates through transcriptional machanisms to preserve true genome architectural features, chromosomes localization and DNA bending. This interaction can be a part of the unknown molecular mechanism of globin switching and regulation of gene expression.

  18. Identifying Quantitative Trait Loci (QTLs) and Developing Diagnostic Markers Linked to Orange Rust Resistance in Sugarcane (Saccharum spp.).

    Science.gov (United States)

    Yang, Xiping; Islam, Md S; Sood, Sushma; Maya, Stephanie; Hanson, Erik A; Comstock, Jack; Wang, Jianping

    2018-01-01

    Sugarcane ( Saccharum spp.) is an important economic crop, contributing up to 80% of table sugar used in the world and has become a promising feedstock for biofuel production. Sugarcane production has been threatened by many diseases, and fungicide applications for disease control have been opted out for sustainable agriculture. Orange rust is one of the major diseases impacting sugarcane production worldwide. Identifying quantitative trait loci (QTLs) and developing diagnostic markers are valuable for breeding programs to expedite release of superior sugarcane cultivars for disease control. In this study, an F 1 segregating population derived from a cross between two hybrid sugarcane clones, CP95-1039 and CP88-1762, was evaluated for orange rust resistance in replicated trails. Three QTLs controlling orange rust resistance in sugarcane (qORR109, qORR4 and qORR102) were identified for the first time ever, which can explain 58, 12 and 8% of the phenotypic variation, separately. We also characterized 1,574 sugarcane putative resistance ( R ) genes. These sugarcane putative R genes and simple sequence repeats in the QTL intervals were further used to develop diagnostic markers for marker-assisted selection of orange rust resistance. A PCR-based Resistance gene-derived maker, G1 was developed, which showed significant association with orange rust resistance. The putative QTLs and marker developed in this study can be effectively utilized in sugarcane breeding programs to facilitate the selection process, thus contributing to the sustainable agriculture for orange rust disease control.

  19. Genome-Wide Association Study of Major Agronomic Traits Related to Domestication in Peanut

    Directory of Open Access Journals (Sweden)

    Xingguo Zhang

    2017-09-01

    Full Text Available Peanut (Arachis hypogaea consists of two subspecies, hypogaea and fastigiata, and has been cultivated worldwide for hundreds of years. Here, 158 peanut accessions were selected to dissect the molecular footprint of agronomic traits related to domestication using specific-locus amplified fragment sequencing (SLAF-seq method. Then, a total of 17,338 high-quality single nucleotide polymorphisms (SNPs in the whole peanut genome were revealed. Eleven agronomic traits in 158 peanut accessions were subsequently analyzed using genome-wide association studies (GWAS. Candidate genes responsible for corresponding traits were then analyzed in genomic regions surrounding the peak SNPs, and 1,429 genes were found within 200 kb windows centerd on GWAS-identified peak SNPs related to domestication. Highly differentiated genomic regions were observed between hypogaea and fastigiata accessions using FST values and sequence diversity (π ratios. Among the 1,429 genes, 662 were located on chromosome A3, suggesting the presence of major selective sweeps caused by artificial selection during long domestication. These findings provide a promising insight into the complicated genetic architecture of domestication-related traits in peanut, and reveal whole-genome SNP markers of beneficial candidate genes for marker-assisted selection (MAS in future breeding programs.

  20. Examining Dark Triad traits in relation to mental toughness and physical activity in young adults.

    Science.gov (United States)

    Sabouri, Sarah; Gerber, Markus; Sadeghi Bahmani, Dena; Lemola, Sakari; Clough, Peter J; Kalak, Nadeem; Shamsi, Mahin; Holsboer-Trachsler, Edith; Brand, Serge

    2016-01-01

    The Dark Triad (DT) describes a set of three closely related personality traits: Machiavellianism, narcissism, and psychopathy. Mental toughness (MT) refers to a psychological construct combining confidence, commitment, control, and challenge. High MT is related to greater physical activity (PA) and, relative to men, women have lower MT scores. The aims of the present study were 1) to investigate the association between DT, MT, and PA, and 2) to compare the DT, MT, and PA scores of men and women. A total of 341 adults (M=29 years; 51.6% women; range: 18-37 years) took part in the study. Participants completed a series of questionnaires assessing DT, MT, and PA. Machiavellianism, narcissism, and psychopathy were all significantly associated with higher MT scores (rs =0.45, 0.50, and 0.20, respectively). DT traits and MT were associated with more vigorous PA. Compared to men, women participants had lower scores for DT traits (overall score and psychopathy), while no differences were found for MT or PA in both sexes. DT traits, high MT, and vigorous PA are interrelated. This pattern of results might explain why, for instance, successful professional athletes can at the same time be tough and ruthless.

  1. Comparison of multipoint linkage analyses for quantitative traits in the CEPH data: parametric LOD scores, variance components LOD scores, and Bayes factors.

    Science.gov (United States)

    Sung, Yun Ju; Di, Yanming; Fu, Audrey Q; Rothstein, Joseph H; Sieh, Weiva; Tong, Liping; Thompson, Elizabeth A; Wijsman, Ellen M

    2007-01-01

    We performed multipoint linkage analyses with multiple programs and models for several gene expression traits in the Centre d'Etude du Polymorphisme Humain families. All analyses provided consistent results for both peak location and shape. Variance-components (VC) analysis gave wider peaks and Bayes factors gave fewer peaks. Among programs from the MORGAN package, lm_multiple performed better than lm_markers, resulting in less Markov-chain Monte Carlo (MCMC) variability between runs, and the program lm_twoqtl provided higher LOD scores by also including either a polygenic component or an additional quantitative trait locus.

  2. Mapping Quantitative Trait Loci (QTL in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL

    Directory of Open Access Journals (Sweden)

    Thomson Peter C

    2010-09-01

    Full Text Available Abstract An (Awassi × Merino × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1 and 3.5 (cohort 2 years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3, 15 significant (LOD ≥ 2, and 11 suggestive QTL (1.7 ≤ LOD P P A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.

  3. Height-related changes in leaf photosynthetic traits in diverse Bornean tropical rain forest trees.

    Science.gov (United States)

    Kenzo, Tanaka; Inoue, Yuta; Yoshimura, Mitsunori; Yamashita, Megumi; Tanaka-Oda, Ayumi; Ichie, Tomoaki

    2015-01-01

    Knowledge of variations in morphophysiological leaf traits with forest height is essential for quantifying carbon and water fluxes from forest ecosystems. Here, we examined changes in leaf traits with forest height in diverse tree species and their role in environmental acclimation in a tropical rain forest in Borneo that does not experience dry spells. Height-related changes in leaf physiological and morphological traits [e.g., maximum photosynthetic rate (Amax), stomatal conductance (gs), dark respiration rate (Rd), carbon isotope ratio (δ(13)C), nitrogen (N) content, and leaf mass per area (LMA)] from understory to emergent trees were investigated in 104 species in 29 families. We found that many leaf area-based physiological traits (e.g., A(max-area), Rd, gs), N, δ(13)C, and LMA increased linearly with tree height, while leaf mass-based physiological traits (e.g., A(max-mass)) only increased slightly. These patterns differed from other biomes such as temperate and tropical dry forests, where trees usually show decreased photosynthetic capacity (e.g., A(max-area), A(max-mass)) with height. Increases in photosynthetic capacity, LMA, and δ(13)C are favored under bright and dry upper canopy conditions with higher photosynthetic productivity and drought tolerance, whereas lower R d and LMA may improve shade tolerance in lower canopy trees. Rapid recovery of leaf midday water potential to theoretical gravity potential during the night supports the idea that the majority of trees do not suffer from strong drought stress. Overall, leaf area-based photosynthetic traits were associated with tree height and the degree of leaf drought stress, even in diverse tropical rain forest trees.

  4. Agreeableness and alcohol-related aggression: the mediating effect of trait aggressivity.

    Science.gov (United States)

    Miller, Cameron A; Parrott, Dominic J; Giancola, Peter R

    2009-12-01

    This study investigated the mediating effect of trait aggressivity on the relation between agreeableness and alcohol-related aggression in a laboratory setting. Participants were 116 healthy male social drinkers between 21 and 30 years of age. Agreeableness and trait aggressivity were measured using the Big Five Inventory and the Buss-Perry Aggression Questionnaire, respectively. Following the consumption of an alcohol or no-alcohol control beverage, participants completed a modified version of the Taylor Aggression Paradigm, in which electric shocks were received from and administered to a fictitious opponent during a competitive task. Aggression was operationalized as the proportion of the most extreme shocks delivered to the fictitious opponent under conditions of low and high provocation. Results indicated that lower levels of agreeableness were associated with higher levels of trait aggressivity. In turn, higher levels of trait aggressivity predicted extreme aggression in intoxicated, but not sober, participants under low, but not high, provocation. Findings highlight the importance of examining determinants of intoxicated aggression within a broader theoretical framework of personality.

