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Sample records for head rot qtl

  1. QTL mapping of fruit rot resistance to the plant pathogen Phytophthora capsici in a recombinant inbred line Capsicum annuum population.

    Science.gov (United States)

    Naegele, R P; Ashrafi, H; Hill, T A; Chin-Wo, S Reyes; Van Deynze, A E; Hausbeck, M K

    2014-05-01

    Phytophthora capsici is an important pepper (Capsicum annuum) pathogen causing fruit and root rot, and foliar blight in field and greenhouse production. Previously, an F6 recombinant inbred line population was evaluated for fruit rot susceptibility. Continuous variation among lines and partial and isolate-specific resistance were found. In this study, Phytophthora fruit rot resistance was mapped in the same F6 population between Criollo del Morelos 334 (CM334), a landrace from Mexico, and 'Early Jalapeno' using a high-density genetic map. Isolate-specific resistance was mapped independently in 63 of the lines evaluated and the two parents. Heritability of the resistance for each isolate at 3 and 5 days postinoculation (dpi) was high (h(2) = 0.63 to 0.68 and 0.74 to 0.83, respectively). Significant additive and epistatic quantitative trait loci (QTL) were identified for resistance to isolates OP97 and 13709 (3 and 5 dpi) and 12889 (3 dpi only). Mapping of fruit traits showed potential linkage with few disease resistance QTL. The partial fruit rot resistance from CM334 suggests that this may not be an ideal source for fruit rot resistance in pepper.

  2. Association mapping in sunflower for sclerotinia head rot resistance

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    Fusari Corina M

    2012-06-01

    Full Text Available Abstract Background Sclerotinia Head Rot (SHR is one of the most damaging diseases of sunflower in Europe, Argentina, and USA, causing average yield reductions of 10 to 20 %, but leading to total production loss under favorable environmental conditions for the pathogen. Association Mapping (AM is a promising choice for Quantitative Trait Locus (QTL mapping, as it detects relationships between phenotypic variation and gene polymorphisms in existing germplasm without development of mapping populations. This article reports the identification of QTL for resistance to SHR based on candidate gene AM. Results A collection of 94 sunflower inbred lines were tested for SHR under field conditions using assisted inoculation with the fungal pathogen Sclerotinia sclerotiorum. Given that no biological mechanisms or biochemical pathways have been clearly identified for SHR, 43 candidate genes were selected based on previous transcript profiling studies in sunflower and Brassica napus infected with S. sclerotiorum. Associations among SHR incidence and haplotype polymorphisms in 16 candidate genes were tested using Mixed Linear Models (MLM that account for population structure and kinship relationships. This approach allowed detection of a significant association between the candidate gene HaRIC_B and SHR incidence (P  Conclusions These results suggest that AM will be useful in dissecting other complex traits in sunflower, thus providing a valuable tool to assist in crop breeding.

  3. The Identification of Two Head Smut Resistance-Related QTL in Maize by the Joint Approach of Linkage Mapping and Association Analysis.

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    Yong-xiang Li

    Full Text Available Head smut, caused by the fungus Sphacelotheca reiliana (Kühn Clint, is a devastating threat to maize production. In this study, QTL mapping of head smut resistance was performed using a recombinant inbred line (RIL population from a cross between a resistant line "QI319" and a susceptible line "Huangzaosi" (HZS with a genetic map constructed from genotyping-by-sequencing (GBS data and composed of 1638 bin markers. Two head smut resistance QTL were identified, located on Chromosome 2 (q2.09HR and Chromosome 5 (q5.03HR, q2.09HR is co-localized with a previously reported QTL for head smut resistance, and the effect of q5.03HR has been validated in backcross populations. It was also observed that pyramiding the resistant alleles of both QTL enhanced the level of resistance to head smut. A genome-wide association study (GWAS using 277 diverse inbred lines was processed to validate the mapped QTL and to identify additional head smut resistance associations. A total of 58 associated SNPs were detected, which were distributed in 31 independent regions. SNPs with significant association to head smut resistance were detected within the q2.09HR and q5.03HR regions, confirming the linkage mapping results. It was also observed that both additive and epistastic effects determine the genetic architecture of head smut resistance in maize. As shown in this study, the combined strategy of linkage mapping and association analysis is a powerful approach in QTL dissection for disease resistance in maize.

  4. Genetic Analysis of Fusarium Head Blight Resistance in CIMMYT Bread Wheat Line C615 Using Traditional and Conditional QTL Mapping.

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    Yi, Xin; Cheng, Jingye; Jiang, Zhengning; Hu, Wenjing; Bie, Tongde; Gao, Derong; Li, Dongsheng; Wu, Ronglin; Li, Yuling; Chen, Shulin; Cheng, Xiaoming; Liu, Jian; Zhang, Yong; Cheng, Shunhe

    2018-01-01

    Fusarium head blight (FHB) is a destructive wheat disease present throughout the world, and host resistance is an effective and economical strategy used to control FHB. Lack of adequate resistance resource is still a main bottleneck for FHB genetics and wheat breeding research. The synthetic-derived bread wheat line C615, which does not carry the Fhb1 gene, is a promising source of FHB resistance for breeding. A population of 198 recombinant inbred lines (RILs) produced by crossing C615 with the susceptible cultivar Yangmai 13 was evaluated for FHB response using point and spray inoculations. As the disease phenotype is frequently complicated by other agronomic traits, we used both traditional and multivariate conditional QTL mapping approaches to investigate the genetic relationships (at the individual QTL level) between FHB resistance and plant height (PH), spike compactness (SC), and days to flowering (FD). A linkage map was constructed from 3,901 polymorphic SNP markers, which covered 2,549.2 cM. Traditional and conditional QTL mapping analyses found 13 and 22 QTL for FHB, respectively; 10 were identified by both methods. Among these 10, three QTL from C615 were detected in multiple years; these QTL were located on chromosomes 2AL, 2DS, and 2DL. Conditional QTL mapping analysis indicated that, at the QTL level, SC strongly influenced FHB in point inoculation; whereas PH and SC contributed more to FHB than did FD in spray inoculation. The three stable QTL ( QFhbs-jaas.2AL, QFhbp-jaas.2DS , and QFhbp-jaas.2DL ) for FHB were partly affected by or were independent of the three agronomic traits. The QTL detected in this study improve our understanding of the genetic relationships between FHB response and related traits at the QTL level and provide useful information for marker-assisted selection for the improvement of FHB resistance in breeding.

  5. Genetic Analysis of Fusarium Head Blight Resistance in CIMMYT Bread Wheat Line C615 Using Traditional and Conditional QTL Mapping

    Science.gov (United States)

    Yi, Xin; Cheng, Jingye; Jiang, Zhengning; Hu, Wenjing; Bie, Tongde; Gao, Derong; Li, Dongsheng; Wu, Ronglin; Li, Yuling; Chen, Shulin; Cheng, Xiaoming; Liu, Jian; Zhang, Yong; Cheng, Shunhe

    2018-01-01

    Fusarium head blight (FHB) is a destructive wheat disease present throughout the world, and host resistance is an effective and economical strategy used to control FHB. Lack of adequate resistance resource is still a main bottleneck for FHB genetics and wheat breeding research. The synthetic-derived bread wheat line C615, which does not carry the Fhb1 gene, is a promising source of FHB resistance for breeding. A population of 198 recombinant inbred lines (RILs) produced by crossing C615 with the susceptible cultivar Yangmai 13 was evaluated for FHB response using point and spray inoculations. As the disease phenotype is frequently complicated by other agronomic traits, we used both traditional and multivariate conditional QTL mapping approaches to investigate the genetic relationships (at the individual QTL level) between FHB resistance and plant height (PH), spike compactness (SC), and days to flowering (FD). A linkage map was constructed from 3,901 polymorphic SNP markers, which covered 2,549.2 cM. Traditional and conditional QTL mapping analyses found 13 and 22 QTL for FHB, respectively; 10 were identified by both methods. Among these 10, three QTL from C615 were detected in multiple years; these QTL were located on chromosomes 2AL, 2DS, and 2DL. Conditional QTL mapping analysis indicated that, at the QTL level, SC strongly influenced FHB in point inoculation; whereas PH and SC contributed more to FHB than did FD in spray inoculation. The three stable QTL (QFhbs-jaas.2AL, QFhbp-jaas.2DS, and QFhbp-jaas.2DL) for FHB were partly affected by or were independent of the three agronomic traits. The QTL detected in this study improve our understanding of the genetic relationships between FHB response and related traits at the QTL level and provide useful information for marker-assisted selection for the improvement of FHB resistance in breeding. PMID:29780395

  6. Integrated Metabolo-Transcriptomics Reveals Fusarium Head Blight Candidate Resistance Genes in Wheat QTL-Fhb2.

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    Dhananjay Dhokane

    Full Text Available Fusarium head blight (FHB caused by Fusarium graminearum not only causes severe losses in yield, but also reduces quality of wheat grain by accumulating mycotoxins. Breeding for host plant resistance is considered as the best strategy to manage FHB. Resistance in wheat to FHB is quantitative in nature, involving cumulative effects of many genes governing resistance. The poor understanding of genetics and lack of precise phenotyping has hindered the development of FHB resistant cultivars. Though more than 100 QTLs imparting FHB resistance have been reported, none discovered the specific genes localized within the QTL region, nor the underlying mechanisms of resistance.In our study recombinant inbred lines (RILs carrying resistant (R-RIL and susceptible (S-RIL alleles of QTL-Fhb2 were subjected to metabolome and transcriptome profiling to discover the candidate genes. Metabolome profiling detected a higher abundance of metabolites belonging to phenylpropanoid, lignin, glycerophospholipid, flavonoid, fatty acid, and terpenoid biosynthetic pathways in R-RIL than in S-RIL. Transcriptome analysis revealed up-regulation of several receptor kinases, transcription factors, signaling, mycotoxin detoxification and resistance related genes. The dissection of QTL-Fhb2 using flanking marker sequences, integrating metabolomic and transcriptomic datasets, identified 4-Coumarate: CoA ligase (4CL, callose synthase (CS, basic Helix Loop Helix (bHLH041 transcription factor, glutathione S-transferase (GST, ABC transporter-4 (ABC4 and cinnamyl alcohol dehydrogenase (CAD as putative resistance genes localized within the QTL-Fhb2 region.Some of the identified genes within the QTL region are associated with structural resistance through cell wall reinforcement, reducing the spread of pathogen through rachis within a spike and few other genes that detoxify DON, the virulence factor, thus eventually reducing disease severity. In conclusion, we report that the wheat

  7. Fine mapping of multiple QTL using combined linkage and linkage disequilibrium mapping – A comparison of single QTL and multi QTL methods

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    Meuwissen Theo HE

    2007-04-01

    Full Text Available Abstract Two previously described QTL mapping methods, which combine linkage analysis (LA and linkage disequilibrium analysis (LD, were compared for their ability to detect and map multiple QTL. The methods were tested on five different simulated data sets in which the exact QTL positions were known. Every simulated data set contained two QTL, but the distances between these QTL were varied from 15 to 150 cM. The results show that the single QTL mapping method (LDLA gave good results as long as the distance between the QTL was large (> 90 cM. When the distance between the QTL was reduced, the single QTL method had problems positioning the two QTL and tended to position only one QTL, i.e. a "ghost" QTL, in between the two real QTL positions. The multi QTL mapping method (MP-LDLA gave good results for all evaluated distances between the QTL. For the large distances between the QTL (> 90 cM the single QTL method more often positioned the QTL in the correct marker bracket, but considering the broader likelihood peaks of the single point method it could be argued that the multi QTL method was more precise. Since the distances were reduced the multi QTL method was clearly more accurate than the single QTL method. The two methods combine well, and together provide a good tool to position single or multiple QTL in practical situations, where the number of QTL and their positions are unknown.

  8. Serious limitations of the QTL/Microarray approach for QTL gene discovery

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    Warden Craig H

    2010-07-01

    Full Text Available Abstract Background It has been proposed that the use of gene expression microarrays in nonrecombinant parental or congenic strains can accelerate the process of isolating individual genes underlying quantitative trait loci (QTL. However, the effectiveness of this approach has not been assessed. Results Thirty-seven studies that have implemented the QTL/microarray approach in rodents were reviewed. About 30% of studies showed enrichment for QTL candidates, mostly in comparisons between congenic and background strains. Three studies led to the identification of an underlying QTL gene. To complement the literature results, a microarray experiment was performed using three mouse congenic strains isolating the effects of at least 25 biometric QTL. Results show that genes in the congenic donor regions were preferentially selected. However, within donor regions, the distribution of differentially expressed genes was homogeneous once gene density was accounted for. Genes within identical-by-descent (IBD regions were less likely to be differentially expressed in chromosome 2, but not in chromosomes 11 and 17. Furthermore, expression of QTL regulated in cis (cis eQTL showed higher expression in the background genotype, which was partially explained by the presence of single nucleotide polymorphisms (SNP. Conclusions The literature shows limited successes from the QTL/microarray approach to identify QTL genes. Our own results from microarray profiling of three congenic strains revealed a strong tendency to select cis-eQTL over trans-eQTL. IBD regions had little effect on rate of differential expression, and we provide several reasons why IBD should not be used to discard eQTL candidates. In addition, mismatch probes produced false cis-eQTL that could not be completely removed with the current strains genotypes and low probe density microarrays. The reviewed studies did not account for lack of coverage from the platforms used and therefore removed genes

  9. Rhizoctonia root rot (Rhizoctoni solani K ü h n of sugar beet in province Vojvodina

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    Stojšin Vera B.

    2006-01-01

    Full Text Available Sugar beet root rot appears regularly each year, but its intensity depends on agro ecological conditions. The predominant causers of root rot in Vojvodina are fungi from Fusarium genus and species Macrophomina phaseolina. Over the last couple of years, more intense occurrence of Rhizoctonia root rot has been observed. Rhizoctonia solani, the causal agent of root rot is present in sugar beet fields. During 2000-2005, on the territory of Vojvodina, the frequency of Rhizoctonia solani in phytopathological isolations from rotted sugar beet roots was between 0,0-18,2%. The intensity of the disease depends on localities, agro ecological conditions and genotypes. Symptoms of Rhizoctonia root rot were registered at some localities in all regions of Vojvodina: Srem, Banat and Bačka. The disease appearance is above all local. It occurs in small patches, on heavy, non-structured soil and on depressed wet parts of plots. Individual diseased plants can be found during July. Brown rot appears on sugar beet roots, with dried tissue on surface, which is present on the tail as well as on the middle part and the head of root. Tissues with described symptoms are deeper regarding the healthy part of root. On vertical root section, the necrotic changes are clearly visible comparing to tissue section without symptoms. The heavily infected tissue forms fissures on roots in most cases. Besides the above-mentioned symptoms on roots, the plant wilting and leaf handle necrosis as well as leaf dying are also observed. When rot spreads to the whole root head, plants quickly die.

  10. Identification of QTLs for resistance to sclerotinia stem rot and BnaC.IGMT5.a as a candidate gene of the major resistant QTL SRC6 in Brassica napus.

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    Jian Wu

    Full Text Available Stem rot caused by Sclerotinia sclerotiorum in many important dicotyledonous crops, including oilseed rape (Brassica napus, is one of the most devastating fungal diseases and imposes huge yield loss each year worldwide. Currently, breeding for Sclerotinia resistance in B. napus, as in other crops, can only rely on germplasms with quantitative resistance genes. Thus, the identification of quantitative trait locus (QTL for S. sclerotiorum resistance/tolerance in this crop holds immediate promise for the genetic improvement of the disease resistance. In this study, ten QTLs for stem resistance (SR at the mature plant stage and three QTLs for leaf resistance (LR at the seedling stage in multiple environments were mapped on nine linkage groups (LGs of a whole genome map for B. napus constructed with SSR markers. Two major QTLs, LRA9 on LG A9 and SRC6 on LG C6, were repeatedly detected across all environments and explained 8.54-15.86% and 29.01%-32.61% of the phenotypic variations, respectively. Genotypes containing resistant SRC6 or LRA9 allele showed a significant reduction in disease lesion after pathogen infection. Comparative mapping with Arabidopsis and data mining from previous gene profiling experiments identified that the Arabidopsis homologous gene of IGMT5 (At1g76790 was related to the SRC6 locus. Four copies of the IGMT5 gene in B. napus were isolated through homologous cloning, among which, only BnaC.IGMT5.a showed a polymorphism between parental lines and can be associated with the SRC6. Furthermore, two parental lines exhibited a differential expression pattern of the BnaC.IGMT5.a gene in responding to pathogen inoculation. Thus, our data suggested that BnaC.IGMT5.a was very likely a candidate gene of this major resistance QTL.

  11. Root rots

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    Kathryn Robbins; Philip M. Wargo

    1989-01-01

    Root rots of central hardwoods are diseases caused by fungi that infect and decay woody roots and sometimes also invade the butt portion of the tree. By killing and decaying roots, root rotting fungi reduce growth, decrease tree vigor, and cause windthrow and death. The most common root diseases of central hardwoods are Armillaria root rot, lnonotus root rot, and...

  12. MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments

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    Charcosset Alain

    2007-02-01

    Full Text Available Abstract Background Integration of multiple results from Quantitative Trait Loci (QTL studies is a key point to understand the genetic determinism of complex traits. Up to now many efforts have been made by public database developers to facilitate the storage, compilation and visualization of multiple QTL mapping experiment results. However, studying the congruency between these results still remains a complex task. Presently, the few computational and statistical frameworks to do so are mainly based on empirical methods (e.g. consensus genetic maps are generally built by iterative projection. Results In this article, we present a new computational and statistical package, called MetaQTL, for carrying out whole-genome meta-analysis of QTL mapping experiments. Contrary to existing methods, MetaQTL offers a complete statistical process to establish a consensus model for both the marker and the QTL positions on the whole genome. First, MetaQTL implements a new statistical approach to merge multiple distinct genetic maps into a single consensus map which is optimal in terms of weighted least squares and can be used to investigate recombination rate heterogeneity between studies. Secondly, assuming that QTL can be projected on the consensus map, MetaQTL offers a new clustering approach based on a Gaussian mixture model to decide how many QTL underly the distribution of the observed QTL. Conclusion We demonstrate using simulations that the usual model choice criteria from mixture model literature perform relatively well in this context. As expected, simulations also show that this new clustering algorithm leads to a reduction in the length of the confidence interval of QTL location provided that across studies there are enough observed QTL for each underlying true QTL location. The usefulness of our approach is illustrated on published QTL detection results of flowering time in maize. Finally, MetaQTL is freely available at http://bioinformatics.org/mqtl.

  13. Molecular mapping of QTLs for resistance to Gibberella ear rot, in corn, caused by Fusarium graminearum.

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    Ali, M Liakat; Taylor, Jeff H; Jie, Liu; Sun, Genlou; William, Manilal; Kasha, Ken J; Reid, Lana M; Pauls, K Peter

    2005-06-01

    Gibberella ear rot, caused by the fungus Fusarium graminearum Schwabe, is a serious disease of corn (Zea mays) grown in northern climates. Infected corn is lower yielding and contains toxins that are dangerous to livestock and humans. Resistance to ear rot in corn is quantitative, specific to the mode of fungal entry (silk channels or kernel wounds), and highly influenced by the environment. Evaluations of ear rot resistance are complex and subjective; and they need to be repeated over several years. All of these factors have hampered attempts to develop F. graminearum resistant corn varieties. The aim of this study was to identify molecular markers linked to the genes for resistance to Gibberella ear rot. A recombinant inbred (RI) population, produced from a cross between a Gibberella ear rot resistant line (CO387) and a susceptible line (CG62), was field-inoculated and scored for Gibberella ear rot symptoms in the F4, F6, and F7 generations. The distributions of disease scores were continuous, indicating that resistance is probably conditioned by multiple loci. A molecular linkage map, based on segregation in the F5 RI population, contained 162 markers distributed over 10 linkage groups and had a total length of 2237 cM with an average distance between markers of 13.8 cM. Composite interval mapping identified 11 quantitative trait loci (QTLs) for Gibberella ear rot resistance following silk inoculation and 18 QTLs following kernel inoculation in 4 environments that accounted for 6.7%-35% of the total phenotypic variation. Only 2 QTLs (on linkage group 7) were detected in more than 1 test for silk resistance, and only 1 QTL (on linkage group 5) was detected in more than 1 test for kernel resistance, confirming the strong influence of the environment on these traits. The majority of the favorable alleles were derived from the resistant parent (CO387). The germplasm and markers for QTLs with significant phenotypic effects may be useful for marker-assisted selection

  14. CaDMR1 Cosegregates with QTL Pc5.1 for Resistance to Phytophthora capsici in Pepper (Capsicum annuum

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    William Z. Rehrig

    2014-07-01

    Full Text Available A major problem for the pepper ( industry is the root rot disease caused by (, to which all commercial varieties suffer yield losses despite good management practices and available landraces with high levels of resistance. A high-density map with 3887 markers was generated in a set of recombinant inbred lines (RIL derived from the highly resistant accession Criollo de Morelos-334 and Early Jalapeño. These lines have been systematically screened for resistance against a set of isolates collected from Mexico, New Mexico, New Jersey, California, Michigan and Tennessee. Quantitative trait loci (QTL associated with effective resistance across isolates have been identified and validated with SNP markers across additional segregating populations. By leveraging transcriptomic and genomic information, we describe , a homoserine kinase (HSK, as a candidate gene responsible for the major QTL on chromosome P5 for resistance to . SNP markers for the resistant allele were validated to facilitate gene pyramiding schemes for recurrent selection in pepper.

  15. Statistical properties of interval mapping methods on quantitative trait loci location: impact on QTL/eQTL analyses

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    Wang Xiaoqiang

    2012-04-01

    Full Text Available Abstract Background Quantitative trait loci (QTL detection on a huge amount of phenotypes, like eQTL detection on transcriptomic data, can be dramatically impaired by the statistical properties of interval mapping methods. One of these major outcomes is the high number of QTL detected at marker locations. The present study aims at identifying and specifying the sources of this bias, in particular in the case of analysis of data issued from outbred populations. Analytical developments were carried out in a backcross situation in order to specify the bias and to propose an algorithm to control it. The outbred population context was studied through simulated data sets in a wide range of situations. The likelihood ratio test was firstly analyzed under the "one QTL" hypothesis in a backcross population. Designs of sib families were then simulated and analyzed using the QTL Map software. On the basis of the theoretical results in backcross, parameters such as the population size, the density of the genetic map, the QTL effect and the true location of the QTL, were taken into account under the "no QTL" and the "one QTL" hypotheses. A combination of two non parametric tests - the Kolmogorov-Smirnov test and the Mann-Whitney-Wilcoxon test - was used in order to identify the parameters that affected the bias and to specify how much they influenced the estimation of QTL location. Results A theoretical expression of the bias of the estimated QTL location was obtained for a backcross type population. We demonstrated a common source of bias under the "no QTL" and the "one QTL" hypotheses and qualified the possible influence of several parameters. Simulation studies confirmed that the bias exists in outbred populations under both the hypotheses of "no QTL" and "one QTL" on a linkage group. The QTL location was systematically closer to marker locations than expected, particularly in the case of low QTL effect, small population size or low density of markers, i

  16. QTL analysis of Fusarium root rot resistance in an Andean x Middle American common bean RIL population

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    Aims Fusarium root rot (FRR) is a soil-borne disease that constrains common bean (Phaseolus vulgaris L.) production. FRR causal pathogens include clade 2 members of the Fusarium solani species complex. Here we characterize common bean reaction to four Fusarium species and identify genomic regions as...

  17. Genetic architecture of fusarium head blight resistance in four winter triticale populations.

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    Kalih, R; Maurer, H P; Miedaner, T

    2015-03-01

    Fusarium head blight (FHB) is a devastating disease that causes significant reductions in yield and quality in wheat, rye, and triticale. In triticale, knowledge of the genetic architecture of FHB resistance is missing but essential due to modern breeding requirements. In our study, four doubled-haploid triticale populations (N=120 to 200) were evaluated for resistance to FHB caused by artificial inoculation with Fusarium culmorum in four environments. DArT markers were used to genotype triticale populations. Seventeen quantitative trait loci (QTL) for FHB resistance were detected across all populations; six of them were derived from rye genome and located on chromosomes 4R, 5R, and 7R, which are here reported for the first time. The total cross-validated ratio of the explained phenotypic variance for all detected QTL in each population was 41 to 68%. In all, 17 QTL for plant height and 18 QTL for heading stage were also detected across all populations; 3 and 5 of them, respectively, were overlapping with QTL for FHB. In conclusion, FHB resistance in triticale is caused by a multitude of QTL, and pyramiding them contributes to higher resistance.

  18. QTLs for heading date and plant height under multiple environments in rice.

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    Han, Zhongmin; Hu, Wei; Tan, Cong; Xing, Yongzhong

    2017-02-01

    Both heading date and plant height are important traits related to grain yield in rice. In this study, a recombinant inbred lines (RILs) population was used to map quantitative trait loci (QTLs) for both traits under 3 long-day (LD) environments and 1 short-day (SD) environment. A total of eight QTLs for heading date and three QTLs for plant height were detected by composite interval mapping under LD conditions. Additional one QTL for heading date and three QTLs for plant height were identified by Two-QTL model under LD conditions. Among them, major QTLs qHd7.1, qHd7.2 and qHd8 for heading date, and qPh1 and qPh7.1 for plant height were commonly detected. qHd7.1 and qHd7.2 were mapped to small regions of less than 1 cM. Genome position comparison of previously cloned genes with QTLs detected in this study revealed that qHd5 and qPh3.1 were two novel QTLs. The alleles of these QTLs increasing trait values were dispersed in both parents, which well explained the transgressive segregation observed in this population. In addition, the interaction between qHd7.1 and qHd8 was detected under all LD conditions. Multiple-QTL model analysis revealed that all QTLs and their interactions explained over 80% of heading date variation and 50% of plant height variation. Two heading date QTLs were detected under SD condition. Of them, qHd10 were commonly identified under LD condition. The difference in QTL detection between LD and SD conditions indicated most heading date QTLs are sensitive to photoperiod. These findings will benefit breeding design for heading date and plant height in rice.

  19. QTL list: QTL1 [PGDBj Registered plant list, Marker list, QTL list, Plant DB link and Genome analysis methods[Archive

    Lifescience Database Archive (English)

    Full Text Available QT58275 Brassica oleracea Brassicaceae QTL1 fusarium resistance fusarium wilt resi...stance trait, Foc-Bo1 (fusarium wilt-resistant) gene (QTL2) 3 ... LG_O04 ... 42.2 2.06 ... 10.1007/s11032-011-9665-8 ...

  20. QTL list: QTL2 [PGDBj Registered plant list, Marker list, QTL list, Plant DB link and Genome analysis methods[Archive

    Lifescience Database Archive (English)

    Full Text Available QT58276 Brassica oleracea Brassicaceae QTL2 fusarium resistance fusarium wilt resi...stance trait, Foc-Bo1 (fusarium wilt-resistant) gene (QTL2) 3 ... LG_O07 ... 30.1 19.5 ... 10.1007/s11032-011-9665-8 ...

  1. Suppression of crown and root rot of wheat by the rhizobacterium Paenibacillus polymyxa

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    Lamia LOUNACI

    2017-01-01

    Full Text Available A seedling bioassay was developed for screening a wheat root-associated rhizobacterial strain of Paenibacillus polymyxa for ability to suppress crown and root rot pathogens of wheat. The primary aim was to evaluate the ability of P. polymyxa to suppress Fusarium graminearum, F. culmorum, F. verticillioides and Microdochium nivale, the fungal pathogens responsible for Fusarium crown and root rot and head blight of wheat in Algeria. Bioassays conducted under controlled conditions indicated that seed treatments with P. polymyxa strain SGK2 significantly reduced disease symptoms caused by all four fungal pathogens. Plant growth promotion (increased shoot and root dry weights, however, depended on the pathogen tested. Our results indicate that seed treatments with a biocontrol agent could be an additional strategy for management of wheat crown and root rot pathogens.

  2. Spatial Heterogeneity of SOM Concentrations Associated with White-rot Versus Brown-rot Wood Decay.

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    Bai, Zhen; Ma, Qiang; Dai, Yucheng; Yuan, Haisheng; Ye, Ji; Yu, Wantai

    2017-10-23

    White- and brown-rot fungal decay via distinct pathways imparts characteristic molecular imprints on decomposing wood. However, the effect that a specific wood-rotting type of fungus has on proximal soil organic matter (SOM) accumulation remains unexplored. We investigated the potential influence of white- and brown-rot fungi-decayed Abies nephrolepis logs on forest SOM stocks (i.e., soil total carbon (C) and nitrogen (N)) and the concentrations of amino sugars (microbial necromass) at different depths and horizontal distances from decaying woody debris. The brown-rot fungal wood decay resulted in higher concentrations of soil C and N and a greater increase in microbial necromass (i.e., 1.3- to 1.7-fold greater) than the white-rot fungal wood decay. The white-rot sets were accompanied by significant differences in the proportions of the bacterial residue index (muramic acid%) with soil depth; however, the brown-rot-associated soils showed complementary shifts, primarily in fungal necromass, across horizontal distances. Soil C and N concentrations were significantly correlated with fungal rather than bacterial necromass in the brown-rot systems. Our findings confirmed that the brown-rot fungi-dominated degradation of lignocellulosic residues resulted in a greater SOM buildup than the white-rot fungi-dominated degradation.

  3. Bayesian multi-QTL mapping for growth curve parameters

    DEFF Research Database (Denmark)

    Heuven, Henri C M; Janss, Luc L G

    2010-01-01

    % for ASYM and SCAL while the heritability for XMID was approximately 24%. The genome wide scan revealed four QTLs affecting ASYM, one QTL affecting XMID and four QTLs affecting SCAL. The size of the QTL differed. QTL with a larger effect could be more precisely located compared to QTL with small effect....... The locations of the QTLs for separate parameters were very close in some cases and probably caused the genetic correlation observed between ASYM and XMID and SCAL respectively. None of the QTL appeared on chromosome five. Conclusions Repeated observations on individuals were affected by at least nine QTLs....... For most QTL a precise location could be determined. The QTL for the inflection point (XMID) was difficult to pinpoint and might actually exist of two closely linked QTL on chromosome one....

  4. QTL global meta-analysis: are trait determining genes clustered?

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    Adelson David L

    2009-04-01

    Full Text Available Abstract Background A key open question in biology is if genes are physically clustered with respect to their known functions or phenotypic effects. This is of particular interest for Quantitative Trait Loci (QTL where a QTL region could contain a number of genes that contribute to the trait being measured. Results We observed a significant increase in gene density within QTL regions compared to non-QTL regions and/or the entire bovine genome. By grouping QTL from the Bovine QTL Viewer database into 8 categories of non-redundant regions, we have been able to analyze gene density and gene function distribution, based on Gene Ontology (GO with relation to their location within QTL regions, outside of QTL regions and across the entire bovine genome. We identified a number of GO terms that were significantly over represented within particular QTL categories. Furthermore, select GO terms expected to be associated with the QTL category based on common biological knowledge have also proved to be significantly over represented in QTL regions. Conclusion Our analysis provides evidence of over represented GO terms in QTL regions. This increased GO term density indicates possible clustering of gene functions within QTL regions of the bovine genome. Genes with similar functions may be grouped in specific locales and could be contributing to QTL traits. Moreover, we have identified over-represented GO terminology that from a biological standpoint, makes sense with respect to QTL category type.

  5. 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.

    Science.gov (United States)

    Cavanagh, Colin R; Jonas, Elisabeth; Hobbs, Matthew; Thomson, Peter C; Tammen, Imke; Raadsma, Herman W

    2010-09-16

    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 < 2) were detected on eleven chromosomes. Regression analysis confirmed 28 of these QTL and an additional 17 suggestive (P < 0.1) and two significant (P < 0.05) QTL were identified using this method. QTL with pleiotropic effects for two or more tissues were identified on chromosomes 1, 6, 10, 14, 16 and 23. No tissue-specific QTL were identified.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.

  6. QTL detection for physicochemical characteristics of cashew apple

    Directory of Open Access Journals (Sweden)

    Francisco Herbeth Costa dos Santos

    2011-08-01

    Full Text Available The identification of quantitative trait loci (QTL and marker-assisted selection have aroused great interest inbreeding programs aiming at fruit quality. The objective of this study was to detect QTL related to the quality of the cashew apple.The physicochemical characteristics oligomeric phenolics, total soluble solids, total titrable acidity and vitamin C contents wereanalyzed in the mapped cashew population. QTL were detected by QTL interval and multiple QTL mapping. The results showedhigh phenotypic variation in the segregating F1 generation for all traits. Eighteen QTL associated with cashew quality wereidentified: three for oligomeric phenolics, five for total soluble solids, six for total acidity and four for vitamin C. QTL are promisingfor marker-assisted selection since they have the greatest phenotypic effects and contribution to phenotypic variation.

  7. Effect and mode of action of the Texel muscling QTL (TM-QTL) on carcass traits in purebred Texel lambs.

    Science.gov (United States)

    Macfarlane, J M; Lambe, N R; Matika, O; Johnson, P L; Wolf, B T; Haresign, W; Bishop, S C; Bünger, L

    2014-07-01

    TM-QTL is a quantitative trait locus (QTL) on ovine chromosome 18 (OAR18) known to affect loin muscling in Texel sheep. Previous work suggested that its mode of inheritance is consistent with paternal polar overdominance, but this has yet to be formally demonstrated. This study used purebred Texel sheep segregating for TM-QTL to confirm its presence in the chromosomal region in which it was first reported and to determine its pattern of inheritance. To do so, this study used the first available data from a Texel flock, which included homozygote TM-QTL carriers (TM/TM; n=34) in addition to homozygote non-carriers (+/+; n=40 and, heterozygote TM-QTL-carriers inheriting TM-QTL from their sire (TM/+; n=53) or their dam (+/TM; n=17). Phenotypes included a wide range of loin muscling, carcass composition and tissue distribution traits. The presence of a QTL affecting ultrasound muscle depth on OAR18 was confirmed with a paternal QTL effect ranging from +0.54 to +2.82 mm UMD (s.e. 0.37 to 0.57 mm) across the sires segregating for TM-QTL. Loin muscle width, depth and area, loin muscle volume and dissected M. longissimus lumborum weight were significantly greater for TM/+ than +/+ lambs (+2.9% to +7.9%; Pcarcass weight; TM/TM animals were significantly (Panimals (+11.9% and +11.7%, respectively), with TM/+ intermediate. Weights of the leg, saddle and shoulder region (corrected for carcass weight) were similar in the genotypic groups. There was a tendency for lambs inheriting TM-QTL from their sire to be less fat with slightly more muscle than non-carriers. For example, carcass muscle weight measured by live animal CT-scanning was 2.8% higher in TM/TM than +/+ lambs (Pcarcass muscle weight measured by carcass CT-scanning was 1.36% higher in TM/+ than +/+ lambs (Pcarcass cuts was significantly lower for TM/+ than +/+ lambs (-11.2%; Pcarcass traits were found. Optimal commercial use of TM-QTL within the sheep industry would require some consideration, due to the apparently

  8. Box-Cox transformation for QTL mapping.

    Science.gov (United States)

    Yang, Runqing; Yi, Nengjun; Xu, Shizhong

    2006-01-01

    The maximum likelihood method of QTL mapping assumes that the phenotypic values of a quantitative trait follow a normal distribution. If the assumption is violated, some forms of transformation should be taken to make the assumption approximately true. The Box-Cox transformation is a general transformation method which can be applied to many different types of data. The flexibility of the Box-Cox transformation is due to a variable, called transformation factor, appearing in the Box-Cox formula. We developed a maximum likelihood method that treats the transformation factor as an unknown parameter, which is estimated from the data simultaneously along with the QTL parameters. The method makes an objective choice of data transformation and thus can be applied to QTL analysis for many different types of data. Simulation studies show that (1) Box-Cox transformation can substantially increase the power of QTL detection; (2) Box-Cox transformation can replace some specialized transformation methods that are commonly used in QTL mapping; and (3) applying the Box-Cox transformation to data already normally distributed does not harm the result.

  9. QTL-mapping in mink (Neovison vison) shows evidence for QTL for guard hair thickness, guard hair length and skin length

    DEFF Research Database (Denmark)

    Thirstrup, Janne Pia; Labouriau, Rodrigo; Guldbrandtsen, Bernt

    2011-01-01

    Fur quality in mink (Neovison vison) is a composite trait, consisting of e.g. guard hair length, guard hair thickness and density of wool. A genome wide QTL search was performed to detect QTL for fur quality traits in mink. Here we present the results of QTL analyses for guard hair length, guard...... hair thickness and density of wool. Data from an F2-cross was analysed across fourteen chromosomes using 100 microsatellites as markers with a spacing of approximately 20 cM. The two lines used for the F2-cross were Nordic wild mink and American short nap mink. In total 1,083 animals (21 wild type, 25...... short nap, 103 F1 and 934 F2) were marker typed and recorded for the three presented fur quality traits. For the QTL-analyses a regression analysis implemented in QTL Express software was used. Evidence was found for the existence of QTL for guard hair length, guard hair thickness and density of wool...

  10. Molecular marker analysis of heading date Hd1 locus in Egyptian ...

    African Journals Online (AJOL)

    Nine molecular markers derived from the heading date QTL Hd1 DNA sequence for cultivated rice were used to study the heading date allelic diversity of the cultivated Egyptian rice varieties. The results showed that among the nine simple sequence repeats (SSR) and sequence tagged-sites (STS) markers used, one SSR ...

  11. Energy balance associated with the degradation of lignocellulosic material by white-rot and brown-rot fungi.

    Science.gov (United States)

    Derrien, Delphine; Bédu, Hélène; Buée, Marc; Kohler, Annegret; Goodell, Barry; Gelhaye, Eric

    2017-04-01

    Forest soils cover about 30% of terrestrial area and comprise between 50 and 80% of the global stock of soil organic carbon (SOC). The major precursor for this forest SOC is lignocellulosic material, which is made of polysaccharides and lignin. Lignin has traditionally been considered as a recalcitrant polymer that hinders access to the much more labile structural polysaccharides. This view appears to be partly incorrect from a microbiology perspective yet, as substrate alteration depends on the metabolic potential of decomposers. In forest ecosystems the wood-rotting Basidiomycota fungi have developed two different strategies to attack the structure of lignin and gain access to structural polysaccharides. White-rot fungi degrade all components of plant cell walls, including lignin, using enzymatic systems. Brown-rot fungi do not remove lignin. They generate oxygen-derived free radicals, such as the hydroxyl radical produced by the Fenton reaction, that disrupt the lignin polymer and depolymerize polysaccharides which then diffuse out to where the enzymes are located The objective of this study was to develop a model to investigate whether the lignin relative persistence could be related to the energetic advantage of brown-rot degradative pathway in comparison to white-rot degradative pathway. The model simulates the changes in substrate composition over time, and determines the energy gained from the conversion of the lost substrate into CO2. The energy cost for the production of enzymes involved in substrate alteration is assessed using information derived from genome and secretome analysis. For brown-rot fungus specifically, the energy cost related to the production of OH radicals is also included. The model was run, using data from the literature on populous wood degradation by Trametes versicolor, a white-rot fungus, and Gloeophyllum trabeum, a brown-rot fungus. It demonstrates that the brown-rot fungus (Gloeophyllum trabeum) was more efficient than the white-rot

  12. Construction of chromosome segment substitution lines enables QTL mapping for flowering and morphological traits in Brassica rapa

    Directory of Open Access Journals (Sweden)

    Xiaonan eLi

    2015-06-01

    Full Text Available Chromosome segment substitution lines (CSSLs represent a powerful method for precise quantitative trait loci (QTL detection of complex agronomical traits in plants. In this study, we used a marker-assisted backcrossing strategy to develop a population consisting of 63 CSSLs, derived from backcrossing of the F1 generated from a cross between two Brassica rapa subspecies: ‘Chiifu’ (ssp. pekinensis, the Brassica A genome-represented line used as the donor, and ‘49caixin’ (ssp. parachinensis, a non-heading cultivar used as the recipient. The 63 CSSLs covered 87.95% of the B. rapa genome. Among them, 39 lines carried a single segment; 15 lines, two segments; and nine lines, three or more segments of the donor parent chromosomes. To verify the potential advantage of these CSSL lines, we used them to locate QTL for six morphology-related traits. A total of 58 QTL were located on eight chromosomes for all six traits: 17 for flowering time, 14 each for bolting time and plant height, 6 for plant diameter, 2 for leaf width, and 5 for flowering stalk diameter. Co-localized QTL were mainly distributed on eight genomic regions in A01, A02, A05, A06, A08, A09, and A10, present in the corresponding CSSLs. Moreover, new chromosomal fragments that harbored QTL were identified using the findings of previous studies. The CSSL population constructed in our study paves the way for fine mapping and cloning of candidate genes involved in late bolting, flowering, and plant architecture-related traits in B. rapa. Furthermore, it has great potential for future marker-aided gene/QTL pyramiding of other interesting traits in B. rapa breeding.

  13. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white rot/ brown rot paradigm for wood decay fungi

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Robert; Salamov, Asaf; Brown, Daren W.; Nagy, Laszlo G.; Floudas, Dimitris; Held, Benjamin; Levasseur, Anthony; Lombard, Vincent; Morin, Emmanuelle; Otillar, Robert; Lindquist, Erika; Sun, Hui; LaButti, Kurt; Schmutz, Jeremy; Jabbour, Dina; Luo, Hong; Baker, Scott E.; Pisabarro, Antonio; Walton, Jonathan D.; Blanchette, Robert; Henrissat, Bernard; Martin, Francis; Cullen, Dan; Hibbett, David; Grigoriev, Igor V.

    2014-03-14

    Basidiomycota (basidiomycetes) make up 32percent of the described fungi and include most wood decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white rot/brown rot classification paradigm we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically-informed Principal Components Analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs, but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown rot fungi. Our results suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.

  14. QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...Policy | Contact Us QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  15. Stand tending and root rot in Norway spruce stands - economical effects caused by root rot at different thinning regimes

    International Nuclear Information System (INIS)

    Johansson, Mats

    1997-01-01

    This report is divided into three parts: 1) a literature study describing the most common fungi causing rot in wood and descriptions of various strategies to reduce economic loss from root rot, 2) a check of a model describing the development of butt rot in pure Norway spruce plantations in southern Sweden, and 3) simulated economic effects of root rot in stands with various stand tending. The rot model was used to estimate future rot frequencies in the economic calculations. In order to avoid overestimations of rot frequencies, the calculations were also executed when assuming slower growth of rot than shown in the model. When analysing the economical effects of rot, the following three thinning programmes were used: Program 1: thinning at the ages of 30- and 45 years. Final felling at the ages 50-, 55-, 60-, 65-, and 70 years. Program 2: thinning at the ages of 40- and 60- years. Final felling at the ages 65 and 75 years. Program 3: thinning at the ages of 30-, 40-, 55-, and 70 years. Final felling at the ages 80 and 90 years. With an interest rate of 3%, programme 2 (final felling at the age of 65 years) had the highest value at present. This result was valid when presuming butt rot in the stand as well as when presuming no butt rot in the stand. There was a small difference between the value at present in programme 1 (final felling at the age of 60 years) and in programme 3 (final felling at the age of 80 years). When presuming butt rot in the stand, the value at present in programme 3 decreased somewhat more in comparison to the value at present in programme 1. Compared to no butt rot in the stand, the optimal final felling time appeared five to ten years earlier when assuming butt rot in the stand. Stand tending programme 1 and an interest rate of 3% were used. Interest rates 2 and 4% did not indicate shorter rotation. The calculated optimal time of final felling appeared at the same stand age whether assuming rot preset or not. The results in this study

  16. 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.

  17. An information-theoretic machine learning approach to expression QTL analysis.

    Directory of Open Access Journals (Sweden)

    Tao Huang

    Full Text Available Expression Quantitative Trait Locus (eQTL analysis is a powerful tool to study the biological mechanisms linking the genotype with gene expression. Such analyses can identify genomic locations where genotypic variants influence the expression of genes, both in close proximity to the variant (cis-eQTL, and on other chromosomes (trans-eQTL. Many traditional eQTL methods are based on a linear regression model. In this study, we propose a novel method by which to identify eQTL associations with information theory and machine learning approaches. Mutual Information (MI is used to describe the association between genetic marker and gene expression. MI can detect both linear and non-linear associations. What's more, it can capture the heterogeneity of the population. Advanced feature selection methods, Maximum Relevance Minimum Redundancy (mRMR and Incremental Feature Selection (IFS, were applied to optimize the selection of the affected genes by the genetic marker. When we applied our method to a study of apoE-deficient mice, it was found that the cis-acting eQTLs are stronger than trans-acting eQTLs but there are more trans-acting eQTLs than cis-acting eQTLs. We compared our results (mRMR.eQTL with R/qtl, and MatrixEQTL (modelLINEAR and modelANOVA. In female mice, 67.9% of mRMR.eQTL results can be confirmed by at least two other methods while only 14.4% of R/qtl result can be confirmed by at least two other methods. In male mice, 74.1% of mRMR.eQTL results can be confirmed by at least two other methods while only 18.2% of R/qtl result can be confirmed by at least two other methods. Our methods provide a new way to identify the association between genetic markers and gene expression. Our software is available from supporting information.

  18. Response of the Andean diversity panel to root rot in a root rot nursery in Puerto Rico

    Science.gov (United States)

    The Andean Diversity Panel (ADP) was evaluated under low-fertility and root rot conditions in two trials conducted in 2013 and 2015 in Isabela, Puerto Rico. About 246 ADP lines were evaluated in the root rot nursery with root rot and stem diseases caused predominantly by Fusarium solani, which cause...

  19. Two distinct classes of QTL determine rust resistance in sorghum.

    Science.gov (United States)

    Wang, Xuemin; Mace, Emma; Hunt, Colleen; Cruickshank, Alan; Henzell, Robert; Parkes, Heidi; Jordan, David

    2014-12-31

    Agriculture is facing enormous challenges to feed a growing population in the face of rapidly evolving pests and pathogens. The rusts, in particular, are a major pathogen of cereal crops with the potential to cause large reductions in yield. Improving stable disease resistance is an on-going major and challenging focus for many plant breeding programs, due to the rapidly evolving nature of the pathogen. Sorghum is a major summer cereal crop that is also a host for a rust pathogen Puccinia purpurea, which occurs in almost all sorghum growing areas of the world, causing direct and indirect yield losses in sorghum worldwide, however knowledge about its genetic control is still limited. In order to further investigate this issue, QTL and association mapping methods were implemented to study rust resistance in three bi-parental populations and an association mapping set of elite breeding lines in different environments. In total, 64 significant or highly significant QTL and 21 suggestive rust resistance QTL were identified representing 55 unique genomic regions. Comparisons across populations within the current study and with rust QTL identified previously in both sorghum and maize revealed a high degree of correspondence in QTL location. Negative phenotypic correlations were observed between rust, maturity and height, indicating a trend for both early maturing and shorter genotypes to be more susceptible to rust. The significant amount of QTL co-location across traits, in addition to the consistency in the direction of QTL allele effects, has provided evidence to support pleiotropic QTL action across rust, height, maturity and stay-green, supporting the role of carbon stress in susceptibility to rust. Classical rust resistance QTL regions that did not co-locate with height, maturity or stay-green QTL were found to be significantly enriched for the defence-related NBS-encoding gene family, in contrast to the lack of defence-related gene enrichment in multi-trait effect

  20. Molecular Basis of Resistance to Fusarium Ear Rot in Maize

    Directory of Open Access Journals (Sweden)

    Alessandra Lanubile

    2017-10-01

    Full Text Available The impact of climate change has been identified as an emerging issue for food security and safety, and the increased incidence of mycotoxin contamination in maize over the last two decades is considered a potential emerging hazard. Disease control by chemical and agronomic approaches is often ineffective and increases the cost of production; for this reason the exploitation of genetic resistance is the most sustainable method for reducing contamination. The review focuses on the significant advances that have been made in the development of transcriptomic, genetic and genomic information for maize, Fusarium verticillioides molds, and their interactions, over recent years. Findings from transcriptomic studies have been used to outline a specific model for the intracellular signaling cascade occurring in maize cells against F. verticillioides infection. Several recognition receptors, such as receptor-like kinases and R genes, are involved in pathogen perception, and trigger down-stream signaling networks mediated by mitogen-associated protein kinases. These signals could be orchestrated primarily by hormones, including salicylic acid, auxin, abscisic acid, ethylene, and jasmonic acid, in association with calcium signaling, targeting multiple transcription factors that in turn promote the down-stream activation of defensive response genes, such as those related to detoxification processes, phenylpropanoid, and oxylipin metabolic pathways. At the genetic and genomic levels, several quantitative trait loci (QTL and single-nucleotide polymorphism markers for resistance to Fusarium ear rot deriving from QTL mapping and genome-wide association studies are described, indicating the complexity of this polygenic trait. All these findings will contribute to identifying candidate genes for resistance and to applying genomic technologies for selecting resistant maize genotypes and speeding up a strategy of breeding to contrast disease, through plants

  1. A comparison of bivariate and univariate QTL mapping in livestock populations

    Directory of Open Access Journals (Sweden)

    Sorensen Daniel

    2003-11-01

    Full Text Available Abstract This study presents a multivariate, variance component-based QTL mapping model implemented via restricted maximum likelihood (REML. The method was applied to investigate bivariate and univariate QTL mapping analyses, using simulated data. Specifically, we report results on the statistical power to detect a QTL and on the precision of parameter estimates using univariate and bivariate approaches. The model and methodology were also applied to study the effectiveness of partitioning the overall genetic correlation between two traits into a component due to many genes of small effect, and one due to the QTL. It is shown that when the QTL has a pleiotropic effect on two traits, a bivariate analysis leads to a higher statistical power of detecting the QTL and to a more precise estimate of the QTL's map position, in particular in the case when the QTL has a small effect on the trait. The increase in power is most marked in cases where the contributions of the QTL and of the polygenic components to the genetic correlation have opposite signs. The bivariate REML analysis can successfully partition the two components contributing to the genetic correlation between traits.

  2. 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.

  3. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white rot/brown rot paradigm for wood decay fungi

    Science.gov (United States)

    Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade ...

  4. Root rot in sugar beet piles at harvest

    Science.gov (United States)

    Sugar beet root rots are not only a concern because of reduced yields, but can also be associated with losses in storage. Our primary sugar beet root rot disease problem in the Amalgamated production area is Rhizoctonia root rot. However, this rot frequently only penetrates a short distance past t...

  5. Characterization of QTL for unique agronomic traits of new-plant-type rice varieties using introgression lines of IR64

    Directory of Open Access Journals (Sweden)

    Analiza G. Tagle

    2016-02-01

    Full Text Available To enhance the yield potential of an elite indica rice cultivar, an introgression (BC3-derived line of IR64, YTH288, was developed using a new-plant-type cultivar, IR66215-44-2-3, as a donor parent. YTH288 has agronomically valuable characteristics such as large panicles, few unproductive tillers, and large leaves inherited from NPT. To identify the genetic basis of these traits, we used 167 F2 plants derived from a cross between IR64 and YTH288 to conduct QTL analysis for five agronomic traits: days to heading (DTH, culm length (CL, flag leaf length (FLL, flag leaf width (FLW, and filled spikelet number per panicle (FSN. Six putative QTL were detected: four on chromosome 4 (for CL, FLL, FLW, and FSN and two on chromosome 2 (for DTH and FLL. All QTL with the IR66215-44-2-3 allele, except that for FLL on chromosome 2, had positive effects on each trait. To confirm the effects of these putative QTL, we developed NILs with the IR64 genetic background by marker-assisted selection. We observed significant differences in several agronomic traits between IR64 and NILs that carried these QTL on chromosomes 2 and 4. Additionally, four IR64-NILs carrying chromosomal segments derived from different NPT varieties on the long arm of chromosome 4 exhibited similar pleiotropic effects for unique agronomic traits. These NILs can be used as research materials for studying each trait and as breeding materials for yield improvement of indica rice cultivars.

  6. QTL mapping of resistance to gray leaf spot in maize.

    Science.gov (United States)

    Zhang, Yan; Xu, Ling; Fan, Xingming; Tan, Jing; Chen, Wei; Xu, Mingliang

    2012-12-01

    Gray leaf spot (GLS), caused by the causal fungal pathogen Cercospora zeae-maydis, is one of the most serious foliar diseases of maize worldwide. In the current study, a highly resistant inbred line Y32 and a susceptible line Q11 were used to produce segregating populations for both genetic analysis and QTL mapping. The broad-sense heritability (H (2)) for GLS resistance was estimated to be as high as 0.85, indicating that genetic factors played key roles in phenotypic variation. In initial QTL analysis, four QTL, located on chromosomes 1, 2, 5, and 8, were detected to confer GLS resistance. Each QTL could explain 2.53-23.90 % of the total phenotypic variation, predominantly due to additive genetic effects. Two major QTL, qRgls1 and qRgls2 on chromosomes 8 and 5, were consistently detected across different locations and replicates. Compared to the previous results, qRgls2 is located in a 'hotspot' for GLS resistance; while, qRgls1 does not overlap with any other known resistance QTL. Furthermore, the major QTL-qRgls1 was fine-mapped into an interval of 1.4 Mb, flanked by the markers GZ204 and IDP5. The QTL-qRgls1 could enhance the resistance percentages by 19.70-61.28 %, suggesting its usefulness to improve maize resistance to GLS.

  7. Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL

    Science.gov (United States)

    Dixit, Shalabh; Kumar Biswal, Akshaya; Min, Aye; Henry, Amelia; Oane, Rowena H.; Raorane, Manish L.; Longkumer, Toshisangba; Pabuayon, Isaiah M.; Mutte, Sumanth K.; Vardarajan, Adithi R.; Miro, Berta; Govindan, Ganesan; Albano-Enriquez, Blesilda; Pueffeld, Mandy; Sreenivasulu, Nese; Slamet-Loedin, Inez; Sundarvelpandian, Kalaipandian; Tsai, Yuan-Ching; Raghuvanshi, Saurabh; Hsing, Yue-Ie C.; Kumar, Arvind; Kohli, Ajay

    2015-01-01

    Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs. Here we demonstrate the requirement of multiple intra-QTL genes for the full impact of QTL qDTY12.1 on rice yield under drought. Multiple evidences are presented for the need of the transcription factor ‘no apical meristem’ (OsNAM12.1) and its co-localized target genes of separate GO categories for qDTY12.1 function, raising a regulon-like model of genetic architecture. The molecular underpinnings of qDTY12.1 support its effectiveness in further improving a drought tolerant genotype and for its validity in multiple genotypes/ecosystems/environments. Resolving the combinatorial value of OsNAM12.1 with individual intra-QTL genes notwithstanding, identification and analyses of qDTY12.1has fast-tracked rice improvement towards food security. PMID:26507552

  8. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

    Science.gov (United States)

    Robert Riley; Asaf A. Salamov; Daren W. Brown; Laszlo G. Nagy; Dimitrios Floudas; Benjamin W. Held; Anthony Levasseur; Vincent Lombard; Emmanuelle Morin; Robert Otillar; Erika A. Lindquist; Hui Sun; Kurt M. LaButti; Jeremy Schmutz; Dina Jabbour; Hong Luo; Scott E. Baker; Antonio G. Pisabarro; Jonathan D. Walton; Robert A. Blanchette; Bernard Henrissat; Francis Martin; Daniel Cullen; David S. Hibbett; Igor V. Grigoriev

    2014-01-01

    Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic...

  9. Bias correction for estimated QTL effects using the penalized maximum likelihood method.

    Science.gov (United States)

    Zhang, J; Yue, C; Zhang, Y-M

    2012-04-01

    A penalized maximum likelihood method has been proposed as an important approach to the detection of epistatic quantitative trait loci (QTL). However, this approach is not optimal in two special situations: (1) closely linked QTL with effects in opposite directions and (2) small-effect QTL, because the method produces downwardly biased estimates of QTL effects. The present study aims to correct the bias by using correction coefficients and shifting from the use of a uniform prior on the variance parameter of a QTL effect to that of a scaled inverse chi-square prior. The results of Monte Carlo simulation experiments show that the improved method increases the power from 25 to 88% in the detection of two closely linked QTL of equal size in opposite directions and from 60 to 80% in the identification of QTL with small effects (0.5% of the total phenotypic variance). We used the improved method to detect QTL responsible for the barley kernel weight trait using 145 doubled haploid lines developed in the North American Barley Genome Mapping Project. Application of the proposed method to other shrinkage estimation of QTL effects is discussed.

  10. Use of maternal information for QTL detection in a (granddaughter design

    Directory of Open Access Journals (Sweden)

    Boichard Didier

    2002-05-01

    Full Text Available Abstract In a (granddaughter design, maternal information is often neglected because the number of progeny per dam is limited. The number of dams per maternal grandsire (MGS, however, could be large enough to contribute to QTL detection. But dams and MGS usually are not genotyped, there are two recombination opportunities between the MGS and the progeny, and at a given location, only half the progeny receive a MGS chromosomal segment. A 3-step procedure was developed to estimate: (1 the marker phenotypes probabilities of the MGS; (2 the probability of each possible MGS haplotype; (3 the probabilities that the progeny receives either the first, or second MGS segment, or a maternal grandam segment. These probabilities were used for QTL detection in a linear model including the effects of sire, MGS, paternal QTL, MGS QTL and maternal grandam QTL. Including the grandam QTL effect makes it possible to detect QTL in the grandam population, even when MGS are not informative. The detection power, studied by simulation, was rather high, provided that MGS family size was greater than 50. Using maternal information in the French dairy cattle granddaughter design made it possible to detect 23 additional QTL genomewise significant.

  11. 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.

  12. Isolation of laccase gene-specific sequences from white rot and brown rot fungi by PCR.

    Science.gov (United States)

    D'Souza, T M; Boominathan, K; Reddy, C A

    1996-01-01

    Degenerate primers corresponding to the consensus sequences of the copper-binding regions in the N-terminal domains of known basidiomycete laccases were used to isolate laccase gene-specific sequences from strains representing nine genera of wood rot fungi. All except three gave the expected PCR product of about 200 bp. Computer searches of the databases identified the sequence of each of the PCR products analyzed as a laccase gene sequence, suggesting the specificity of the primers. PCR products of the white rot fungi Ganoderma lucidum, Phlebia brevispora, and Trametes versicolor showed 65 to 74% nucleotide sequence similarity to each other; the similarity in deduced amino acid sequences was 83 to 91%. The PCR products of Lentinula edodes and Lentinus tigrinus, on the other hand, showed relatively low nucleotide and amino acid similarities (58 to 64 and 62 to 81%, respectively); however, these similarities were still much higher than when compared with the corresponding regions in the laccases of the ascomycete fungi Aspergillus nidulans and Neurospora crassa. A few of the white rot fungi, as well as Gloeophyllum trabeum, a brown rot fungus, gave a 144-bp PCR fragment which had a nucleotide sequence similarity of 60 to 71%. Demonstration of laccase activity in G. trabeum and several other brown rot fungi was of particular interest because these organisms were not previously shown to produce laccases. PMID:8837429

  13. Comparative studies on thermochemical characterization of corn stover pretreated by white-rot and brown-rot fungi.

    Science.gov (United States)

    Zeng, Yelin; Yang, Xuewei; Yu, Hongbo; Zhang, Xiaoyu; Ma, Fuying

    2011-09-28

    The effects of white-rot and brown-rot fungal pretreatment on the chemical composition and thermochemical conversion of corn stover were investigated. Fungus-pretreated corn stover was analyzed by Fourier transform infrared spectroscopy and X-ray diffraction analysis to characterize the changes in chemical composition. Differences in thermochemical conversion of corn stover after fungal pretreatment were investigated using thermogravimetric and pyrolysis analysis. The results indicated that the white-rot fungus Irpex lacteus CD2 has great lignin-degrading ability, whereas the brown-rot fungus Fomitopsis sp. IMER2 preferentially degrades the amorphous regions of the cellulose. The biopretreatment favors thermal decomposition of corn stover. The weight loss of IMER2-treated acid detergent fiber became greater, and the oil yield increased from 32.7 to 50.8%. After CD2 biopretreatment, 58% weight loss of acid detergent lignin was achieved and the oil yield increased from 16.8 to 26.8%.

  14. Detection and modelling of time-dependent QTL in animal populations

    DEFF Research Database (Denmark)

    Lund, Mogens S; Sørensen, Peter; Madsen, Per

    2008-01-01

    A longitudinal approach is proposed to map QTL affecting function-valued traits and to estimate their effect over time. The method is based on fitting mixed random regression models. The QTL allelic effects are modelled with random coefficient parametric curves and using a gametic relationship...... matrix. A simulation study was conducted in order to assess the ability of the approach to fit different patterns of QTL over time. It was found that this longitudinal approach was able to adequately fit the simulated variance functions and considerably improved the power of detection of time-varying QTL...... effects compared to the traditional univariate model. This was confirmed by an analysis of protein yield data in dairy cattle, where the model was able to detect QTL with high effect either at the beginning or the end of the lactation, that were not detected with a simple 305 day model....

  15. QTLTableMiner++: semantic mining of QTL tables in scientific articles.

    Science.gov (United States)

    Singh, Gurnoor; Kuzniar, Arnold; van Mulligen, Erik M; Gavai, Anand; Bachem, Christian W; Visser, Richard G F; Finkers, Richard

    2018-05-25

    A quantitative trait locus (QTL) is a genomic region that correlates with a phenotype. Most of the experimental information about QTL mapping studies is described in tables of scientific publications. Traditional text mining techniques aim to extract information from unstructured text rather than from tables. We present QTLTableMiner ++ (QTM), a table mining tool that extracts and semantically annotates QTL information buried in (heterogeneous) tables of plant science literature. QTM is a command line tool written in the Java programming language. This tool takes scientific articles from the Europe PMC repository as input, extracts QTL tables using keyword matching and ontology-based concept identification. The tables are further normalized using rules derived from table properties such as captions, column headers and table footers. Furthermore, table columns are classified into three categories namely column descriptors, properties and values based on column headers and data types of cell entries. Abbreviations found in the tables are expanded using the Schwartz and Hearst algorithm. Finally, the content of QTL tables is semantically enriched with domain-specific ontologies (e.g. Crop Ontology, Plant Ontology and Trait Ontology) using the Apache Solr search platform and the results are stored in a relational database and a text file. The performance of the QTM tool was assessed by precision and recall based on the information retrieved from two manually annotated corpora of open access articles, i.e. QTL mapping studies in tomato (Solanum lycopersicum) and in potato (S. tuberosum). In summary, QTM detected QTL statements in tomato with 74.53% precision and 92.56% recall and in potato with 82.82% precision and 98.94% recall. QTM is a unique tool that aids in providing QTL information in machine-readable and semantically interoperable formats.

  16. Mapping of QTLs for frost tolerance and heading time using SSR ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-10-19

    Oct 19, 2008 ... using SSR markers in bread wheat. Omid Sofalian1*, Seyyed A. ... Key words: Bread wheat, frost tolerance, heading time, QTL mapping, single marker analysis, SSR. INTRODUCTION. Abiotic stresses are crucial ... cultivars are divided into two types (winter and spring growth habit) depending on their need ...

  17. Identification of QTL for UV-protective eye area pigmentation in cattle by progeny phenotyping and genome-wide association analysis.

    Directory of Open Access Journals (Sweden)

    Hubert Pausch

    Full Text Available Pigmentation patterns allow for the differentiation of cattle breeds. A dominantly inherited white head is characteristic for animals of the Fleckvieh (FV breed. However, a minority of the FV animals exhibits peculiar pigmentation surrounding the eyes (ambilateral circumocular pigmentation, ACOP. In areas where animals are exposed to increased solar ultraviolet radiation, ACOP is associated with a reduced susceptibility to bovine ocular squamous cell carcinoma (BOSCC, eye cancer. Eye cancer is the most prevalent malignant tumour affecting cattle. Selection for animals with ACOP rapidly reduces the incidence of BOSCC. To identify quantitative trait loci (QTL underlying ACOP, we performed a genome-wide association study using 658,385 single nucleotide polymorphisms (SNPs. The study population consisted of 3579 bulls of the FV breed with a total of 320,186 progeny with phenotypes for ACOP. The proportion of progeny with ACOP was used as a quantitative trait with high heritability (h(2 = 0.79. A variance component based approach to account for population stratification uncovered twelve QTL regions on seven chromosomes. The identified QTL point to MCM6, PAX3, ERBB3, KITLG, LEF1, DKK2, KIT, CRIM1, ATRN, GSDMC, MITF and NBEAL2 as underlying genes for eye area pigmentation in cattle. The twelve QTL regions explain 44.96% of the phenotypic variance of the proportion of daughters with ACOP. The chromosomes harbouring significantly associated SNPs account for 54.13% of the phenotypic variance, while another 19.51% of the phenotypic variance is attributable to chromosomes without identified QTL. Thus, the missing heritability amounts to 7% only. Our results support a polygenic inheritance pattern of ACOP in cattle and provide the basis for efficient genomic selection of animals that are less susceptible to serious eye diseases.

  18. RESISTANCE TO POST-HARVEST MICROBIAL ROT IN YAM ...

    African Journals Online (AJOL)

    ACSS

    for resistance to internal rot, with Olordor and Kplondzo recording the lowest internal microbial rot, suggesting their potential in .... material. Dried maize stocks were then used to cover the pile of tubers. There were four .... effort in breeding for host plant resistance. Also, ... rot in Dioscorea species under all storage methods.

  19. Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis

    Directory of Open Access Journals (Sweden)

    Doerge RW

    2003-06-01

    Full Text Available Abstract Background It has been reported in the quantitative trait locus (QTL literature that when testing for QTL location and effect, the statistical power supporting methodologies based on two markers and their estimated genetic map is higher than for the genetic map independent methodologies known as single marker analyses. Close examination of these reports reveals that the two marker approaches are more powerful than single marker analyses only in certain cases. Simulation studies are a commonly used tool to determine the behavior of test statistics under known conditions. We conducted a simulation study to assess the general behavior of an intersection test and a two marker test under a variety of conditions. The study was designed to reveal whether two marker tests are always more powerful than intersection tests, or whether there are cases when an intersection test may outperform the two marker approach. We present a reanalysis of a data set from a QTL study of ovariole number in Drosophila melanogaster. Results Our simulation study results show that there are situations where the single marker intersection test equals or outperforms the two marker test. The intersection test and the two marker test identify overlapping regions in the reanalysis of the Drosophila melanogaster data. The region identified is consistent with a regression based interval mapping analysis. Conclusion We find that the intersection test is appropriate for analysis of QTL data. This approach has the advantage of simplicity and for certain situations supplies equivalent or more powerful results than a comparable two marker test.

  20. 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.

  1. Robust Linear Models for Cis-eQTL Analysis.

    Science.gov (United States)

    Rantalainen, Mattias; Lindgren, Cecilia M; Holmes, Christopher C

    2015-01-01

    Expression Quantitative Trait Loci (eQTL) analysis enables characterisation of functional genetic variation influencing expression levels of individual genes. In outbread populations, including humans, eQTLs are commonly analysed using the conventional linear model, adjusting for relevant covariates, assuming an allelic dosage model and a Gaussian error term. However, gene expression data generally have noise that induces heavy-tailed errors relative to the Gaussian distribution and often include atypical observations, or outliers. Such departures from modelling assumptions can lead to an increased rate of type II errors (false negatives), and to some extent also type I errors (false positives). Careful model checking can reduce the risk of type-I errors but often not type II errors, since it is generally too time-consuming to carefully check all models with a non-significant effect in large-scale and genome-wide studies. Here we propose the application of a robust linear model for eQTL analysis to reduce adverse effects of deviations from the assumption of Gaussian residuals. We present results from a simulation study as well as results from the analysis of real eQTL data sets. Our findings suggest that in many situations robust models have the potential to provide more reliable eQTL results compared to conventional linear models, particularly in respect to reducing type II errors due to non-Gaussian noise. Post-genomic data, such as that generated in genome-wide eQTL studies, are often noisy and frequently contain atypical observations. Robust statistical models have the potential to provide more reliable results and increased statistical power under non-Gaussian conditions. The results presented here suggest that robust models should be considered routinely alongside other commonly used methodologies for eQTL analysis.

  2. 7 CFR 29.6039 - Stem rot.

    Science.gov (United States)

    2010-01-01

    ... Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... INSPECTION Standards Definitions § 29.6039 Stem rot. The deterioration of an uncured or frozen stem resulting from bacterial action. Although stem rot results from bacterial action, it is inactive in cured tobacco...

  3. Discovering genes underlying QTL

    Energy Technology Data Exchange (ETDEWEB)

    Vanavichit, Apichart [Kasetsart University, Kamphaengsaen, Nakorn Pathom (Thailand)

    2002-02-01

    A map-based approach has allowed scientists to discover few genes at a time. In addition, the reproductive barrier between cultivated rice and wild relatives has prevented us from utilizing the germ plasm by a map-based approach. Most genetic traits important to agriculture or human diseases are manifested as observable, quantitative phenotypes called Quantitative Trait Loci (QTL). In many instances, the complexity of the phenotype/genotype interaction and the general lack of clearly identifiable gene products render the direct molecular cloning approach ineffective, thus additional strategies like genome mapping are required to identify the QTL in question. Genome mapping requires no prior knowledge of the gene function, but utilizes statistical methods to identify the most likely gene location. To completely characterize genes of interest, the initially mapped region of a gene location will have to be narrowed down to a size that is suitable for cloning and sequencing. Strategies for gene identification within the critical region have to be applied after the sequencing of a potentially large clone or set of clones that contains this gene(s). Tremendous success of positional cloning has been shown for cloning many genes responsible for human diseases, including cystic fibrosis and muscular dystrophy as well as plant disease resistance genes. Genome and QTL mapping, positional cloning: the pre-genomics era, comparative approaches to gene identification, and positional cloning: the genomics era are discussed in the report. (M. Suetake)

  4. A quick method to calculate QTL confidence interval

    Indian Academy of Sciences (India)

    2011-08-19

    Aug 19, 2011 ... experimental design and analysis to reveal the real molecular nature of the ... strap sample form the bootstrap distribution of QTL location. The 2.5 and ..... ative probability to harbour a true QTL, hence x-LOD rule is not stable ... Darvasi A. and Soller M. 1997 A simple method to calculate resolv- ing power ...

  5. Fusarium basal rot in the Netherlands

    NARCIS (Netherlands)

    Visser, de C.L.M.; Broek, van den R.C.F.M.; Brink, van den L.

    2006-01-01

    Fusarium basal rot of onion, caused by Fusarium oxysporum f.sp. cepae, is a steadily increasing problem in The Netherlands. Financial losses for Dutch farmers confronted with Fusarium basal rot is substantial, due to yield reduction and high storage costs. This paper describes the development and

  6. BIOMODIFICATION OF KENAF USING WHITE ROT FUNGI

    OpenAIRE

    Rasmina Halis,; Hui Rus Tan,; Zaidon Ashaari,; Rozi Mohamed

    2012-01-01

    White rot fungi can be used as a pretreatment of biomass to degrade lignin. It also alters the structure of the lignocellulosic matter, thus increasing its accessibility to enzymes able to convert polysaccharides into simple sugars. This study compares the ability of two species of white rot fungi, Pycnoporous sanguineus and Oxyporus latemarginatus FRIM 31, to degrade lignin in kenaf chips. The white rot fungi were originally isolated from the tropical forest in Malaysia. Kenaf chips were fir...

  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. Age-dependent QTL affecting body weight in gilthead seabream (Sparus aurata L.

    Directory of Open Access Journals (Sweden)

    D. LOUKOVITIS

    2016-09-01

    Full Text Available We examined 24 maternal half-sib families of gilthead seabream to identify quantitative trait loci (QTL associated with body weight at four time points during a production cycle. 57 brooders and 637 offspring were genotyped for 14 informative microsatellite markers, spanning linkage groups 1 and 21. The QTL detection method was based on half-sib interval mapping analysis through a linear regression approach. One QTL was found significant at all time points in linkage group 1, with its effect having different profile across time, and one QTL in linkage group 21 that seems to impact body weight at a later growth stage of the species. Current results verified previously published QTL for growth in the above linkage groups, using a different genetic background of seabream. These QTL can be considered as valuable candidates for use in marker-assisted selective breeding programs, aiming at high rates of genetic improvement for growth in S. aurata.

  9. Isolation of laccase gene-specific sequences from white rot and brown rot fungi by PCR

    Energy Technology Data Exchange (ETDEWEB)

    D`Souza, T.M.; Boominathan, K.; Reddy, C.A. [Michigan State Univ., East Lansing, MI (United States)

    1996-10-01

    Degenerate primers corresponding to the consensus sequences of the copper-binding regions in the N-terminal domains of known basidiomycete laccases were used to isolate laccase gene-specific sequences from strains representing nine genera of wood rot fungi. All except three gave the expected PCR product of about 200 bp. Computer searches of the databases identified the sequences of each of the PCR product of about 200 bp. Computer searches of the databases identified the sequence of each of the PCR products analyzed as a laccase gene sequence, suggesting the specificity of the primers. PCR products of the white rot fungi Ganoderma lucidum, Phlebia brevispora, and Trametes versicolor showed 65 to 74% nucleotide sequence similarity to each other; the similarity in deduced amino acid sequences was 83 to 91%. The PCR products of Lentinula edodes and Lentinus tigrinus, on the other hand, showed relatively low nucleotide and amino acid similarities (58 to 64 and 62 to 81%, respectively); however, these similarities were still much higher than when compared with the corresponding regions in the laccases of the ascomycete fungi Aspergillus nidulans and Neurospora crassa. A few of the white rot fungi, as well as Gloeophyllum trabeum, a brown rot fungus, gave a 144-bp PCR fragment which had a nucleotide sequence similarity of 60 to 71%. Demonstration of laccase activity in G. trabeum and several other brown rot fungi was of particular interest because these organisms were not previously shown to produce laccases. 36 refs., 6 figs., 2 tabs.