  5. Exploring the relation between childhood trauma, temperamental traits and mindfulness in borderline personality disorder.

    Science.gov (United States)

    Elices, Matilde; Pascual, Juan C; Carmona, Cristina; Martín-Blanco, Ana; Feliu-Soler, Albert; Ruiz, Elisabet; Gomà-I-Freixanet, Montserrat; Pérez, Víctor; Soler, Joaquim

    2015-07-29

    Deficits in mindfulness-related capacities have been described in borderline personality disorder (BPD). However, little research has been conducted to explore which factors could explain these deficits. This study assesses the relationship between temperamental traits and childhood maltreatment with mindfulness in BPD. A total of 100 individuals diagnosed with BPD participated in the study. Childhood maltreatment was assessed using the Childhood Trauma Questionnaire (CTQ-SF), temperamental traits were assessed using the Zuckerman-Khulman Personality Questionnaire (ZKPQ), and mindfulness capabilities were evaluated with the Five Facet Mindfulness Questionnaire (FFMQ). Hierarchical regression analyses were performed including only those CTQ-SF and ZKPQ subscales that showed simultaneous significant correlations with mindfulness facets. Results indicated that neuroticism and sexual abuse were predictors of acting with awareness; and neuroticism, impulsiveness and sexual abuse were significant predictors of non-judging. Temperamental traits did not have a moderator effect on the relationship between childhood sexual abuse and mindfulness facets. These results provide preliminary evidence for the effects of temperamental traits and childhood trauma on mindfulness capabilities in BPD individuals. Further studies are needed to better clarify the impact of childhood traumatic experiences on mindfulness capabilities and to determine the causal relations between these variables.

  6. PERCEPTION OF SUPERVISOR SUPPORT, PERSONALITY TRAITS OF EMPLOYEES AND THEIR SATISFACTION WITH WORK-RELATED FACETS

    Directory of Open Access Journals (Sweden)

    Olga Hadzic

    2009-09-01

    Full Text Available The planned downsizing in many organizations which are under the state ownership in Serbia produce a high level of uncertainty and a very specific organi-zational environment. Investigation of the satisfaction with work-related facets of the employees at the beginning of organizational changes is a very important step toward the building of an appropriate strategy for human resource management. We investigate the moderating effect of the variable “supervisor support“ on the correla-tions between variables “Big Five personality traits of employees” and “satisfaction with work-related facets”.Sample consists of 117 employees from a big state owned organization during an important organizational change. The following instruments are used: Big Five Locator - BFL, Communication Satisfaction Questionnaire - CSQ and Job Satisfac-tion Questionnaire - JS.Our results prove that the variable “supervisor support” moderate the correlati-ons between variable “personality trait conscientiousness” and variables “satisfacti-on with pay” and “satisfaction with benefit”; the correlation between variable “personality trait openness” and variable “satisfaction with pay”; the correlations between variable “personality trait negative affectivity” and variables ”satisfaction with pay”, “satisfaction with benefit”, and “satisfaction with recognition”.

  7. Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits.

    Directory of Open Access Journals (Sweden)

    Angelo Scuteri

    2007-07-01

    Full Text Available The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not only of several environmental risk factors, but also of genetic predisposition. To take advantage of recent advances in gene-mapping technology, we executed a genome-wide association scan to identify genetic variants associated with obesity-related quantitative traits in the genetically isolated population of Sardinia. Initial analysis suggested that several SNPs in the FTO and PFKP genes were associated with increased BMI, hip circumference, and weight. Within the FTO gene, rs9930506 showed the strongest association with BMI (p = 8.6 x10(-7, hip circumference (p = 3.4 x 10(-8, and weight (p = 9.1 x 10(-7. In Sardinia, homozygotes for the rare "G" allele of this SNP (minor allele frequency = 0.46 were 1.3 BMI units heavier than homozygotes for the common "A" allele. Within the PFKP gene, rs6602024 showed very strong association with BMI (p = 4.9 x 10(-6. Homozygotes for the rare "A" allele of this SNP (minor allele frequency = 0.12 were 1.8 BMI units heavier than homozygotes for the common "G" allele. To replicate our findings, we genotyped these two SNPs in the GenNet study. In European Americans (N = 1,496 and in Hispanic Americans (N = 839, we replicated significant association between rs9930506 in the FTO gene and BMI (p-value for meta-analysis of European American and Hispanic American follow-up samples, p = 0.001, weight (p = 0.001, and hip circumference (p = 0.0005. We did not replicate association between rs6602024 and obesity-related traits in the GenNet sample, although we found that in European Americans, Hispanic Americans, and African Americans, homozygotes for the rare "A" allele were, on average, 1.0-3.0 BMI units heavier than homozygotes for the more common "G" allele. In summary, we have completed a whole genome-association scan for

  8. The complete linkage disequilibrium test: a test that points to causative mutations underlying quantitative traits

    Directory of Open Access Journals (Sweden)

    Uleberg Eivind

    2011-05-01

    Full Text Available Abstract Background Genetically, SNP that are in complete linkage disequilibrium with the causative SNP cannot be distinguished from the causative SNP. The Complete Linkage Disequilibrium (CLD test presented here tests whether a SNP is in complete LD with the causative mutation or not. The performance of the CLD test is evaluated in 1000 simulated datasets. Methods The CLD test consists of two steps i.e. analysis I and analysis II. Analysis I consists of an association analysis of the investigated region. The log-likelihood values from analysis I are next ranked in descending order and in analysis II the CLD test evaluates differences in log-likelihood ratios between the best and second best markers. Under the null-hypothesis distribution, the best SNP is in greater LD with the QTL than the second best, while under the alternative-CLD-hypothesis, the best SNP is alike-in-state with the QTL. To find a significance threshold, the test was also performed on data excluding the causative SNP. The 5th, 10th and 50th highest TCLD value from 1000 replicated analyses were used to control the type-I-error rate of the test at p = 0.005, p = 0.01 and p = 0.05, respectively. Results In a situation where the QTL explained 48% of the phenotypic variance analysis I detected a QTL in 994 replicates (p = 0.001, where 972 were positioned in the correct QTL position. When the causative SNP was excluded from the analysis, 714 replicates detected evidence of a QTL (p = 0.001. In analysis II, the CLD test confirmed 280 causative SNP from 1000 simulations (p = 0.05, i.e. power was 28%. When the effect of the QTL was reduced by doubling the error variance, the power of the test reduced relatively little to 23%. When sequence data were used, the power of the test reduced to 16%. All SNP that were confirmed by the CLD test were positioned in the correct QTL position. Conclusions The CLD test can provide evidence for a causative SNP, but its power may be low in situations

  9. Dysfunctional error-related processing in incarcerated youth with elevated psychopathic traits

    Science.gov (United States)

    Maurer, J. Michael; Steele, Vaughn R.; Cope, Lora M.; Vincent, Gina M.; Stephen, Julia M.; Calhoun, Vince D.; Kiehl, Kent A.

    2016-01-01

    Adult psychopathic offenders show an increased propensity towards violence, impulsivity, and recidivism. A subsample of youth with elevated psychopathic traits represent a particularly severe subgroup characterized by extreme behavioral problems and comparable neurocognitive deficits as their adult counterparts, including perseveration deficits. Here, we investigate response-locked event-related potential (ERP) components (the error-related negativity [ERN/Ne] related to early error-monitoring processing and the error-related positivity [Pe] involved in later error-related processing) in a sample of incarcerated juvenile male offenders (n = 100) who performed a response inhibition Go/NoGo task. Psychopathic traits were assessed using the Hare Psychopathy Checklist: Youth Version (PCL:YV). The ERN/Ne and Pe were analyzed with classic windowed ERP components and principal component analysis (PCA). Using linear regression analyses, PCL:YV scores were unrelated to the ERN/Ne, but were negatively related to Pe mean amplitude. Specifically, the PCL:YV Facet 4 subscale reflecting antisocial traits emerged as a significant predictor of reduced amplitude of a subcomponent underlying the Pe identified with PCA. This is the first evidence to suggest a negative relationship between adolescent psychopathy scores and Pe mean amplitude. PMID:26930170

  10. Effects of parental emotional warmth on the relationship between regional gray matter volume and depression-related personality traits.