  10. Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus.

    Science.gov (United States)

    Swamy, B P Mallikarjuna; Vikram, Prashant; Dixit, Shalabh; Ahmed, H U; Kumar, Arvind

    2011-06-16

    In the last few years, efforts have been made to identify large effect QTL for grain yield under drought in rice. However, identification of most precise and consistent QTL across the environments and genetics backgrounds is essential for their successful use in Marker-assisted Selection. In this study, an attempt was made to locate consistent QTL regions associated with yield increase under drought by applying a genome-wide QTL meta-analysis approach. The integration of 15 maps resulted in a consensus map with 531 markers and a total map length of 1821 cM. Fifty-three yield QTL reported in 15 studies were projected on a consensus map and meta-analysis was performed. Fourteen meta-QTL were obtained on seven chromosomes. MQTL1.2, MQTL1.3, MQTL1.4, and MQTL12.1 were around 700 kb and corresponded to a reasonably small genetic distance of 1.8 to 5 cM and they are suitable for use in marker-assisted selection (MAS). The meta-QTL for grain yield under drought coincided with at least one of the meta-QTL identified for root and leaf morphology traits under drought in earlier reports. Validation of major-effect QTL on a panel of random drought-tolerant lines revealed the presence of at least one major QTL in each line. DTY12.1 was present in 85% of the lines, followed by DTY4.1 in 79% and DTY1.1 in 64% of the lines. Comparative genomics of meta-QTL with other cereals revealed that the homologous regions of MQTL1.4 and MQTL3.2 had QTL for grain yield under drought in maize, wheat, and barley respectively. The genes in the meta-QTL regions were analyzed by a comparative genomics approach and candidate genes were deduced for grain yield under drought. Three groups of genes such as stress-inducible genes, growth and development-related genes, and sugar transport-related genes were found in clusters in most of the meta-QTL. Meta-QTL with small genetic and physical intervals could be useful in Marker-assisted selection individually and in combinations. Validation and comparative

  11. Linear models for joint association and linkage QTL mapping

    Directory of Open Access Journals (Sweden)

    Fernando Rohan L

    2009-09-01

    Full Text Available Abstract Background Populational linkage disequilibrium and within-family linkage are commonly used for QTL mapping and marker assisted selection. The combination of both results in more robust and accurate locations of the QTL, but models proposed so far have been either single marker, complex in practice or well fit to a particular family structure. Results We herein present linear model theory to come up with additive effects of the QTL alleles in any member of a general pedigree, conditional to observed markers and pedigree, accounting for possible linkage disequilibrium among QTLs and markers. The model is based on association analysis in the founders; further, the additive effect of the QTLs transmitted to the descendants is a weighted (by the probabilities of transmission average of the substitution effects of founders' haplotypes. The model allows for non-complete linkage disequilibrium QTL-markers in the founders. Two submodels are presented: a simple and easy to implement Haley-Knott type regression for half-sib families, and a general mixed (variance component model for general pedigrees. The model can use information from all markers. The performance of the regression method is compared by simulation with a more complex IBD method by Meuwissen and Goddard. Numerical examples are provided. Conclusion The linear model theory provides a useful framework for QTL mapping with dense marker maps. Results show similar accuracies but a bias of the IBD method towards the center of the region. Computations for the linear regression model are extremely simple, in contrast with IBD methods. Extensions of the model to genomic selection and multi-QTL mapping are straightforward.

  12. Mapeamento de QTL para conteúdos de proteína e óleo em soja Mapping QTL for protein and oil content in soybean

    Directory of Open Access Journals (Sweden)

    Josiane Isabela da Silva Rodrigues

    2010-05-01

    Full Text Available O objetivo deste trabalho foi detectar e mapear locos de caracteres quantitativos (QTL que afetam os conteúdos de proteína e óleo em soja (Glycine max L. Merr.. Plantas F2, derivadas do cruzamento entre a linhagem CS3032PTA276 e a variedade UFVS2012, foram cultivadas em casa de vegetação e forneceram as folhas para extração e análise de DNA. Quarenta e oito marcadores microssatélites (SSR polimórficos foram avaliados na população F2. A avaliação dos fenótipos foi realizada em 207 famílias das progênies F2:3, em um delineamento em blocos ao acaso, com três repetições, conduzido em Viçosa, MG, em 2006. Foram detectados quatro QTL associados ao conteúdo de proteína, nos grupos de ligação D1a, G, A1, e I, e três QTL associados ao conteúdo de óleo, nos grupos A1, I e O. A variação fenotípica explicada pelos QTL variou de 6,24 a 18,94% e 17,26 a 25,93%, respectivamente, para os conteúdos de proteína e óleo. Foram detectados novos QTL associados aos conteúdos de proteína e óleo, além dos previamente relatados em outros estudos. Regiões distintas das atualmente conhecidas podem estar envolvidas no controle genético do teor de proteína e óleo na soja.The objective of this study was to detect and map quantitative trait loci (QTL affecting soybean (Glycine max L. Merr. protein and oil contents. F2 plants, derived from the cross between the CS3032PTA276 line and the variety UFVS2012, were grown in a greenhouse and provided the leaves for DNA extraction and analysis. Forty-eight polymorphic microsatelite markers (SSR were evaluated in the F2 population. Evaluation of the phenotype was performed in 207 families from F2:3 progenies, in a complete block design with three replicates, carried out in Viçosa, MG, Brazil, in 2006. Four QTL associated with protein content, in linkage groups D1a, G, A1, and I, and three QTL for oil content in groups A1, I and O were identified. Phenotypic variation for protein and oil

  13. Consistent effects of a major QTL for thermal resistance in field-released Drosophila melanogaster

    DEFF Research Database (Denmark)

    Loeschcke, Volker; Kristensen, Torsten Nygård; Norry, Fabian M

    2011-01-01

    Molecular genetic markers can be used to identify quantitative trait loci (QTL) for thermal resistance and this has allowed characterization of a major QTL for knockdown resistance to high temperature in Drosophila melanogaster. The QTL showed trade-off associations with cold resistance under lab...... of field fitness at different environmental temperatures with genotypic variation in a QTL for thermal tolerance. Graphical abstract...

  14. QTL mapping and correlation analysis for 1000-grain weight and ...

    Indian Academy of Sciences (India)

    in both environments, nine QTL for 1000-paddy-grain weight (PTGW), five QTL for 1000-brown-grain weight .... at the middle of chromosome 4 (defined by Bb38P21a), one ..... tive traits for panicle architecture by using chromosomal segment.

  15. Main Effect QTL with Dominance Determines Heterosis for Dynamic Plant Height in Upland Cotton

    Directory of Open Access Journals (Sweden)

    Lianguang Shang

    2016-10-01

    Full Text Available Plant height, which shows dynamic development and heterosis, is a major trait affecting plant architecture and has an indirect influence on economic yield related to biological yield in cotton. In the present study, we carried out dynamic analysis for plant height and its heterosis by quantitative trait loci (QTL mapping at multiple developmental stages using two recombinant inbred lines (RILs and their backcross progeny. At the single-locus level, 47 QTL were identified at five developmental stages in two hybrids. In backcross populations, QTL identified at an early stage mainly showed partial effects and QTL detected at a later stage mostly displayed overdominance effects. At the two-locus level, we found that main effect QTL played a more important role than epistatic QTL in the expression of heterosis in backcross populations. Therefore, this study implies that the genetic basis of plant height heterosis shows dynamic character and main effect QTL with dominance determines heterosis for plant height in Upland cotton.

  16. Mapping carcass and meat quality QTL on Sus Scrofa chromosome 2 in commercial finishing pigs

    Directory of Open Access Journals (Sweden)

    van Kampen Tony A

    2009-01-01

    Full Text Available Abstract Quantitative trait loci (QTL affecting carcass and meat quality located on SSC2 were identified using variance component methods. A large number of traits involved in meat and carcass quality was detected in a commercial crossbred population: 1855 pigs sired by 17 boars from a synthetic line, which where homozygous (A/A for IGF2. Using combined linkage and linkage disequilibrium mapping (LDLA, several QTL significantly affecting loin muscle mass, ham weight and ham muscles (outer ham and knuckle ham and meat quality traits, such as Minolta-L* and -b*, ultimate pH and Japanese colour score were detected. These results agreed well with previous QTL-studies involving SSC2. Since our study is carried out on crossbreds, different QTL may be segregating in the parental lines. To address this question, we compared models with a single QTL-variance component with models allowing for separate sire and dam QTL-variance components. The same QTL were identified using a single QTL variance component model compared to a model allowing for separate variances with minor differences with respect to QTL location. However, the variance component method made it possible to detect QTL segregating in the paternal line (e.g. HAMB, the maternal lines (e.g. Ham or in both (e.g. pHu. Combining association and linkage information among haplotypes improved slightly the significance of the QTL compared to an analysis using linkage information only.

  17. eQTL Networks Reveal Complex Genetic Architecture in the Immature Soybean Seed

    Directory of Open Access Journals (Sweden)

    Yung-Tsi Bolon

    2014-03-01

    Full Text Available The complex network of regulatory factors and interactions involved in transcriptional regulation within the seed is not well understood. To evaluate gene expression regulation in the immature seed, we utilized a genetical genomics approach on a soybean [ (L. Merr.] recombinant inbred line (RIL population and produced a genome-wide expression quantitative trait loci (eQTL dataset. The validity of the dataset was confirmed by mapping the eQTL hotspot for flavonoid biosynthesis-related genes to a region containing repeats of chalcone synthase (CHS genes known to correspond to the soybean inhibitor locus that regulates seed color. We then identified eQTL for genes with seed-specific expression and discovered striking eQTL hotspots at distinct genomic intervals on chromosomes (Chr 20, 7, and 13. The main eQTL hotspot for transcriptional regulation of fatty acid biosynthesis genes also coincided with regulation of oleosin genes. Transcriptional upregulation of genesets from eQTL with opposite allelic effects were also found. Gene–eQTL networks were constructed and candidate regulatory genes were identified from these three key loci specific to seed expression and enriched in genes involved in seed oil accumulation. Our data provides new insight into the complex nature of gene networks in the immature soybean seed and the genetic architecture that contributes to seed development.

  18. A General Method for QTL Mapping in Multiple Related Populations Derived from Multiple Parents

    Directory of Open Access Journals (Sweden)

    Yan AO

    2009-03-01

    Full Text Available It's well known that incorporating some existing populations derived from multiple parents may improve QTL mapping and QTL-based breeding programs. However, no general maximum likelihood method has been available for this strategy. Based on the QTL mapping in multiple related populations derived from two parents, a maximum likelihood estimation method was proposed, which can incorporate several populations derived from three or more parents and also can be used to handle different mating designs. Taking a circle design as an example, we conducted simulation studies to study the effect of QTL heritability and sample size upon the proposed method. The results showed that under the same heritability, enhanced power of QTL detection and more precise and accurate estimation of parameters could be obtained when three F2 populations were jointly analyzed, compared with the joint analysis of any two F2 populations. Higher heritability, especially with larger sample sizes, would increase the ability of QTL detection and improve the estimation of parameters. Potential advantages of the method are as follows: firstly, the existing results of QTL mapping in single population can be compared and integrated with each other with the proposed method, therefore the ability of QTL detection and precision of QTL mapping can be improved. Secondly, owing to multiple alleles in multiple parents, the method can exploit gene resource more adequately, which will lay an important genetic groundwork for plant improvement.

  19. QTL Mapping of Grain Quality Traits Using Introgression Lines Carrying Oryza rufipogon Chromosome Segments in Japonica Rice.

    Science.gov (United States)

    Yun, Yeo-Tae; Chung, Chong-Tae; Lee, Young-Ju; Na, Han-Jung; Lee, Jae-Chul; Lee, Sun-Gye; Lee, Kwang-Won; Yoon, Young-Hwan; Kang, Ju-Won; Lee, Hyun-Sook; Lee, Jong-Yeol; Ahn, Sang-Nag

    2016-12-01

    Improved eating quality is a major breeding target in japonica rice due to market demand. Consequently, quantitative trait loci (QTL) for glossiness of cooked rice and amylose content associated with eating quality have received much research focus because of their importance in rice quality. In this study, QTL associated with 12 grain quality traits were identified using 96 introgression lines (IL) of rice developed from an interspecific cross between the Korean elite O. sativa japonica cultivar 'Hwaseong' and O. rufipogon over 7 years. QTL analyses indicated that QTL qDTH6 for heading date, detected on chromosome 6 is associated with variance in grain traits. Most QTLs detected in this study clustered near the qDTH6 locus on chromosome 6, suggesting the effect of qDTH6. O. rufipogon alleles negatively affected grain quality traits except for a few QTLs, including qGCR9 for glossiness of cooked rice on chromosome 9. To characterize the effect of the O. rufipogon locus harboring qGCR9, four lines with a single but different O. rufipogon segment near qGCR9 were compared to Hwaseong. Three lines (O. rufipopgon ILs) having O. rufipogon segment between RM242 and RM245 in common showed higher glossiness of cooked rice than Hwaseong and the other line (Hwaseong IL), indicating that qGCR9 is located in the 3.4-Mb region between RM242 and RM245. Higher glossiness of cooked rice conferred by the O. rufipogon allele might be associated with protein content considering that three lines had lower protein content than Hwaseong (P < 0.1). These three O. rufipogon ILs showed higher yield than Hwaseong and Hwaseong IL due to increase in spikelets per panicle and grain weight indicating the linkage of qGCR9 and yield component QTLs. The qGCR9 locus is of particular interest because of its independence from other undesirable grain quality traits in O. rufipogon. SSR markers linked to qGCR9 can be used to develop high-quality japonica lines and offer a starting point for map

  20. 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.

  1. Foot Rot of Ulluco Caused by Pythium aphanidermatum

    OpenAIRE

    Keisuke, TOMIOKA; Toyozo, SATO; Tateo, NAKANISHI; National Agricultural Research Center for Western Region; National Institute of Agrobiological Sciences; National Agricultural Research Center for Western Region

    2002-01-01

    Severe rot of stem bases caused by Pythium aphanidermatum was found on ulluco (Ullucus tuberosus) grown in Kagawa Prefecture, Japan, in September 1999. The name "foot rot of ulluco" is proposed for this new disease.

  2. 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.

  3. Impact of management strategies in the basal rot, charcoal rots epidemiology and Phaseolus vulgaris L. yield.

    Directory of Open Access Journals (Sweden)

    Ulacio Osorio Dilcia

    2013-02-01

    Full Text Available The effect of chemical, physical, biologycal and cultural strategies individually or combinated were evaluated in the epidemiology of the basal rot (Sclerotium rolfsii, charcoal rot (Macrophomina phaseolina and the Phaseolus vulgaris cv Tacarigua yield at Barinas state from Venezuela. In the experiment, Tebuconazole (Teb was applicated at seed (1 L/Ton and at soil, a los 30 y 60 days after of the sow (1 L/ha; Trichoderma harzianum (Tri was applicated at seed (15 g for each 1.5 k and to 15, 30, 45 y 60 days after of the sow (30 g/10 L of water. On the other hand, soil was solarizated (Sol during 15 days and calcium nitrate (Ca (60 g/10 L of water was applicated each 15 days until 60 days of growth of cultivated plants. Basal rot was registered as far as 42 days after of the sow, showing less of 5.3% in Teb y the combination SolTeb. The hightest incidence of this disease was observed in the treatment Tri with 28.5%, being highter that control (14.5%. Last to 42 days predominated the charcoal rot in the rest of the plants for a total of 100% of incidente in everything the treatments. Nevertheless, Teb showed the hightest yield with 555 k/ha, being different estatistically at treatment TriCa, which showed the lowest yield with 31 k/ha, however, the roots not formed nodules nitrogen uptake in these replications with the fungicide and Ca. It is concluded that S. rolfsii was sensible at action of some of the treatments; but not M. phaseolina; nevertheless, the plants were capables to produce seeds health apparently in treatments in which observed less severity of charcoal rot.

  4. Biodegrading effects of some rot fungi on Pinus caribaea wood

    African Journals Online (AJOL)

    STORAGESEVER

    2008-05-16

    May 16, 2008 ... species of white-rot fungi; Corioliopsis polyzona and Pleurotus squarrosulus, and two species of brown- rot fungi; Lentinus ... The results indicated that biodegradation by rot fungi differs in intensity according to the fungus ..... wood of coast red wood Sequoia Sempervirens (D. Don). For. Prod. J. 33(5): 15-20 ...

  5. Fine-mapping of a QTL influencing pork tenderness on porcine chromosome 2

    Directory of Open Access Journals (Sweden)

    Beever Jonathan E

    2007-10-01

    Full Text Available Abstract Background In a previous study, a quantitative trait locus (QTL exhibiting large effects on both Instron shear force and taste panel tenderness was detected within the Illinois Meat Quality Pedigree (IMQP. This QTL mapped to the q arm of porcine chromosome 2 (SSC2q. Comparative analysis of SSC2q indicates that it is orthologous to a segment of human chromosome 5 (HSA5 containing a strong positional candidate gene, calpastatin (CAST. CAST polymorphisms have recently been shown to be associated with meat quality characteristics; however, the possible involvement of other genes and/or molecular variation in this region cannot be excluded, thus requiring fine-mapping of the QTL. Results Recent advances in porcine genome resources, including high-resolution radiation hybrid and bacterial artificial chromosome (BAC physical maps, were utilized for development of novel informative markers. Marker density in the ~30-Mb region surrounding the most likely QTL position was increased by addition of eighteen new microsatellite markers, including nine publicly-available and nine novel markers. Two newly-developed markers were derived from a porcine BAC clone containing the CAST gene. Refinement of the QTL position was achieved through linkage and haplotype analyses. Within-family linkage analyses revealed at least two families segregating for a highly-significant QTL in strong positional agreement with CAST markers. A combined analysis of these two families yielded QTL intervals of 36 cM and 7 cM for Instron shear force and taste panel tenderness, respectively, while haplotype analyses suggested further refinement to a 1.8 cM interval containing CAST markers. The presence of additional tenderness QTL on SSC2q was also suggested. Conclusion These results reinforce CAST as a strong positional candidate. Further analysis of CAST molecular variation within the IMQP F1 boars should enhance understanding of the molecular basis of pork tenderness, and thus

  6. Multi-environment QTL mixed models for drought stress adaptation in wheat

    NARCIS (Netherlands)

    Mathews, K.L.; Malosetti, M.; Chapman, S.; McIntyre, L.; Reynolds, M.; Shorter, R.; Eeuwijk, van F.A.

    2008-01-01

    Many quantitative trait loci (QTL) detection methods ignore QTL-by-environment interaction (QEI) and are limited in accommodation of error and environment-specific variance. This paper outlines a mixed model approach using a recombinant inbred spring wheat population grown in six drought stress

  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. Dynamic QTL analysis and candidate gene mapping for waterlogging tolerance at maize seedling stage.

    Directory of Open Access Journals (Sweden)

    Khalid A Osman

    Full Text Available Soil waterlogging is one of the major abiotic stresses adversely affecting maize growth and yield. To identify dynamic expression of genes or quantitative trait loci (QTL, QTL associated with plant height, root length, root dry weight, shoot dry weight and total dry weight were identified via conditional analysis in a mixed linear model and inclusive composite interval mapping method at three respective periods under waterlogging and control conditions. A total of 13, 19 and 23 QTL were detected at stages 3D|0D (the period during 0-3 d of waterlogging, 6D|3D and 9D|6D, respectively. The effects of each QTL were moderate and distributed over nine chromosomes, singly explaining 4.14-18.88% of the phenotypic variation. Six QTL (ph6-1, rl1-2, sdw4-1, sdw7-1, tdw4-1 and tdw7-1 were identified at two consistent stages of seedling development, which could reflect a continuous expression of genes; the remaining QTL were detected at only one stage. Thus, expression of most QTL was influenced by the developmental status. In order to provide additional evidence regarding the role of corresponding genes in waterlogging tolerance, mapping of Expressed Sequence Tags markers and microRNAs were conducted. Seven candidate genes were observed to co-localize with the identified QTL on chromosomes 1, 4, 6, 7 and 9, and may be important candidate genes for waterlogging tolerance. These results are a good starting point for understanding the genetic basis for selectively expressing of QTL in different stress periods and the common genetic control mechanism of the co-localized traits.

  9. QTL mapping for yield components and agronomic traits in a Brazilian soybean population

    Directory of Open Access Journals (Sweden)

    Josiane Isabela da Silva Rodrigues

    2016-11-01

    Full Text Available The objective of this work was to map QTL for agronomic traits in a Brazilian soybean population. For this, 207 F2:3 progenies from the cross CS3035PTA276-1-5-2x UFVS2012 were genotyped and cultivated in Viçosa-MG, using randomized block design with three replications. QTL detection was carried out by linear regression and composite interval mapping. Thirty molecular markers linked to QTL were detected by linear regression for the total of nine agronomic traits. QTL for SWP (seed weight per plant, W100S (weight of 100 seeds, NPP (number of pods per plant, and NSP (number of seeds per plant were detected by composite interval mapping. Four QTL with additive effect are promising for marker-assisted selection (MAS. Particularly, the markers Satt155 and Satt300 could be useful in simultaneous selection for greater SWP, NPP, and NSP.

  10. Mapping and introgression of QTL for yield and related traits in two ...

    Indian Academy of Sciences (India)

    1Directorate of Rice Research, Rajendranagar, Hyderabad 500 030, India ... Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box ... Advanced backcross QTL (AB-QTL) analysis was carried out in two Oryza ...

  11. QTL analysis of falling number and seed longevity in wheat (Triticum aestivum L.).

    Science.gov (United States)

    Börner, Andreas; Nagel, Manuela; Agacka-Mołdoch, Monika; Gierke, Peter Ulrich; Oberforster, Michael; Albrecht, Theresa; Mohler, Volker

    2018-02-01

    Pre-harvest sprouting (PHS) and seed longevity (SL) are complex biological processes of major importance for agricultural production. In the present study, a recombinant inbred line (RIL) population derived from a cross between the German winter wheat (Triticum aestivum L.) cultivars History and Rubens was used to identify genetic factors controlling these two physiological seed traits. A falling number (FN) test was employed to evaluate PHS, while SL was measured using a germination test (and the speed of germination) after controlled deterioration. FN of the population was assessed in four environments; SL traits were measured in one environment. Four major quantitative trait loci (QTL) for FN were detected on chromosomes 4D, 5A, 5D, and 7B, whereas for SL traits, a major QTL was found on chromosome 1A. The FN QTL on chromosome 4D that coincided with the position of the dwarfing gene Rht-D1b only had effects in environments that were free of PHS. The remaining three QTL for FN were mostly pronounced under conditions conducive to PHS. The QTL on the long arm of chromosome 7B corresponded to the major gene locus controlling late maturity α-amylase (LMA) in wheat. The severity of the LMA phenotype became truly apparent under sprouting conditions. The position on the long arm of chromosome 1A of the QTL for SL points to a new QTL for this important regenerative seed trait.

  12. Identification of major and minor QTL for ecologically important morphological traits in three-spined sticklebacks (Gasterosteus aculeatus).

    Science.gov (United States)

    Liu, Jun; Shikano, Takahito; Leinonen, Tuomas; Cano, José Manuel; Li, Meng-Hua; Merilä, Juha

    2014-04-16

    Quantitative trait locus (QTL) mapping studies of Pacific three-spined sticklebacks (Gasterosteus aculeatus) have uncovered several genomic regions controlling variability in different morphological traits, but QTL studies of Atlantic sticklebacks are lacking. We mapped QTL for 40 morphological traits, including body size, body shape, and body armor, in a F2 full-sib cross between northern European marine and freshwater three-spined sticklebacks. A total of 52 significant QTL were identified at the 5% genome-wide level. One major QTL explaining 74.4% of the total variance in lateral plate number was detected on LG4, whereas several major QTL for centroid size (a proxy for body size), and the lengths of two dorsal spines, pelvic spine, and pelvic girdle were mapped on LG21 with the explained variance ranging from 27.9% to 57.6%. Major QTL for landmark coordinates defining body shape variation also were identified on LG21, with each explaining ≥15% of variance in body shape. Multiple QTL for different traits mapped on LG21 overlapped each other, implying pleiotropy and/or tight linkage. Thus, apart from providing confirmatory data to support conclusions born out of earlier QTL studies of Pacific sticklebacks, this study also describes several novel QTL of both major and smaller effect for ecologically important traits. The finding that many major QTL mapped on LG21 suggests that this linkage group might be a hotspot for genetic determinants of ecologically important morphological traits in three-spined sticklebacks.

  13. Bacterial Infection Potato Tuber Soft Rot Disease Detection Based on Electronic Nose

    Directory of Open Access Journals (Sweden)

    Chang Zhiyong

    2017-11-01

    Full Text Available Soft rot is a severe bacterial disease of potatoes, and soft rot infection can cause significant economic losses during the storage period of potatoes. In this study, potato soft rot was selected as the research object, and a type of potato tuber soft rot disease early detection method based on the electronic nose technology was proposed. An optimized bionic electronic nose gas chamber and a scientific and reasonable sampling device were designed to detect a change in volatile substances of the infected soft rot disease of potato tuber. The infection of soft rot disease in potato tuber samples was detected and identified by using the RBF NN algorithm and SVM algorithm. The results revealed that the proposed bionic electronic nose system can be utilized for early detection of potato tuber soft rot disease. Through comparison and analysis, the recognition rate using the SVM algorithm reached up to 89.7%, and the results were superior to the RBF NN algorithm.

  14. Power analysis of QTL detection in half-sib families using selective DNA pooling

    Directory of Open Access Journals (Sweden)

    López Teresa

    2001-05-01

    Full Text Available Abstract Individual loci of economic importance (QTL can be detected by comparing the inheritance of a trait and the inheritance of loci with alleles readily identifiable by laboratory methods (genetic markers. Data on allele segregation at the individual level are costly and alternatives have been proposed that make use of allele frequencies among progeny, rather than individual genotypes. Among the factors that may affect the power of the set up, the most important are those intrinsic to the QTL: the additive effect of the QTL, and its dominance, and distance between markers and QTL. Other factors are relative to the choice of animals and markers, such as the frequency of the QTL and marker alleles among dams and sires. Data collection may affect the detection power through the size of half-sib families, selection rate within families, and the technical error incurred when estimating genetic frequencies. We present results for a sensitivity analysis for QTL detection using pools of DNA from selected half-sibs. Simulations showed that conclusive detection may be achieved with families of at least 500 half-sibs if sires are chosen on the criteria that most of their marker alleles are either both missing, or one is fixed, among dams.

  15. Role of Rot in bacterial autolysis regulation of Staphylococcus aureus NCTC8325.

    Science.gov (United States)

    Chu, Xinmin; Xia, Rui; He, Nianan; Fang, Yuting

    2013-09-01

    Autolysis is an important process in cell wall turnover in Staphylococcus aureus, performed by several peptidoglycan hydrolases or so-called autolysins and controlled by many regulators. Rot is a global regulator that regulates numerous virulence genes, including genes encoding lipase, hemolysins, proteases and genes related to cell surface adhesion. The aim of our study was to determine whether Rot has the ability to regulate autolysis. We compared Triton-X-100-induced autolysis of S. aureus NCTC8325 and its rot knock-out mutant. We found that the rot mutant showed increased autolysis rates. By examining the transcript level of several autolysins and some known regulators responsible for regulating autolysis using real-time RT-PCR assays, we found that transcription of two autolysins (lytM, lytN) and one regulatory operon (lrgAB) was changed in the rot mutant. An in vitro approach was undertaken to determine which of these genes are directly controlled by Rot. Rot proteins were overproduced in Escherichia coli and purified. Gel mobility shift DNA binding assays were used and showed that in-vitro-purified Rot can directly bind to the promoter region of lytM, lytN, lrgA and lytS. We also tested biofilm formation of the rot mutant, and it showed enhancement in biofilm formation. Taken together, our results reveal that Rot affects autolysis by directly regulating autolysins LytM and LytN, and, via a regulatory system, LrgAB. Copyright © 2013 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  16. lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals.

    Science.gov (United States)

    Ziyatdinov, Andrey; Vázquez-Santiago, Miquel; Brunel, Helena; Martinez-Perez, Angel; Aschard, Hugues; Soria, Jose Manuel

    2018-02-27

    Quantitative trait locus (QTL) mapping in genetic data often involves analysis of correlated observations, which need to be accounted for to avoid false association signals. This is commonly performed by modeling such correlations as random effects in linear mixed models (LMMs). The R package lme4 is a well-established tool that implements major LMM features using sparse matrix methods; however, it is not fully adapted for QTL mapping association and linkage studies. In particular, two LMM features are lacking in the base version of lme4: the definition of random effects by custom covariance matrices; and parameter constraints, which are essential in advanced QTL models. Apart from applications in linkage studies of related individuals, such functionalities are of high interest for association studies in situations where multiple covariance matrices need to be modeled, a scenario not covered by many genome-wide association study (GWAS) software. To address the aforementioned limitations, we developed a new R package lme4qtl as an extension of lme4. First, lme4qtl contributes new models for genetic studies within a single tool integrated with lme4 and its companion packages. Second, lme4qtl offers a flexible framework for scenarios with multiple levels of relatedness and becomes efficient when covariance matrices are sparse. We showed the value of our package using real family-based data in the Genetic Analysis of Idiopathic Thrombophilia 2 (GAIT2) project. Our software lme4qtl enables QTL mapping models with a versatile structure of random effects and efficient computation for sparse covariances. lme4qtl is available at https://github.com/variani/lme4qtl .

  17. Power of QTL detection by either fixed or random models in half-sib designs

    Directory of Open Access Journals (Sweden)

    Schaeffer Lawrence R

    2005-11-01

    Full Text Available Abstract The aim of this study was to compare the variance component approach for QTL linkage mapping in half-sib designs to the simple regression method. Empirical power was determined by Monte Carlo simulation in granddaughter designs. The factors studied (base values in parentheses included the number of sires (5 and sons per sire (80, ratio of QTL variance to total genetic variance (λ = 0.1, marker spacing (10 cM, and QTL allele frequency (0.5. A single bi-allelic QTL and six equally spaced markers with six alleles each were simulated. Empirical power using the regression method was 0.80, 0.92 and 0.98 for 5, 10, and 20 sires, respectively, versus 0.88, 0.98 and 0.99 using the variance component method. Power was 0.74, 0.80, 0.93, and 0.95 using regression versus 0.77, 0.88, 0.94, and 0.97 using the variance component method for QTL variance ratios (λ of 0.05, 0.1, 0.2, and 0.3, respectively. Power was 0.79, 0.85, 0.80 and 0.87 using regression versus 0.80, 0.86, 0.88, and 0.85 using the variance component method for QTL allele frequencies of 0.1, 0.3, 0.5, and 0.8, respectively. The log10 of type I error profiles were quite flat at close marker spacing (1 cM, confirming the inability to fine-map QTL by linkage analysis in half-sib designs. The variance component method showed slightly more potential than the regression method in QTL mapping.

  18. Comparative QTL mapping of resistance to sugarcane mosaic virus in maize based on bioinformatics

    Institute of Scientific and Technical Information of China (English)

    Xiangling L(U); Xinhai LI; Chuanxiao XIE; Zhuanfang HAO; Hailian JI; Liyu SHI; Shihuang ZHANG

    2008-01-01

    The development of genomics and bioinfor-matics offers new tools for comparative gene mapping. In this paper, an integrated QTL map for sugarcane mosaic virus (SCMV) resistance in maize was constructed by compiling a total of 81 QTL loci available, using the Genetic Map IBM2 2005 Neighbors as reference. These 81 QTL loci were scattered on 7 chromosomes of maize, and most of them were clustered on chromosomes 3 and 6. By using the method of meta-analysis, we identified one "consensus QTL" on chromosome 3 covering a genetic distance of 6.44 cM, and two on chromosome 6 covering genetic distances of 16 cM and 27.48 cM, respectively. Four positional candidate resistant genes were identified within the "consensus QTL" on chromosome 3 via the strategy of comparative genomics. These results suggest that application of a combination of meta-analysis within a species with sequence homology comparison in a related model plant is an efficient approach to identify the major QTL and its candidate gene(s) for the target traits. The results of this study provide useful information for iden-tifying and cloning the major gene(s) conferring resistance to SCMV in maize.

  19. Maize Cob Rot in Kenya and Its Association with Stalk Borer Damage

    International Nuclear Information System (INIS)

    Ajanga, S.I.

    2002-01-01

    Cob rots are a major cause of crop loss in areas such as western Kenya that experience prolonged rainfall during the period of crop maturation. Cob rot fungi cause spoilage of the grain and some of them produce mycotoxins which can pose a health risk to humans and animals consuming foods prepared from contaminate grain. survey conducted in western Kenya in 1998 showed that cob rot incidence exceeded 20%. In the following year when rainfall was greater around the harvest period, cob rot fungi affected 68% of cobs. in 1998 stalk borer larvae (mainly Busseola fusca) damaged 20% of the cobs and there was a strong correlation (R= 0.87) between cob rot incidence and borer damage. In 1999 almost half of the cobs sampled showed evidence of borer damage. The result indicate that the high cob rot incidence in this pert of Kenya is due to stalk bore damage, which predisposes the cobs to fungal infection, and that management of the borer would greatly decrease cob rot incidence

  20. QTL Information Table: 454 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available 61 rgn Zhuang, J.Y., Fan, Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Mapping major and minor QTL for rice CMS-WA fertility restoration. Rice Genetics Newsletter 17, 56-59. ...

  1. Botanicals to Control Soft Rot Bacteria of Potato

    Directory of Open Access Journals (Sweden)

    M. M. Rahman

    2012-01-01

    Full Text Available Extracts from eleven different plant species such as jute (Corchorus capsularis L., cheerota (Swertia chiraita Ham., chatim (Alstonia scholaris L., mander (Erythrina variegata, bael (Aegle marmelos L., marigold (Tagetes erecta, onion (Allium cepa, garlic (Allium sativum L., neem (Azadiracta indica, lime (Citrus aurantifolia, and turmeric (Curcuma longa L. were tested for antibacterial activity against potato soft rot bacteria, E. carotovora subsp. carotovora (Ecc P-138, under in vitro and storage conditions. Previously, Ecc P-138 was identified as the most aggressive soft rot bacterium in Bangladeshi potatoes. Of the 11 different plant extracts, only extracts from dried jute leaves and cheerota significantly inhibited growth of Ecc P-138 in vitro. Finally, both plant extracts were tested to control the soft rot disease of potato tuber under storage conditions. In a 22-week storage condition, the treated potatoes were significantly more protected against the soft rot infection than those of untreated samples in terms of infection rate and weight loss. The jute leaf extracts showed more pronounced inhibitory effects on Ecc-138 growth both in in vitro and storage experiments.

  2. BIOMODIFICATION OF KENAF USING WHITE ROT FUNGI

    Directory of Open Access Journals (Sweden)

    Rasmina Halis,

    2012-01-01

    Full Text Available White rot fungi can be used as a pretreatment of biomass to degrade lignin. It also alters the structure of the lignocellulosic matter, thus increasing its accessibility to enzymes able to convert polysaccharides into simple sugars. This study compares the ability of two species of white rot fungi, Pycnoporous sanguineus and Oxyporus latemarginatus FRIM 31, to degrade lignin in kenaf chips. The white rot fungi were originally isolated from the tropical forest in Malaysia. Kenaf chips were first inoculated with each fungus separately using corn steep liquor as a fungal growth promoter. The kenaf chips were inoculated with white rot fungus for a period of 1, 2, 4, 8 and 16 weeks, after which they were observed under the scanning electron microscope (SEM. Chemical analyses were conducted following TAPPI Standard Methods and Fourier Transmission Infra Red (FTIR. SEM observations showed evidence of fungal colonization. When calculating weight loss, both P. sanguineus and O. latemarginatus FRIM 31 showed the greatest reduction. Amounts by mass of cellulose, hemicelluloses, extractives, and lignin in the treated kenaf chips all were lowered. The results show that O. latemarginatus FRIM 31 had a greater ability to degrade lignin when compared to P. sanguineus.

  3. Survival of Fusarium graminearum, the causal agent of Fusarium head blight. A review

    OpenAIRE

    Leplat , Johann; Friberg , Hanna; Abid , Muhammad; Steinberg , Christian

    2012-01-01

    International audience; Wheat is one of the most cultivated crops worldwide. In 2010, 20 % of wheat and durum wheat were cultivated in Europe, 17 % in China and 9 % in Russia and in North America. Wheat yield can be highly decreased by several factors. In particular Fusarium graminearum Schwabe is a worldwide fungal pest impacting wheat production. F. graminearum is the causal agent of Fusarium head blight, root and stem-base rot of cereals. Losses caused by Fusarium head blight in Northern a...

  4. Detection of QTL for Carcass Quality on Chromosome 6 by Exploiting Linkage and Linkage Disequilibrium in Hanwoo

    Directory of Open Access Journals (Sweden)

    J.-H. Lee

    2012-01-01

    Full Text Available The purpose of this study was to improve mapping power and resolution for the QTL influencing carcass quality in Hanwoo, which was previously detected on the bovine chromosome (BTA 6. A sample of 427 steers were chosen, which were the progeny from 45 Korean proven sires in the Hanwoo Improvement Center, Seosan, Korea. The samples were genotyped with the set of 2,535 SNPs on BTA6 that were imbedded in the Illumina bovine 50 k chip. A linkage disequilibrium variance component mapping (LDVCM method, which exploited both linkage between sires and their steers and population-wide linkage disequilibrium, was applied to detect QTL for four carcass quality traits. Fifteen QTL were detected at 0.1% comparison-wise level, for which five, three, five, and two QTL were associated with carcass weight (CWT, backfat thickness (BFT, longissimus dorsi muscle area (LMA, and marbling score (Marb, respectively. The number of QTL was greater compared with our previous results, in which twelve QTL for carcass quality were detected on the BTA6 in the same population by applying other linkage disequilibrium mapping approaches. One QTL for LMA was detected on the distal region (110,285,672 to 110,633,096 bp with the most significant evidence for linkage (p<10−5. Another QTL that was detected on the proximal region (33,596,515 to 33,897,434 bp was pleiotrophic, i.e. influencing CWT, BFT, and LMA. Our results suggest that the LDVCM is a good alternative method for QTL fine-mapping in detection and characterization of QTL.

  5. 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.

  6. QTL analyses on genotype-specific component traits in a crop simulation model for capsicum annuum L.

    NARCIS (Netherlands)

    Wubs, A.M.; Heuvelink, E.; Dieleman, J.A.; Magan, J.J.; Palloix, A.; Eeuwijk, van F.A.

    2012-01-01

    Abstract: QTL for a complex trait like yield tend to be unstable across environments and show QTL by environment interaction. Direct improvement of complex traits by selecting on QTL is therefore difficult. For improvement of complex traits, crop growth models can be useful, as such models can

  7. Adaptive linear rank tests for eQTL studies.

    Science.gov (United States)

    Szymczak, Silke; Scheinhardt, Markus O; Zeller, Tanja; Wild, Philipp S; Blankenberg, Stefan; Ziegler, Andreas

    2013-02-10

    Expression quantitative trait loci (eQTL) studies are performed to identify single-nucleotide polymorphisms that modify average expression values of genes, proteins, or metabolites, depending on the genotype. As expression values are often not normally distributed, statistical methods for eQTL studies should be valid and powerful in these situations. Adaptive tests are promising alternatives to standard approaches, such as the analysis of variance or the Kruskal-Wallis test. In a two-stage procedure, skewness and tail length of the distributions are estimated and used to select one of several linear rank tests. In this study, we compare two adaptive tests that were proposed in the literature using extensive Monte Carlo simulations of a wide range of different symmetric and skewed distributions. We derive a new adaptive test that combines the advantages of both literature-based approaches. The new test does not require the user to specify a distribution. It is slightly less powerful than the locally most powerful rank test for the correct distribution and at least as powerful as the maximin efficiency robust rank test. We illustrate the application of all tests using two examples from different eQTL studies. Copyright © 2012 John Wiley & Sons, Ltd.

  8. Soft rot erwiniae: from genes to genomes.

    Science.gov (United States)

    Toth, Ian K; Bell, Kenneth S; Holeva, Maria C; Birch, Paul R J

    2003-01-01

    SUMMARY The soft rot erwiniae, Erwinia carotovora ssp. atroseptica (Eca), E. carotovora ssp. carotovora (Ecc) and E. chrysanthemi (Ech) are major bacterial pathogens of potato and other crops world-wide. We currently understand much about how these bacteria attack plants and protect themselves against plant defences. However, the processes underlying the establishment of infection, differences in host range and their ability to survive when not causing disease, largely remain a mystery. This review will focus on our current knowledge of pathogenesis in these organisms and discuss how modern genomic approaches, including complete genome sequencing of Eca and Ech, may open the door to a new understanding of the potential subtlety and complexity of soft rot erwiniae and their interactions with plants. The soft rot erwiniae are members of the Enterobacteriaceae, along with other plant pathogens such as Erwinia amylovora and human pathogens such as Escherichia coli, Salmonella spp. and Yersinia spp. Although the genus name Erwinia is most often used to describe the group, an alternative genus name Pectobacterium was recently proposed for the soft rot species. Ech mainly affects crops and other plants in tropical and subtropical regions and has a wide host range that includes potato and the important model host African violet (Saintpaulia ionantha). Ecc affects crops and other plants in subtropical and temperate regions and has probably the widest host range, which also includes potato. Eca, on the other hand, has a host range limited almost exclusively to potato in temperate regions only. Disease symptoms: Soft rot erwiniae cause general tissue maceration, termed soft rot disease, through the production of plant cell wall degrading enzymes. Environmental factors such as temperature, low oxygen concentration and free water play an essential role in disease development. On potato, and possibly other plants, disease symptoms may differ, e.g. blackleg disease is associated

  9. QTL for the species-specific male and female genital morphologies in Ohomopterus ground beetles.

    Science.gov (United States)

    Sasabe, Masataka; Takami, Yasuoki; Sota, Teiji

    2010-12-01

    Animals with internal fertilization often exhibit marked diversification in genital morphology among closely related species. However, our knowledge of the genetic architecture underlying genital evolution is still limited. We constructed genetic linkage maps and analysed quantitative trait loci (QTL) for F(2) hybrids of two closely related species of the carabid beetles Carabus (Ohomopterus) iwawakianus and C. (O.) maiyasanus, which show matching male and female genital shapes within species, but marked differences in genital morphologies between species. The linkage maps comprised both amplified fragment length polymorphism and microsatellite markers. Composite interval mapping to detect QTL for three traits of male copulatory piece (length, width, weight) and two traits for female vaginal appendix (length, width) resulted in the detection of one to five significant QTL for each trait. The QTL explained large proportions of phenotypic variance. Thus, the interspecific difference in the genital morphologies appeared to be determined by relatively small numbers of genes with large genetic effects. QTL of different traits for the same or different sexes co-occurred on five of eight linkage groups with significant QTL; in particular, three QTL for different male and female genital traits occurred almost at the same position. Each of the male genital traits showed uniform signs of additive genetic effects, suggesting that directional selection has led to species-specific morphologies. However, the signs of additive genetic effects in each female genital trait were not uniform, suggesting that coevolution between sexes is not necessarily concerted. This result requires further assessment because the sample size of F(2) females was small. © 2010 Blackwell Publishing Ltd.

  10. Structure of Rot, a global regulator of virulence genes in Staphylococcus aureus.

    Science.gov (United States)

    Zhu, Yuwei; Fan, Xiaojiao; Zhang, Xu; Jiang, Xuguang; Niu, Liwen; Teng, Maikun; Li, Xu

    2014-09-01

    Staphylococcus aureus is a highly versatile pathogen that can infect human tissue by producing a large arsenal of virulence factors that are tightly regulated by a complex regulatory network. Rot, which shares sequence similarity with SarA homologues, is a global regulator that regulates numerous virulence genes. However, the recognition model of Rot for the promoter region of target genes and the putative regulation mechanism remain elusive. In this study, the 1.77 Å resolution X-ray crystal structure of Rot is reported. The structure reveals that two Rot molecules form a compact homodimer, each of which contains a typical helix-turn-helix module and a β-hairpin motif connected by a flexible loop. Fluorescence polarization results indicate that Rot preferentially recognizes AT-rich dsDNA with ~30-base-pair nucleotides and that the conserved positively charged residues on the winged-helix motif are vital for binding to the AT-rich dsDNA. It is proposed that the DNA-recognition model of Rot may be similar to that of SarA, SarR and SarS, in which the helix-turn-helix motifs of each monomer interact with the major grooves of target dsDNA and the winged motifs contact the minor grooves. Interestingly, the structure shows that Rot adopts a novel dimerization model that differs from that of other SarA homologues. As expected, perturbation of the dimer interface abolishes the dsDNA-binding ability of Rot, suggesting that Rot functions as a dimer. In addition, the results have been further confirmed in vivo by measuring the transcriptional regulation of α-toxin, a major virulence factor produced by most S. aureus strains.

  11. Multi-environment analysis and improved mapping of a yield-related QTL on chromosome 3B of wheat.

    Science.gov (United States)

    Bonneau, Julien; Taylor, Julian; Parent, Boris; Bennett, Dion; Reynolds, Matthew; Feuillet, Catherine; Langridge, Peter; Mather, Diane

    2013-03-01

    Improved mapping, multi-environment quantitative trait loci (QTL) analysis and dissection of allelic effects were used to define a QTL associated with grain yield, thousand grain weight and early vigour on chromosome 3BL of bread wheat (Triticum aestivum L.) under abiotic stresses. The QTL had pleiotropic effects and showed QTL x environment interactions across 21 diverse environments in Australia and Mexico. The occurrence and the severity of water deficit combined with high temperatures during the growing season affected the responsiveness of this QTL, resulting in a reversal in the direction of allelic effects. The influence of this QTL can be substantial, with the allele from one parent (RAC875) increasing grain yield by up to 12.5 % (particularly in environments where both heat and drought stress occurred) and the allele from the other parent (Kukri) increasing grain yield by up to 9 % in favourable environments. With the application of additional markers and the genotyping of additional recombinant inbred lines, the genetic map in the QTL region was refined to provide a basis for future positional cloning.

  12. Short communication: QTL mapping for ear tip-barrenness in maize

    Energy Technology Data Exchange (ETDEWEB)

    Ding, J.; Ma, J.; Chen, J.; Ai, T.; Li, Z.; Tian, Z.; Wu, S.; Chen, W.; Wu, J.

    2016-11-01

    Barren tip on corn ear is an important agronomic trait in maize, which is highly associated with grain yield. Understanding the genetic basis of tip-barrenness may help to reduce the ear tip-barrenness in breeding programs. In this study, ear tip-barrenness was evaluated in two environments in a F2:3 population, and it showed significant genotypic variation for ear tip-barrenness in both environments. Using mixed-model composite interval mapping method, three additive effects quantitative trait loci (QTL) for ear tip-barrenness were mapped on chromosomes 2, 3 and 6, respectively. They explained 16.6% of the phenotypic variation, and no significant QTL × Environment interactions and digenic interactions were detected. The results indicated that additive effect was the main genetic basis for ear tip-barrenness in maize. This is the first report of QTL mapped for ear tip-barrenness in maize. (Author)

  13. Detection of nitrogen deficiency QTL in juvenile wild barley introgression lines growing in a hydroponic system.

    Science.gov (United States)

    Hoffmann, Astrid; Maurer, Andreas; Pillen, Klaus

    2012-10-20

    In this report we studied the genetic regulation of juvenile development of wild barley introgression lines (S42ILs) under two contrasting hydroponic nitrogen (N) supplies. Ten shoot and root related traits were examined among 42 S42ILs and the recurrent parent 'Scarlett'. The traits included tiller number, leaf number, plant height, leaf and root length, leaf to root length ratio, shoots and root dry weight, shoot to root weight ratio, and chlorophyll content. Our aims were (1) to test the suitability of a hydroponic system for early detection of favourable S42ILs, (2) to locate quantitative trait loci (QTL) that control the examined traits, (3) to identify favourable wild barley alleles that improve trait performances in regard to N treatment and, finally, (4) to validate the identified QTL through comparison with previously reported QTL originating from the same parental cross. The phenotypic data were analysed in a mixed model association study to detect QTL. The post-hoc Dunnett test identified 28 S42ILs that revealed significant (P hydroponic N study corresponded to QTL that were also detected in field trials with adult plants of a similar S42IL set or of the original S42 population. For instance, S42IL-135, -136 and -137, revealed increasing Hsp effects for tiller number, leaf number, leaf length, plant height and leaf to root ratio on the long arm of chromosome 7H. These QTL correspond to QTL for ears per plant and plant height that were previously detected in field trials conducted with the same S42ILs or with the S42 population. Our results suggest that the QTL we identified under hydroponic N cultivation partly correspond to QTL detected in field experiments. Due to this finding, screening of plants in early developmental stages grown in a hydroponic system may be a fast and cost effective method for early QTL detection and marker-assisted allelic selection, potentially speeding up elite barley breeding programs.

  14. Weevil - red rot associations in eastern white pine

    Science.gov (United States)

    Myron D. Ostrander; Clifford H. Foster

    1957-01-01

    The presence of red rot (Fomes pini) in pruned white pine stands has often been attributed to the act of pruning. This assumption may well be true for heavily stocked stands where thinning has been neglected and pruning scars are slow to heal. The question then arises: How do we account for the red rot often found in vigorous unpruned white pine stands? Evidence...

  15. Fine Mapping of qroot-yield-1.06, a QTL for Root, Plant Vigor and Yield in Maize

    OpenAIRE

    Martinez Ascanio, Ana Karine

    2015-01-01

    Root-yield-1.06 is a major QTL affecting root system architecture (RSA) and other agronomic traits in maize. The effect of this QTL has been evaluated with the development of near isogenic lines (NILs) differing at the QTL position. The objective of this study was to fine map qroot-yield-1.06 by marker-assisted searching for chromosome recombinants in the QTL interval and concurrent root phenotyping in both controlled and field conditions, through successive generations. Complementary approac...

  16. A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification

    Directory of Open Access Journals (Sweden)

    Daniel Fulop

    2016-10-01

    Full Text Available Quantitative Trait Loci (QTL mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum and its more distant interfertile relatives typically follow a near isogenic line (NIL design, such as the S. pennellii Introgression Line (IL population, with a single wild introgression per line in an otherwise domesticated genetic background. Here, we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennellii. This so-called Backcrossed Inbred Line (BIL population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs, we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous hidden Markov model for genotyping the lines, and by using state-of-the-art sparse regression techniques for QTL mapping.

  17. Detection of nitrogen deficiency QTL in juvenile wild barley introgression lines growing in a hydroponic system

    Directory of Open Access Journals (Sweden)

    Hoffmann Astrid

    2012-10-01

    Full Text Available Abstract Background In this report we studied the genetic regulation of juvenile development of wild barley introgression lines (S42ILs under two contrasting hydroponic nitrogen (N supplies. Ten shoot and root related traits were examined among 42 S42ILs and the recurrent parent ‘Scarlett’. The traits included tiller number, leaf number, plant height, leaf and root length, leaf to root length ratio, shoots and root dry weight, shoot to root weight ratio, and chlorophyll content. Our aims were (1 to test the suitability of a hydroponic system for early detection of favourable S42ILs, (2 to locate quantitative trait loci (QTL that control the examined traits, (3 to identify favourable wild barley alleles that improve trait performances in regard to N treatment and, finally, (4 to validate the identified QTL through comparison with previously reported QTL originating from the same parental cross. Results The phenotypic data were analysed in a mixed model association study to detect QTL. The post-hoc Dunnett test identified 28 S42ILs that revealed significant (P Hsp effects for tiller number, leaf number, leaf length, plant height and leaf to root ratio on the long arm of chromosome 7H. These QTL correspond to QTL for ears per plant and plant height that were previously detected in field trials conducted with the same S42ILs or with the S42 population. Conclusion Our results suggest that the QTL we identified under hydroponic N cultivation partly correspond to QTL detected in field experiments. Due to this finding, screening of plants in early developmental stages grown in a hydroponic system may be a fast and cost effective method for early QTL detection and marker-assisted allelic selection, potentially speeding up elite barley breeding programs.

  18. Reaction of Cauliflower Genotypes to Black Rot of Crucifers

    Directory of Open Access Journals (Sweden)

    Lincon Rafael da Silva

    2015-06-01

    Full Text Available This study aimed to evaluate six cauliflower genotypes regarding their resistance to black rot and their production performance. To do so, it was conducted two field experiments in Ipameri, Goiás, Brazil, in 2012 and 2013. It was used a randomized block design, with four replications (total of 24 plots. Each plot consisted of three planting lines 2.5 m long (six plants/line, spaced 1.0 m apart, for a total area of 7.5 m². Evaluations of black rot severity were performed at 45 days after transplanting, this is, 75 days after sowing (DAS, and yield evaluations at 90 to 105 DAS. The Verona 184 genotype was the most resistant to black rot, showing 1.87 and 2.25% of leaf area covered by black rot symptom (LACBRS in 2012 and 2013. However, it was not among the most productive materials. The yield of the genotypes varied between 15.14 and 25.83 t/ha in both years, Lisvera F1 (21.78 and 24.60 t/ha and Cindy (19.95 and 23.56 t/ha being the most productive. However, Lisvera F1 showed 6.37 and 9.37% of LACBRS and Cindy showed 14.25 and 14.87% of LACBRS in 2012 and 2013, being both considered as tolerant to black rot.

  19. A network based covariance test for detecting multivariate eQTL in saccharomyces cerevisiae.

    Science.gov (United States)

    Yuan, Huili; Li, Zhenye; Tang, Nelson L S; Deng, Minghua

    2016-01-11

    Expression quantitative trait locus (eQTL) analysis has been widely used to understand how genetic variations affect gene expressions in the biological systems. Traditional eQTL is investigated in a pair-wise manner in which one SNP affects the expression of one gene. In this way, some associated markers found in GWAS have been related to disease mechanism by eQTL study. However, in real life, biological process is usually performed by a group of genes. Although some methods have been proposed to identify a group of SNPs that affect the mean of gene expressions in the network, the change of co-expression pattern has not been considered. So we propose a process and algorithm to identify the marker which affects the co-expression pattern of a pathway. Considering two genes may have different correlations under different isoforms which is hard to detect by the linear test, we also consider the nonlinear test. When we applied our method to yeast eQTL dataset profiled under both the glucose and ethanol conditions, we identified a total of 166 modules, with each module consisting of a group of genes and one eQTL where the eQTL regulate the co-expression patterns of the group of genes. We found that many of these modules have biological significance. We propose a network based covariance test to identify the SNP which affects the structure of a pathway. We also consider the nonlinear test as considering two genes may have different correlations under different isoforms which is hard to detect by linear test.

  20. An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome.

    Science.gov (United States)

    Ng, Bernard; White, Charles C; Klein, Hans-Ulrich; Sieberts, Solveig K; McCabe, Cristin; Patrick, Ellis; Xu, Jishu; Yu, Lei; Gaiteri, Chris; Bennett, David A; Mostafavi, Sara; De Jager, Philip L

    2017-10-01

    We report a multi-omic resource generated by applying quantitative trait locus (xQTL) analyses to RNA sequence, DNA methylation and histone acetylation data from the dorsolateral prefrontal cortex of 411 older adults who have all three data types. We identify SNPs significantly associated with gene expression, DNA methylation and histone modification levels. Many of these SNPs influence multiple molecular features, and we demonstrate that SNP effects on RNA expression are fully mediated by epigenetic features in 9% of these loci. Further, we illustrate the utility of our new resource, xQTL Serve, by using it to prioritize the cell type(s) most affected by an xQTL. We also reanalyze published genome wide association studies using an xQTL-weighted analysis approach and identify 18 new schizophrenia and 2 new bipolar susceptibility variants, which is more than double the number of loci that can be discovered with a larger blood-based expression eQTL resource.

  1. Cellulose Degradation by Cellulose-Clearing and Non-Cellulose-Clearing Brown-Rot Fungi

    OpenAIRE

    Highley, Terry L.

    1980-01-01

    Cellulose degradation by four cellulose-clearing brown-rot fungi in the Coniophoraceae—Coniophora prasinoides, C. puteana, Leucogyrophana arizonica, and L. olivascens—is compared with that of a non-cellulose-clearing brown-rot fungus, Poria placenta. The cellulose- and the non-cellulose-clearing brown-rot fungi apparently employ similar mechanisms to depolymerize cellulose; most likely a nonenzymatic mechanism is involved.

  2. Biological Control of White Rot in Garlic Using Burkholderia pyrrocinia CAB08106-4

    Directory of Open Access Journals (Sweden)

    Kwang Seop Han

    2013-03-01

    Full Text Available White rot caused by Sclerotium cepivorum was reported to be severe soil-born disease on garlic. Disease progress of white rot of garlic (Allium sativum L. was investigated during the growing season of 2009 to 2011 at Taean and Seosan areas. The white rot disease on bulb began to occur from late April and peaked in late May. The antifungal bacteria, Burkholderia pyrrocinia CAB08106-4 was tested in field bioassay for suppression of white rot disease. As a result of the nucleotide sequence of the gene 16S rRNA, CAB008106-4 strain used in this study has been identified as B. pyrrocinia. B. pyrrocinia CAB080106-4 isolate suppressed the white rot with 69.6% control efficacy in field test. These results suggested that B. pyrrocinia CAB08106-4 isolate could be an effective biological control agent against white rot of garlic.

  3. Mapping QTL for Sex and Growth Traits in Salt-Tolerant Tilapia (Oreochromis spp. X O. mossambicus).

    Science.gov (United States)

    Lin, Grace; Chua, Elaine; Orban, Laszlo; Yue, Gen Hua

    2016-01-01

    In aquaculture, growth and sex are economically important traits. To accelerate genetic improvement in increasing growth in salt-tolerant tilapia, we conducted QTL mapping for growth traits and sex with an F2 family, including 522 offspring and two parents. We used 144 polymorphic microsatellites evenly covering the genome of tilapia to genotype the family. QTL analyses were carried out using interval mapping for all individuals, males and females in the family, respectively. Using all individuals, three suggestive QTL for body weight, body length and body thickness respectively were detected in LG20, LG22 and LG12 and explained 2.4% to 3.1% of phenotypic variance (PV). When considering only males, five QTL for body weight were detected on five LGs, and explained 4.1 to 6.3% of PV. Using only females from the F2 family, three QTL for body weight were detected on LG1, LG6 and LG8, and explained 7.9-14.3% of PV. The QTL for body weight in males and females were located in different LGs, suggesting that in salt-tolerant tilapia, different set of genes 'switches' control the growth in males and females. QTL for sex were mapped on LG1 and LG22, indicating multigene sex determination in the salt-tolerant tilapia. This study provides new insights on the locations and effects of QTL for growth traits and sex, and sets the foundation for fine mapping for future marker-assisted selection for growth and sex in salt-tolerant tilapia aquaculture.

  4. Biocontrol of charcoal-rot of sorghum by actinomycetes isolated from ...

    African Journals Online (AJOL)

    use

    2011-12-12

    Dec 12, 2011 ... Streptomyces but with different species in BLAST analysis. This study indicates that the selected actinomycetes have the potential for PGP and control of charcoal-rot disease in sorghum. Key words: Antagonistic actinomycetes, biocontrol, charcoal-rot, Macrophomina phaseolina. INTRODUCTION.

  5. Improvement of resistance to Fusarium root rot through gene ...

    African Journals Online (AJOL)

    Fusarium root rot (FRR), caused by Fusarium solani f.sp. , is one of the most serious root rot diseases of common bean (Phaseolus vulgaris L.) throughout the world. Yield losses of up to 84% have been attributed to the disease. Development and deployment of resistant materials is the most feasible approach to managing ...

  6. Efficient computation of the inverse of gametic relationship matrix for a marked QTL

    Directory of Open Access Journals (Sweden)

    Iwaisaki Hiroaki

    2006-04-01

    Full Text Available Abstract Best linear unbiased prediction of genetic merits for a marked quantitative trait locus (QTL using mixed model methodology includes the inverse of conditional gametic relationship matrix (G-1 for a marked QTL. When accounting for inbreeding, the conditional gametic relationships between two parents of individuals for a marked QTL are necessary to build G-1 directly. Up to now, the tabular method and its adaptations have been used to compute these relationships. In the present paper, an indirect method was implemented at the gametic level to compute these few relationships. Simulation results showed that the indirect method can perform faster with significantly less storage requirements than adaptation of the tabular method. The efficiency of the indirect method was mainly due to the use of the sparseness of G-1. The indirect method can also be applied to construct an approximate G-1 for populations with incomplete marker data, providing approximate probabilities of descent for QTL alleles for individuals with incomplete marker data.

  7. High-throughput phenotyping to detect drought tolerance QTL in wild barley introgression lines

    KAUST Repository

    Honsdorf, Nora

    2014-05-13

    Drought is one of the most severe stresses, endangering crop yields worldwide. In order to select drought tolerant genotypes, access to exotic germplasm and efficient phenotyping protocols are needed. In this study the high-throughput phenotyping platform "The Plant Accelerator", Adelaide, Australia, was used to screen a set of 47 juvenile (six week old) wild barley introgression lines (S42ILs) for drought stress responses. The kinetics of growth development was evaluated under early drought stress and well watered treatments. High correlation (r = 0.98) between image based biomass estimates and actual biomass was demonstrated, and the suitability of the system to accurately and non-destructively estimate biomass was validated. Subsequently, quantitative trait loci (QTL) were located, which contributed to the genetic control of growth under drought stress. In total, 44 QTL for eleven out of 14 investigated traits were mapped, which for example controlled growth rate and water use efficiency. The correspondence of those QTL with QTL previously identified in field trials is shown. For instance, six out of eight QTL controlling plant height were also found in previous field and glasshouse studies with the same introgression lines. This indicates that phenotyping juvenile plants may assist in predicting adult plant performance. In addition, favorable wild barley alleles for growth and biomass parameters were detected, for instance, a QTL that increased biomass by approximately 36%. In particular, introgression line S42IL-121 revealed improved growth under drought stress compared to the control Scarlett. The introgression line showed a similar behavior in previous field experiments, indicating that S42IL-121 may be an attractive donor for breeding of drought tolerant barley cultivars. © 2014 Honsdorf et al.

  8. High-throughput phenotyping to detect drought tolerance QTL in wild barley introgression lines.

    Directory of Open Access Journals (Sweden)

    Nora Honsdorf

    Full Text Available Drought is one of the most severe stresses, endangering crop yields worldwide. In order to select drought tolerant genotypes, access to exotic germplasm and efficient phenotyping protocols are needed. In this study the high-throughput phenotyping platform "The Plant Accelerator", Adelaide, Australia, was used to screen a set of 47 juvenile (six week old wild barley introgression lines (S42ILs for drought stress responses. The kinetics of growth development was evaluated under early drought stress and well watered treatments. High correlation (r=0.98 between image based biomass estimates and actual biomass was demonstrated, and the suitability of the system to accurately and non-destructively estimate biomass was validated. Subsequently, quantitative trait loci (QTL were located, which contributed to the genetic control of growth under drought stress. In total, 44 QTL for eleven out of 14 investigated traits were mapped, which for example controlled growth rate and water use efficiency. The correspondence of those QTL with QTL previously identified in field trials is shown. For instance, six out of eight QTL controlling plant height were also found in previous field and glasshouse studies with the same introgression lines. This indicates that phenotyping juvenile plants may assist in predicting adult plant performance. In addition, favorable wild barley alleles for growth and biomass parameters were detected, for instance, a QTL that increased biomass by approximately 36%. In particular, introgression line S42IL-121 revealed improved growth under drought stress compared to the control Scarlett. The introgression line showed a similar behavior in previous field experiments, indicating that S42IL-121 may be an attractive donor for breeding of drought tolerant barley cultivars.

  9. A high-density SNP map for accurate mapping of seed fibre QTL in Brassica napus L.

    Directory of Open Access Journals (Sweden)

    Liezhao Liu

    Full Text Available A high density genetic linkage map for the complex allotetraploid crop species Brassica napus (oilseed rape was constructed in a late-generation recombinant inbred line (RIL population, using genome-wide single nucleotide polymorphism (SNP markers assayed by the Brassica 60 K Infinium BeadChip Array. The linkage map contains 9164 SNP markers covering 1832.9 cM. 1232 bins account for 7648 of the markers. A subset of 2795 SNP markers, with an average distance of 0.66 cM between adjacent markers, was applied for QTL mapping of seed colour and the cell wall fiber components acid detergent lignin (ADL, cellulose and hemicellulose. After phenotypic analyses across four different environments a total of 11 QTL were detected for seed colour and fiber traits. The high-density map considerably improved QTL resolution compared to the previous low-density maps. A previously identified major QTL with very high effects on seed colour and ADL was pinpointed to a narrow genome interval on chromosome A09, while a minor QTL explaining 8.1% to 14.1% of variation for ADL was detected on chromosome C05. Five and three QTL accounting for 4.7% to 21.9% and 7.3% to 16.9% of the phenotypic variation for cellulose and hemicellulose, respectively, were also detected. To our knowledge this is the first description of QTL for seed cellulose and hemicellulose in B. napus, representing interesting new targets for improving oil content. The high density SNP genetic map enables navigation from interesting B. napus QTL to Brassica genome sequences, giving useful new information for understanding the genetics of key seed quality traits in rapeseed.

  10. DEGRADATION OF TEXTILE DYES BY WHITE ROT BASIDIOMYCETES

    OpenAIRE

    B.P. PARMAR, P.N. MERVANA B.R.M. VYAS*

    2014-01-01

    ABSTRACT: Dyes released by the textile industries pose a threat to environmental quality. Ligninolytic white-rot basidiomycetes can effectively degrade colored effluents and conventional dyes. White-rot fungi produce various isoforms of extracellular oxidases including laccase, Mn peroxidase and lignin peroxidase (LiP), which are involved in the degradation of lignin in their natural lignocellulosic substrates.  The textile industry, by far the most avid user of synthetic dyes, is in need...

  11. QTL and QTL x environment effects on agronomic and nitrogen acquisition traits in rice.

    Science.gov (United States)

    Senthilvel, Senapathy; Vinod, Kunnummal Kurungara; Malarvizhi, Palaniappan; Maheswaran, Marappa

    2008-09-01

    Agricultural environments deteriorate due to excess nitrogen application. Breeding for low nitrogen responsive genotypes can reduce soil nitrogen input. Rice genotypes respond variably to soil available nitrogen. The present study attempted quantification of genotype x nitrogen level interaction and mapping of quantitative trait loci (QTLs) associated with nitrogen use efficiency (NUE) and other associated agronomic traits. Twelve parameters were observed across a set of 82 double haploid (DH) lines derived from IR64/Azucena. Three nitrogen regimes namely, native (0 kg/ha; no nitrogen applied), optimum (100 kg/ha) and high (200 kg/ha) replicated thrice were the environments. The parents and DH lines were significantly varying for all traits under different nitrogen regimes. All traits except plant height recorded significant genotype x environment interaction. Individual plant yield was positively correlated with nitrogen use efficiency and nitrogen uptake. Sixteen QTLs were detected by composite interval mapping. Eleven QTLs showed significant QTL x environment interactions. On chromosome 3, seven QTLs were detected associated with nitrogen use, plant yield and associated traits. A QTL region between markers RZ678, RZ574 and RZ284 was associated with nitrogen use and yield. This chromosomal region was enriched with expressed gene sequences of known key nitrogen assimilation genes.

  12. Molecular mapping of QTL alleles of Brassica oleracea affecting days to flowering and photosensitivity in spring Brassica napus.

    Science.gov (United States)

    Rahman, Habibur; Bennett, Rick A; Kebede, Berisso

    2018-01-01

    Earliness of flowering and maturity are important traits in spring Brassica napus canola-whether grown under long- or short-day condition. By use of a spring B. napus mapping population carrying the genome content of B. oleracea and testing this population under 10 to 18 h photoperiod and 18 to 20 0C (day) temperature conditions, we identified a major QTL on the chromosome C1 affecting flowering time without being influenced by photoperiod and temperature, and a major QTL on C9 affecting flowering time under a short photoperiod (10 h); in both cases, the QTL alleles reducing the number of days to flowering in B. napus were introgressed from the late flowering species B. oleracea. Additive effect of the C1 QTL allele at 14 to18 h photoperiod was 1.1 to 2.9 days; however, the same QTL allele exerted an additive effect of 6.2 days at 10 h photoperiod. Additive effect of the C9 QTL at 10 h photoperiod was 2.8 days. These two QTL also showed significant interaction in the control of flowering only under a short-day (10 h photoperiod) condition with an effect of 2.3 days. A few additional QTL were also detected on the chromosomes C2 and C8; however, none of these QTL could be detected under all photoperiod and temperature conditions. BLASTn search identified several putative flowering time genes on the chromosomes C1 and C9 and located the physical position of the QTL markers in the Brassica genome; however, only a few of these genes were found within the QTL region. Thus, the molecular markers and the genomic regions identified in this research could potentially be used in breeding for the development of early flowering photoinsensitive B. napus canola cultivars, as well as for identification of candidate genes involved in flowering time variation and photosensitivity.

  13. Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs.

    Science.gov (United States)

    Jouffe, Vincent; Rowe, Suzanne; Liaubet, Laurence; Buitenhuis, Bart; Hornshøj, Henrik; SanCristobal, Magali; Mormède, Pierre; de Koning, D J

    2009-07-16

    Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link this with information on published QTL. The starting point is a set of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH). Different approaches to localize the differentially expressed (DE) genes to the pig genome showed different levels of success and a clear lack of concordance for some genes between the various approaches. For a focused analysis on 12 genes, overlapping QTL from the public domain were presented. Also, differentially expressed genes underlying QTL for ACTH response were described. Using the latest version of the draft sequence, the differentially expressed genes were mapped to the pig genome. This enabled co-location of DE genes and previously studied QTL regions, but the draft genome sequence is still incomplete and will contain many errors. A further step to explore links between DE genes and QTL at the pathway level was largely unsuccessful due to the lack of annotation of the pig genome. This could be improved by further comparative mapping analyses but this would be time consuming. This paper provides a case study for the integration of QTL data and microarray data for a species with limited genome sequence information and annotation. The results illustrate the challenges that must be addressed but also provide a roadmap for future work that is applicable to other non-model species.

  14. ( Azadirachta Indica ) Leaf Extracts on the Rot Fungus ( Fusarium ...

    African Journals Online (AJOL)

    The storage lifespan of kola nuts is challenged by the problem of decay of nuts in storage as a result of the attack by the rot fungus (Fusarium spp). The effect of the neem leaf (Azadirachta indica) extracts on the rot fungus was investigated in order to aid extended kola nuts storage. The aqueous and ethanolic leaf extracts of ...

  15. Identification of seed-related QTL in Brassica rapa

    Directory of Open Access Journals (Sweden)

    H. Bagheri

    2013-10-01

    Full Text Available To reveal the genetic variation, and loci involved, for a range of seed-related traits, a new F2 mapping population was developed by crossing Brassica rapa ssp. parachinensis L58 (CaiXin with B. rapa ssp. trilocularis R-o-18 (spring oil seed, both rapid flowering and self-compatible. A linkage map was constructed using 97 AFLPs and 21 SSRs, covering a map distance of 757 cM with an average resolution of 6.4 cM, and 13 quantitative trait loci (QTL were detected for nine traits. A strong seed colour QTL (LOD 26 co-localized with QTL for seed size (LOD 7, seed weight (LOD 4.6, seed oil content (LOD 6.6, number of siliques (LOD 3 and number of seeds per silique (LOD 3. There was only a significant positive correlation between seed colour and seed oil content in the yellow coloured classes. Seed coat colour and seed size were controlled by the maternal plant genotype. Plants with more siliques tended to have more, but smaller, seeds and higher seed oil content. Seed colour and seed oil content appeared to be controlled by two closely linked loci in repulsion phase. Thus, it may not always be advantageous to select for yellow-seededness when breeding for high seed oil content in Brassicas.

  16. Genome-wide association mapping of partial resistance to Phytophthora sojae in soybean plant introductions from the Republic of Korea.

    Science.gov (United States)

    Schneider, Rhiannon; Rolling, William; Song, Qijian; Cregan, Perry; Dorrance, Anne E; McHale, Leah K

    2016-08-11

    Phytophthora root and stem rot is one of the most yield-limiting diseases of soybean [Glycine max (L.) Merr], caused by the oomycete Phytophthora sojae. Partial resistance is controlled by several genes and, compared to single gene (Rps gene) resistance to P. sojae, places less selection pressure on P. sojae populations. Thus, partial resistance provides a more durable resistance against the pathogen. In previous work, plant introductions (PIs) originating from the Republic of Korea (S. Korea) have shown to be excellent sources for high levels of partial resistance against P. sojae. Resistance to two highly virulent P. sojae isolates was assessed in 1395 PIs from S. Korea via a greenhouse layer test. Lines exhibiting possible Rps gene immunity or rot due to other pathogens were removed and the remaining 800 lines were used to identify regions of quantitative resistance using genome-wide association mapping. Sixteen SNP markers on chromosomes 3, 13 and 19 were significantly associated with partial resistance to P. sojae and were grouped into seven quantitative trait loci (QTL) by linkage disequilibrium blocks. Two QTL on chromosome 3 and three QTL on chromosome 19 represent possible novel loci for partial resistance to P. sojae. While candidate genes at QTL varied in their predicted functions, the coincidence of QTLs 3-2 and 13-1 on chromosomes 3 and 13, respectively, with Rps genes and resistance gene analogs provided support for the hypothesized mechanism of partial resistance involving weak R-genes. QTL contributing to partial resistance towards P. sojae in soybean germplasm originating from S. Korea were identified. The QTL identified in this study coincide with previously reported QTL, Rps genes, as well as novel loci for partial resistance. Molecular markers associated with these QTL can be used in the marker-assisted introgression of these alleles into elite cultivars. Annotations of genes within QTL allow hypotheses on the possible mechanisms of partial

  17. QTL meta-analysis of root traits in Brassica napus under contrasting phosphorus supply in two growth systems.

    Science.gov (United States)

    Zhang, Ying; Thomas, Catherine L; Xiang, Jinxia; Long, Yan; Wang, Xiaohua; Zou, Jun; Luo, Ziliang; Ding, Guangda; Cai, Hongmei; Graham, Neil S; Hammond, John P; King, Graham J; White, Philip J; Xu, Fangsen; Broadley, Martin R; Shi, Lei; Meng, Jinling

    2016-09-14

    A high-density SNP-based genetic linkage map was constructed and integrated with a previous map in the Tapidor x Ningyou7 (TNDH) Brassica napus population, giving a new map with a total of 2041 molecular markers and an average marker density which increased from 0.39 to 0.97 (0.82 SNP bin) per cM. Root and shoot traits were screened under low and 'normal' phosphate (Pi) supply using a 'pouch and wick' system, and had been screened previously in an agar based system. The P-efficient parent Ningyou7 had a shorter primary root length (PRL), greater lateral root density (LRD) and a greater shoot biomass than the P-inefficient parent Tapidor under both treatments and growth systems. Quantitative trait loci (QTL) analysis identified a total of 131 QTL, and QTL meta-analysis found four integrated QTL across the growth systems. Integration reduced the confidence interval by ~41%. QTL for root and shoot biomass were co-located on chromosome A3 and for lateral root emergence were co-located on chromosomes A4/C4 and C8/C9. There was a major QTL for LRD on chromosome C9 explaining ~18% of the phenotypic variation. QTL underlying an increased LRD may be a useful breeding target for P uptake efficiency in Brassica.