    Science.gov (United States)

    Yang, Junyi; Yin, Ping; Wei, Dongtao; Wang, Kangcheng; Li, Yongmei; Qiu, Jiang

    2017-06-01

    The depression-related personality trait is associated with the severity of patients' current depressive symptoms and with the vulnerability to depression within the nonclinical groups. However, little is known about the anatomical structure associated with the depression-related personality traits within the nonclinical sample. Parenting behavior is associated with the depression symptoms; however, whether or not parenting behavior influence the neural basis of the depression-related personality traits is unclear. Thus in current study, first, we used voxel-based morphometry to identify the brain regions underlying individual differences in depression-related personality traits, as measured by the revised Neuroticism-Extraversion-Openness Personality Inventory, in a large sample of young healthy adults. Second, we use mediation analysis to investigate the relationship between parenting behavior and neural basis of depression-related personality traits. The results revealed that depression-related personality traits were positively correlated with gray matter volume mainly in medial frontal gyrus (MFG) that is implicated in the self-referential processing and emotional regulation. Furthermore, parental emotional warmth acted as a mediational mechanism underlying the association between the MFG volume and the depression-related personality trait. Together, our findings suggested that the family environment might play an important role in the acquisition and process of the depression-related personality traits.

  11. Variation in relative growth rate and growth traits in wild and cultivated Capsicum accessions grown under different temperatures

    NARCIS (Netherlands)

    Swart, de E.A.M.; Marcelis, L.F.M.; Voorrips, R.E.

    2006-01-01

    Differences in environmental conditions are known to influence plant growth and growth-related traits. The aim of this study was to identify the variation in relative growth rate (RGR), and its underlying physiological and morphological traits, in a group of ten wild and cultivated Capsicum

  12. A trait database for marine copepods

    DEFF Research Database (Denmark)

    Brun, Philipp Georg; Payne, Mark R.; Kiørboe, Thomas

    2016-01-01

    was more limited for quantitative traits related to reproduction and physiology. The database may be used to investigate relationships between traits, to produce trait biogeographies, or to inform and validate trait-based marine ecosystem models. The data can be downloaded from PANGAEA, doi:10.1594/PANGAEA......, and organised the data into a structured database. We collected 9345 records for 14 functional traits. Particular attention was given to body size, feeding mode, egg size, spawning strategy, respiration rate and myelination (presence of nerve sheathing). Most records were reported on the species level, but some...

  13. A trait database for marine copepods

    DEFF Research Database (Denmark)

    Brun, Philipp Georg; Payne, Mark; Kiørboe, Thomas

    2017-01-01

    , while information was more limited for quantitative traits related to reproduction and physiology. The database may be used to investigate relationships between traits, to produce trait biogeographies, or to inform and validate trait-based marine ecosystem models. The data can be downloaded from PANGAEA...... and organized the data into a structured database. We collected 9306 records for 14 functional traits. Particular attention was given to body size, feeding mode, egg size, spawning strategy, respiration rate, and myelination (presence of nerve sheathing). Most records were reported at the species level...

  14. The Relation Between Supervisors' Big Five Personality Traits and Employees' Experiences of Abusive Supervision.

    Science.gov (United States)

    Camps, Jeroen; Stouten, Jeroen; Euwema, Martin

    2016-01-01

    The present study investigates the relation between supervisors' personality traits and employees' experiences of supervisory abuse, an area that - to date - remained largely unexplored in previous research. Field data collected from 103 supervisor-subordinate dyads showed that contrary to our expectations supervisors' agreeableness and neuroticism were not significantly related to abusive supervision, nor were supervisors' extraversion or openness to experience. Interestingly, however, our findings revealed a positive relation between supervisors' conscientiousness and abusive supervision. That is, supervisors high in conscientiousness were more likely to be perceived as an abusive supervisor by their employees. Overall, our findings do suggest that supervisors' Big Five personality traits explain only a limited amount of the variability in employees' experiences of abusive supervision.

  15. The Relation Between Supervisors’ Big Five Personality Traits and Employees’ Experiences of Abusive Supervision

    Science.gov (United States)

    Camps, Jeroen; Stouten, Jeroen; Euwema, Martin

    2016-01-01

    The present study investigates the relation between supervisors’ personality traits and employees’ experiences of supervisory abuse, an area that – to date – remained largely unexplored in previous research. Field data collected from 103 supervisor-subordinate dyads showed that contrary to our expectations supervisors’ agreeableness and neuroticism were not significantly related to abusive supervision, nor were supervisors’ extraversion or openness to experience. Interestingly, however, our findings revealed a positive relation between supervisors’ conscientiousness and abusive supervision. That is, supervisors high in conscientiousness were more likely to be perceived as an abusive supervisor by their employees. Overall, our findings do suggest that supervisors’ Big Five personality traits explain only a limited amount of the variability in employees’ experiences of abusive supervision. PMID:26903919

  16. Urgency traits moderate daily relations between affect and drinking to intoxication among young adults.

    Science.gov (United States)

    Bold, Krysten W; Fucito, Lisa M; DeMartini, Kelly S; Leeman, Robert F; Kranzler, Henry R; Corbin, William R; O'Malley, Stephanie S

    2017-01-01

    Young adults with higher trait urgency (i.e., a tendency to act rashly in response to heightened affect) may be especially vulnerable to heavy drinking. The current study examined 1) the influence of urgency on daily relations between affect and drinking to intoxication, and 2) whether urgency influenced the effectiveness of naltrexone (vs. placebo) for reducing alcohol use. This study is a secondary analysis of data from 126 (n=40 female) heavy drinking young adults, ages 18-25, enrolled in a double-blind, 8-week clinical trial comparing brief motivational intervention and either naltrexone or placebo. Multilevel models examined whether trait urgency moderated daily relations between positive and negative affect and drinking to intoxication, measured by an estimated blood-alcohol concentration (eBAC) at or above the legal limit (≥0.08g%). Person-level interactions examined whether naltrexone was more effective than placebo at reducing the odds of eBAC≥0.08g% for individuals with higher vs. lower trait urgency. On days of greater within-person positive or negative affect, young adults with higher urgency were more likely to drink to intoxication than those with lower urgency. Naltrexone reduced the odds of drinking to intoxication significantly more than placebo, independent of positive or negative urgency. Although naltrexone treatment reduced drinking overall, young adults with higher trait urgency were still at increased risk for hazardous drinking following times of strong positive or negative mood. Targeted interventions are needed to reduce the risk of heavy drinking among young adults with high trait urgency. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  17. The modulating effect of personality traits on neural error monitoring: evidence from event-related FMRI.

    Science.gov (United States)

    Sosic-Vasic, Zrinka; Ulrich, Martin; Ruchsow, Martin; Vasic, Nenad; Grön, Georg

    2012-01-01

    The present study investigated the association between traits of the Five Factor Model of Personality (Neuroticism, Extraversion, Openness for Experiences, Agreeableness, and Conscientiousness) and neural correlates of error monitoring obtained from a combined Eriksen-Flanker-Go/NoGo task during event-related functional magnetic resonance imaging in 27 healthy subjects. Individual expressions of personality traits were measured using the NEO-PI-R questionnaire. Conscientiousness correlated positively with error signaling in the left inferior frontal gyrus and adjacent anterior insula (IFG/aI). A second strong positive correlation was observed in the anterior cingulate gyrus (ACC). Neuroticism was negatively correlated with error signaling in the inferior frontal cortex possibly reflecting the negative inter-correlation between both scales observed on the behavioral level. Under present statistical thresholds no significant results were obtained for remaining scales. Aligning the personality trait of Conscientiousness with task accomplishment striving behavior the correlation in the left IFG/aI possibly reflects an inter-individually different involvement whenever task-set related memory representations are violated by the occurrence of errors. The strong correlations in the ACC may indicate that more conscientious subjects were stronger affected by these violations of a given task-set expressed by individually different, negatively valenced signals conveyed by the ACC upon occurrence of an error. Present results illustrate that for predicting individual responses to errors underlying personality traits should be taken into account and also lend external validity to the personality trait approach suggesting that personality constructs do reflect more than mere descriptive taxonomies.