  18. 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).

  19. Internal Rot Detection with the Use of Low-Frequency Flaw Detector

    Science.gov (United States)

    Proskórnicki, Marek; Ligus, Grzegorz

    2014-12-01

    The issue of rot detection in standing timber or stocked wood is very important in forest management. Rot flaw detection used for that purpose is represented by invasive and non-invasive devices. Non-invasive devices are very accurate, but due to the cost and complicated operation they have not been applied on a large scale in forest management. Taking into account the practical needs of foresters a prototype of low-frequency flaw was developed. The principle of its operation is based on the difference in acoustic wave propagation in sound wood and wood with rot.

  20. Genetic dissection of the Drosophila melanogaster female head transcriptome reveals widespread allelic heterogeneity.

    Science.gov (United States)

    King, Elizabeth G; Sanderson, Brian J; McNeil, Casey L; Long, Anthony D; Macdonald, Stuart J

    2014-05-01

    Modern genetic mapping is plagued by the "missing heritability" problem, which refers to the discordance between the estimated heritabilities of quantitative traits and the variance accounted for by mapped causative variants. One major potential explanation for the missing heritability is allelic heterogeneity, in which there are multiple causative variants at each causative gene with only a fraction having been identified. The majority of genome-wide association studies (GWAS) implicitly assume that a single SNP can explain all the variance for a causative locus. However, if allelic heterogeneity is prevalent, a substantial amount of genetic variance will remain unexplained. In this paper, we take a haplotype-based mapping approach and quantify the number of alleles segregating at each locus using a large set of 7922 eQTL contributing to regulatory variation in the Drosophila melanogaster female head. Not only does this study provide a comprehensive eQTL map for a major community genetic resource, the Drosophila Synthetic Population Resource, but it also provides a direct test of the allelic heterogeneity hypothesis. We find that 95% of cis-eQTLs and 78% of trans-eQTLs are due to multiple alleles, demonstrating that allelic heterogeneity is widespread in Drosophila eQTL. Allelic heterogeneity likely contributes significantly to the missing heritability problem common in GWAS studies.

  1. 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.

  2. Phenotypic plasticity, QTL mapping and genomic characterization of bud set in black poplar

    Directory of Open Access Journals (Sweden)

    Fabbrini Francesco

    2012-04-01

    Full Text Available Abstract Background The genetic control of important adaptive traits, such as bud set, is still poorly understood in most forest trees species. Poplar is an ideal model tree to study bud set because of its indeterminate shoot growth. Thus, a full-sib family derived from an intraspecific cross of P. nigra with 162 clonally replicated progeny was used to assess the phenotypic plasticity and genetic variation of bud set in two sites of contrasting environmental conditions. Results Six crucial phenological stages of bud set were scored. Night length appeared to be the most important signal triggering the onset of growth cessation. Nevertheless, the effect of other environmental factors, such as temperature, increased during the process. Moreover, a considerable role of genotype × environment (G × E interaction was found in all phenological stages with the lowest temperature appearing to influence the sensitivity of the most plastic genotypes. Descriptors of growth cessation and bud onset explained the largest part of phenotypic variation of the entire process. Quantitative trait loci (QTL for these traits were detected. For the four selected traits (the onset of growth cessation (date2.5, the transition from shoot to bud (date1.5, the duration of bud formation (subproc1 and bud maturation (subproc2 eight and sixteen QTL were mapped on the maternal and paternal map, respectively. The identified QTL, each one characterized by small or modest effect, highlighted the complex nature of traits involved in bud set process. Comparison between map location of QTL and P. trichocarpa genome sequence allowed the identification of 13 gene models, 67 bud set-related expressional and six functional candidate genes (CGs. These CGs are functionally related to relevant biological processes, environmental sensing, signaling, and cell growth and development. Some strong QTL had no obvious CGs, and hold great promise to identify unknown genes that affect bud set

  3. Concordance analysis for QTL detection in dairy cattle: a case study of leg morphology

    DEFF Research Database (Denmark)

    van den Berg, Irene; Rodrigue; Fritz, Sebastien

    2014-01-01

    The present availability of sequence data gives new opportunities to narrow down from QTL (quantitative trait locus) regions to causative mutations. Our objective was to decrease the number of candidate causative mutations in a QTL region. For this, a concordance analysis was applied for a leg co...

  4. Across Breed QTL Detection and Genomic Prediction in French and Danish Dairy Cattle Breeds

    DEFF Research Database (Denmark)

    van den Berg, Irene; Guldbrandtsen, Bernt; Hozé, C

    Our objective was to investigate the potential benefits of using sequence data to improve across breed genomic prediction, using data from five French and Danish dairy cattle breeds. First, QTL for protein yield were detected using high density genotypes. Part of the QTL detected within breed was...

  5. Fungi associated with base rot disease of aloe vera (Aloe ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-12-17

    Dec 17, 2008 ... full base rot disease after 6 days of inoculation. Key words: Fungi, base rot, Aloe vera. INTRODUCTION. Aloe barbadensis Miller, popularly called Aloe vera is a phanerogame angiosperm which belongs to the family. Liliaceae. The plant is a perennial drought resistant succulent plant (Figure 1). Aloe vera is ...

  6. The influence of root rot incidence on cassava genotype on ...

    African Journals Online (AJOL)

    In Nigeria cassava root rot causes serious yield losses in cassava tuber production every year. However, the influence of root rot incidence on cassava genotype at harvest on consumers' acceptability of the gari produced from it has not been studied. A sensory evaluation was conducted on gari processed from the tuberous ...

  7. Resistance to post-harvest microbial rot in yam: Integration of ...

    African Journals Online (AJOL)

    Post-harvest microbial rot is an important disease that causes severe losses in yam (Dioscorea spp.) storage. Rot from microbial infection of healthy yam tubers reduces their table quality and renders them unappealing to consumers. A study was carried out at Bimbilla in the Nanumba North District of Ghana to evaluate ...

  8. Removal of phenanthrene in contaminated soil by combination of alfalfa, white-rot fungus, and earthworms.

    Science.gov (United States)

    Deng, Shuguang; Zeng, Defang

    2017-03-01

    The aim of this study was to investigate the removal of phenanthrene by combination of alfalfa, white-rot fungus, and earthworms in soil. A 60-day experiment was conducted. Inoculation with earthworms and/or white-rot fungus increased alfalfa biomass and phenanthrene accumulation in alfalfa. However, inoculations of alfalfa and white-rot fungus can significantly decrease the accumulation of phenanthrene in earthworms. The removal rates for phenanthrene in soil were 33, 48, 66, 74, 85, and 93% under treatments control, only earthworms, only alfalfa, earthworms + alfalfa, alfalfa + white-rot fungus, and alfalfa + earthworms + white-rot fungus, respectively. The present study demonstrated that the combination of alfalfa, earthworms, and white-rot fungus is an effective way to remove phenanthrene in the soil. The removal is mainly via stimulating both microbial development and soil enzyme activity.

  9. 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

  10. An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice.

    Science.gov (United States)

    Daware, Anurag; Das, Sweta; Srivastava, Rishi; Badoni, Saurabh; Singh, Ashok K; Agarwal, Pinky; Parida, Swarup K; Tyagi, Akhilesh K

    2016-01-01

    Development and use of genome-wide informative simple sequence repeat (SSR) markers and novel integrated genomic strategies are vital to drive genomics-assisted breeding applications and for efficient dissection of quantitative trait loci (QTLs) underlying complex traits in rice. The present study developed 6244 genome-wide informative SSR markers exhibiting in silico fragment length polymorphism based on repeat-unit variations among genomic sequences of 11 indica, japonica, aus , and wild rice accessions. These markers were mapped on diverse coding and non-coding sequence components of known cloned/candidate genes annotated from 12 chromosomes and revealed a much higher amplification (97%) and polymorphic potential (88%) along with wider genetic/functional diversity level (16-74% with a mean 53%) especially among accessions belonging to indica cultivar group, suggesting their utility in large-scale genomics-assisted breeding applications in rice. A high-density 3791 SSR markers-anchored genetic linkage map (IR 64 × Sonasal) spanning 2060 cM total map-length with an average inter-marker distance of 0.54 cM was generated. This reference genetic map identified six major genomic regions harboring robust QTLs (31% combined phenotypic variation explained with a 5.7-8.7 LOD) governing grain weight on six rice chromosomes. One strong grain weight major QTL region ( OsqGW5.1 ) was narrowed-down by integrating traditional QTL mapping with high-resolution QTL region-specific integrated SSR and single nucleotide polymorphism markers-based QTL-seq analysis and differential expression profiling. This led us to delineate two natural allelic variants in two known cis -regulatory elements (RAV1AAT and CARGCW8GAT) of glycosyl hydrolase and serine carboxypeptidase genes exhibiting pronounced seed-specific differential regulation in low (Sonasal) and high (IR 64) grain weight mapping parental accessions. Our genome-wide SSR marker resource (polymorphic within/between diverse

  11. QTL mapping of downy and powdery mildew resistances in PI 197088 cucumber with genotyping-by-sequencing in RIL population.

    Science.gov (United States)

    Wang, Yuhui; VandenLangenberg, Kyle; Wen, Changlong; Wehner, Todd C; Weng, Yiqun

    2018-03-01

    Host resistances in PI 197088 cucumber to downy and powdery mildew pathogens are conferred by 11 (3 with major effect) and 4 (1 major effect) QTL, respectively, and three of which are co-localized. The downy mildew (DM) and powdery mildew (PM) are the two most important foliar diseases of cucurbit crops worldwide. The cucumber accession PI 197088 exhibits high-level resistances to both pathogens. Here, we reported QTL mapping results for DM and PM resistances with 148 recombinant inbred lines from a cross between PI 197088 and the susceptible line 'Coolgreen'. Phenotypic data on responses to natural DM and PM infection were collected in multi-year and multi-location replicated field trials. A high-density genetic map with 2780 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing and 55 microsatellite markers was developed, which revealed genomic regions with segregation distortion and mis-assemblies in the '9930' cucumber draft genome. QTL analysis identified 11 and 4 QTL for DM and PM resistances accounting for more than 73.5 and 63.0% total phenotypic variance, respectively. Among the 11 DM resistance QTL, dm5.1, dm5.2, and dm5.3 were major-effect contributing QTL, whereas dm1.1, dm2.1, and dm6.2 conferred susceptibility. Of the 4 QTL for PM resistance, pm5.1 was the major-effect QTL explaining 32.4% phenotypic variance and the minor-effect QTL pm6.1 contributed to disease susceptibility. Three PM QTL, pm2.1, pm5.1, and pm6.1, were co-localized with DM QTL dm2.1, dm5.2, and dm6.1, respectively, which was consistent with the observed linkage of PM and DM resistances in PI 197088. The genetic architecture of DM resistance in PI 197088 and another resistant line WI7120 (PI 330628) was compared, and the potential of using PI 197088 in cucumber breeding for downy and powdery mildew resistances is discussed.

  12. Application of alternative models to identify QTL for growth traits in an F2 Duroc x Pietrain pig resource population

    Directory of Open Access Journals (Sweden)

    Rumph Janice M

    2010-11-01

    Full Text Available Abstract Background A variety of analysis approaches have been applied to detect quantitative trait loci (QTL in experimental populations. The initial genome scan of our Duroc x Pietrain F2 resource population included 510 F2 animals genotyped with 124 microsatellite markers and analyzed using a line-cross model. For the second scan, 20 additional markers on 9 chromosomes were genotyped for 954 F2 animals and 20 markers used in the first scan were genotyped for 444 additional F2 animals. Three least-squares Mendelian models for QTL analysis were applied for the second scan: a line-cross model, a half-sib model, and a combined line-cross and half-sib model. Results In total, 26 QTL using the line-cross model, 12 QTL using the half-sib model and 3 additional QTL using the combined line-cross and half-sib model were detected for growth traits with a 5% false discovery rate (FDR significance level. In the line-cross analysis, highly significant QTL for fat deposition at 10-, 13-, 16-, 19-, and 22-wk of age were detected on SSC6. In the half-sib analysis, a QTL for loin muscle area at 19-wk of age was detected on SSC7 and QTL for 10th-rib backfat at 19- and 22-wk of age were detected on SSC15. Conclusions Additional markers and animals contributed to reduce the confidence intervals and increase the test statistics for QTL detection. Different models allowed detection of new QTL which indicated differing frequencies for alternative alleles in parental breeds.

  13. Genome-wide linkage analysis of QTL for growth and body composition employing the PorcineSNP60 BeadChip

    Directory of Open Access Journals (Sweden)

    Fernández Ana I

    2012-05-01

    Full Text Available Abstract Background The traditional strategy to map QTL is to use linkage analysis employing a limited number of markers. These analyses report wide QTL confidence intervals, making very difficult to identify the gene and polymorphisms underlying the QTL effects. The arrival of genome-wide panels of SNPs makes available thousands of markers increasing the information content and therefore the likelihood of detecting and fine mapping QTL regions. The aims of the current study are to confirm previous QTL regions for growth and body composition traits in different generations of an Iberian x Landrace intercross (IBMAP and especially identify new ones with narrow confidence intervals by employing the PorcineSNP60 BeadChip in linkage analyses. Results Three generations (F3, Backcross 1 and Backcross 2 of the IBMAP and their related animals were genotyped with PorcineSNP60 BeadChip. A total of 8,417 SNPs equidistantly distributed across autosomes were selected after filtering by quality, position and frequency to perform the QTL scan. The joint and separate analyses of the different IBMAP generations allowed confirming QTL regions previously identified in chromosomes 4 and 6 as well as new ones mainly for backfat thickness in chromosomes 4, 5, 11, 14 and 17 and shoulder weight in chromosomes 1, 2, 9 and 13; and many other to the chromosome-wide signification level. In addition, most of the detected QTLs displayed narrow confidence intervals, making easier the selection of positional candidate genes. Conclusions The use of higher density of markers has allowed to confirm results obtained in previous QTL scans carried out with microsatellites. Moreover several new QTL regions have been now identified in regions probably not covered by markers in previous scans, most of these QTLs displayed narrow confidence intervals. Finally, prominent putative biological and positional candidate genes underlying those QTL effects are listed based on recent porcine

  14. 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.

  15. Management of Potato Soft Rot by Gamma Irradiation

    International Nuclear Information System (INIS)

    Abd El-Ghany, H.; Moussa, Z.; Abd El-Rahman, A.F.; Salem, E.A.

    2017-01-01

    This investigation aims to apply a safe practice to minimize potato losses due to soft rot disease of tubers kept under ambient temperature. In this regard, gamma irradiation was used to extend keeping quality through its effect on soft rot bacteria. Eight bacterial isolates were recovered on Logan’s medium from kitchen kept tubers with symptoms of soft rot disease. Five isolates were found pathogenic and tentatively identified as Pectobacterium atrosepticum and Pectobacterium carotovorum sub sp. brasiliense on the basis of the usual bacteriological methods. A molecular method using 16SrDNA sequence analysis for verification of the identity of two isolates was made. The two bacterial isolates, Pectobacterium atrosepticum and Pectobacterium carotovorum sub sp. brasiliense, were irradiated by different doses of gamma rays. Complete inhibition occurred at doses 2.5 and 2.0 KGy for high densities (Approximately 4.0x10"9 CFU/ml) of P. atrosepticum and P. carotovorum sub sp. brasiliense, respectively. The D10 value of gamma irradiation was 0.24 KGy for P. atrosepticum and 0.20 KGy for P. carotovorum subsp. brasiliense. Irradiation of artificially infected tubers with soft rot bacteria using the two mentioned D10 doses for the two bacterial species increased the shelf life of tubers kept under ambient temperature. The internal chemical quality of tubers was shown to be improved by keeping the tubers under ambient temperature after irradiation by the two D10 doses 0.24 and 0.20 KGy

  16. Fine Mapping QTL for mastitis resistance on BTA9 in three Nordic red cattle breeds

    DEFF Research Database (Denmark)

    Sahana, G; Lund, M S; Andersson-Eklund, L

    2008-01-01

    A QTL affecting clinical mastitis and/or somatic cell score (SCS) has been reported previously on chromosome 9 from studies in 16 families from the Swedish Red and White (SRB), Finnish Ayrshire (FA) and Danish Red (DR) breeds. In order to refine the QTL location, 67 markers were genotyped over...... the whole chromosome in the 16 original families and 18 additional half-sib families. This enabled linkage disequilibrium information to be used in the analysis. Data were analysed by an approach that combines information from linkage and linkage disequilibrium, which allowed the QTL affecting clinical...... mastitis to be mapped to a small interval (BM4208 and INRA084. This QTL showed a pleiotropic effect on SCS in the DR and SRB breeds. Haplotypes associated with variations in mastitis resistance were identified. The haplotypes were predictive in the general population and can be used in marker...

  17. Distribution and prevalence of crown rot pathogens affecting wheat crops in southern Chile

    Directory of Open Access Journals (Sweden)

    Ernesto Moya-Elizondo

    2015-03-01

    Full Text Available Crown rot pathogens are associated with higher losses for wheat crop farmers, but information about the distribution and prevalence of these pathogens in Chile is inadequate. Distribution and prevalence of wheat (Triticum aestivum L. crown rot pathogens were examined in a survey of 48 commercial fields from December 2011 to February 2012 in southern Chile. These fields were located between Collipulli (37°56'00" S; 72°26'39" W and Purranque (40°50'30" S; 73°22'03" W. Severity of crown rot disease was determined through visual assessment of the first internode of 20 tillers obtained from each field. Incidence of crown rot pathogens per field was determined by plating the 20 tillers on Petri plates with 20% potato dextrose agar amended with lactic acid (aPDA medium. Resulting fungal colonies from monoxenic culture were identified by morphological or molecular-assisted identification. Severity of crown rot varied between 11.3% and 80% for individual fields. Culture plate analysis showed 72.2% of stems were infected with some fungus. Fusarium avenaceum, F. graminearum, and F. culmorum, pathogens associated with Fusarium crown rot disease were isolated from 13.5% of tillers. Gaeumannomyces graminis, causal agent of take-all disease in cereals, was isolated from 11.1% of culms. Phaeosphaeria sp., an endophyte and possibly a non-pathogenic fungus, was isolated from 13.9% of tillers. Pathogenic fungi such as Rhizoctonia spp. and Microdochium nivale, other saprophyte, and several unidentified non-sporulating fungi were isolated at frequencies lower than 3% of the total. Fusarium crown rot and take-all were the most prevalent and distributed crown rot diseases present in wheat crops in southern Chile.

  18. Cell-Based Phenotyping Reveals QTL for Membrane Potential Maintenance Associated with Hypoxia and Salinity Stress Tolerance in Barley

    Directory of Open Access Journals (Sweden)

    Muhammad B. Gill

    2017-11-01

    Full Text Available Waterlogging and salinity are two major abiotic stresses that hamper crop production world-wide resulting in multibillion losses. Plant abiotic stress tolerance is conferred by many interrelated mechanisms. Amongst these, the cell’s ability to maintain membrane potential (MP is considered to be amongst the most crucial traits, a positive relationship between the ability of plants to maintain highly negative MP and its tolerance to both salinity and waterlogging stress. However, no attempts have been made to identify quantitative trait loci (QTL conferring this trait. In this study, the microelectrode MIFE technique was used to measure the plasma membrane potential of epidermal root cells of 150 double haploid (DH lines of barley (Hordeum vulgare L. from a cross between a Chinese landrace TX9425 and Japanese malting cultivar Naso Nijo under hypoxic conditions. A major QTL for the MP in the epidermal root cells in hypoxia-exposed plants was identified. This QTL was located on 2H, at a similar position to the QTL for waterlogging and salinity tolerance reported in previous studies. Further analysis confirmed that MP showed a significant contribution to both waterlogging and salinity tolerance. The fact that the QTL for MP was controlled by a single major QTL illustrates the power of the single-cell phenotyping approach and opens prospects for fine mapping this QTL and thus being more effective in marker assisted selection.

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

    African Journals Online (AJOL)

    fire7-

    2016-10-05

    Oct 5, 2016 ... The genes for host basal resistance seem to play similar roles in basal .... purpose DNA of each QTL-NILs was isolated following the CTAB isolation method ..... never sleep: non-host resistance in plants. J. Plant Physiol.

  20. Mapping QTL for Omega-3 Content in Hybrid Saline Tilapia.

    Science.gov (United States)

    Lin, Grace; Wang, Le; Ngoh, Si Te; Ji, Lianghui; Orbán, Laszlo; Yue, Gen Hua

    2018-02-01

    Tilapia is one of most important foodfish species. The low omega-3 to omega-6 fatty acid ratio in freshwater tilapia meat is disadvantageous for human health. Increasing omega-3 content is an important task in breeding to increase the nutritional value of tilapia. However, conventional breeding to increase omega-3 content is difficult and slow. To accelerate the increase of omega-3 through marker-assisted selection (MAS), we conducted QTL mapping for fatty acid contents and profiles in a F 2 family of saline tilapia generated by crossing red tilapia and Mozambique tilapia. The total omega-3 content in F 2 hybrid tilapia was 2.5 ± 1.0 mg/g, higher than that (2.00 mg/g) in freshwater tilapia. Genotyping by sequencing (GBS) technology was used to discover and genotype SNP markers, and microsatellites were also genotyped. We constructed a linkage map with 784 markers (151 microsatellites and 633 SNPs). The linkage map was 2076.7 cM long and consisted of 22 linkage groups. Significant and suggestive QTL for total lipid content were mapped on six linkage groups (LG3, -4, -6, -8, -13, and -15) and explained 5.8-8.3% of the phenotypic variance. QTL for omega-3 fatty acids were located on four LGs (LG11, -18, -19, and -20) and explained 5.0 to 7.5% of the phenotypic variance. Our data suggest that the total lipid and omega-3 fatty acid content were determined by multiple genes in tilapia. The markers flanking the QTL for omega-3 fatty acids can be used in MAS to accelerate the genetic improvements of these traits in salt-tolerant tilapia.

  1. Identification of milling and baking quality QTL in multiple soft wheat mapping populations.

    Science.gov (United States)

    Cabrera, Antonio; Guttieri, Mary; Smith, Nathan; Souza, Edward; Sturbaum, Anne; Hua, Duc; Griffey, Carl; Barnett, Marla; Murphy, Paul; Ohm, Herb; Uphaus, Jim; Sorrells, Mark; Heffner, Elliot; Brown-Guedira, Gina; Van Sanford, David; Sneller, Clay

    2015-11-01

    Two mapping approaches were use to identify and validate milling and baking quality QTL in soft wheat. Two LG were consistently found important for multiple traits and we recommend the use marker-assisted selection on specific markers reported here. Wheat-derived food products require a range of characteristics. Identification and understanding of the genetic components controlling end-use quality of wheat is important for crop improvement. We assessed the underlying genetics controlling specific milling and baking quality parameters of soft wheat including flour yield, softness equivalent, flour protein, sucrose, sodium carbonate, water absorption and lactic acid, solvent retention capacities in a diversity panel and five bi-parental mapping populations. The populations were genotyped with SSR and DArT markers, with markers specific for the 1BL.1RS translocation and sucrose synthase gene. Association analysis and composite interval mapping were performed to identify quantitative trait loci (QTL). High heritability was observed for each of the traits evaluated, trait correlations were consistent over populations, and transgressive segregants were common in all bi-parental populations. A total of 26 regions were identified as potential QTL in the diversity panel and 74 QTL were identified across all five bi-parental mapping populations. Collinearity of QTL from chromosomes 1B and 2B was observed across mapping populations and was consistent with results from the association analysis in the diversity panel. Multiple regression analysis showed the importance of the two 1B and 2B regions and marker-assisted selection for the favorable alleles at these regions should improve quality.

  2. Adaptive divergence in flowering time among natural populations of Arabidopsis thaliana: Estimates of selection and QTL mapping.

    Science.gov (United States)

    Ågren, Jon; Oakley, Christopher G; Lundemo, Sverre; Schemske, Douglas W

    2017-03-01

    To identify the ecological and genetic mechanisms of local adaptation requires estimating selection on traits, identifying their genetic basis, and evaluating whether divergence in adaptive traits is due to conditional neutrality or genetic trade-offs. To this end, we conducted field experiments for three years using recombinant inbred lines (RILs) derived from two ecotypes of Arabidopsis thaliana (Italy, Sweden), and at each parental site examined selection on flowering time and mapped quantitative trait loci (QTL). There was strong selection for early flowering in Italy, but weak selection in Sweden. Eleven distinct flowering time QTL were detected, and for each the Italian genotype caused earlier flowering. Twenty-seven candidate genes were identified, two of which (FLC and VIN3) appear under major flowering time QTL in Italy. Seven of eight QTL in Italy with narrow credible intervals colocalized with previously reported fitness QTL, in comparison to three of four in Sweden. The results demonstrate that the magnitude of selection on flowering time differs strikingly between our study populations, that the genetic basis of flowering time variation is multigenic with some QTL of large effect, and suggest that divergence in flowering time between ecotypes is due mainly to conditional neutrality. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  3. Identification of qSOR1, a major rice QTL involved in soil-surface rooting in paddy fields.

    Science.gov (United States)

    Uga, Yusaku; Hanzawa, Eiko; Nagai, Shinsei; Sasaki, Kazuhiro; Yano, Masahiro; Sato, Tadashi

    2012-01-01

    Specific Indonesian lowland rice (Oryza sativa L.) cultivars elongate thick primary roots on the soil surface of paddy fields. To clarify the genetic factors controlling soil-surface rooting, we performed quantitative trait locus (QTL) analyses using 124 recombinant inbred lines (RILs) derived from a cross between Gemdjah Beton, an Indonesian lowland rice cultivar with soil-surface roots, and Sasanishiki, a Japanese lowland rice cultivar without soil-surface roots. These cultivars and the RILs were tested for soil-surface rooting in a paddy field. We identified four regions of chromosomes 3, 4, 6, and 7 that were associated with soil-surface rooting in the field. Among them, one major QTL was located on the long arm of chromosome 7. This QTL explained 32.5-53.6% of the total phenotypic variance across three field evaluations. To perform fine mapping of this QTL, we measured the basal root growth angle of crown roots at the seedling stage in seven BC(2)F(3) recombinant lines grown in small cups in a greenhouse. The QTL was mapped between markers RM21941 and RM21976, which delimit an 812-kb interval in the reference cultivar Nipponbare. We have designated this QTL qSOR1 (quantitative trait locus for SOIL SURFACE ROOTING 1).

  4. Antifungal Effects Of Botanical Leaf Extracts On Tuber Rots Of Yam ...

    African Journals Online (AJOL)

    The fungicidal effects of dry and fresh leaf extracts of Axardirachta indica (L) and Ocimum grattissimum on the rot of yam tubers were investigated. Fusaruim oxysporium, Rhjzopus stolonifer, Botryodiplodia theobromae and Aspergillus Niger (root pathogens) were isolated from the rotted yam. Both dry and fresh leaf extracts ...

  5. Root rot diseases of sugarbeet (Beta vulgaris L as affected by defloliation intensity

    Directory of Open Access Journals (Sweden)

    Karadimos Dimitros A.

    2006-01-01

    Full Text Available The aim of this work was to study the effect of sugar beet re-growth after water stress defoliation on root rots of three cultivars (Europa, Rival Corsica, which were spring sown in Thessaly, central Greece, for two growing seasons (2003-04. At the beginning of July, sugar beets were subjected to water deficit with irrigation withholding. A month later, three defoliation levels (control - C, moderate - MD, severe - SD and irrigation were applied. Thus, sugar beets were forced to re-grow and three harvests (15, 30 and 40 days after defoliation - DAD were conducted. Rotted roots per hectare were counted and pathogens were identified. Data were analyzed as a four-factor randomized complete block design with years, defoliation levels, sampling times and cultivars as main factors. The number of rotted roots was increased with the defoliation level and was significantly higher for SD sugar beets (3748 roots ha–1. No significant differences were found between C and MD treatments (1543 and 2116 roots ha–1, respectively. Rival was the most susceptible cultivar to root rots. Sugar beets were more susceptible to rotting 15 and 40 DAD (2778 and 2998 roots ha–1. The causal agents of root rots were the fungi, Fusarium spp., Rhizopus stolonifer, Macrophomina phaseolina and Rhizoctonia solani.

  6. QTL MAPPING FOR GRAIN QUALITY TRAITS IN TESTCROSSES OF A MAIZE BIPARENTAL POPULATION USING GENOTYPING-BY-SEQUENCING DATA

    Directory of Open Access Journals (Sweden)

    Mario Franić

    2017-01-01

    Full Text Available We performed QTL mapping in testcrosses of maize population IBMSyn4 for three grain quality traits: oil and protein contents and test weight. 191 phenotyped and genotyped lines were used as a training set while 85 genotyped only lines comprised a validation set used to calculate best linear unbiased predictions (BLUP, making a total of 276 phenotypes for the QTL analysis. 92000 filtered Genotyping-By-Sequencing (GBS SNP markers were used to calculate BLUPs, while a set of 2178 genetically mapped SSRs was used in QTL analysis. By simple QTL scan, we scored several minor effect QTLs: one for oil content (chromosome 1, one for protein content (chromosome 10 and four for test weight (chromosomes 1, 3, 5 and 10. QTLs associated with test weight were found to be additive, and 18.25% of phenotypic variance was explained by their joint effect. Only one QTL for test weight was found to be significant in composite interval mapping and it was mapped on chromosome 5. This QTL accounted for 9.97% of phenotypic variance. QTLs detected in this study represent monitoring of commercially most successful elite maize germplasm for grain quality traits.

  7. Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex.

    Science.gov (United States)

    Portis, Ezio; Scaglione, Davide; Acquadro, Alberto; Mauromicale, Giovanni; Mauro, Rosario; Knapp, Steven J; Lanteri, Sergio

    2012-05-23

    The Asteraceae species Cynara cardunculus (2n = 2x = 34) includes the two fully cross-compatible domesticated taxa globe artichoke (var. scolymus L.) and cultivated cardoon (var. altilis DC). As both are out-pollinators and suffer from marked inbreeding depression, linkage analysis has focussed on the use of a two way pseudo-test cross approach. A set of 172 microsatellite (SSR) loci derived from expressed sequence tag DNA sequence were integrated into the reference C. cardunculus genetic maps, based on segregation among the F1 progeny of a cross between a globe artichoke and a cultivated cardoon. The resulting maps each detected 17 major linkage groups, corresponding to the species' haploid chromosome number. A consensus map based on 66 co-dominant shared loci (64 SSRs and two SNPs) assembled 694 loci, with a mean inter-marker spacing of 2.5 cM. When the maps were used to elucidate the pattern of inheritance of head production earliness, a key commercial trait, seven regions were shown to harbour relevant quantitative trait loci (QTL). Together, these QTL accounted for up to 74% of the overall phenotypic variance. The newly developed consensus as well as the parental genetic maps can accelerate the process of tagging and eventually isolating the genes underlying earliness in both the domesticated C. cardunculus forms. The largest single effect mapped to the same linkage group in each parental maps, and explained about one half of the phenotypic variance, thus representing a good candidate for marker assisted selection.

  8. QTL Mapping of Sex Determination Loci Supports an Ancient Pathway in Ants and Honey Bees.

    Directory of Open Access Journals (Sweden)

    Misato O Miyakawa

    2015-11-01

    Full Text Available Sex determination mechanisms play a central role in life-history characteristics, affecting mating systems, sex ratios, inbreeding tolerance, etc. Downstream components of sex determination pathways are highly conserved, but upstream components evolve rapidly. Evolutionary dynamics of sex determination remain poorly understood, particularly because mechanisms appear so diverse. Here we investigate the origins and evolution of complementary sex determination (CSD in ants and bees. The honey bee has a well-characterized CSD locus, containing tandemly arranged homologs of the transformer gene [complementary sex determiner (csd and feminizer (fem]. Such tandem paralogs appear frequently in aculeate hymenopteran genomes. However, only comparative genomic, but not functional, data support a broader role for csd/fem in sex determination, and whether species other than the honey bee use this pathway remains controversial. Here we used a backcross to test whether csd/fem acts as a CSD locus in an ant (Vollenhovia emeryi. After sequencing and assembling the genome, we computed a linkage map, and conducted a quantitative trait locus (QTL analysis of diploid male production using 68 diploid males and 171 workers. We found two QTLs on separate linkage groups (CsdQTL1 and CsdQTL2 that jointly explained 98.0% of the phenotypic variance. CsdQTL1 included two tandem transformer homologs. These data support the prediction that the same CSD mechanism has indeed been conserved for over 100 million years. CsdQTL2 had no similarity to CsdQTL1 and included a 236-kb region with no obvious CSD gene candidates, making it impossible to conclusively characterize it using our data. The sequence of this locus was conserved in at least one other ant genome that diverged >75 million years ago. By applying QTL analysis to ants for the first time, we support the hypothesis that elements of hymenopteran CSD are ancient, but also show that more remains to be learned about the

  9. A score-statistic approach for determining threshold values in QTL mapping.

    Science.gov (United States)

    Kao, Chen-Hung; Ho, Hsiang-An

    2012-06-01

    Issues in determining the threshold values of QTL mapping are often investigated for the backcross and F2 populations with relatively simple genome structures so far. The investigations of these issues in the progeny populations after F2 (advanced populations) with relatively more complicated genomes are generally inadequate. As these advanced populations have been well implemented in QTL mapping, it is important to address these issues for them in more details. Due to an increasing number of meiosis cycle, the genomes of the advanced populations can be very different from the backcross and F2 genomes. Therefore, special devices that consider the specific genome structures present in the advanced populations are required to resolve these issues. By considering the differences in genome structure between populations, we formulate more general score test statistics and gaussian processes to evaluate their threshold values. In general, we found that, given a significance level and a genome size, threshold values for QTL detection are higher in the denser marker maps and in the more advanced populations. Simulations were performed to validate our approach.

  10. Persistence of Gliocephalotrichum spp. causing fruit rot of rambutan (Nephelium lappaceum L.) in Puerto Rico

    Science.gov (United States)

    Worldwide, fruit rot of rambutan is an important problem that limits the storage, marketing and long-distance transportation of the fruit. A complex of pathogens has been reported to cause fruit rot of rambutan and significant post-harvest economic losses. During 2009 and 2011 rambutan fruit rot was...

  11. MANAGEMENT OF ROOT ROT IN AVOCADO TREES

    Directory of Open Access Journals (Sweden)

    SIMONE RODRIGUES DA SILVA

    Full Text Available ABSTRACT Root rot (Phytophthora cinnamomi Rands is one of the most restrictive factors to avocado growing in main producing regions worldwide. In Brazil, scientific reports on the effectiveness of control methods are scarce. The objective of this study was to evaluate the efficiency of gypsum applications and dolomitic limestone to the soil and potassium phosphite sprays in controlling this disease in ‘Hass’ avocado, grown without irrigation. The application of dolomitic limestone or gypsum alone is not effective to recover plants affected by root rot. The application of potassium phosphite, combined or not with dolomitic lime or gypsum enables the partial recovery ‘Hass’ avocado plants affected by the disease.

  12. Genetic linkage map and QTL identification for adventitious rooting traits in red gum eucalypts.

    Science.gov (United States)

    Sumathi, Murugan; Bachpai, Vijaya Kumar Waman; Mayavel, A; Dasgupta, Modhumita Ghosh; Nagarajan, Binai; Rajasugunasekar, D; Sivakumar, Veerasamy; Yasodha, Ramasamy

    2018-05-01

    The eucalypt species, Eucalyptus tereticornis and Eucalyptus camaldulensis , show tolerance to drought and salinity conditions, respectively, and are widely cultivated in arid and semiarid regions of tropical countries. In this study, genetic linkage map was developed for interspecific cross E. tereticornis  ×  E. camaldulensis using pseudo-testcross strategy with simple sequence repeats (SSRs), intersimple sequence repeats (ISSRs), and sequence-related amplified polymorphism (SRAP) markers. The consensus genetic map comprised totally 283 markers with 84 SSRs, 94 ISSRs, and 105 SRAP markers on 11 linkage groups spanning 1163.4 cM genetic distance. Blasting the SSR sequences against E. grandis sequences allowed an alignment of 64% and the average ratio of genetic-to-physical distance was 1.7 Mbp/cM, which strengths the evidence that high amount of synteny and colinearity exists among eucalypts genome. Blast searches also revealed that 37% of SSRs had homologies with genes, which could potentially be used in the variety of downstream applications including candidate gene polymorphism. Quantitative trait loci (QTL) analysis for adventitious rooting traits revealed six QTL for rooting percent and root length on five chromosomes with interval and composite interval mapping. All the QTL explained 12.0-14.7% of the phenotypic variance, showing the involvement of major effect QTL on adventitious rooting traits. Increasing the density of markers would facilitate the detection of more number of small-effect QTL and also underpinning the genes involved in rooting process.

  13. Analysis of morphine responses in mice reveals a QTL on Chromosome 7 [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Wim E. Crusio

    2016-09-01

    Full Text Available In this study we identified a quantitative trait locus (QTL on mouse Chromosome 7 associated with locomotor activity and rearing post morphine treatment. This QTL was revealed after correcting for the effects of another QTL peak on Chromosome 10 using composite interval mapping. The positional candidate genes are Syt9 and Ppfibp2. Several other genes within the interval are linked to neural processes, locomotor activity, and the defensive response to harmful stimuli.

  14. Analysis of morphine responses in mice reveals a QTL on Chromosome 7 [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Wim E. Crusio

    2016-10-01

    Full Text Available In this study we identified a quantitative trait locus (QTL on mouse Chromosome 7 associated with locomotor activity and rearing post morphine treatment. This QTL was revealed after correcting for the effects of another QTL peak on Chromosome 10 using composite interval mapping. The positional candidate genes are Syt9 and Ppfibp2. Several other genes within the interval are linked to neural processes, locomotor activity, and the defensive response to harmful stimuli.

  15. 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 ...

  16. Assessment of Sugarcane Germplasm ( Saccharum spp. complex Against Red Rot Pathogen Colletotrichum Falcatum

    Directory of Open Access Journals (Sweden)

    Atul Singh

    2017-08-01

    Full Text Available ABSTRACT Red rot, caused by Colletotrichum falcatum Went is the most important disease of sugarcane in India inflicting substantial loss to both cane industry and cane growers. To keep in view the importance of red rot disease of sugarcane, 117 accession of sugarcane germplasm including different Saccharum species and Indian and foreign commercial hybrids were tested against red rot with Cf 07, Cf 08 & Cf 09 (national pathotypes by plug method of inoculation. Out of 117, 6 were found resistant and 12 were moderately resistant against red rot and rest were moderately susceptible/susceptible/highly susceptible. Theses resistance and moderately resistant accession can be further utilize to produce resistance varieties against the most devastating pathogen of sugarcane.

  17. Effect of irradiation and insect pest control on rots and sensory ...

    African Journals Online (AJOL)

    The coffee bean weevil, Araecerus fasciculatus Degeer (Coleoptera: Curculionidae) is associated with rots in stored yam tubers. The current study was designed to assess the effect of irradiation and other insect pest control strategies on rots and sensory quality of stored yams. 450 tubers each of two varieties of white yam ...

  18. Genetic determinism of bone and mineral metabolism in meat-type chickens: A QTL mapping study.

    Science.gov (United States)

    Mignon-Grasteau, Sandrine; Chantry-Darmon, Céline; Boscher, Marie-Yvonne; Sellier, Nadine; Chabault-Dhuit, Marie; Le Bihan-Duval, Elisabeth; Narcy, Agnès

    2016-12-01

    Skeletal integrity in meat-type chickens is affected by many factors including rapid growth rate, nutrition and genetics. To investigate the genetic basis of bone and mineral metabolism, a QTL detection study was conducted in an intercross between two lines of meat-type chickens divergently selected for their high (D +) or low (D -) digestive efficiency. Tibia size (length, diameter, volume) and ash content were determined at 3 weeks of age as well as phosphorus (P) retention and plasma concentration. Heritability of these traits and their genetic correlations with digestive efficiency were estimated. A QTL mapping study was performed using 3379 SNP markers. Tibia size, weight, ash content and breaking strength were highly heritable (0.42 to 0.61). Relative tibia diameter and volume as well as P retention were strongly and positively genetically correlated with digestive efficiency (0.57 to 0.80). A total of 35 QTL were identified (9 for tibia weight, 13 for tibia size, 5 for bone strength, 5 for bone mineralization, 2 for plasma P concentration and 1 for P retention). Six QTL were genome-wide significant, and 3 QTL for tibia relative volume, weight and ash weight on chromosome 6 were fixed, the positive allele coming from the D-line. For two QTL for ash content on chromosome 18 and relative tibia length on chromosome 26, the confidence intervals were small enough to identify potential candidate genes. These findings support the evidence of multiple genetic loci controlling bone and mineral metabolism. The identification of candidate genes may provide new perspectives in the understanding of bone regulation, even beyond avian species.

  19. First report of Fusarium proliferatum causing dry rot in Michigan commercial potato (Solanum tuberosum) production

    Science.gov (United States)

    Fusarium dry rot of potato is a postharvest disease caused by several Fusarium spp. and is of worldwide importance. Thirteen Fusarium spp. have been implicated in fungal dry rots of potatoes worldwide. Among them, 11 species have been reported causing potato dry rot of seed tubers in the northern Un...

  20. CHARACTERIZATION OF WOOD DECAY BY ROT FUNGI USING COLORIMETRY AND INFRARED SPECTROSCOPY

    Directory of Open Access Journals (Sweden)

    Mírian de Almeida Costa

    2011-09-01

    Full Text Available Wood samples of marupá (Simarouba amara and andiroba (Carapa guianenis were submitted to Trametes versicolor (white rot and Gloeophylum trabeum (brown rot fungi attack. Colorimetry was used to determine the color of the wood before and after wood decaying fungi. To evaluate the changes in chemical compounds levels in the wood samples, the diffuse reflectance medium infrared spectroscopy was used. Both wood were non resistant against white rot fungus, while with brown rot attack andiroba was resistant and marupá was not. After Gloeophyllum trabeum attack both woods changed to a darken color, and after Trametes versicolor attack andiroba changed to a lighter color and marupá darkened slightly, The analysis showed a reduction in the peak intensity of cellulose, hemicellulose and lignin, for both species, after Trametes versicolor attack and a reduction in the peak intensity of cellulose after Gloeophyllum trabeum attack.

  1. Genetic dissection of the Drosophila melanogaster female head transcriptome reveals widespread allelic heterogeneity.

    Directory of Open Access Journals (Sweden)

    Elizabeth G King

    2014-05-01

    Full Text Available Modern genetic mapping is plagued by the "missing heritability" problem, which refers to the discordance between the estimated heritabilities of quantitative traits and the variance accounted for by mapped causative variants. One major potential explanation for the missing heritability is allelic heterogeneity, in which there are multiple causative variants at each causative gene with only a fraction having been identified. The majority of genome-wide association studies (GWAS implicitly assume that a single SNP can explain all the variance for a causative locus. However, if allelic heterogeneity is prevalent, a substantial amount of genetic variance will remain unexplained. In this paper, we take a haplotype-based mapping approach and quantify the number of alleles segregating at each locus using a large set of 7922 eQTL contributing to regulatory variation in the Drosophila melanogaster female head. Not only does this study provide a comprehensive eQTL map for a major community genetic resource, the Drosophila Synthetic Population Resource, but it also provides a direct test of the allelic heterogeneity hypothesis. We find that 95% of cis-eQTLs and 78% of trans-eQTLs are due to multiple alleles, demonstrating that allelic heterogeneity is widespread in Drosophila eQTL. Allelic heterogeneity likely contributes significantly to the missing heritability problem common in GWAS studies.

  2. Efficacy of gaseous ozone to counteract postharvest table grape sour rot.

    Science.gov (United States)

    Pinto, L; Caputo, L; Quintieri, L; de Candia, S; Baruzzi, F

    2017-09-01

    This work aims at studying the efficacy of low doses of gaseous ozone in postharvest control of the table grape sour rot, a disease generally attributed to a consortium of non-Saccharomyces yeasts (NSY) and acetic acid bacteria (AAB). Sour rot incidence of wounded berries, inoculated with 8 NSYstrains, or 7 AAB, or 56 yeast-bacterium associations, was monitored at 25 °C up to six days. Sour rot incidence in wounded berries inoculated with yeast-bacterium associations resulted higher than in berries inoculated with one single NSY or AAB strain. Among all NSY-AAB associations, the yeast-bacterium association composed of Candida zemplinina CBS 9494 (Cz) and Acetobacter syzygii LMG 21419 (As) showed the highest prevalence of sour rot; thus, after preliminary in vitro assays, this simplified As-Cz microbial consortium was inoculated in wounded berries that were stored at 4 °C for ten days under ozone (2.14 mg m -3 ) or in air. At the end of cold storage, no berries showed sour-rot symptoms although ozonation mainly affected As viable cell count. After additional 12 days at 25 °C, the sour rot index of inoculated As-Cz berries previously cold-stored under ozone or in air accounted for 22.6 ± 3.7% and 66.7 ± 4.5%, respectively. Molecular analyses of dominant AAB and NSY populations of both sound and rotten berries during post-refrigeration period revealed the appearance of new strains mainly belonging to Gluconobacter albidus and Hanseniaspora uvarum species, respectively. Cold ozonation resulted an effective approach to extend the shelf-life of table grapes also after cold storage. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Serpula lacrymans, The Dry Rot Fungus and Tolerance Towards Copper-Based Wood Preservatives

    DEFF Research Database (Denmark)

    Hastrup, Anne Christine Steenkjær; Jensen, Bo; Clausen, Carol

    2005-01-01

    -rot fungi is thought to be due in part to oxalic acid production and accumulation. Oxalic acid has been implicated in copper tolerance by the formation of copper oxalate crystals. Twelve isolates of the dry rot fungus, S. lacrymans and four other brown rot species were evaluated for weight loss on wood...

  4. Identification of QTL with effects on intramuscular fat content and fatty acid composition in a Duroc × Large White cross

    Directory of Open Access Journals (Sweden)

    Legault Christian

    2007-08-01

    Full Text Available Abstract Background Improving pork quality can be done by increasing intramuscular fat (IMF content. This trait is influenced by quantitative trait loci (QTL sought out in different pig populations. Considering the high IMF content observed in the Duroc pig, it was appealing to determine whether favourable alleles at a major gene or QTL could be found. The detection was performed in an experimental F2 Duroc × Large White population first by segregation analysis, then by QTL mapping using additional molecular information. Results Segregation analysis provided evidence for a major gene, with a recessive Duroc allele increasing IMF by 1.8% in Duroc homozygous pigs. However, results depended on whether data were normalised or not. After Box-Cox transformation, likelihood ratio was indeed 12 times lower and no longer significant. The QTL detection results were partly consistent with the segregation analysis. Three QTL significant at the chromosome wide level were evidenced. Two QTL, located on chromosomes 13 and 15, showed a high IMF Duroc recessive allele with an overall effect slightly lower than that expected from segregation analysis (+0.4 g/100 g muscle. The third QTL was located on chromosome 1, with a dominant Large White allele inducing high IMF content (+0.5 g/100 g muscle. Additional QTL were detected for muscular fatty acid composition. Conclusion The study presented results from two complementary approaches, a segregation analysis and a QTL detection, to seek out genes involved in the higher IMF content observed in the Duroc population. Discrepancies between both methods might be partially explained by the existence of at least two QTL with similar characteristics located on two different chromosomes for which different boars were heterozygous. The favourable and dominant allele detected in the Large White population was unexpected. Obviously, in both populations, the favourable alleles inducing high IMF content were not fixed and

  5. Soft rot decay capabilities and interactions of fungi and bacteria from fumigated utility poles

    International Nuclear Information System (INIS)

    Wang, C.J.K.; Worrall, J.J.

    1992-11-01

    The objectives were to (1) identify microfungi and bacterial associates isolated from fumigated southern pine poles from EPRI project RP 1471-72, (2) study the soft-rot capabilities of predominant fungi, and (3) study interactions among microorganisms in relation to wood decay. Methods for identification followed standard techniques using morphological and physiological criteria. Soft-rot by microfungi alone and with bacteria was determined as weight loss and anatomical examination of wood blocks using light microscopy and limited electron microscopy. Acinetobacter calcoaceticus was the predominant bacterium. Twenty-one species of microfungi were identified including four new species. A book entitled IDENTIFICATION MANUAL FOR FUNGI FROM UTILITY POLES IN THE EASTERN UNITED STATES was published. An improved soft-rot test was devised. Fifty-one of 84 species (60%) of microfungi from poles tested were soft-rot positive; that is much greater than previously reported. Three types of anatomical damage of wood of pine or birch caused by soft-rot fungi were described. Interaction tests showed that, in some cases, there was a strong synergism between bacteria and fungi in causing weight loss, but results were inconsistent. Although soft rot is often most apparent under conditions of very high moisture, intermediate moisture levels appear to be optimal, as with basidiomycete decayers

  6. Erwinia carotovora extracellular proteases : characterization and role in soft rot

    OpenAIRE

    Kyöstiö, Sirkka R. M.

    1990-01-01

    Erwinia carotovora subsp. carotovora (Ecc) strain EC14, a Gram-negative bacterium, causes soft rot on several crops, including potato. Maceration of potato tuber tissue is caused by secreted pectolytic enzymes. Other cell-degrading enzymes may also have roles in pathogenesis, including cellulases, phospholipases, and protease(s). The objectives of this research were to (1) characterize Ecc extracellular protease (Prt) and (2) elucidate its role in potato soft rot. A gene enc...

  7. Mapping QTL for Seed Germinability under Low Temperature Using a New High-Density Genetic Map of Rice

    Directory of Open Access Journals (Sweden)

    Ningfei Jiang

    2017-07-01

    Full Text Available Mapping major quantitative trait loci (QTL responsible for rice seed germinability under low temperature (GULT can provide valuable genetic source for improving cold tolerance in rice breeding. In this study, 124 rice backcross recombinant inbred lines (BRILs derived from a cross indica cv. Changhui 891 and japonica cv. 02428 were genotyped through re-sequencing technology. A bin map was generated which includes 3057 bins covering distance of 1266.5 cM with an average of 0.41 cM between markers. On the basis of newly constructed high-density genetic map, six QTL were detected ranging from 40 to 140 kb on Nipponbare genome. Among these, two QTL qCGR8 and qGRR11 alleles shared by 02428 could increase GULT and seed germination recovery rate after cold stress, respectively. However, qNGR1 and qNGR4 may be two major QTL affecting indica Changhui 891germination under normal condition. QTL qGRR1 and qGRR8 affected the seed germination recovery rate after cold stress and the alleles with increasing effects were shared by the Changhui 891 could improve seed germination rate after cold stress dramatically. These QTL could be a highly valuable genetic factors for cold tolerance improvement in rice lines. Moreover, the BRILs developed in this study will serve as an appropriate choice for mapping and studying genetic basis of rice complex traits.

  8. QTL mapping in multiple populations and development stages reveals dynamic quantitative trait loci for fruit size in cucumbers of different market classes.

    Science.gov (United States)

    Weng, Yiqun; Colle, Marivi; Wang, Yuhui; Yang, Luming; Rubinstein, Mor; Sherman, Amir; Ophir, Ron; Grumet, Rebecca

    2015-09-01

    QTL analysis in multi-development stages with different QTL models identified 12 consensus QTLs underlying fruit elongation and radial growth presenting a dynamic view of genetic control of cucumber fruit development. Fruit size is an important quality trait in cucumber (Cucumis sativus L.) of different market classes. However, the genetic and molecular basis of fruit size variations in cucumber is not well understood. In this study, we conducted QTL mapping of fruit size in cucumber using F2, F2-derived F3 families and recombinant inbred lines (RILs) from a cross between two inbred lines Gy14 (North American picking cucumber) and 9930 (North China fresh market cucumber). Phenotypic data of fruit length and diameter were collected at three development stages (anthesis, immature and mature fruits) in six environments over 4 years. QTL analysis was performed with three QTL models including composite interval mapping (CIM), Bayesian interval mapping (BIM), and multiple QTL mapping (MQM). Twenty-nine consistent and distinct QTLs were detected for nine traits from multiple mapping populations and QTL models. Synthesis of information from available fruit size QTLs allowed establishment of 12 consensus QTLs underlying fruit elongation and radial growth, which presented a dynamic view of genetic control of cucumber fruit development. Results from this study highlighted the benefits of QTL analysis with multiple QTL models and different mapping populations in improving the power of QTL detection. Discussion was presented in the context of domestication and diversifying selection of fruit length and diameter, marker-assisted selection of fruit size, as well as identification of candidate genes for fruit size QTLs in cucumber.

  9. Differences in crystalline cellulose modification due to degradation by brown and white rot fungi.

    Science.gov (United States)

    Hastrup, Anne Christine Steenkjær; Howell, Caitlin; Larsen, Flemming Hofmann; Sathitsuksanoh, Noppadon; Goodell, Barry; Jellison, Jody

    2012-10-01

    Wood-decaying basidiomycetes are some of the most effective bioconverters of lignocellulose in nature, however the way they alter wood crystalline cellulose on a molecular level is still not well understood. To address this, we examined and compared changes in wood undergoing decay by two species of brown rot fungi, Gloeophyllum trabeum and Meruliporia incrassata, and two species of white rot fungi, Irpex lacteus and Pycnoporus sanguineus, using X-ray diffraction (XRD) and (13)C solid-state nuclear magnetic resonance (NMR) spectroscopy. The overall percent crystallinity in wood undergoing decay by M. incrassata, G. trabeum, and I. lacteus appeared to decrease according to the stage of decay, while in wood decayed by P. sanguineus the crystallinity was found to increase during some stages of degradation. This result is suggested to be potentially due to the different decay strategies employed by these fungi. The average spacing between the 200 cellulose crystal planes was significantly decreased in wood degraded by brown rot, whereas changes observed in wood degraded by the two white rot fungi examined varied according to the selectivity for lignin. The conclusions were supported by a quantitative analysis of the structural components in the wood before and during decay confirming the distinct differences observed for brown and white rot fungi. The results from this study were consistent with differences in degradation methods previously reported among fungal species, specifically more non-enzymatic degradation in brown rot versus more enzymatic degradation in white rot. Copyright © 2012 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  10. Stem rots of oil palm caused by Ganoderma boninense: pathogen biology and epidemiology.

    Science.gov (United States)

    Pilotti, C A

    2005-01-01

    Oil palm (Elaeis guineensis Jacq.) has been grown in Papua New Guinea since the early 1960s. The most important disease of oil palm in PNG is a stem rot of the palm base. This is the same disease that constitutes a major threat to sustainable oil palm production in SE Asia. Investigations into the causal pathogen have revealed that the stem rots in PNG are caused predominantly by the basidiomycete Ganoderma boninense, with a minor pathogen identified as G. tornatum G. tornatum was found to have a broad host range whereas G. boninense appears to be restricted to palms. The population structure of G. boninense was investigated using inter-fertility studies between isolates collected from basal stem rots on oil palm. Although the G. boninense field populations are predominantly comprised of distinct individuals, a number of isolates were found that share single mating alleles. This indicates that out-crossing had occurred over several generations in the resident or wild population of G. boninense prior to colonization of oil palm. No direct hereditary relationship between isolates on neighbouring diseased palms was found, although an indirect link between isolates causing upper stem rot and basal stem rot was detected.

  11. New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL

    Directory of Open Access Journals (Sweden)

    Riccardo Rinaldi

    2016-07-01

    Full Text Available Eggplant, pepper and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage.Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits.The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp.Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation.In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10% affecting key agronomic traits. Most were confirmed to cluster in

  12. QTL identification of grain protein concentration and its genetic ...

    Indian Academy of Sciences (India)

    culated using the statistical software package SPSS 12.0. (SPSS, Chicago, USA). ... Joint QTL analysis for PC and GWP/SC was carried out according to the multiple interval ..... testing for epistasis: an application in maize. Theor. Appl. Genet.

  13. Major QTL Conferring Resistance to Rice Bacterial Leaf Streak

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Bacterial leaf streak (BLS) is one of the important limiting factors to rice production in southern China and other tropical and sub-tropical areas in Asia. Resistance to BLS was found to be a quantitative trait and no major resistant gene was located in rice until date. In the present study, a new major quantitative trait locus (QTL) conferring resistance to BLS was identified from a highly resistant variety Dular by the employment of Dular/Balilla (DB) and Dular/IR24 (DI) segregation populations and was designated qBLSR-11-1. This QTL was located between the simple sequence repeat (SSR) markers RM120 and RM441 on chromosome 11 and could account for 18.1-21.7% and 36.3% of the variance in DB and DI populations, respectively. The genetic pattern of rice resistance to BLS was discussed.

  14. Detecting parent of origin and dominant QTL in a two-generation commercial poultry pedigree using variance component methodology

    Directory of Open Access Journals (Sweden)

    Haley Christopher S

    2009-01-01

    Full Text Available Abstract Introduction Variance component QTL methodology was used to analyse three candidate regions on chicken chromosomes 1, 4 and 5 for dominant and parent-of-origin QTL effects. Data were available for bodyweight and conformation score measured at 40 days from a two-generation commercial broiler dam line. One hundred dams were nested in 46 sires with phenotypes and genotypes on 2708 offspring. Linear models were constructed to simultaneously estimate fixed, polygenic and QTL effects. Different genetic models were compared using likelihood ratio test statistics derived from the comparison of full with reduced or null models. Empirical thresholds were derived by permutation analysis. Results Dominant QTL were found for bodyweight on chicken chromosome 4 and for bodyweight and conformation score on chicken chromosome 5. Suggestive evidence for a maternally expressed QTL for bodyweight and conformation score was found on chromosome 1 in a region corresponding to orthologous imprinted regions in the human and mouse. Conclusion Initial results suggest that variance component analysis can be applied within commercial populations for the direct detection of segregating dominant and parent of origin effects.

  15. Enhanced bioprocessing of lignocellulose: Wood-rot fungal saccharification and fermentation of corn fiber to ethanol

    Science.gov (United States)

    Shrestha, Prachand

    This research aims at developing a biorefinery platform to convert corn-ethanol coproduct, corn fiber, into fermentable sugars at a lower temperature with minimal use of chemicals. White-rot (Phanerochaete chrysosporium), brown-rot (Gloeophyllum trabeum) and soft-rot (Trichoderma reesei) fungi were used in this research to biologically break down cellulosic and hemicellulosic components of corn fiber into fermentable sugars. Laboratory-scale simultaneous saccharification and fermentation (SSF) process proceeded by in-situ cellulolytic enzyme induction enhanced overall enzymatic hydrolysis of hemi/cellulose from corn fiber into simple sugars (mono-, di-, tri-saccharides). The yeast fermentation of hydrolyzate yielded 7.1, 8.6 and 4.1 g ethanol per 100 g corn fiber when saccharified with the white-, brown-, and soft-rot fungi, respectively. The highest corn-to-ethanol yield (8.6 g ethanol/100 g corn fiber) was equivalent to 42 % of the theoretical ethanol yield from starch and cellulose in corn fiber. Cellulase, xylanase and amylase activities of these fungi were also investigated over a week long solid-substrate fermentation of corn fiber. G. trabeum had the highest activities for starch (160 mg glucose/mg protein.min) and on day three of solid-substrate fermentation. P. chrysosporium had the highest activity for xylan (119 mg xylose/mg protein.min) on day five and carboxymethyl cellulose (35 mg glucose/mg protein.min) on day three of solid-substrate fermentation. T. reesei showed the highest activity for Sigma cell 20 (54.8 mg glucose/mg protein.min) on day 5 of solid-substrate fermentation. The effect of different pretreatments on SSF of corn fiber by fungal processes was examined. Corn fiber was treated at 30 °C for 2 h with alkali [2% NaOH (w/w)], alkaline peroxide [2% NaOH (w/w) and 1% H2O 2 (w/w)], and by steaming at 100 °C for 2 h. Mild pretreatment resulted in improved ethanol yields for brown- and soft-rot SSF, while white-rot and Spezyme CP SSFs showed

  16. First Report of Calonectria hongkongensis Causing Fruit Rot of Rambutan (Nephelium lappaceum)

    NARCIS (Netherlands)

    Serrato-Diaz, L.M.; Latoni-Brailowsky, E.I.; Rivera-Vargas, L.I.; Goenaga, R.J.; Crous, P.W.; French-Monar, R.D.

    2013-01-01

    Fruit rot of rambutan is a pre- and post-harvest disease problem of rambutan orchards. In 2011, fruit rot was observed at USDA-ARS orchards in Mayaguez, Puerto Rico. Infected fruit were collected and 1 mm2 tissue sections were surface disinfested with 70% ethanol followed by 0.5% sodium

  17. Fusarium spp. causing dry rot of seed potato tubers in Michigan and their sensitivity to fungicides

    Science.gov (United States)

    Fusarium dry rot of potato (Solanum tuberosum L.) is a postharvest disease that can be caused by several Fusarium spp. A survey was conducted to establish the composition of Fusarium species causing dry rot of seed tubers in Michigan. A total of 370 dry rot symptomatic tubers were collected in 2009 ...

  18. Genome-wide identification of QTL for seed yield and yield-related traits and construction of a high-density consensus map for QTL comparison in Brassica napus

    Directory of Open Access Journals (Sweden)

    Weiguo eZhao

    2016-01-01

    Full Text Available Seed yield (SY is the most important trait in rapeseed, which was determined by multiple seed yield-related traits (SYRTs and also easily subject to environmental influence. Lots of quantitative trait loci (QTL for SY and SYRTs were reported in Brassica napus. However, no studies have focused on SY and seven agronomic traits affecting SY simultaneous. Genome-wide QTL analysis for SY and seven SYRTs in eight environments was conducted in a doubled haploid population containing 348 lines. Totally, 18 and 208 QTLs for SY and SYRTs were observed, respectively, and then these QTLs were integrated into 144 consensus QTLs by a meta-analysis. Three major QTLs for SY were observed, including cqSY-C6-2 and cqSY-C6-3 that expressed stably in winter cultivation area for three years and cqSY-A2-2 only expressed in spring rapeseed area. Trait-by-trait meta-analysis revealed that the 144 consensus QTLs were integrated into 72 pleiotropic unique QTLs. Among them, all the unique QTLs affected SY, except for uq-A6-1, including uq.A2-3, uq.C1-2, uq.C1-3, uq.C6-1, uq.C6-5 and uq.C6-6 could also affect more than two SYRTs. According to high density consensus map construction and QTL comparison from literature, 36 QTLs from five populations were co-localized with QTLs identified in this study. In addition, 13 orthologs genes were observed, including five each genes for SY and SW, one each gene for BY, BH and PH, respectively. The genomic information of these QTLs would be valuable in hybrid cultivar breeding, and be helpful to analyze QTL expression in different environments.

  19. Nonchemical, cultural management strategies to suppress phytophthora root rot in northern highbush blueberry

    Science.gov (United States)

    Phytophthora cinnamomi causes root rot of highbush blueberry and decreases plant growth, yield, and profitability for growers. Fungicides can suppress root rot, but cannot be used in certified organic production systems and fungicide resistance may develop. Alternative, non-chemical, cultural manag...

  20. Saturation mapping of QTL region determining resistance specificity ...

    African Journals Online (AJOL)

    Genetic improvement for biotic resistance in rice involves the quantitative nature of inheritance, which reflects the additive effects of several genetic loci throughout the genome. To in silico identify putative candidate genes involved in defense response, we performed in silico anchoring of the QTL genetic marker data to the ...

  1. QTL analysis of frost damage in pea suggests different mechanisms involved in frost tolerance.

    Science.gov (United States)

    Klein, Anthony; Houtin, Hervé; Rond, Céline; Marget, Pascal; Jacquin, Françoise; Boucherot, Karen; Huart, Myriam; Rivière, Nathalie; Boutet, Gilles; Lejeune-Hénaut, Isabelle; Burstin, Judith

    2014-06-01

    Avoidance mechanisms and intrinsic resistance are complementary strategies to improve winter frost tolerance and yield potential in field pea. The development of the winter pea crop represents a major challenge to expand plant protein production in temperate areas. Breeding winter cultivars requires the combination of freezing tolerance as well as high seed productivity and quality. In this context, we investigated the genetic determinism of winter frost tolerance and assessed its genetic relationship with yield and developmental traits. Using a newly identified source of frost resistance, we developed a population of recombinant inbred lines and evaluated it in six environments in Dijon and Clermont-Ferrand between 2005 and 2010. We developed a genetic map comprising 679 markers distributed over seven linkage groups and covering 947.1 cM. One hundred sixty-one quantitative trait loci (QTL) explaining 9-71 % of the phenotypic variation were detected across the six environments for all traits measured. Two clusters of QTL mapped on the linkage groups III and one cluster on LGVI reveal the genetic links between phenology, morphology, yield-related traits and frost tolerance in winter pea. QTL clusters on LGIII highlighted major developmental gene loci (Hr and Le) and the QTL cluster on LGVI explained up to 71 % of the winter frost damage variation. This suggests that a specific architecture and flowering ideotype defines frost tolerance in winter pea. However, two consistent frost tolerance QTL on LGV were independent of phenology and morphology traits, showing that different protective mechanisms are involved in frost tolerance. Finally, these results suggest that frost tolerance can be bred independently to seed productivity and quality.

  2. Ancestral QTL alleles from wild emmer wheat improve drought resistance and productivity in modern wheat cultivars

    Directory of Open Access Journals (Sweden)

    Lianne eMerchuk-Ovnat

    2016-04-01

    Full Text Available Wild emmer wheat (Triticum turgidum ssp. dicoccoides is considered a promising source for improving stress resistances in domesticated wheat. Here we explored the potential of selected quantitative trait loci (QTLs from wild emmer wheat, introgressed via marker-assisted selection, to enhance drought resistance in elite durum (T. turgidum ssp. durum and bread (T. aestivum wheat cultivars. The resultant near-isogenic lines (BC3F3 and BC3F4 were genotyped using SNP array to confirm the introgressed genomic regions and evaluated in two consecutive years under well-watered (690–710 mm and water-limited (290–320 mm conditions. Three of the introgressed QTLs were successfully validated, two in the background of durum wheat cv. Uzan (on chromosomes 1BL and 2BS, and one in the background of bread wheat cvs. Bar Nir and Zahir (chromosome 7AS. In most cases, the QTL x environment interaction was validated in terms of improved grain yield and biomass - specifically under drought (7AS QTL in cv. Bar Nir background, under both treatments (2BS QTL, and a greater stability across treatments (1BL QTL. The results provide a first demonstration that introgression of wild emmer QTL alleles can enhance productivity and yield stability across environments in domesticated wheat, thereby enriching the modern gene pool with essential diversity for the improvement of drought resistance.

  3. Combining powers of linkage and association mapping for precise dissection of QTL controlling resistance to gray leaf spot disease in maize (Zea mays L.).

    Science.gov (United States)

    Mammadov, Jafar; Sun, Xiaochun; Gao, Yanxin; Ochsenfeld, Cherie; Bakker, Erica; Ren, Ruihua; Flora, Jonathan; Wang, Xiujuan; Kumpatla, Siva; Meyer, David; Thompson, Steve

    2015-11-10

    Gray Leaf Spot (GLS causal agents Cercospora zeae-maydis and Cercospora zeina) is one of the most important foliar diseases of maize in all areas where the crop is being cultivated. Although in the USA the situation with GLS severity is not as critical as in sub-Saharan Africa or Brazil, the evidence of climate change, increasing corn monoculture as well as the narrow genetic base of North American resistant germplasm can turn the disease into a serious threat to US corn production. The development of GLS resistant cultivars is one way to control the disease. In this study we combined the high QTL detection power of genetic linkage mapping with the high resolution power of genome-wide association study (GWAS) to precisely dissect QTL controlling GLS resistance and identify closely linked molecular markers for robust marker-assisted selection and trait introgression. Using genetic linkage analysis with a small bi-parental mapping population, we identified four GLS resistance QTL on chromosomes 1, 6, 7, and 8, which were validated by GWAS. GWAS enabled us to dramatically increase the resolution within the confidence intervals of the above-mentioned QTL. Particularly, GWAS revealed that QTLGLSchr8, detected by genetic linkage mapping as a locus with major effect, was likely represented by two QTL with smaller effects. Conducted in parallel, GWAS of days-to-silking demonstrated the co-localization of flowering time QTL with GLS resistance QTL on chromosome 7 indicating that either QTLGLSchr7 is a flowering time QTL or it is a GLS resistance QTL that co-segregates with the latter. As a result, this genetic linkage - GWAS hybrid mapping system enabled us to identify one novel GLS resistance QTL (QTLGLSchr8a) and confirm with more refined positions four more previously mapped QTL (QTLGLSchr1, QTLGLSchr6, QTLGLSchr7, and QTLGLSchr8b). Through the novel Single Donor vs. Elite Panel method we were able to identify within QTL confidence intervals SNP markers that would be

  4. Impact of QTL minor allele frequency on genomic evaluation using real genotype data and simulated phenotypes in Japanese Black cattle.

    Science.gov (United States)

    Uemoto, Yoshinobu; Sasaki, Shinji; Kojima, Takatoshi; Sugimoto, Yoshikazu; Watanabe, Toshio

    2015-11-19

    Genetic variance that is not captured by single nucleotide polymorphisms (SNPs) is due to imperfect linkage disequilibrium (LD) between SNPs and quantitative trait loci (QTLs), and the extent of LD between SNPs and QTLs depends on different minor allele frequencies (MAF) between them. To evaluate the impact of MAF of QTLs on genomic evaluation, we performed a simulation study using real cattle genotype data. In total, 1368 Japanese Black cattle and 592,034 SNPs (Illumina BovineHD BeadChip) were used. We simulated phenotypes using real genotypes under different scenarios, varying the MAF categories, QTL heritability, number of QTLs, and distribution of QTL effect. After generating true breeding values and phenotypes, QTL heritability was estimated and the prediction accuracy of genomic estimated breeding value (GEBV) was assessed under different SNP densities, prediction models, and population size by a reference-test validation design. The extent of LD between SNPs and QTLs in this population was higher in the QTLs with high MAF than in those with low MAF. The effect of MAF of QTLs depended on the genetic architecture, evaluation strategy, and population size in genomic evaluation. In genetic architecture, genomic evaluation was affected by the MAF of QTLs combined with the QTL heritability and the distribution of QTL effect. The number of QTL was not affected on genomic evaluation if the number of QTL was more than 50. In the evaluation strategy, we showed that different SNP densities and prediction models affect the heritability estimation and genomic prediction and that this depends on the MAF of QTLs. In addition, accurate QTL heritability and GEBV were obtained using denser SNP information and the prediction model accounted for the SNPs with low and high MAFs. In population size, a large sample size is needed to increase the accuracy of GEBV. The MAF of QTL had an impact on heritability estimation and prediction accuracy. Most genetic variance can be captured

  5. Major Co-localized QTL for Plant Height, Branch Initiation Height, Stem Diameter, and Flowering Time in an Alien Introgression Derived Brassica napus DH Population

    Directory of Open Access Journals (Sweden)

    Yusen Shen

    2018-03-01

    Full Text Available Plant height (PH, branch initiation height (BIH, and stem diameter (SD are three stem-related traits that play crucial roles in plant architecture and lodging resistance. Herein, we show one doubled haploid (DH population obtained from a cross between Y689 (one Capsella bursa-pastoris derived Brassica napus intertribal introgression and Westar (B. napus cultivar that these traits were significantly positively correlated with one another and with flowering time (FT. Based on a high-density SNP map, a total of 102 additive quantitative trait loci (QTL were identified across six environments. Seventy-two consensus QTL and 49 unique QTL were identified using a two-round strategy of QTL meta-analysis. Notably, a total of 19 major QTL, including 11 novel ones, were detected for these traits, which comprised two QTL clusters on chromosomes A02 and A07. Conditional QTL mapping was performed to preliminarily evaluate the genetic basis (pleiotropy or tight linkage of the co-localized QTL. In addition, QTL by environment interactions (QEI mapping was performed to verify the additive QTL and estimate the QEI effect. In the genomic regions of all major QTL, orthologs of the genes involved in phytohormone biosynthesis, phytohormone signaling, flower development, and cell differentiation in Arabidopsis were proposed as candidate genes. Of these, BnaA02g02560, an ortholog of Arabidopsis GASA4, was suggested as a candidate gene for PH, SD, and FT; and BnaA02g08490, an ortholog of Arabidopsis GNL, was associated with PH, BIH and FT. These results provide useful information for further genetic studies on stem-related traits and plant growth adaptation.