  18. The modulating effect of personality traits on neural error monitoring: evidence from event-related FMRI.

    Directory of Open Access Journals (Sweden)

    Zrinka Sosic-Vasic

    Full Text Available The present study investigated the association between traits of the Five Factor Model of Personality (Neuroticism, Extraversion, Openness for Experiences, Agreeableness, and Conscientiousness and neural correlates of error monitoring obtained from a combined Eriksen-Flanker-Go/NoGo task during event-related functional magnetic resonance imaging in 27 healthy subjects. Individual expressions of personality traits were measured using the NEO-PI-R questionnaire. Conscientiousness correlated positively with error signaling in the left inferior frontal gyrus and adjacent anterior insula (IFG/aI. A second strong positive correlation was observed in the anterior cingulate gyrus (ACC. Neuroticism was negatively correlated with error signaling in the inferior frontal cortex possibly reflecting the negative inter-correlation between both scales observed on the behavioral level. Under present statistical thresholds no significant results were obtained for remaining scales. Aligning the personality trait of Conscientiousness with task accomplishment striving behavior the correlation in the left IFG/aI possibly reflects an inter-individually different involvement whenever task-set related memory representations are violated by the occurrence of errors. The strong correlations in the ACC may indicate that more conscientious subjects were stronger affected by these violations of a given task-set expressed by individually different, negatively valenced signals conveyed by the ACC upon occurrence of an error. Present results illustrate that for predicting individual responses to errors underlying personality traits should be taken into account and also lend external validity to the personality trait approach suggesting that personality constructs do reflect more than mere descriptive taxonomies.

  19. Factorial correspondence analysis of fear-related behaviour traits in Japanese quail.

    Science.gov (United States)

    Mignon-Grasteau, S; Roussot, O; Delaby, C; Faure, J M.; Mills, A; Leterrier, C; Guéméné, D; Constantin, P; Mills, M; Lepape, G; Beaumont, C

    2003-02-28

    Factorial correspondence analysis was performed on 341 quails from a F2 cross between two lines divergently selected on the duration of tonic immobility over 29 generations. Several fear- or stress-related traits were recorded, i.e. tonic immobility duration, number of inductions needed to induce tonic immobility, open-field behaviour (time spent walking, latency before first movement and number of defecations), asymmetry of tibia lengths and corticosterone concentration after restraint stress. Variables were categorised in classes and analysed by factorial correspondence analysis. The first axis was mostly described by open-field behaviour, and the second by tonic immobility traits (duration of tonic immobility and number of inductions), which showed that these behaviours were almost independent. No relationship was found between axes of the factorial correspondence analysis and corticosterone concentration or asymmetry of tibia lengths, showing that these variables reflected other characteristics of stress susceptibility than those described by tonic immobility and open-field behaviour. These results show that reaction to stress of quails is a multidimensional trait and cannot be summarised by one trait.

  20. The relation between trait mindfulness and aggression in men seeking residential substance use treatment.

    Science.gov (United States)

    Shorey, Ryan C; Anderson, Scott; Stuart, Gregory L

    2015-06-01

    There has been an abundance of research in recent years on mindfulness, including mindfulness within individuals seeking substance use treatment. However, to date, there has been no research on whether trait mindfulness is associated with increased aggression among individuals seeking substance use treatment. Past research has demonstrated that individuals in substance use treatment evidence higher levels of aggression than non-substance abusers, and preliminary research has shown that trait mindfulness is inversely associated with aggression in non-substance-use treatment-seeking populations. The current study examined whether trait mindfulness was associated with aggression among men seeking residential substance use treatment (N = 116). Results demonstrated that lower trait mindfulness was associated with increased aggression (physical, verbal, and aggressive attitude). Moreover, this relation held for both verbal aggression and aggressive attitude after controlling for alcohol use, drug use, and age, all known predictors of aggression. Findings provide the first evidence that mindfulness is negatively associated with aggression among men in substance use treatment, which could have important implications for intervention. That is, mindfulness-based interventions may prove helpful for the treatment of both substance use and aggression. © The Author(s) 2014.

  1. Affective touch awareness in mental health and disease relates to autistic traits - An explorative neurophysiological investigation.

    Science.gov (United States)

    Croy, Ilona; Geide, Helen; Paulus, Martin; Weidner, Kerstin; Olausson, Håkan

    2016-11-30

    Affective touch is important for social interaction within families and groups and there is evidence that unmyelinated C tactile fibers are involved in this process. Individuals with autism spectrum disorders show alterations in the perception and processing of affective touch. sThus, we hypothesized that affective touch awareness based on C tactile fiber activation is impaired in individuals with high levels of autistic trait. The pleasantness perception of optimal and suboptimal C tactile stimuli was tested in an explorative study in 70 patients recruited from an outpatient psychotherapy clinic and 69 healthy comparison subjects. All participants completed questionnaires about autistic traits, depressive symptomatology, childhood maltreatment, and about the daily amount of touch. Relative to comparison subjects, patients reported engaging in touch less frequently in daily life and rated touch less pleasant. Reduced valence ratings of touch were explained by childhood maltreatment but not by any particular disorder or depression severity. Among all tested variables, the affective touch awareness correlated with autistic traits only - in patients as well as in comparison subjects. Taken together, individuals with mental health issues have a lower baseline of expression and reception of affective touch. Autistic traits and childhood maltreatment modulate the experience of affective touch. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  2. Preliminary evidence for associations between molecular markers and quantitative traits in a set of bread wheat (Triticum aestivum L.) cultivars and breeding lines.

    Science.gov (United States)

    Abdollahi Mandoulakani, Babak; Nasri, Shilan; Dashchi, Sahar; Arzhang, Sorour; Bernousi, Iraj; Abbasi Holasou, Hossein

    The identification of polymorphic markers associated with various quantitative traits allows us to test their performance for the exploitation of the extensive quantitative variation maintained in gene banks. In the current study, a set of 97 wheat germplasm accessions including 48 cultivars and 49 breeding lines were evaluated for 18 agronomic traits. The accessions were also genotyped with 23 ISSR, nine IRAP and 20 REMAP markers, generating a total of 658 clear and scorable bands, 86% of which were polymorphic. Both neighbor-joining dendrogram and Bayesian analysis of clustering of individuals revealed that the accessions could be divided into four genetically distinct groups, indicating the presence of a population structure in current wheat germplasm. Associations between molecular markers and 18 agronomic traits were analyzed using the mixed linear model (MLM) approach. A total of 94 loci were found to be significantly associated with agronomic traits (P≤0.01). The highest number of bands significantly associated with the 18 traits varied from 11 for number of spikelets spike -1 (NSS) to two for grain yield in row (GRY). Loci ISSR16-9 and REMAP13-10 were associated with three different traits. The results of the current study provide useful information about the performance of retrotransposon-based and ISSR molecular markers that could be helpful in selecting potentially elite gene bank samples for wheat-breeding programs. Copyright © 2017 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

  3. Metabolomic Quantitative Trait Loci (mQTL Mapping Implicates the Ubiquitin Proteasome System in Cardiovascular Disease Pathogenesis.

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    William E Kraus

    2015-11-01

    Full Text Available Levels of certain circulating short-chain dicarboxylacylcarnitine (SCDA, long-chain dicarboxylacylcarnitine (LCDA and medium chain acylcarnitine (MCA metabolites are heritable and predict cardiovascular disease (CVD events. Little is known about the biological pathways that influence levels of most of these metabolites. Here, we analyzed genetics, epigenetics, and transcriptomics with metabolomics in samples from a large CVD cohort to identify novel genetic markers for CVD and to better understand the role of metabolites in CVD pathogenesis. Using genomewide association in the CATHGEN cohort (N = 1490, we observed associations of several metabolites with genetic loci. Our strongest findings were for SCDA metabolite levels with variants in genes that regulate components of endoplasmic reticulum (ER stress (USP3, HERC1, STIM1, SEL1L, FBXO25, SUGT1 These findings were validated in a second cohort of CATHGEN subjects (N = 2022, combined p = 8.4x10-6-2.3x10-10. Importantly, variants in these genes independently predicted CVD events. Association of genomewide methylation profiles with SCDA metabolites identified two ER stress genes as differentially methylated (BRSK2 and HOOK2. Expression quantitative trait loci (eQTL pathway analyses driven by gene variants and SCDA metabolites corroborated perturbations in ER stress and highlighted the ubiquitin proteasome system (UPS arm. Moreover, culture of human kidney cells in the presence of levels of fatty acids found in individuals with cardiometabolic disease, induced accumulation of SCDA metabolites in parallel with increases in the ER stress marker BiP. Thus, our integrative strategy implicates the UPS arm of the ER stress pathway in CVD pathogenesis, and identifies novel genetic loci associated with CVD event risk.