  6. Copper tolerance of brown-rot fungi : time course of oxalic acid production

    Science.gov (United States)

    Frederick Green; Carol A. Clausen

    2003-01-01

    The increase in the use of non-arsenical copper-based wood preservatives in response to environmental concerns has been accompanied by interest in copper-tolerant decay fungi. Oxalic acid production by brown-rot fungi has been proposed as one mechanism of copper tolerance. Fifteen brown-rot fungi representing the genera Postia, Wolfiporia, Meruliporia, Gloeophyllum,...

  7. Developmental and Metabolic Plasticity of White-Skinned Grape Berries in Response to Botrytis cinerea during Noble Rot1[OPEN

    Science.gov (United States)

    Collins, Thomas S.; Vicente, Ariel R.; Doyle, Carolyn L.; Ye, Zirou; Allen, Greg; Heymann, Hildegarde

    2015-01-01

    Noble rot results from exceptional infections of ripe grape (Vitis vinifera) berries by Botrytis cinerea. Unlike bunch rot, noble rot promotes favorable changes in grape berries and the accumulation of secondary metabolites that enhance wine grape composition. Noble rot-infected berries of cv Sémillon, a white-skinned variety, were collected over 3 years from a commercial vineyard at the same time that fruit were harvested for botrytized wine production. Using an integrated transcriptomics and metabolomics approach, we demonstrate that noble rot alters the metabolism of cv Sémillon berries by inducing biotic and abiotic stress responses as well as ripening processes. During noble rot, B. cinerea induced the expression of key regulators of ripening-associated pathways, some of which are distinctive to the normal ripening of red-skinned cultivars. Enhancement of phenylpropanoid metabolism, characterized by a restricted flux in white-skinned berries, was a common outcome of noble rot and red-skinned berry ripening. Transcript and metabolite analyses together with enzymatic assays determined that the biosynthesis of anthocyanins is a consistent hallmark of noble rot in cv Sémillon berries. The biosynthesis of terpenes and fatty acid aroma precursors also increased during noble rot. We finally characterized the impact of noble rot in botrytized wines. Altogether, the results of this work demonstrated that noble rot causes a major reprogramming of berry development and metabolism. This desirable interaction between a fruit and a fungus stimulates pathways otherwise inactive in white-skinned berries, leading to a greater accumulation of compounds involved in the unique flavor and aroma of botrytized wines. PMID:26450706

  8. Filamentous fungi associated with natural infection of noble rot on withered grapes.

    Science.gov (United States)

    Lorenzini, M; Simonato, B; Favati, F; Bernardi, P; Sbarbati, A; Zapparoli, G

    2018-05-02

    The effects of noble rot infection of grapes on the characteristics of different types of wine, including Italian passito wine, are well known. Nevertheless, there is still little information on filamentous fungi associated with noble-rotten grapes. In this study, withered Garganega grapes for passito wine production, naturally infected by noble rot, were analyzed and compared to sound grapes. Skin morphology and fungal population on berry surfaces were analyzed. Scanning electron microscopy analysis revealed microcracks, germination conidia and branched hyphae on noble-rotten berries. Penicillium, Aureobasidium and Cladosporium were the most frequent genera present. Analysis of single berries displayed higher heterogeneity of epiphytic fungi in those infected by noble-rot than in sound berries. Penicillium adametzoides, Cladosporium cladospoirioides and Coniochaeta polymorpha were recovered. These, to the best of our knowledge, had never been previously isolated from withered grapes and, for C. polymorpha, from grapevine. This study provided novel data on noble rot mycobiota and suggests that fungi that co-habit with B. cinerea could have an important role on grape and wine quality. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Association mapping and favorable QTL alleles for fiber quality traits ...

    Indian Academy of Sciences (India)

    A total of 201 markers were polymorphic and generated 394 ... identified favorable QTL alleles and typical accessions for fiber quality are excellent genetic resources for future cotton .... Field management followed respective local practices.

  10. Simultaneous estimation of QTL parameters for mapping multiple traits

    Indian Academy of Sciences (India)

    LIANG TONG

    2018-03-13

    XM ji ) denotes the conditional probability of the QTL genotype. X. ∗ ji (QiQi, Qiqi or ... random error of the ith trait value of the jth subject, with mean zero and ..... to adjust the conditional probabilities in table 1 when conducting ...

  11. Grapevine bunch rots: impacts on wine composition, quality, and potential procedures for the removal of wine faults.

    Science.gov (United States)

    Steel, Christopher C; Blackman, John W; Schmidtke, Leigh M

    2013-06-05

    Bunch rot of grape berries causes economic loss to grape and wine production worldwide. The organisms responsible are largely filamentous fungi, the most common of these being Botrytis cinerea (gray mold); however, there are a range of other fungi responsible for the rotting of grapes such as Aspergillus spp., Penicillium spp., and fungi found in subtropical climates (e.g., Colletotrichum spp. (ripe rot) and Greeneria uvicola (bitter rot)). A further group more commonly associated with diseases of the vegetative tissues of the vine can also infect grape berries (e.g., Botryosphaeriaceae, Phomopsis viticola ). The impact these fungi have on wine quality is poorly understood as are remedial practices in the winery to minimize wine faults. Compounds found in bunch rot affected grapes and wine are typically described as having mushroom, earthy odors and include geosmin, 2-methylisoborneol, 1-octen-3-ol, 2-octen-1-ol, fenchol, and fenchone. This review examines the current state of knowledge about bunch rot of grapes and how this plant disease complex affects wine chemistry. Current wine industry practices to minimize wine faults and gaps in our understanding of how grape bunch rot diseases affect wine production and quality are also identified.

  12. Progeny-testing of full-sibs IBD in a SSC2 QTL region highlights epistatic interactions for fatness traits in pigs

    Directory of Open Access Journals (Sweden)

    Iannuccelli Nathalie

    2011-10-01

    Full Text Available Abstract Background Many QTL have been detected in pigs, but very few of them have been fine-mapped up to the causal mutation. On SSC2, the IGF2-intron3-G3072A mutation has been described as the causative polymorphism for a QTL underlying muscle mass and backfat deposition, but further studies have demonstrated that at least one additional QTL should segregate downstream of this mutation. A marker-assisted backcrossing design was set up in order to confirm the segregation of this second locus, reduce its confidence interval and better understand its mode of segregation. Results Five recombinant full-sibs, with genotype G/G at the IGF2 mutation, were progeny-tested. Only two of them displayed significant QTL for fatness traits although four inherited the same paternal and maternal chromosomes, thus exhibiting the same haplotypic contrast in the QTL region. The hypothesis of an interaction with another region in the genome was proposed to explain these discrepancies and after a genome scan, four different regions were retained as potential interacting regions with the SSC2 QTL. A candidate interacting region on SSC13 was confirmed by the analysis of an F2 pedigree, and in the backcross pedigree one haplotype in this region was found to mask the SSC2 QTL effect. Conclusions Assuming the hypothesis of interactions with other chromosomal regions, the QTL could be unambiguously mapped to a 30 cM region delimited by recombination points. The marker-assisted backcrossing design was successfully used to confirm the segregation of a QTL on SSC2 and, because full-sibs that inherited the same alleles from their two parents were analysed, the detection of epistatic interactions could be performed between alleles and not between breeds as usually done with the traditional Line-Cross model. Additional analyses of other recombinant sires should provide more information to further improve the fine-mapping of this locus, and confirm or deny the interaction

  13. First report of in-vitro fludioxonil-resistant isolates of Fusarium spp. causing potato dry rot in Michigan

    Science.gov (United States)

    Fusarium dry rot of potato (Solanum tuberosum) is a postharvest disease caused by several Fusarium species and is of worldwide importance. Measures for controlling dry rot in storage are limited. Dry rot has been managed primarily by reducing tuber bruising, providing conditions for rapid wound heal...

  14. Characterizing butt-rot fungi on USA-affiliated islands in the western Pacific

    Science.gov (United States)

    Phil Cannon; Ned B. Klopfenstein; Robert L. Schlub; Mee-Sook Kim; Yuko Ota; Norio Sahashi; Roland J. Quitugua; John W. Hanna; Amy L. Ross-Davis; J. D. Sweeney

    2014-01-01

    Ganoderma and Phellinus are genera that commonly cause tree butt-rot on USA-affiliated islands of the western Pacific. These fungal genera can be quite prevalent, especially in older mangrove stands. Although the majority of infections caused by these fungi lead to severe rotting of the heartwood, they typically do not directly kill the living tissues of the sapwood,...

  15. Field Efficiency Trial of 72% Streptomycin against Konjac Bacterial Soft Rot

    Institute of Scientific and Technical Information of China (English)

    Huang; Yongsheng; Li; Xiaojun; Zhu; Shijin; Ma; Yongsheng; Wang; Li

    2014-01-01

    72% Streptomycin soluble powder was used to control konjac bacterial soft rot in the study. The control efficiency and yield of different treatments were investigated,and the benefit was analyzed. The control scheme against konjac bacterial soft rot was as follows: spraying 72% atreptomycinon twice on rotation fields after all the seedlings were strong and uniform,or irrigating roots with 72% atreptomycinon once and spraying twice on continuous cropping fields.

  16. Mapping Late Leaf Spot Resistance in Peanut (Arachis hypogaea Using QTL-seq Reveals Markers for Marker-Assisted Selection

    Directory of Open Access Journals (Sweden)

    Josh Clevenger

    2018-02-01

    Full Text Available Late leaf spot (LLS; Cercosporidium personatum is a major fungal disease of cultivated peanut (Arachis hypogaea. A recombinant inbred line population segregating for quantitative field resistance was used to identify quantitative trait loci (QTL using QTL-seq. High rates of false positive SNP calls using established methods in this allotetraploid crop obscured significant QTLs. To resolve this problem, robust parental SNPs were first identified using polyploid-specific SNP identification pipelines, leading to discovery of significant QTLs for LLS resistance. These QTLs were confirmed over 4 years of field data. Selection with markers linked to these QTLs resulted in a significant increase in resistance, showing that these markers can be immediately applied in breeding programs. This study demonstrates that QTL-seq can be used to rapidly identify QTLs controlling highly quantitative traits in polyploid crops with complex genomes. Markers identified can then be deployed in breeding programs, increasing the efficiency of selection using molecular tools.Key Message: Field resistance to late leaf spot is a quantitative trait controlled by many QTLs. Using polyploid-specific methods, QTL-seq is faster and more cost effective than QTL mapping.

  17. Genomewide association study to detect QTL for twinning rate in ...

    Indian Academy of Sciences (India)

    2014-07-14

    Jul 14, 2014 ... Strongly suggestive quantitative trait loci (QTL) were also ... Journal of Genetics, Vol. .... fied in the different analysis, the GWAS showed three differ- .... also acknowledge the financial support of the Iran National Science.

  18. Genome-wide QTL and bulked transcriptomic analysis reveals new candidate genes for the control of tuber carotenoid content in potato (Solanum tuberosum L.).

    Science.gov (United States)

    Campbell, Raymond; Pont, Simon D A; Morris, Jenny A; McKenzie, Gaynor; Sharma, Sanjeev Kumar; Hedley, Pete E; Ramsay, Gavin; Bryan, Glenn J; Taylor, Mark A

    2014-09-01

    Genome-wide QTL analysis of potato tuber carotenoid content was investigated in populations of Solanum tuberosum Group Phureja that segregate for flesh colour, revealing a novel major QTL on chromosome 9. The carotenoid content of edible plant storage organs is a key nutritional and quality trait. Although the structural genes that encode the biosynthetic enzymes are well characterised, much less is known about the factors that determine overall storage organ content. In this study, genome-wide QTL mapping, in concert with an efficient 'genetical genomics' analysis using bulked samples, has been employed to investigate the genetic architecture of potato tuber carotenoid content. Two diploid populations of Solanum tuberosum Group Phureja were genotyped (AFLP, SSR and DArT markers) and analysed for their tuber carotenoid content over two growing seasons. Common to both populations were QTL that explained relatively small proportions of the variation in constituent carotenoids and a major QTL on chromosome 3 explaining up to 71 % of the variation in carotenoid content. In one of the populations (01H15), a second major carotenoid QTL was identified on chromosome 9, explaining up to 20 % of the phenotypic variation. Whereas the major chromosome 3 QTL was likely to be due to an allele of a gene encoding β-carotene hydroxylase, no known carotenoid biosynthetic genes are located in the vicinity of the chromosome 9 QTL. A unique expression profiling strategy using phenotypically distinct bulks comprised individuals with similar carotenoid content provided further support for the QTL mapping to chromosome 9. This study shows the potential of using the potato genome sequence to link genetic maps to data arising from eQTL approaches to enhance the discovery of candidate genes underlying QTLs.

  19. Mapping QTL Contributing to Variation in Posterior Lobe Morphology between Strains of Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Jennifer L Hackett

    Full Text Available Closely-related, and otherwise morphologically similar insect species frequently show striking divergence in the shape and/or size of male genital structures, a phenomenon thought to be driven by sexual selection. Comparative interspecific studies can help elucidate the evolutionary forces acting on genital structures to drive this rapid differentiation. However, genetic dissection of sexual trait divergence between species is frequently hampered by the difficulty generating interspecific recombinants. Intraspecific variation can be leveraged to investigate the genetics of rapidly-evolving sexual traits, and here we carry out a genetic analysis of variation in the posterior lobe within D. melanogaster. The lobe is a male-specific process emerging from the genital arch of D. melanogaster and three closely-related species, is essential for copulation, and shows radical divergence in form across species. There is also abundant variation within species in the shape and size of the lobe, and while this variation is considerably more subtle than that seen among species, it nonetheless provides the raw material for QTL mapping. We created an advanced intercross population from a pair of phenotypically-different inbred strains, and after phenotyping and genotyping-by-sequencing the recombinants, mapped several QTL contributing to various measures of lobe morphology. The additional generations of crossing over in our mapping population led to QTL intervals that are smaller than is typical for an F2 mapping design. The intervals we map overlap with a pair of lobe QTL we previously identified in an independent mapping cross, potentially suggesting a level of shared genetic control of trait variation. Our QTL additionally implicate a suite of genes that have been shown to contribute to the development of the posterior lobe. These loci are strong candidates to harbor naturally-segregating sites contributing to phenotypic variation within D. melanogaster, and

  20. Improving cost-effectiveness of brown rot control: the value of bio-economic modelling

    NARCIS (Netherlands)

    Breukers, A.; Werf, van der W.; Mourits, M.C.M.; Oude Lansink, A.G.J.M.

    2007-01-01

    Since 1995, the Dutch potato production chain has been hit by several outbreaks of brown rot, a quarantine disease caused by Ralstonia solanacearum race 3, biovar 2. To avoid establishment of brown rot in the potato production chain and avert the consequences on potato export, the Dutch government

  1. Mapping QTL for fatty acid composition that segregates between the ...

    African Journals Online (AJOL)

    Mapping QTL for fatty acid composition that segregates between the Japanese Black and Limousin cattle breeds (Short communication). NOM Tshipuliso, LJ Alexander, TW Geary, VM Snelling, DC Rule, JE Koltes, BE Mote, MD MacNeil ...

  2. Identification and dissection of four major QTL affecting milk fat content in the German Holstein-Friesian population.

    Directory of Open Access Journals (Sweden)

    Xiaolong Wang

    Full Text Available Milk composition traits exhibit a complex genetic architecture with a small number of major quantitative trait loci (QTL explaining a large fraction of the genetic variation and numerous QTL with minor effects. In order to identify QTL for milk fat percentage (FP in the German Holstein-Friesian (HF population, a genome-wide association study (GWAS was performed. The study population consisted of 2327 progeny-tested bulls. Genotypes were available for 44,280 SNPs. Phenotypes in the form of estimated breeding values (EBVs for FP were used as highly heritable traits. A variance components-based approach was used to account for population stratification. The GWAS identified four major QTL regions explaining 46.18% of the FP EBV variance. Besides two previously known FP QTL on BTA14 (P = 8.91×10-(198 and BTA20 (P = 7.03×10(-12 within DGAT1 and GHR, respectively, we uncovered two additional QTL regions on BTA5 (P = 2.00×10(-13 and BTA27 (P = 9.83×10(-5 encompassing EPS8 and GPAT4, respectively. EPS8 and GPAT4 are involved in lipid metabolism in mammals. Re-sequencing of EPS8 and GPAT4 revealed 50 polymorphisms. Genotypes for five of them were inferred for the entire study population. Two polymorphisms affecting potential transcription factor binding sites of EPS8 (P = 1.40×10(-12 and GPAT4 (P = 5.18×10(-5, respectively, were highly significantly associated with the FP EBV. Our results provide evidence that alteration of regulatory sites is an important aspect of genetic variation of complex traits in cattle.

  3. First report of Calonectria hongkongensis causing fruit rot of rambutan (Nephelium lappaceum L.)

    Science.gov (United States)

    Fruit rot is a major pre- and post-harvest disease problem in rambutan orchards. In 2011, fruit rot was observed at the USDA-TARS orchards in Mayaguez, Puerto Rico. Infected fruit were collected and tissue sections (1 mm2) were superficially sterilized with 70% ethanol and 0.5% sodium hypochlorite. ...

  4. License - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...t list, Marker list, QTL list, Plant DB link & Genome analysis methods © Satoshi ... Policy | Contact Us License - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  5. Demonstration of inaccuracy of QTL mapping due to sampling error€

    African Journals Online (AJOL)

    Bertrand Collard

    2012-06-12

    Jun 12, 2012 ... finding in simple terms so that findings and implications can be easily ... While sampling from the true populations for n = 94 and n =190, individual mapping .... Overview of QTL mapping experimental design. Four true ...

  6. Dro1, a major QTL involved in deep rooting of rice under upland field conditions.

    Science.gov (United States)

    Uga, Yusaku; Okuno, Kazutoshi; Yano, Masahiro

    2011-05-01

    Developing a deep root system is an important strategy for avoiding drought stress in rice. Using the 'basket' method, the ratio of deep rooting (RDR; the proportion of total roots that elongated through the basket bottom) was calculated to evaluate deep rooting. A new major quantitative trait locus (QTL) controlling RDR was detected on chromosome 9 by using 117 recombinant inbred lines (RILs) derived from a cross between the lowland cultivar IR64, with shallow rooting, and the upland cultivar Kinandang Patong (KP), with deep rooting. This QTL explained 66.6% of the total phenotypic variance in RDR in the RILs. A BC(2)F(3) line homozygous for the KP allele of the QTL had an RDR of 40.4%, compared with 2.6% for the homozygous IR64 allele. Fine mapping of this QTL was undertaken using eight BC(2)F(3) recombinant lines. The RDR QTL Dro1 (Deeper rooting 1) was mapped between the markers RM24393 and RM7424, which delimit a 608.4 kb interval in the reference cultivar Nipponbare. To clarify the influence of Dro1 in an upland field, the root distribution in different soil layers was quantified by means of core sampling. A line homozygous for the KP allele of Dro1 (Dro1-KP) and IR64 did not differ in root dry weight in the shallow soil layers (0-25 cm), but root dry weight of Dro1-KP in deep soil layers (25-50 cm) was significantly greater than that of IR64, suggesting that Dro1 plays a crucial role in increased deep rooting under upland field conditions.

  7. Pathogenicity and genetic diversity of Fusarium oxysporum causing soybean root rot in northeast China

    Science.gov (United States)

    Soybean is an important edible legume cultivated around the world. However, soybean production is seriously impacted by the widespread occurrence of root rot disease. In this study, genetic diversity and pathogenicity of Fusarium oxysporum associated with root rot of soybean in Heilongjiang province...

  8. Fungicide rotation schemes for managing Phytophthora fruit rot of watermelon across southeastern United States

    Science.gov (United States)

    Southeastern states produce about 50% of the watermelons in the United States (U.S.) where conditions are optimal for development of Phytophthora fruit rot prevail. Phytophthora fruit rot significantly limits watermelon production by causing serious yield losses to growers before and after harvest. ...

  9. Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean

    Directory of Open Access Journals (Sweden)

    Puji eLestari

    2013-06-01

    Full Text Available Understanding several modes of duplication contributing on the present genome structure is getting an attention because it could be related to numerous agronomically important traits. Since soybean serves as a rich protein source for animal feeds and human consumption, breeding efforts in soybean have been directed toward enhancing seed protein content. The publicly available soybean sequences and its genomically featured elements facilitate comprehending of quantitative trait loci (QTL for seed protein content in concordance with homeologous regions in soybean genome. Although parts of chromosome (Chr 20 and Chr 10 showed synteny, QTLs for seed protein content present only on Chr 20. Using comparative analysis of gene contents in recently duplicated genomic regions harboring QTL for protein/oil content on Chrs 20 and 10, a total of 27 genes are present in duplicated regions of both chromosomes. Notably, 4 tandem duplicates of the putative homeobox protein 22 (HB22 are present only on Chr 20 and this Medicago truncatula homolog expressed in endosperm at seed filling stage. These tandem duplicates could contribute on the protein/oil QTL of Chr 20. Our study suggests that non-shared gene contents within the duplicated genomic regions might lead to absence/presence of QTL related to protein/oil content.

  10. Biodegradation of hazardous waste using white rot fungus: Project planning and concept development document

    International Nuclear Information System (INIS)

    Luey, J.; Brouns, T.M.; Elliott, M.L.

    1990-11-01

    The white rot fungus Phanerochaete chrysosporium has been shown to effectively degrade pollutants such as trichlorophenol, polychlorinated biphenyls (PCBs), dioxins and other halogenated aromatic compounds. These refractory organic compounds and many others have been identified in the tank waste, groundwater and soil of various US Department of Energy (DOE) sites. The treatment of these refractory organic compounds has been identified as a high priority for DOE's Research, Development, Demonstration, Testing, and Evaluation (RDDT ampersand E) waste treatment programs. Unlike many bacteria, the white rot fungus P. chrysosporium is capable of degrading these types of refractory organics and may be valuable for the treatment of wastes containing multiple pollutants. The objectives of this project are to identify DOE waste problems amenable to white rot fungus treatment and to develop and demonstrate white rot fungus treatment process for these hazardous organic compounds. 32 refs., 6 figs., 7 tabs

  11. Paraphoma crown rot of pyrethrum (Tanacetum cinerariifolium)

    NARCIS (Netherlands)

    Moslemi, Azin; Ades, Peter Kevin; Groom, Tim; Crous, Pedro; Nicolas, Marc Edward; Taylor, Paul William James

    2016-01-01

    Pyrethrum (Tanacetum cinerariifolium) is commercially cultivated for the extraction of natural pyrethrin insecticides from the oil glands inside seeds. Yield-decline has caused significant yield losses in Tasmania during the last decade. A new pathogen of pyrethrum causing crown rot and reduced

  12. A genome scan revealed significant associations of growth traits with a major QTL and GHR2 in tilapia

    Science.gov (United States)

    Liu, Feng; Sun, Fei; Xia, Jun Hong; Li, Jian; Fu, Gui Hong; Lin, Grace; Tu, Rong Jian; Wan, Zi Yi; Quek, Delia; Yue, Gen Hua

    2014-01-01

    Growth is an important trait in animal breeding. However, the genetic effects underpinning fish growth variability are still poorly understood. QTL mapping and analysis of candidate genes are effective methods to address this issue. We conducted a genome-wide QTL analysis for growth in tilapia. A total of 10, 7 and 8 significant QTLs were identified for body weight, total length and standard length at 140 dph, respectively. The majority of these QTLs were sex-specific. One major QTL for growth traits was identified in the sex-determining locus in LG1, explaining 71.7%, 67.2% and 64.9% of the phenotypic variation (PV) of body weight, total length and standard length, respectively. In addition, a candidate gene GHR2 in a QTL was significantly associated with body weight, explaining 13.1% of PV. Real-time qPCR revealed that different genotypes at the GHR2 locus influenced the IGF-1 expression level. The markers located in the major QTL for growth traits could be used in marker-assisted selection of tilapia. The associations between GHR2 variants and growth traits suggest that the GHR2 gene should be an important gene that explains the difference in growth among tilapia species. PMID:25435025

  13. Identifying QTL and genetic correlations between fur quality traits in mink (Neovison vison)

    DEFF Research Database (Denmark)

    Thirstrup, Janne Pia; Anistoroaei, Razvan Marian; Guldbrandtsen, Bernt

    2014-01-01

    Mapping of QTL affecting fur quality traits (guard hair length, guard hair thickness, density of wool, surface of the fur and quality) and skin length was performed in a three-generation mink population (F2 design). In the parental generation, Nordic Brown mink were crossed reciprocally with Amer......Mapping of QTL affecting fur quality traits (guard hair length, guard hair thickness, density of wool, surface of the fur and quality) and skin length was performed in a three-generation mink population (F2 design). In the parental generation, Nordic Brown mink were crossed reciprocally...... with American Black short nap mink. In all, 1082 mink encompassing three generations were used for the analyses. The mink were genotyped for 104 microsatellites covering all 14 autosomes. The QTL analyses were performed by least-square regression implemented in gridqtl software. Genetic and phenotypic...

  14. Variation in oxalate and oxalate decarboxylase production by six species of brown and white rot fungi

    DEFF Research Database (Denmark)

    Hastrup, Anne Christine Steenkjær; Oliver, Jason; Howell, Caitlin

      Oxalic acid (C2O4H2), the strongest of the organic acids is produced by both brown and white rot decay fungi and has been connected to various aspects of brown- and white rot decay including the Fenton reaction (Green and Highley, 1997; Munir et al.,2001). Oxalic acid is secreted into the wood...... cell lumen where it quickly dissociates into hydrogen ions and oxalate, resulting in a pH decrease of the environment, and oxalate-cation complexes. Generally, brown rot fungi accumulate larger quantities of oxalic acid in the wood than white rot fungi. The amount of oxalic acid has been shown to vary...... of formic acid and CO2 (Makela et al., 2002). So far only a few species of brown rot fungi have been shown to accumulate this enzyme (Micales, 1995, Howell and Jellison, 2006).   The purpose of this study was to investigate the variation in the levels of soluble oxalate and total oxalate, in correlation...

  15. Identification of QTL for reaction to three races of Colletotrichum trifolii and further analysis of inheritance of resistance in autotetraploid lucerne.

    Science.gov (United States)

    Mackie, J M; Musial, J M; Armour, D J; Phan, H T T; Ellwood, S E; Aitken, K S; Irwin, J A G

    2007-05-01

    Anthracnose, caused by Colletotrichum trifolii, is one of the most serious diseases of lucerne worldwide. The disease is managed through deployment of resistant cultivars, but new pathotypes present a challenge to the successful implementation of this strategy. This paper reports the genetic map locations of quantitative trait loci (QTL) for reaction to races 1, 2 and 4 of C. trifolii in a single autotetraploid lucerne clone, designated W126 from the Australian cv. Trifecta. Resistance was mapped in a backcross population of 145 individuals, and reaction was assessed both by spray and injection inoculation of stems. Resistance to injection inoculation with races 1 and 4 was incompletely dominant and closely linked (phenotypic markers 2.2 cM apart); these resistances mapped to a linkage group homologous to Medicago truncatula linkage group 8. When the spray inoculation data were subjected to QTL analysis, the strongest QTL for resistance was located on linkage group 8; six QTL were identified for race 1 and four for race 4. Resistance to race 2 was incompletely recessive; four QTL were identified and these include one QTL on linkage group 4 that was also identified for race 1. Modelling of the interactions between individual QTL and marker effects allowed a total of 52-63% of the phenotypic variation to be described for each of the different races. These markers will have value in breeding lucerne, carrying multiple sources of resistance to the three known races of C. trifolii.

  16. Effectiveness of Neutral Electrolyzed Water on Incidence of Fungal Rot on Tomato Fruits ( Solanum lycopersicum L.).

    Science.gov (United States)

    Vásquez-López, Alfonso; Villarreal-Barajas, Tania; Rodríguez-Ortiz, Gerardo

    2016-10-01

    We assessed the effect of neutral electrolyzed water (NEW) on the incidence of rot on tomato ( Solanum lycopersicum L.) fruits inoculated with Fusarium oxysporum , Galactomyces geotrichum , and Alternaria sp. at sites with lesions. The inoculated fruits were treated with NEW at 10, 30, and 60 mg liter -1 active chlorine, with copper oxychloride fungicide, and with sterile distilled water (control) for 3, 5, and 10 min. In the experiment with F. oxysporum , 50 to 80% of the control fruits and 50 to 60% of the fruits treated with the fungicide exhibited symptoms of rot at the inoculated sites. The lowest incidence recorded was 30% for fruits treated with NEW at 60 mg liter -1 active chlorine with an immersion time of 5 min. In the experiment with G. geotrichum , incidence of rot on control fruits was 70 to 90%, and for treatment with fungicide rot incidence was 50 to 90%. NEW at 60 mg liter -1 active chlorine significantly reduced incidence of symptomatic fruit: only 30% of the inoculated fruits washed for 5 min had damage from rot. In the experiment with Alternaria sp., 60 to 90% of the fruits in the control group and 60 to 70% of the fruits in the fungicide group were symptomatic. The lowest incidence was recorded for the treatment in which the fruits were submerged in NEW with 60 mg liter -1 active chlorine for 3 min. In this group, 40 to 50% of the fruits exhibited symptoms of rot. These results were obtained 8 days after inoculation. NEW, with 60 mg liter -1 active chlorine, significantly reduced incidence of rot symptoms on fruits inoculated with one of the experimental fungi relative to the control (P ≤ 0.05). NEW at 60 mg liter -1 is effective in the control of fungal rot in tomatoes.

  17. Insight into the genetic components of community genetics: QTL mapping of insect association in a fast-growing forest tree.

    Directory of Open Access Journals (Sweden)

    Jennifer DeWoody

    Full Text Available Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL analyses conducted on data from a common garden experiment. The F2 offspring of a hybrid poplar (Populus trichocarpa x P. deltoides cross were assessed for seven categories of insect leaf damage at two time points, June and August. Positive and negative correlations were detected among damage categories and between sampling times. For example, sap suckers on leaves in June were positively correlated with sap suckers on leaves (P<0.001 but negatively correlated with skeletonizer damage (P<0.01 in August. The seven forms of leaf damage were used as a proxy for seven functional groups of insect species. Significant variation in insect association occurred among the hybrid offspring, including transgressive segregation of susceptibility to damage. NMDS analyses revealed significant variation and modest broad-sense heritability in insect community structure among genets. QTL analyses identified 14 genomic regions across 9 linkage groups that correlated with insect association. We used three genomics tools to test for putative mechanisms underlying the QTL. First, shikimate-phenylpropanoid pathway genes co-located to 9 of the 13 QTL tested, consistent with the role of phenolic glycosides as defensive compounds. Second, two insect association QTL corresponded to genomic hotspots for leaf trait QTL as identified in previous studies, indicating that, in addition to biochemical attributes, leaf morphology may influence insect preference. Third, network analyses identified categories of gene models over-represented in QTL for certain damage types, providing direction for future functional studies. These results provide insight into the genetic components involved in insect community structure in a fast

  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. QTL-seq for rapid identification of candidate genes for flowering time in broccoli × cabbage.

    Science.gov (United States)

    Shu, Jinshuai; Liu, Yumei; Zhang, Lili; Li, Zhansheng; Fang, Zhiyuan; Yang, Limei; Zhuang, Mu; Zhang, Yangyong; Lv, Honghao

    2018-04-01

    A major QTL controlling early flowering in broccoli × cabbage was identified by marker analysis and next-generation sequencing, corresponding to GRF6 gene conditioning flowering time in Arabidopsis. Flowering is an important agronomic trait for hybrid production in broccoli and cabbage, but the genetic mechanism underlying this process is unknown. In this study, segregation analysis with BC 1 P1, BC 1 P2, F 2 , and F 2:3 populations derived from a cross between two inbred lines "195" (late-flowering) and "93219" (early flowering) suggested that flowering time is a quantitative trait. Next, employing a next-generation sequencing-based whole-genome QTL-seq strategy, we identified a major genomic region harboring a robust flowering time QTL using an F 2 mapping population, designated Ef2.1 on cabbage chromosome 2 for early flowering. Ef2.1 was further validated by indel (insertion or deletion) marker-based classical QTL mapping, explaining 51.5% (LOD = 37.67) and 54.0% (LOD = 40.5) of the phenotypic variation in F 2 and F 2:3 populations, respectively. Combined QTL-seq and classical QTL analysis narrowed down Ef1.1 to a 228-kb genomic region containing 29 genes. A cabbage gene, Bol024659, was identified in this region, which is a homolog of GRF6, a major gene regulating flowering in Arabidopsis, and was designated BolGRF6. qRT-PCR study of the expression level of BolGRF6 revealed significantly higher expression in the early flowering genotypes. Taken together, our results provide support for BolGRF6 as a possible candidate gene for early flowering in the broccoli line 93219. The identified candidate genomic regions and genes may be useful for molecular breeding to improve broccoli and cabbage flowering times.

  20. Studies on storage rot of cocoyam

    African Journals Online (AJOL)

    uc network

    42(3): 2059-2068. Eze, C.S (1984). Studies on storage rot of cocoyam (Colocasia esculenta (L.) Schott) at Nsukka. MSc. Dissertation, Dept of Botany, Univ of Nigeria, Nsukka. 73pp. Loyonga, S. N and Nzietchueng S. (1987). Cocoyam and African food crisi. In: Tropical Root Crops: Root crops and the African food crisis Terry ...

  1. BAC-derived markers converted from RFLP linked to Phytophthora capsici resistance in pepper (Capsicum annuum L.).

    Science.gov (United States)

    Kim, Hyoun-Joung; Nahm, Seok-Hyeon; Lee, Heung-Ryul; Yoon, Gi-Bo; Kim, Ki-Taek; Kang, Byoung-Cheorl; Choi, Doil; Kweon, Oh Yeol; Cho, Myeong-Cheoul; Kwon, Jin-Kyung; Han, Jung-Heon; Kim, Jeong-Ho; Park, Minkyu; Ahn, Jong Hwa; Choi, Soon Ho; Her, Nam Han; Sung, Joo-Hee; Kim, Byung-Dong

    2008-12-01

    Phytophthora capsici Leonian, an oomycete pathogen, is a serious problem in pepper worldwide. Its resistance in pepper is controlled by quantitative trait loci (QTL). To detect QTL associated with P. capsici resistance, a molecular linkage map was constructed using 100 F(2) individuals from a cross between Capsicum annuum 'CM334' and C. annuum 'Chilsungcho'. This linkage map consisted of 202 restriction fragment length polymorphisms (RFLPs), 6 WRKYs and 1 simple sequence repeat (SSR) covering 1482.3 cM, with an average interval marker distance of 7.09 cM. QTL mapping of Phytophthora root rot and damping-off resistance was performed in F(2:3) originated from a cross between resistant Mexican landrace C. annuum 'CM334' and susceptible Korean landrace C. annuum 'Chilsungcho' using composite interval mapping (CIM) analysis. Four QTL explained 66.3% of the total phenotypic variations for root rot resistance and three 44.9% for damping-off resistance. Of these QTL loci, two were located close to RFLP markers CDI25 on chromosome 5 (P5) and CT211A on P9. A bacterial artificial chromosome (BAC) library from C. annuum 'CM334' was screened with these two RFLP probes to obtain sequence information around the RFLP marker loci for development of PCR-based markers. CDI25 and CT211 probes identified seven and eight BAC clones, respectively. Nine positive BAC clones containing probe regions were sequenced and used for cytogenetic analysis. One single-nucleotide amplified polymorphism (SNAP) for the CDI25 locus, and two SSRs and cleaved amplified polymorphic sequence (CAPS) for CT211 were developed using sequences of the positive BAC clones. These markers will be valuable for rapid selection of genotypes and map-based cloning for resistance genes against P. capsici.

  2. Confirmation and fine-mapping of clinical mastitis and somatic cell score QTL in Nordic Holstein cattle

    DEFF Research Database (Denmark)

    Sahana, Goutam; Guldbrandtsen, Bernt; Thomsen, Bo

    2013-01-01

    observed on bovine autosomes 6, 13, 14 and 20. Possible candidate genes for these QTL were identified. Identification of SNPs in linkage disequilibrium with QTL will enable marker-based selection for mastitis resistance. The candidate genes identified should be further studied to detect candidate......A genome-wide association study of 2098 progeny-tested Nordic Holstein bulls genotyped for 36 387 SNPs on 29 autosomes was conducted to confirm and fine-map quantitative trait loci (QTL) for mastitis traits identified earlier using linkage analysis with sparse microsatellite markers in the same...... population. We used linear mixed model analysis where a polygenic genetic effect was fitted as a random effect and single SNPs were successively included as fixed effects in the model. We detected 143 SNP-by-trait significant associations (P mastitis-related traits...