  4. Quantitative Trait Loci and Inter-Organ Partitioning for Essential Metal and Toxic Analogue Accumulation in Barley.

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    Stefan Reuscher

    Full Text Available The concentrations of both essential nutrients and chemically similar toxic analogues accumulated in cereal grains have a major impact on the nutritional quality and safety of crops. Naturally occurring genetic diversity can be exploited for the breeding of improved varieties through introgression lines (ILs. In this study, multi-element analysis was conducted on vegetative leaves, senesced flag leaves and mature grains of a set of 54 ILs of the wild ancestral Hordeum vulgare ssp. spontaneum in the cultivated variety Hordeum vulgare ssp. vulgare cv. Scarlett. Plants were cultivated on an anthropogenically heavy metal-contaminated soil collected in an agricultural field, thus allowing simultaneous localization of quantitative trait loci (QTL for the accumulation of both essential nutrients and toxic trace elements in barley as a model cereal crop. For accumulation of the micronutrients Fe and Zn and the interfering toxin Cd, we identified 25, 16 and 5 QTL, respectively. By examining the gene content of the introgressions, we associated QTL with candidate genes based on homology to known metal homeostasis genes of Arabidopsis and rice. Global comparative analyses suggested the preferential remobilization of Cu and Fe, over Cd, from the flag leaf to developing grains. Our data identifies grain micronutrient filling as a regulated and nutrient-specific process, which operates differently from vegetative micronutrient homoeostasis. In summary, this study provides novel QTL for micronutrient accumulation in the presence of toxic analogues and supports a higher degree of metal specificity of trace element partitioning during grain filling in barley than previously reported for other cereals.

  5. PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies.

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    Wenchao Zhang

    2016-05-01

    Full Text Available The term epistasis refers to interactions between multiple genetic loci. Genetic epistasis is important in regulating biological function and is considered to explain part of the 'missing heritability,' which involves marginal genetic effects that cannot be accounted for in genome-wide association studies. Thus, the study of epistasis is of great interest to geneticists. However, estimating epistatic effects for quantitative traits is challenging due to the large number of interaction effects that must be estimated, thus significantly increasing computing demands. Here, we present a new web server-based tool, the Pipeline for estimating EPIStatic genetic effects (PEPIS, for analyzing polygenic epistatic effects. The PEPIS software package is based on a new linear mixed model that has been used to predict the performance of hybrid rice. The PEPIS includes two main sub-pipelines: the first for kinship matrix calculation, and the second for polygenic component analyses and genome scanning for main and epistatic effects. To accommodate the demand for high-performance computation, the PEPIS utilizes C/C++ for mathematical matrix computing. In addition, the modules for kinship matrix calculations and main and epistatic-effect genome scanning employ parallel computing technology that effectively utilizes multiple computer nodes across our networked cluster, thus significantly improving the computational speed. For example, when analyzing the same immortalized F2 rice population genotypic data examined in a previous study, the PEPIS returned identical results at each analysis step with the original prototype R code, but the computational time was reduced from more than one month to about five minutes. These advances will help overcome the bottleneck frequently encountered in genome wide epistatic genetic effect analysis and enable accommodation of the high computational demand. The PEPIS is publically available at http://bioinfo.noble.org/PolyGenic_QTL/.

  6. PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies.

    Science.gov (United States)

    Zhang, Wenchao; Dai, Xinbin; Wang, Qishan; Xu, Shizhong; Zhao, Patrick X

    2016-05-01

    The term epistasis refers to interactions between multiple genetic loci. Genetic epistasis is important in regulating biological function and is considered to explain part of the 'missing heritability,' which involves marginal genetic effects that cannot be accounted for in genome-wide association studies. Thus, the study of epistasis is of great interest to geneticists. However, estimating epistatic effects for quantitative traits is challenging due to the large number of interaction effects that must be estimated, thus significantly increasing computing demands. Here, we present a new web server-based tool, the Pipeline for estimating EPIStatic genetic effects (PEPIS), for analyzing polygenic epistatic effects. The PEPIS software package is based on a new linear mixed model that has been used to predict the performance of hybrid rice. The PEPIS includes two main sub-pipelines: the first for kinship matrix calculation, and the second for polygenic component analyses and genome scanning for main and epistatic effects. To accommodate the demand for high-performance computation, the PEPIS utilizes C/C++ for mathematical matrix computing. In addition, the modules for kinship matrix calculations and main and epistatic-effect genome scanning employ parallel computing technology that effectively utilizes multiple computer nodes across our networked cluster, thus significantly improving the computational speed. For example, when analyzing the same immortalized F2 rice population genotypic data examined in a previous study, the PEPIS returned identical results at each analysis step with the original prototype R code, but the computational time was reduced from more than one month to about five minutes. These advances will help overcome the bottleneck frequently encountered in genome wide epistatic genetic effect analysis and enable accommodation of the high computational demand. The PEPIS is publically available at http://bioinfo.noble.org/PolyGenic_QTL/.

  7. Inheritance analysis and mapping of quantitative trait loci (QTL controlling individual anthocyanin compounds in purple barley (Hordeum vulgare L. grains.

    Directory of Open Access Journals (Sweden)

    Xiao-Wei Zhang

    Full Text Available Anthocyanin-rich barley can have great potential in promoting human health and in developing nutraceuticals and functional foods. As different anthocyanin compounds have different antioxidant activities, breeding cultivars with pre-designed anthocyanin compositions could be highly desirable. Working toward this possibility, we assessed and reported for the first time the genetic control of individual anthocyanin compounds in barley. Of the ten anthocyanins assessed, two, peonidin-3-glucoside (P3G and cyanidin-3-glucoside (C3G, were major components in the purple pericarp barley genotype RUSSIA68. Quantitative trait locus (QTL mapping showed that both anthocyanin compounds were the interactive products of two loci, one located on chromosome arm 2HL and the other on 7HS. However, the two different anthocyanin components seem to be controlled by different interactions between the two loci. The effects of the 7HS locus on P3G and C3G were difficult to detect without removing the effect of the 2HL locus. At least one copy of the 2HL alleles from the purple pericarp parent was required for the synthesis of P3G. This does not seem to be the case for the production of C3G which was produced in each of all the different allele combinations between the two loci. Typical maternal effect was also observed in the inheritance of purple pericarp grains in barley. The varied values of different compounds, coupled with their different genetic controls, highlight the need for targeting individual anthocyanins in crop breeding and food processing.

  8. Are leaf physiological traits related to leaf water isotopic enrichment in restinga woody species?

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    BRUNO H.P. ROSADO

    2013-09-01

    Full Text Available During plant-transpiration, water molecules having the lighter stable isotopes of oxygen and hydrogen evaporate and diffuse at a faster rate through the stomata than molecules having the heavier isotopes, which cause isotopic enrichment of leaf water. Although previous models have assumed that leaf water is well-mixed and isotopically uniform, non-uniform stomatal closure, promoting different enrichments between cells, and different pools of water within leaves, due to morpho-physiological traits, might lead to inaccuracies in isotopic models predicting leaf water enrichment. We evaluate the role of leaf morpho-physiological traits on leaf water isotopic enrichment in woody species occurring in a coastal vegetation of Brazil known as restinga. Hydrogen and oxygen stable isotope values of soil, plant stem and leaf water and leaf traits were measured in six species from restinga vegetation during a drought and a wet period. Leaf water isotopic enrichment relative to stem water was more homogeneous among species during the drought in contrast to the wet period suggesting convergent responses to deal to temporal heterogeneity in water availability. Average leaf water isotopic enrichment relative to stem water during the drought period was highly correlated with relative apoplastic water content. We discuss this observation in the context of current models of leaf water isotopic enrichment as a function of the Péclet effect. We suggest that future studies should include relative apoplastic water content in isotopic models.

  9. Are leaf physiological traits related to leaf water isotopic enrichment in restinga woody species?

    Science.gov (United States)

    Rosado, Bruno H P; De Mattos, Eduardo A; Sternberg, Leonel Da S L

    2013-09-01

    During plant-transpiration, water molecules having the lighter stable isotopes of oxygen and hydrogen evaporate and diffuse at a faster rate through the stomata than molecules having the heavier isotopes, which cause isotopic enrichment of leaf water. Although previous models have assumed that leaf water is well-mixed and isotopically uniform, non-uniform stomatal closure, promoting different enrichments between cells, and different pools of water within leaves, due to morpho-physiological traits, might lead to inaccuracies in isotopic models predicting leaf water enrichment. We evaluate the role of leaf morpho-physiological traits on leaf water isotopic enrichment in woody species occurring in a coastal vegetation of Brazil known as restinga. Hydrogen and oxygen stable isotope values of soil, plant stem and leaf water and leaf traits were measured in six species from restinga vegetation during a drought and a wet period. Leaf water isotopic enrichment relative to stem water was more homogeneous among species during the drought in contrast to the wet period suggesting convergent responses to deal to temporal heterogeneity in water availability. Average leaf water isotopic enrichment relative to stem water during the drought period was highly correlated with relative apoplastic water content. We discuss this observation in the context of current models of leaf water isotopic enrichment as a function of the Péclet effect. We suggest that future studies should include relative apoplastic water content in isotopic models.

  10. The relations between personality traits and psychopathy as measured by ratings and self-report

    Directory of Open Access Journals (Sweden)

    Kujačić Daliborka

    2015-01-01

    Full Text Available The objective of this study was to examine the relations between psychopathy - as assessed by ratings (PCL-R and by self-report (SRP3 - on one side, and The Five-Factor personality Model - expanded to include the traits Amorality and Disintegration - on the other. Both methods examined four traits of psychopathy: interpersonal, affective, lifestyle and antisocial characteristics. Data were collected on a sample of 112 male convicts. The results show the absence of congruence between the two methods - self-report and rating - in case of interpersonal and affective psychopathic dispositions. This incongruence is also reflected in their relations with personality traits. The self-report measures and the ratings of Lifestyle and Antisocial tendencies are related to amorality, aggressiveness, schizotypy, Neuroticism and impulsivity. However, the ratings of affective and interpersonal style are related to the integrated, organized, and emotionally stable aspects of personality. The results are interpreted in the light of differences between the methods of assessment and in the light of the essential characteristics of the psychopathic phenomena.

  11. Exploring alternative models for sex-linked quantitative trait loci in outbred populations: application to an iberian x landrace pig intercross.

    OpenAIRE

    Pérez-Enciso, Miguel; Clop, Alex; Folch, Josep M; Sánchez, Armand; Oliver, Maria A; Ovilo, Cristina; Barragán, C; Varona, Luis; Noguera, José L

    2002-01-01

    We present a very flexible method that allows us to analyze X-linked quantitative trait loci (QTL) in crosses between outbred lines. The dosage compensation phenomenon is modeled explicitly in an identity-by-descent approach. A variety of models can be fitted, ranging from considering alternative fixed alleles within the founder breeds to a model where the only genetic variation is within breeds, as well as mixed models. Different genetic variances within each founder breed can be estimated. ...

  12. Coordination of Leaf Photosynthesis, Transpiration, and Structural Traits in Rice and Wild Relatives (Genus Oryza).

    Science.gov (United States)

    Giuliani, Rita; Koteyeva, Nuria; Voznesenskaya, Elena; Evans, Marc A; Cousins, Asaph B; Edwards, Gerald E

    2013-07-01

    The genus Oryza, which includes rice (Oryza sativa and Oryza glaberrima) and wild relatives, is a useful genus to study leaf properties in order to identify structural features that control CO(2) access to chloroplasts, photosynthesis, water use efficiency, and drought tolerance. Traits, 26 structural and 17 functional, associated with photosynthesis and transpiration were quantified on 24 accessions (representatives of 17 species and eight genomes). Hypotheses of associations within, and between, structure, photosynthesis, and transpiration were tested. Two main clusters of positively interrelated leaf traits were identified: in the first cluster were structural features, leaf thickness (Thick(leaf)), mesophyll (M) cell surface area exposed to intercellular air space per unit of leaf surface area (S(mes)), and M cell size; a second group included functional traits, net photosynthetic rate, transpiration rate, M conductance to CO(2) diffusion (g(m)), stomatal conductance to gas diffusion (g(s)), and the g(m)/g(s) ratio.While net photosynthetic rate was positively correlated with gm, neither was significantly linked with any individual structural traits. The results suggest that changes in gm depend on covariations of multiple leaf (S(mes)) and M cell (including cell wall thickness) structural traits. There was an inverse relationship between Thick(leaf) and transpiration rate and a significant positive association between Thick(leaf) and leaf transpiration efficiency. Interestingly, high g(m) together with high g(m)/g(s) and a low S(mes)/g(m) ratio (M resistance to CO(2) diffusion per unit of cell surface area exposed to intercellular air space) appear to be ideal for supporting leaf photosynthesis while preserving water; in addition, thick M cell walls may be beneficial for plant drought tolerance.

  13. Dark personality traits and impulsivity among adolescents: Differential links to problem behaviors and family relations.

    Science.gov (United States)

    Dubas, Judith Semon; Baams, Laura; Doornwaard, Suzan M; van Aken, Marcel A G

    2017-10-01

    Research on how dark personality traits develop and relate to risky behaviors and family relations during adolescence is scarce. This study used a person-oriented approach to examine (a) whether distinct groups of adolescents could be identified based on their developmental profiles of callous-unemotional (CU), grandiose manipulative (GM), and dysfunctional impulsivity (DI) traits and (b) whether these groups differ in their problem behaviors and parent-adolescent relationship quality. Latent class growth analyses on 4-wave data of 1,131 Dutch adolescents revealed 3 personality profiles: (1) a dark impulsive group (13.9%), with high scores on all 3 traits (CU, GM, and DI) that were stable over time; (2) an impulsive group (26.1%), with high and increasing levels of impulsivity and relatively low scores on CU and GM; and (3) and a low risk group (60.0%), with relatively low levels on all 3 personality characteristics, with impulsivity decreasing over time. Compared with adolescents in the low risk group, adolescents in the dark impulsive and impulsive groups reported higher initial levels of substance use, sexual risk behaviors, permissive sexual attitudes, parent-adolescent conflict, and lower parent-adolescent satisfaction, as well as greater increases in sexual risk behavior over time. Compared with adolescents in the impulsive group, those in the dark impulsive group showed the highest levels of risk behaviors. Hence, dark personality traits coupled with impulsivity may be indicative of an earlier and more severe trajectory of problem behaviors that may differ from the trajectory of youth who are only impulsive. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  14. Estimation of Relative Economic Weights of Hanwoo Carcass Traits Based on Carcass Market Price

    Science.gov (United States)

    Choy, Yun Ho; Park, Byoung Ho; Choi, Tae Jung; Choi, Jae Gwan; Cho, Kwang Hyun; Lee, Seung Soo; Choi, You Lim; Koh, Kyung Chul; Kim, Hyo Sun

    2012-01-01

    The objective of this study was to estimate economic weights of Hanwoo carcass traits that can be used to build economic selection indexes for selection of seedstocks. Data from carcass measures for determining beef yield and quality grades were collected and provided by the Korean Institute for Animal Products Quality Evaluation (KAPE). Out of 1,556,971 records, 476,430 records collected from 13 abattoirs from 2008 to 2010 after deletion of outlying observations were used to estimate relative economic weights of bid price per kg carcass weight on cold carcass weight (CW), eye muscle area (EMA), backfat thickness (BF) and marbling score (MS) and the phenotypic relationships among component traits. Price of carcass tended to increase linearly as yield grades or quality grades, in marginal or in combination, increased. Partial regression coefficients for MS, EMA, BF, and for CW in original scales were +948.5 won/score, +27.3 won/cm2, −95.2 won/mm and +7.3 won/kg when all three sex categories were taken into account. Among four grade determining traits, relative economic weight of MS was the greatest. Variations in partial regression coefficients by sex categories were great but the trends in relative weights for each carcass measures were similar. Relative economic weights of four traits in integer values when standardized measures were fit into covariance model were +4:+1:−1:+1 for MS:EMA:BF:CW. Further research is required to account for the cost of production per unit carcass weight or per unit production under different economic situations. PMID:25049531

  15. Introgression of novel traits from a wild wheat relative improves drought adaptation in wheat.

    Science.gov (United States)

    Placido, Dante F; Campbell, Malachy T; Folsom, Jing J; Cui, Xinping; Kruger, Greg R; Baenziger, P Stephen; Walia, Harkamal

    2013-04-01

    Root architecture traits are an important component for improving water stress adaptation. However, selection for aboveground traits under favorable environments in modern cultivars may have led to an inadvertent loss of genes and novel alleles beneficial for adapting to environments with limited water. In this study, we elucidate the physiological and molecular consequences of introgressing an alien chromosome segment (7DL) from a wild wheat relative species (Agropyron elongatum) into cultivated wheat (Triticum aestivum). The wheat translocation line had improved water stress adaptation and higher root and shoot biomass compared with the control genotypes, which showed significant drops in root and shoot biomass during stress. Enhanced access to water due to higher root biomass enabled the translocation line to maintain more favorable gas-exchange and carbon assimilation levels relative to the wild-type wheat genotypes during water stress. Transcriptome analysis identified candidate genes associated with root development. Two of these candidate genes mapped to the site of translocation on chromosome 7DL based on single-feature polymorphism analysis. A brassinosteroid signaling pathway was predicted to be involved in the novel root responses observed in the A. elongatum translocation line, based on the coexpression-based gene network generated by seeding the network with the candidate genes. We present an effective and highly integrated approach that combines root phenotyping, whole-plant physiology, and functional genomics to discover novel root traits and the underlying genes from a wild related species to improve drought adaptation in cultivated wheat.

  16. Reproductive traits and evolutionary divergence between Mediterranean crops and their wild relatives.

    Science.gov (United States)

    Iriondo, J M; Milla, R; Volis, S; Rubio de Casas, R

    2018-01-01

    Changes in reproductive traits associated with domestication critically determine the evolutionary divergence between crops and their wild relatives, as well as the potential of crop plants to become feral. In this review, we examine the genetic mechanisms of plant domestication and the different types of selection involved, and describe the particularities of domestication of Mediterranean field crops with regard to their reproductive traits, showing illustrative examples. We also explore gene flow patterns between Mediterranean field crops and their wild relatives, along with their ecological, evolutionary and economic implications. Domestication entails multiple selective processes, including direct selection, environmental adaptation and developmental constraints. In contrast to clonal propagation in perennials, sexual reproduction and seed propagation in annuals and biennials have led to a distinct pathway of evolution of reproductive traits. Thus, the initial domestication and further breeding of Mediterranean field crops has brought about changes in reproductive traits, such as higher mean values and variance of seed and fruit sizes, reduced fruit and seed toxicity, non-shattering seeds and loss of seed dormancy. Evolution under domestication is not a linear process, and bi-directional gene flow between wild and crop taxa is a frequent phenomenon. Thus, hybridisation and introgression have played a very important role in determining the genetics of current cultivars. In turn, gene flow from crops to wild relatives can lead to introgression of crop genes into wild populations and potentially alter the characteristics of natural communities. In conclusion, plant evolution under domestication has not only changed the reproductive biology of cultivated taxa, its effects are multifaceted and have implications beyond agriculture. © 2017 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

  17. Examining Dark Triad traits in relation to mental toughness and physical activity in young adults

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    Sabouri S

    2016-01-01

    Full Text Available Sarah Sabouri,1 Markus Gerber,2 Dena Sadeghi Bahmani,3 Sakari Lemola,4 Peter J Clough,5 Nadeem Kalak,3 Mahin Shamsi,1 Edith Holsboer-Trachsler,3 Serge Brand2,3 1Faculty of Educational Sciences and Psychology, AllamehTabataba’i University, Tehran, Iran; 2Department of Sport, Exercise and Health, Sport Science Section, University of Basel, 3Center for Affective, Stress and Sleep Disorders, Psychiatric Clinics of the University of Basel, 4Faculty of Psychology, University of Basel, Basel, Switzerland; 5Department of Psychology, Manchester Metropolitan University, Manchester, UK Objective: The Dark Triad (DT describes a set of three closely related personality traits: Machiavellianism, narcissism, and psychopathy. Mental toughness (MT refers to a psychological construct combining confidence, commitment, control, and challenge. High MT is related to greater physical activity (PA and, relative to men, women have lower MT scores. The aims of the present study were 1 to investigate the association between DT, MT, and PA, and 2 to compare the DT, MT, and PA scores of men and women.Methods: A total of 341 adults (M=29 years; 51.6% women; range: 18–37 years took part in the study. Participants completed a series of questionnaires assessing DT, MT, and PA.Results: Machiavellianism, narcissism, and psychopathy were all significantly associated with higher MT scores (rs =0.45, 0.50, and 0.20, respectively. DT traits and MT were associated with more vigorous PA. Compared to men, women participants had lower scores for DT traits (overall score and psychopathy, while no differences were found for MT or PA in both sexes.Conclusion: DT traits, high MT, and vigorous PA are interrelated. This pattern of results might explain why, for instance, successful professional athletes can at the same time be tough and ruthless. Keywords: dark triad, mental toughness, physical activity, young adults, sex

  18. The Longitudinal Relation between Childhood Autistic Traits and Psychosexual Problems in Early Adolescence: The Tracking Adolescents' Individual Lives Survey Study

    Science.gov (United States)

    Dekker, Linda P.; Hartman, Catharina A.; van der Vegt, Esther J. M.; Verhulst, Frank C.; van Oort, Floor V. A.; Greaves-Lord, Kirstin

    2015-01-01

    Individuals with autistic traits are considered to be prone to develop psychosexual problems due to their limited social skills and insight. This study investigated the longitudinal relation between autistic traits in childhood (T1; age 10-12 years) and parent-reported psychosexual problems in early adolescence (T2; age 12-15 years). In a general…

  19. The longitudinal relation between childhood autistic traits and psychosexual problems in early adolescence : The Tracking Adolescents' Individual Lives Survey study

    NARCIS (Netherlands)

    Dekker, Linda P.; Hartman, Catharina A.; van der Vegt, Esther J. M.; Verhulst, Frank C.; van Oort, Floor V. A.; Greaves-Lord, Kirstin

    Individuals with autistic traits are considered to be prone to develop psychosexual problems due to their limited social skills and insight. This study investigated the longitudinal relation between autistic traits in childhood (T1; age 10-12 years) and parent-reported psychosexual problems in early

  20. A new method of linkage analysis using LOD scores for quantitative traits supports linkage of monoamine oxidase activity to D17S250 in the Collaborative Study on the Genetics of Alcoholism pedigrees.

    Science.gov (United States)

    Curtis, David; Knight, Jo; Sham, Pak C

    2005-09-01

    , suggesting that QMFLINK may have been able to detect a true linkage which was not picked up by the other methods. The application of model-free LOD score analysis to quantitative traits is novel and deserves further evaluation of its merits and disadvantages relative to other methods.

  1. High Density Linkage Map Construction and QTL Detection for Three Silique-Related Traits in Orychophragmus violaceus Derived Brassica napus Population

    Directory of Open Access Journals (Sweden)

    Yi Yang

    2017-09-01

    Full Text Available Seeds per silique (SS, seed weight (SW, and silique length (SL are important determinant traits of seed yield potential in rapeseed (Brassica napus L., and are controlled by naturally occurring quantitative trait loci (QTLs. Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits. Orychophragmus violaceus is a crucifer with long siliques, many SS, and heavy seeds. A novel B. napus introgression line with many SS was previously selected from multiple crosses (B. rapa ssp. chinesis × O. violaceus × B. napus. In present study, a doubled haploid (DH population with 167 lines was established from a cross between the introgression line and a line with far fewer SS, in order to detect QTLs for silique-related traits. By screening with a Brassica 60K single nucleotide polymorphism (SNP array, a high-density linkage map consisting of 1,153 bins and spanning a cumulative length of 2,209.1 cM was constructed, using 12,602 high-quality polymorphic SNPs in the DH population. The average recombination bin densities of the A and C subgenomes were 1.7 and 2.4 cM, respectively. 45 QTLs were identified for the three traits in all, which explained 4.0–34.4% of the total phenotypic variation; 20 of them were integrated into three unique QTLs by meta-analysis. These unique QTLs revealed a significant positive correlation between SS and SL and a significant negative correlation between SW and SS, and were mapped onto the linkage groups A05, C08, and C09. A trait-by-trait meta-analysis revealed eight, four, and seven consensus QTLs for SS, SW, and SL, respectively, and five major QTLs (cqSS.A09b, cqSS.C09, cqSW.A05, cqSW.C09, and cqSL.C09 were identified. Five, three, and four QTLs for SS, SW, and SL, respectively, might be novel QTLs because of the existence of alien genetic loci for these traits in the alien introgression. Thirty-eight candidate genes underlying nine QTLs for silique-related

  2. Methylomic analysis of monozygotic twins discordant for autism spectrum disorder and related behavioural traits.

    Science.gov (United States)

    Wong, C C Y; Meaburn, E L; Ronald, A; Price, T S; Jeffries, A R; Schalkwyk, L C; Plomin, R; Mill, J

    2014-04-01

    Autism spectrum disorder (ASD) defines a group of common, complex neurodevelopmental disorders. Although the aetiology of ASD has a strong genetic component, there is considerable monozygotic (MZ) twin discordance indicating a role for non-genetic factors. Because MZ twins share an identical DNA sequence, disease-discordant MZ twin pairs provide an ideal model for examining the contribution of environmentally driven epigenetic factors in disease. We performed a genome-wide analysis of DNA methylation in a sample of 50 MZ twin pairs (100 individuals) sampled from a representative population cohort that included twins discordant and concordant for ASD, ASD-associated traits and no autistic phenotype. Within-twin and between-group analyses identified numerous differentially methylated regions associated with ASD. In addition, we report significant correlations between DNA methylation and quantitatively measured autistic trait scores across our sample cohort. This study represents the first systematic epigenomic analyses of MZ twins discordant for ASD and implicates a role for altered DNA methylation in autism.

  3. Stability of agronomic and yield related traits of Jatropha curcas accessions raised from cuttings

    Science.gov (United States)

    Mat, Nurul Hidayah Che; Yaakob, Zahira; Ratnam, Wickneswari

    2016-11-01

    Monitoring stability of agronomic and yield related traits is important for prediction of crop yields. This study was a latter study for the evaluation of 295 J. curcas individuals representing 21 accessions from eight countries at Biodiesel Research Station of Universiti Kebangsaan Malaysia, Kuala Pilah planted in December 2012. In this study, 183 J. curcas individuals were selected randomly from the population and their growth performance evaluated from December 2013 to December 2014. All the individual plants were raised from cuttings. The yield related data were recorded periodically and performance of each accession was analyzed using Statistical Analysis System (SAS) 9.4. Five traits which were number of fruits per plant (NFPP), number of fruits per inflorescence (NFPI), hundred seed weight (g) (HSW), number of seeds per plant (NSPP) and yield per plant (g) (YPP) showed significant differences among the accessions after two years of planting. Maximum values for each trait were 208 cm for plant height (PH), 31 for number of branches per plant (BPP), 115 for number of inflorescence per plant (NIPP), 582 for NFPP, 7 for NFPI, 307 for number of flowers per inflorescence (NFI), 17 for number of female flowers per inflorescence (NFFPI), 91.6 g for HSW, 1647.1 for NSPP and 927.6 g for YPP. Most of the plants which had performed well in the first year were among the best performers in the second year.

  4. Age-related reduced prefrontal-amygdala structural connectivity is associated with lower trait anxiety.

    Science.gov (United States)

    Clewett, David; Bachman, Shelby; Mather, Mara

    2014-07-01

    A current neuroanatomical model of anxiety posits that greater structural connectivity between the amygdala and ventral prefrontal cortex (vPFC) facilitates regulatory control over the amygdala and helps reduce anxiety. However, some neuroimaging studies have reported contradictory findings, demonstrating a positive rather than negative association between trait anxiety and amygdala-vPFC white matter integrity. To help reconcile these findings, we tested the regulatory hypothesis of anxiety circuitry using aging as a model of white matter decline in the amygdala-vPFC pathway. We used probabilistic tractography to trace connections between the amygdala and vPFC in 21 younger, 18 middle-aged, and 15 healthy older adults. The resulting tract estimates were used to extract 3 indices of white-matter integrity: fractional anisotropy (FA), radial diffusivity (RD), and axial diffusivity (AD). The relationship between these amygdala-vPFC structural connectivity measures and age and State-Trait Anxiety Inventory (STAI) scores were assessed. The tractography results revealed age-related decline in the FA (p = .005) and radial diffusivity (p = .002) of the amygdala-vPFC pathway. Contrary to the regulatory hypothesis, we found a positive rather than negative association between trait anxiety and right amygdala-vPFC FA (p = .01). These findings argue against the notion that greater amygdala-vPFC structural integrity facilitates better anxiety outcomes in healthy adults. Instead, our results suggest that white matter degeneration in this network relates to lower anxiety in older adults.

  5. Age-related reduced prefrontal-amygdala structural connectivity is associated with lower trait anxiety

    Science.gov (United States)

    Clewett, David; Bachman, Shelby; Mather, Mara

    2014-01-01

    Objective A current neuroanatomical model of anxiety posits that greater structural connectivity between the amygdala and ventral prefrontal cortex (vPFC) facilitates regulatory control over the amygdala and helps reduce anxiety. However, some neuroimaging studies have reported contradictory findings, demonstrating a positive rather than negative association between trait anxiety and amygdala-vPFC white matter integrity. To help reconcile these findings, we tested the regulatory hypothesis of anxiety circuitry using aging as a model of white matter decline in the amygdala-vPFC pathway. Methods We used probabilistic tractography to trace connections between the amygdala and vPFC in 21 younger, 18 middle-aged, and 15 healthy older adults. The resulting tract estimates were used to extract three indices of white-matter integrity: fractional anisotropy (FA), radial diffusivity (RD) and axial diffusivity (AD). The relationship between these amygdala-vPFC structural connectivity measures and age and State-Trait Anxiety Inventory (STAI) scores were assessed. Results The tractography results revealed age-related decline in the FA (p = .005) and radial diffusivity (p = .002) of the amygdala-vPFC pathway. Contrary to the regulatory hypothesis, we found a positive rather than negative association between trait anxiety and right amygdala-vPFC FA (p = .01). Conclusion These findings argue against the notion that greater amygdala-vPFC structural integrity facilitates better anxiety outcomes in healthy adults. Instead, our results suggest that white matter degeneration in this network relates to lower anxiety in older adults. PMID:24635708

  6. Roles in violent interactions in early adolescence: Relations with personality traits, friendship and gender

    Directory of Open Access Journals (Sweden)

    Čolović Petar

    2015-01-01

    Full Text Available The aim of this study is to examine the relations between roles in violent interactions and personality traits (congruent to dimensions of Big Seven lexical model, number of friends, and gender. The study was conducted on a sample of 1095 elementary school students from Serbia (51.4% female, aged 11-14. The results revealed that membership in the victims group corresponds to smaller number of friends, low Extraversion, high Neuroticism and Conscientiousness and male gender, while higher Aggressiveness, Negative and Positive Valence, lower Neuroticism, and male gender increase the odds of membership in the bullies group. The role of bully-victims corresponds to smaller number of friends, higher Negative Valence and Neuroticism, and male gender. The results point to differences between roles in violent interaction with regard to patterns of personality traits and social behavior. [Projekat Ministarstva nauke Republike Srbije, br. ON179006: Psychological foundations of mental health: hereditary and environmental factors

  7. Phenotypic Microdiversity and Phylogenetic Signal Analysis of Traits Related to Social Interaction in Bacillus spp. from Sediment Communities.

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    Rodríguez-Torres, María Dolores; Islas-Robles, África; Gómez-Lunar, Zulema; Delaye, Luis; Hernández-González, Ismael; Souza, Valeria; Travisano, Michael; Olmedo-Álvarez, Gabriela

    2017-01-01

    Understanding the relationship between phylogeny and predicted traits is important to uncover the dimension of the predictive power of a microbial composition approach. Numerous works have addressed the taxonomic composition of bacteria in communities, but little is known about trait heterogeneity in closely related bacteria that co-occur in communities. We evaluated a sample of 467 isolates from the Churince water system of the Cuatro Cienegas Basin (CCB), enriched for Bacillus spp. The 16S rRNA gene revealed a random distribution of taxonomic groups within this genus among 11 sampling sites. A subsample of 141 Bacillus spp. isolates from sediment, with seven well-represented species was chosen to evaluate the heterogeneity and the phylogenetic signal of phenotypic traits that are known to diverge within small clades, such as substrate utilization, and traits that are conserved deep in the lineage, such as prototrophy, swarming and biofilm formation. We were especially interested in evaluating social traits, such as swarming and biofilm formation, for which cooperation is needed to accomplish a multicellular behavior and for which there is little information from natural communities. The phylogenetic distribution of traits, evaluated by the Purvis and Fritz's D statistics approached a Brownian model of evolution. Analysis of the phylogenetic relatedness of the clusters of members sharing the trait using