  3. Interactions of Salmonella enterica Serovar Typhimurium and Pectobacterium carotovorum within a Tomato Soft Rot.

    Science.gov (United States)

    George, Andrée S; Cox, Clayton E; Desai, Prerak; Porwollik, Steffen; Chu, Weiping; de Moraes, Marcos H; McClelland, Michael; Brandl, Maria T; Teplitski, Max

    2018-03-01

    Salmonella spp. are remarkably adaptable pathogens, and this adaptability allows these bacteria to thrive in a variety of environments and hosts. The mechanisms with which these pathogens establish within a niche amid the native microbiota remain poorly understood. Here, we aimed to uncover the mechanisms that enable Salmonella enterica serovar Typhimurium strain ATCC 14028 to benefit from the degradation of plant tissue by a soft rot plant pathogen, Pectobacterium carotovorum The hypothesis that in the soft rot, the liberation of starch (not utilized by P. carotovorum ) makes this polymer available to Salmonella spp., thus allowing it to colonize soft rots, was tested first and proven null. To identify the functions involved in Salmonella soft rot colonization, we carried out transposon insertion sequencing coupled with the phenotypic characterization of the mutants. The data indicate that Salmonella spp. experience a metabolic shift in response to the changes in the environment brought on by Pectobacterium spp. and likely coordinated by the csrBC small regulatory RNA. While csrBC and flhD appear to be of importance in the soft rot, the global two-component system encoded by barA sirA (which controls csrBC and flhDC under laboratory conditions) does not appear to be necessary for the observed phenotype. Motility and the synthesis of nucleotides and amino acids play critical roles in the growth of Salmonella spp. in the soft rot. IMPORTANCE Outbreaks of produce-associated illness continue to be a food safety concern. Earlier studies demonstrated that the presence of phytopathogens on produce was a significant risk factor associated with increased Salmonella carriage on fruits and vegetables. Here, we genetically characterize some of the requirements for interactions between Salmonella and phytobacteria that allow Salmonella spp. to establish a niche within an alternate host (tomato). Pathways necessary for nucleotide synthesis, amino acid synthesis, and motility

  4. Survey of root rot diseases of sugar bett in Central Greece

    Directory of Open Access Journals (Sweden)

    Karadimos Dimitros A.

    2006-01-01

    Full Text Available An extensive survey was conducted during the summer and autumn of 2004 in sugar beet fields in the area of Larissa, Thessaly region, with plants showing symptoms of root rot diseases. The aim of the monitoring was to identify the causal agents of root rot diseases. In total, 76 sugar beet fields were surveyed and 5-10 diseased roots were examined from each field. Isolations, carried out on PDA, showed that two main fungal pathogens causing root rot were Rhizoctonia solani and Phytophthora cryptogea. The former was isolated in 46% of the fields and the latter in 38% of the fields. In addition, Rhizopus stolonifer, Fusarium spp., Scerotium rolfsii and Rhizoctonia violacea were isolated in 14%, 7%, 4% and 1% of the fields respectively. In most of the surveyed fields only one pathogen species was isolated and only in a few of them more than one fungal species was identified.

  5. Rhizopus Soft Rot on Lily Caused by Rhizopus oryzae in Korea

    Directory of Open Access Journals (Sweden)

    Soo-Sang Hahm

    2014-03-01

    Full Text Available Rhizopus soft rot of lily (Lilium longiflorum caused by Rhizopus oryzae was observed in the experimental field in Taean Lily Experiment Station in Korea, 2012. The typical symptoms were water-soaked lesions on bottom stem and leaf rot. The lesion rapidly expanded and the plant was softened totally. The fungus grew vigorously at an optimum temperature (25oC and brownish colony and black sporangia were formed on potato dextrose agar medium. Sporangiophores formed on end of sporangia were sub-globose, brownish and 6-10 μm in size. Sporangia were globose, blackish and 87-116 μm in size. Sporangiospores were irregularly oval and sub-globose, brownish 4-8 μm in size. On the basis of mycological characteristics, analyzing sequences of internal transcribed spacer region of ribosomal DNA, and pathogenicity test on host plants, the causal fungus was identified as R. oryzae. This is the first report of Rhizopus soft rot on lily caused by R. oryzae in Korea.

  6. Chemical and biological control of Sclerotinia stem rot in the soybean crop

    Directory of Open Access Journals (Sweden)

    Ciro Hideki Sumida

    2015-05-01

    Full Text Available It was evaluated the effect of fungicides and the microbial control agent Trichoderma harzianum on the inhibition of the carpogenic and ascospore germination of Sclerotinia sclerotiorum. This study also evaluated the chemical, fungicidal and microbial control of white mold or Sclerotinia stem rot of soybean in the field. Three experiments were conducted, as follows: 1 inhibition of carpogenic germination of sclerotia, 2 inhibition of ascospore germination, and 3 control of Sclerotinia stem rot in a soybean crop under field conditions. The treatments evaluated were fluazinam, procymidone, iprodione, thiophanate-methyl, carbendazim, benzalkonium chloride + fluazinam, and T. harzianum. Procymidone resulted in an inhibition of 13.5% and benzalkonium chloride in an inhibition of 13.9% in an ascospore germination test. Fluazinam and procymidone were the most effective in reducing the production of ascospores/apothecium, representing 65.6% and 82.4% of inhibition. Procymidone and fluazinam if combined or not with benzalkonium chloride were the most effective in controlling sclerotinia stem rot under field conditions when applied at the onset of flowering and 15 days later. In the 2009-10 harvest, these two fungicides reduced the incidence of Sclerotinia stem rot by 73.1 and 71.6% and in the 2010-11 harvest by 75.7 and 77.6%, respectively.

  7. An Integrated Resource for Barley Linkage Map and Malting Quality QTL Alignment

    Directory of Open Access Journals (Sweden)

    Péter Szűcs

    2009-07-01

    Full Text Available Barley ( L. is an economically important model plant for genetics research. Barley is currently served by an increasingly comprehensive set of tools for genetic analysis that have recently been augmented by high-density genetic linkage maps built with gene-based single nucleotide polymorphisms (SNPs. These SNP-based maps need to be aligned with earlier generation maps, which were used for quantitative trait locus (QTL detection, by integrating multiple types of markers into a single map. A 2383 locus linkage map was developed using the Oregon Wolfe Barley (OWB Mapping Population to allow such alignments. The map is based on 1472 SNP, 722 DArT, and 189 prior markers which include morphological, simple sequence repeat (SSR, Restriction Fragment Length Polymorphism (RFLP, and sequence tagged site (STS loci. This new OWB map forms, therefore, a useful bridge between high-density SNP-only maps and prior QTL reports. The application of this bridge concept is shown using malting-quality QTLs from multiple mapping populations, as reported in the literature. This is the first step toward developing a Barley QTL Community Curation workbook for all types of QTLs and maps, on the GrainGenes website. The OWB-related resources are available at OWB Data and GrainGenes Tools (OWB-DGGT (.

  8. The fungus that came in from the cold: dry rot's pre-adapted ability to invade buildings.

    Science.gov (United States)

    Balasundaram, S V; Hess, J; Durling, M B; Moody, S C; Thorbek, L; Progida, C; LaButti, K; Aerts, A; Barry, K; Grigoriev, I V; Boddy, L; Högberg, N; Kauserud, H; Eastwood, D C; Skrede, I

    2018-03-01

    Many organisms benefit from being pre-adapted to niches shaped by human activity, and have successfully invaded man-made habitats. One such species is the dry rot fungus Serpula lacrymans, which has a wide distribution in buildings in temperate and boreal regions, where it decomposes coniferous construction wood. Comparative genomic analyses and growth experiments using this species and its wild relatives revealed that S. lacrymans evolved a very effective brown rot decay compared to its wild relatives, enabling an extremely rapid decay in buildings under suitable conditions. Adaptations in intracellular transport machineries promoting hyphal growth, and nutrient and water transport may explain why it is has become a successful invader of timber in houses. Further, we demonstrate that S. lacrymans has poor combative ability in our experimental setup, compared to other brown rot fungi. In sheltered indoor conditions, the dry rot fungus may have limited encounters with other wood decay fungi compared to its wild relatives. Overall, our analyses indicate that the dry rot fungus is an ecological specialist with poor combative ability against other fungi.

  9. Stripe rust and leaf rust resistance QTL mapping, epistatic interactions, and co-localization with stem rust resistance loci in spring wheat evaluated over three continents.

    Science.gov (United States)

    Singh, A; Knox, R E; DePauw, R M; Singh, A K; Cuthbert, R D; Campbell, H L; Shorter, S; Bhavani, S

    2014-11-01

    In wheat, advantageous gene-rich or pleiotropic regions for stripe, leaf, and stem rust and epistatic interactions between rust resistance loci should be accounted for in plant breeding strategies. Leaf rust (Puccinia triticina Eriks.) and stripe rust (Puccinia striiformis f. tritici Eriks) contribute to major production losses in many regions worldwide. The objectives of this research were to identify and study epistatic interactions of quantitative trait loci (QTL) for stripe and leaf rust resistance in a doubled haploid (DH) population derived from the cross of Canadian wheat cultivars, AC Cadillac and Carberry. The relationship of leaf and stripe rust resistance QTL that co-located with stem rust resistance QTL previously mapped in this population was also investigated. The Carberry/AC Cadillac population was genotyped with DArT(®) and simple sequence repeat markers. The parents and population were phenotyped for stripe rust severity and infection response in field rust nurseries in Kenya (Njoro), Canada (Swift Current), and New Zealand (Lincoln); and for leaf rust severity and infection response in field nurseries in Canada (Swift Current) and New Zealand (Lincoln). AC Cadillac was a source of stripe rust resistance QTL on chromosomes 2A, 2B, 3A, 3B, 5B, and 7B; and Carberry was a source of resistance on chromosomes 2B, 4B, and 7A. AC Cadillac contributed QTL for resistance to leaf rust on chromosome 2A and Carberry contributed QTL on chromosomes 2B and 4B. Stripe rust resistance QTL co-localized with previously reported stem rust resistance QTL on 2B, 3B, and 7B, while leaf rust resistance QTL co-localized with 4B stem rust resistance QTL. Several epistatic interactions were identified both for stripe and leaf rust resistance QTL. We have identified useful combinations of genetic loci with main and epistatic effects. Multiple disease resistance regions identified on chromosomes 2A, 2B, 3B, 4B, 5B, and 7B are prime candidates for further investigation and

  10. Enzymatic oxalic acid regulation correlated with wood degradation in four brown-rot fungi

    Science.gov (United States)

    Anne Christine Steenkjær Hastrup; Frederick Green III; Patricia K. Lebow; Bo Jensen

    2012-01-01

    Oxalic acid is a key component in the initiation of brown-rot decay and it has been suggested that it plays multiple roles during the degradation process. Oxalic acid is accumulated to varying degrees among brown-rot fungi; however, details on active regulation are scarce. The accumulation of oxalic acid was measured in this study from wood degraded by the four brown-...

  11. First report of Fusarium redolens causing crown rot of wheat (Triticum spp.) in Turkey

    Science.gov (United States)

    Fusarium crown rot, caused by a complex of Fusarium spp., is a yield-limiting disease of wheat world-wide, especially in dry Mediterranean climates. In order to identify Fusarium species associated with crown rot of wheat, a survey was conducted in summer 2013 in the major wheat growing regions of T...

  12. Laminated Root Rot of Western Conifers

    Science.gov (United States)

    E.E. Nelson; N.E. Martin; R.E. Williams

    1981-01-01

    Laminated root rot is caused by the native fungus Phellinus weirii (Murr.) Gilb. It occurs throughout the Northwestern United States and in southern British Columbia, Canada. The disease has also been reported in Japan and Manchuria. In the United States, the pathogen is most destructive in pure Douglas-fir stands west of the crest of the Cascade Range in Washington...

  13. Rhizoctonia crown and root rot disease nursery

    Science.gov (United States)

    The BSDF cooperative CRR Eastern Evaluation Nursery Rhizoctonia crown and root rot Evaluation Nursery in 2016 was a randomized complete-block design with five replications in 15 feet long, one-row plots (20 in row spacing), at the Saginaw Valley Research and Education Center near Frankenmuth, MI. F...

  14. 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.

  15. Validation of a 1DL earliness per se (eps) flowering QTL in bread wheat (Triticum aestivum).

    Science.gov (United States)

    Zikhali, Meluleki; Leverington-Waite, Michelle; Fish, Lesley; Simmonds, James; Orford, Simon; Wingen, Luzie U; Goram, Richard; Gosman, Nick; Bentley, Alison; Griffiths, Simon

    2014-01-01

    Vernalization, photoperiod and the relatively poorly defined earliness per se ( eps ) genes regulate flowering in plants. We report here the validation of a major eps quantitative trait locus (QTL) located on wheat 1DL using near isogenic lines (NILs). We used four independent pairs of NILs derived from a cross between Spark and Rialto winter wheat varieties, grown in both the field and controlled environments. NILs carrying the Spark allele, defined by QTL flanking markers Xgdm111 and Xbarc62 , consistently flowered 3-5 days earlier when fully vernalized relative to those with the Rialto. The effect was independent of photoperiod under field conditions, short days (10-h light), long days (16-h light) and very long days (20-h light). These results validate our original QTL identified using doubled haploid (DH) populations. This QTL represents variation maintained in elite north-western European winter wheat germplasm. The two DH lines used to develop the NILs, SR9 and SR23 enabled us to define the location of the 1DL QTL downstream of marker Xgdm111 . SR9 has the Spark 1DL arm while SR23 has a recombinant 1DL arm with the Spark allele from Xgdm111 to the distal end. Our work suggests that marker assisted selection of eps effects is feasible and useful even before the genes are cloned. This means eps genes can be defined and positionally cloned in the same way as the photoperiod and vernalization genes have been. This validation study is a first step towards fine mapping and eventually cloning the gene directly in hexaploid wheat.

  16. Structured association analysis leads to insight into Saccharomyces cerevisiae gene regulation by finding multiple contributing eQTL hotspots associated with functional gene modules.

    Science.gov (United States)

    Curtis, Ross E; Kim, Seyoung; Woolford, John L; Xu, Wenjie; Xing, Eric P

    2013-03-21

    Association analysis using genome-wide expression quantitative trait locus (eQTL) data investigates the effect that genetic variation has on cellular pathways and leads to the discovery of candidate regulators. Traditional analysis of eQTL data via pairwise statistical significance tests or linear regression does not leverage the availability of the structural information of the transcriptome, such as presence of gene networks that reveal correlation and potentially regulatory relationships among the study genes. We employ a new eQTL mapping algorithm, GFlasso, which we have previously developed for sparse structured regression, to reanalyze a genome-wide yeast dataset. GFlasso fully takes into account the dependencies among expression traits to suppress false positives and to enhance the signal/noise ratio. Thus, GFlasso leverages the gene-interaction network to discover the pleiotropic effects of genetic loci that perturb the expression level of multiple (rather than individual) genes, which enables us to gain more power in detecting previously neglected signals that are marginally weak but pleiotropically significant. While eQTL hotspots in yeast have been reported previously as genomic regions controlling multiple genes, our analysis reveals additional novel eQTL hotspots and, more interestingly, uncovers groups of multiple contributing eQTL hotspots that affect the expression level of functional gene modules. To our knowledge, our study is the first to report this type of gene regulation stemming from multiple eQTL hotspots. Additionally, we report the results from in-depth bioinformatics analysis for three groups of these eQTL hotspots: ribosome biogenesis, telomere silencing, and retrotransposon biology. We suggest candidate regulators for the functional gene modules that map to each group of hotspots. Not only do we find that many of these candidate regulators contain mutations in the promoter and coding regions of the genes, in the case of the Ribi group

  17. The evolution of gene expression QTL in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    James Ronald

    2007-08-01

    Full Text Available Understanding the evolutionary forces that influence patterns of gene expression variation will provide insights into the mechanisms of evolutionary change and the molecular basis of phenotypic diversity. To date, studies of gene expression evolution have primarily been made by analyzing how gene expression levels vary within and between species. However, the fundamental unit of heritable variation in transcript abundance is the underlying regulatory allele, and as a result it is necessary to understand gene expression evolution at the level of DNA sequence variation. Here we describe the evolutionary forces shaping patterns of genetic variation for 1206 cis-regulatory QTL identified in a cross between two divergent strains of Saccharomyces cerevisiae. We demonstrate that purifying selection against mildly deleterious alleles is the dominant force governing cis-regulatory evolution in S. cerevisiae and estimate the strength of selection. We also find that essential genes and genes with larger codon bias are subject to slightly stronger cis-regulatory constraint and that positive selection has played a role in the evolution of major trans-acting QTL.

  18. Gnomoniopsis castanea is the main agent of chestnut nut rot in Switzerland

    Directory of Open Access Journals (Sweden)

    Francesca G. DENNERT

    2015-09-01

    Full Text Available Nuts of sweet chestnut have been an important food source for the alpine population in Switzerland since the Middle Ages and are still valued today for the preparation of traditional food commodities. Nut quality is reduced by insect damage and by various pathogenic fungi. In the last few years, producers and consumers perceived an increase of brown nut rot; while the nut rot agent Gnomoniopsis castanea was reported locally in southern Switzerland, its presence has not been investigated over large areas until now. This study assessed the incidence of brown nut rot and identified the causal agent present in Switzerland. Fully ripened nuts were collected from the main sweet chestnut growing areas of Switzerland. A filamentous fungus morphologically identified as G. castanea was isolated from 10 to 91% of the sampled nuts, despite only 3 to 21% of the sampled nuts showing brown rot symptoms. This fungus was isolated from symptomatic chestnuts as well as from apparently healthy chestnuts. Our results suggest a possible endophytic lifestyle in ripened nuts as well as in branches, leaves and unripe nuts as previously found. Species identity of 45 isolates was confirmed by EF-1alpha, beta-tubulin and ITS sequencing. Concatenation of β-tubulin and calmodulin sequences showed that several haplotypes were present at each sampling locality. No other nut rot pathogens could be isolated in this study, suggesting that G. castanea is the main causal agent of nut rot in Switzerland. The presence of this species is reported for the first time in a site in northern Switzerland. Further studies are needed to assess the influence of meteorological conditions and chestnut varieties on the incidence of G. castanea in order to provide prevention strategies for chestnut growers. Normal 0 21 false false false FR-CH X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso

  19. Genetic analysis of partial resistance to basal stem rot (Sclerotinia sclerotiorum in sunflower

    Directory of Open Access Journals (Sweden)

    Amouzadeh Masoumeh

    2013-01-01

    Full Text Available Basal stem rot, caused by Sclerotinia sclerotiorum (Lib. de Bary, is one of the major diseases of sunflower (Helianthus annuus L. in the world. Quantitative trait loci (QTLs implicated in partial resistance to basal stem rot disease were identified using 99 recombinant inbred lines (RILs from the cross between sunflower parental lines PAC2 and RHA266. The study was undertaken in a completely randomized design with three replications under controlled conditions. The RILs and their parental lines were inoculated with a moderately aggressive isolate of S. sclerotiorum (SSKH41. Resistance to disease was evaluated by measuring the percentage of necrosis area three days after inoculation. QTLs were mapped using an updated high-density SSR and SNP linkage map. ANOVA showed significant differences among sunflower lines for resistance to basal stem rot (P≤0.05. The frequency distribution of lines for susceptibility to disease showed a continuous pattern. Composite interval mapping analysis revealed 5 QTLs for percentage of necrotic area, localized on linkage groups 1, 3, 8, 10 and 17. The sign of additive effect was positive in 5 QTLs, suggesting that the additive allele for partial resistance to basal stem rot came from the paternal line (RHA266. The phenotypic variance explained by QTLs (R2 ranged from 0.5 to 3.16%. Identified genes (HUCL02246_1, GST and POD, and SSR markers (ORS338, and SSL3 encompassing the QTLs for partial resistance to basal stem rot could be good candidates for marker assisted selection.

  20. Potential of bulb-associated bacteria for biocontrol of hyacinth soft rot caused by Dickeya zeae

    NARCIS (Netherlands)

    Jafra, S.; Przysowa, J.; Gwizdek-Wisniewska, A.; Wolf, van der J.M.

    2009-01-01

    Dickeya zeae is a pectinolytic bacterium responsible for soft rot disease in flower bulb crops. In this study, the possibility of controlling soft rot disease in hyacinth by using antagonistic bacteria isolated from hyacinth bulbs was explored. Bacterial isolates with potential for biocontrol were

  1. Trichoderma rot on ‘Fallglo’ Tangerine Fruit

    Science.gov (United States)

    In September 2009, brown rot symptoms were observed on ‘Fallglo’ fruit after 7 weeks of storage. Fourteen days prior to harvest, fruit were treated by dipping into one of four different fungicide solutions. Control fruit were dipped in tap water. After harvest, the fruit were degreened with 5 ppm et...

  2. Scholarly context not found: one in five articles suffers from reference rot.

    Directory of Open Access Journals (Sweden)

    Martin Klein

    Full Text Available The emergence of the web has fundamentally affected most aspects of information communication, including scholarly communication. The immediacy that characterizes publishing information to the web, as well as accessing it, allows for a dramatic increase in the speed of dissemination of scholarly knowledge. But, the transition from a paper-based to a web-based scholarly communication system also poses challenges. In this paper, we focus on reference rot, the combination of link rot and content drift to which references to web resources included in Science, Technology, and Medicine (STM articles are subject. We investigate the extent to which reference rot impacts the ability to revisit the web context that surrounds STM articles some time after their publication. We do so on the basis of a vast collection of articles from three corpora that span publication years 1997 to 2012. For over one million references to web resources extracted from over 3.5 million articles, we determine whether the HTTP URI is still responsive on the live web and whether web archives contain an archived snapshot representative of the state the referenced resource had at the time it was referenced. We observe that the fraction of articles containing references to web resources is growing steadily over time. We find one out of five STM articles suffering from reference rot, meaning it is impossible to revisit the web context that surrounds them some time after their publication. When only considering STM articles that contain references to web resources, this fraction increases to seven out of ten. We suggest that, in order to safeguard the long-term integrity of the web-based scholarly record, robust solutions to combat the reference rot problem are required. In conclusion, we provide a brief insight into the directions that are explored with this regard in the context of the Hiberlink project.

  3. Neofusicoccum luteum associated with leaf necrosis and fruit rot of olives in New South Wales, Australia

    Directory of Open Access Journals (Sweden)

    V. Sergeeva

    2009-09-01

    Full Text Available Neofusicoccum luteum is reported for the first time from olives (Olea europaea, causing fruit rot and leaf necrosis. Affected fruits initially became brown with pycnidia developing on the surface, later drying out and becoming mummified. The fungus was shown to be pathogenic on both fruits and leaves. The association of Botryosphaeriaceae with rotting olive fruits in Mediterranean regions and in New South Wales, Australia indicates that these fungi play a significant role in fruit rots of olives and deserve greater attention.

  4. Distribution of cranberry fruit-rotting fungi in new jersey and evidence for nonspecific host resistance.

    Science.gov (United States)

    Stiles, C M; Oudemans, P V

    1999-03-01

    ABSTRACT A survey was conducted over a 3-year period to determine the frequencies and distributions of fruit-rotting fungi in New Jersey cranberry beds. In the first 2 years of the study, Physalospora vaccinii and Glomerella cingulata were the most prevalent and widespread field-rotting fungi. In the third year, the frequency of G. cingulata declined markedly. Other species such as Coleophoma empetri, Phyllosticta vaccinii, and Phomopsis vaccinii were isolated at high frequencies from a limited number of locations. Storage-rotting fungi including Allantophomopsis cytisporea and A. lycopodina were isolated at low frequencies, but were widely distributed within the growing region. On sound fruit, a somewhat different profile emerged. Fungi such as Phyllosticta elongata, Alternaria spp., and Physalospora vaccinii were commonly isolated. In comparisons among different cranberry cultivars, no differences in the fungal profiles were seen. This was interpreted to indicate that if differences in fruit-rot resistance exist, they are likely to be general forms of resistance rather than fungal species-specific mechanisms.

  5. Production and optimization of ligninolytic enzymes by white rot ...

    African Journals Online (AJOL)

    Production and optimization of ligninolytic enzymes by white rot fungus Schizophyllum ... size and nutritional factors (carbon and nitrogen ratio, mediators and metal ions). ... scale production of these enzymes for diverse industrial applications.

  6. QTL mapping of genome regions controlling temephos resistance in larvae of the mosquito Aedes aegypti.

    Science.gov (United States)

    Reyes-Solis, Guadalupe Del Carmen; Saavedra-Rodriguez, Karla; Suarez, Adriana Flores; Black, William C

    2014-10-01

    The mosquito Aedes aegypti is the principal vector of dengue and yellow fever flaviviruses. Temephos is an organophosphate insecticide used globally to suppress Ae. aegypti larval populations but resistance has evolved in many locations. Quantitative Trait Loci (QTL) controlling temephos survival in Ae. aegypti larvae were mapped in a pair of F3 advanced intercross lines arising from temephos resistant parents from Solidaridad, México and temephos susceptible parents from Iquitos, Peru. Two sets of 200 F3 larvae were exposed to a discriminating dose of temephos and then dead larvae were collected and preserved for DNA isolation every two hours up to 16 hours. Larvae surviving longer than 16 hours were considered resistant. For QTL mapping, single nucleotide polymorphisms (SNPs) were identified at 23 single copy genes and 26 microsatellite loci of known physical positions in the Ae. aegypti genome. In both reciprocal crosses, Multiple Interval Mapping identified eleven QTL associated with time until death. In the Solidaridad×Iquitos (SLD×Iq) cross twelve were associated with survival but in the reciprocal IqxSLD cross, only six QTL were survival associated. Polymorphisms at acetylcholine esterase (AchE) loci 1 and 2 were not associated with either resistance phenotype suggesting that target site insensitivity is not an organophosphate resistance mechanism in this region of México. Temephos resistance is under the control of many metabolic genes of small effect and dispersed throughout the Ae. aegypti genome.

  7. A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection.

    Directory of Open Access Journals (Sweden)

    George Nicholson

    2011-09-01

    Full Text Available We have performed a metabolite quantitative trait locus (mQTL study of the (1H nuclear magnetic resonance spectroscopy ((1H NMR metabolome in humans, building on recent targeted knowledge of genetic drivers of metabolic regulation. Urine and plasma samples were collected from two cohorts of individuals of European descent, with one cohort comprised of female twins donating samples longitudinally. Sample metabolite concentrations were quantified by (1H NMR and tested for association with genome-wide single-nucleotide polymorphisms (SNPs. Four metabolites' concentrations exhibited significant, replicable association with SNP variation (8.6×10(-11QTL associations. The study's longitudinal twin design allowed detailed variance-components analysis of the sources of population variation in metabolite levels. The mQTLs explained 40%-64% of biological population variation in the corresponding metabolites' concentrations. These effect sizes are stronger than those reported in a recent, targeted mQTL study of metabolites in serum using the targeted-metabolomics Biocrates platform. By re-analysing our plasma samples using the Biocrates platform, we replicated the mQTL findings of the previous study and discovered a previously uncharacterized yet substantial familial component of variation in metabolite levels in addition to the heritability contribution from

  8. Rapid polyether cleavage via extracellular one-electron oxidation by a brown-rot basidiomycete

    OpenAIRE

    Kerem, Zohar; Bao, Wuli; Hammel, Kenneth E.

    1998-01-01

    Fungi that cause brown rot of wood are essential biomass recyclers and also the principal agents of decay in wooden structures, but the extracellular mechanisms by which they degrade lignocellulose remain unknown. To test the hypothesis that brown-rot fungi use extracellular free radical oxidants as biodegradative tools, Gloeophyllum trabeum was examined for its ability to depolymerize an environmentally recalcitrant polyether, poly(ethylene oxide) (PEO), that cannot penetrate cell membranes....

  9. Detecting cotton boll rot with an electronic nose

    Science.gov (United States)

    South Carolina Boll Rot is an emerging disease of cotton, Gossypium hirsutum L., caused by the opportunistic bacteria, Pantoea agglomerans (Ewing and Fife). Unlike typical fungal diseases, bolls infected with P. agglomerans continue to appear normal externally, complicating early and rapid detectio...

  10. 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.

  11. Studies on the epidemiology of spear rot in oil palm (Elaeis guineensis Jacq.) in Suriname

    NARCIS (Netherlands)

    Lande, van de H.L.

    1993-01-01

    The epidemiology of spear rot, an infectious disease of unknown etiology, was studied over 10 years at three government-owned oil palm plantations in Suriname. As with other and similar diseases, amarelecimento fatal in Brazil and pudrición del cogollo in Latin America, which too show rot

  12. Refining QTL with high-density SNP genotyping and whole genome sequence in three cattle breeds

    DEFF Research Database (Denmark)

    Sahana, Goutam; Guldbrandtsen, Bernt; Lund, Mogens Sandø

    2012-01-01

    Genome-wide association study was carried out in Nordic Holsteins, Nordic Red and Jersey breeds for functional traits using BovineHD Genotyping BreadChip (Illumina, San Diego, CA). The association analyses were carried out using both linear mixed model approach and a Bayesian variable selection...... method. Principal components were used to account for population structure. The QTL segregating in all three breeds were selected and a few of the most significant ones were followed in further analyses. The polymorphisms in the identified QTL regions were imputed using 90 whole genome sequences...

  13. 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.

  14. Genomic dissection and prioritizing of candidate genes of QTL for ...

    Indian Academy of Sciences (India)

    Genomic dissection and prioritizing of candidate genes of QTL for regulating spontaneous arthritis on chromosome 1 in mice deficient for interleukin-1 receptor antagonist. Yanhong Cao, Jifei Zhang, Yan Jiao, Jian Yan, Feng Jiao, XiaoYun Liu, Robert W. Williams, Karen A. Hasty,. John M. Stuart and Weikuan Gu. J. Genet.

  15. Control of Ralstonia Solanacearum The Causal Agent of Brown Rot in Potato Using Essential Oils

    International Nuclear Information System (INIS)

    Salem, E.A.

    2011-01-01

    Five essential oils, namely peppermint (Mentha piperita L.), caraway (Carium carvum L.), fennel (Foeniculum vulgare Mill.), lemongrass (Cymbopogon citratus Staph.) and thyme (Thymus vulgaris), were used separately against Ralstonia solanacearum; the causal agent of brown rot in potato. The most two effective oils (peppermint and thyme) were used in vitro and in vivo after testing their effects on potato tubers buds germination. Peppermint inhibited buds germination but thyme have no effects on buds germination. In vivo, the control of brown rot using thyme oil in glass house experiment reduced the percentage of brown rot infection to 30.6% and reduced the severity of disease from 5 to 3.

  16. A High Density Genetic Map Derived from RAD Sequencing and Its Application in QTL Analysis of Yield-Related Traits in Vigna unguiculata

    Directory of Open Access Journals (Sweden)

    Lei Pan

    2017-09-01

    Full Text Available Cowpea [Vigna unguiculata (L. Walp.] is an annual legume of economic importance and widely grown in the semi-arid tropics. However, high-density genetic maps of cowpea are still lacking. Here, we identified 34,868 SNPs (single nucleotide polymorphisms that were distributed in the cowpea genome based on the RAD sequencing (restriction-site associated DNA sequencing technique using a population of 170 individuals (two cowpea parents and 168 F2:3 progenies. Of these, 17,996 reliable SNPs were allotted to 11 consensus linkage groups (LGs. The length of the genetic map was 1,194.25 cM in total with a mean distance of 0.066 cM/SNP marker locus. Using this map and the F2:3 population, combined with the CIM (composite interval mapping method, eleven quantitative trait loci (QTL of yield-related trait were detected on seven LGs (LG4, 5, 6, 7, 9, 10, and 11 in cowpea. These QTL explained 0.05–17.32% of the total phenotypic variation. Among these, four QTL were for pod length, four QTL for thousand-grain weight (TGW, two QTL for grain number per pod, and one QTL for carpopodium length. Our results will provide a foundation for understanding genes related to grain yield in the cowpea and genus Vigna.

  17. Rapid polyether cleavage via extracellular one-electron oxidation by a brown-rot basidiomycete.

    Science.gov (United States)

    Kerem, Z; Bao, W; Hammel, K E

    1998-09-01

    Fungi that cause brown rot of wood are essential biomass recyclers and also the principal agents of decay in wooden structures, but the extracellular mechanisms by which they degrade lignocellulose remain unknown. To test the hypothesis that brown-rot fungi use extracellular free radical oxidants as biodegradative tools, Gloeophyllum trabeum was examined for its ability to depolymerize an environmentally recalcitrant polyether, poly(ethylene oxide) (PEO), that cannot penetrate cell membranes. Analyses of degraded PEOs by gel permeation chromatography showed that the fungus cleaved PEO rapidly by an endo route. 13C NMR analyses of unlabeled and perdeuterated PEOs recovered from G. trabeum cultures showed that a major route for depolymerization was oxidative C---C bond cleavage, a reaction diagnostic for hydrogen abstraction from a PEO methylene group by a radical oxidant. Fenton reagent (Fe(II)/H2O2) oxidized PEO by the same route in vitro and therefore might account for PEO biodegradation if it is produced by the fungus, but the data do not rule out involvement of less reactive radicals. The reactivity and extrahyphal location of this PEO-degrading system suggest that its natural function is to participate in the brown rot of wood and that it may enable brown-rot fungi to degrade recalcitrant organopollutants.

  18. Biocontrol with Trichoderma species for the management of postharvest crown rot of banana

    Directory of Open Access Journals (Sweden)

    G. Sangeetha

    2009-09-01

    Full Text Available Lasiodiplodia theobromae and Colletotrichum musae cause the postharvest crown rot disease complex of banana. In vitro experiments evaluated the effect of twelve isolates of Trichoderma spp. from the soil of organic banana orchards (‘native isolates’ and eight isolates of Trichoderma spp. from culture collections (‘introduced isolates’ on the two pathogens. The native and introduced Trichoderma spp. had varied antagonistic effects against the two pathogens. Eight Trichoderma spp. isolates effective in the in vitro assays were evaluated singly on fruits both at room temperature and in cold storage. Single antagonists did not satisfactorily control crown rot on the fruits as compared with the fungicide carbendazim. However, two isolates of T. viride, one of T. harzianum and one of T. koningii performed well when applied singly, and these were selected for evaluation in isolate mixtures. There was very little antagonism between these isolates. Of 11 two-way, three-way and four-way mixtures of these isolates, the four-way and a three-way mixtures reduced crown rot incidence, both at room temperature and in cold storage, giving better control than carbendazim. The study identified consortia of compatible Trichoderma antagonists with superior biocontrol potential for the management of the postharvest crown rot complex of banana.

  19. Relationship between QTL for grain shape, grain weight, test weight, milling yield, and plant height in the spring wheat cross RL4452/'AC Domain'.

    Science.gov (United States)

    Cabral, Adrian L; Jordan, Mark C; Larson, Gary; Somers, Daryl J; Humphreys, D Gavin; McCartney, Curt A

    2018-01-01

    Kernel morphology characteristics of wheat are complex and quantitatively inherited. A doubled haploid (DH) population of the cross RL4452/'AC Domain' was used to study the genetic basis of seed shape. Quantitative trait loci (QTL) analyses were conducted on a total of 18 traits: 14 grain shape traits, flour yield (Fyd), and three agronomic traits (Plant height [Plht], 1000 Grain weight [Gwt], Test weight [Twt]), using data from trial locations at Glenlea, Brandon, and Morden in Manitoba, Canada, between 1999 and 2004. Kernel shape was studied through digital image analysis with an Acurum® grain analyzer. Plht, Gwt, Twt, Fyd, and grain shape QTL were correlated with each other and QTL analysis revealed that QTL for these traits often mapped to the same genetic locations. The most significant QTL for the grain shape traits were located on chromosomes 4B and 4D, each accounting for up to 24.4% and 53.3% of the total phenotypic variation, respectively. In addition, the most significant QTL for Plht, Gwt, and Twt were all detected on chromosome 4D at the Rht-D1 locus. Rht-D1b decreased Plht, Gwt, Twt, and kernel width relative to the Rht-D1a allele. A narrow genetic interval on chromosome 4B contained significant QTL for grain shape, Gwt, and Plht. The 'AC Domain' allele reduced Plht, Gwt, kernel length and width traits, but had no detectable effect on Twt. The data indicated that this variation was inconsistent with segregation at Rht-B1. Numerous QTL were identified that control these traits in this population.

  20. New record of Phytophthora root and stem rot of Lavandula angustifolia

    Directory of Open Access Journals (Sweden)

    Leszek B. Orlikowski

    2013-12-01

    Full Text Available Phytophthora cinnamomi was isolated from rotted root and stem parts of lavender as well as from soil taken from containers with diseased plants. Additionally Botrytis cinerea, Fusarium spp. and Sclerotinia sclerotiorum were often isolated from diseased tissues. P. cinnamomi colonised leaves and stem parts of 4 lavender species in laboratory trials and caused stem rot of plants in greenhouse experiments. Cardinal temperature for in vitro growth were about 7,5 and 32°C with optimum 25-27,5°C. The species colonised stem tissues at temperature ranged from 10° to 32°C.

  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. A Predictive Model for Time-to-Flowering in the Common Bean Based on QTL and Environmental Variables

    Directory of Open Access Journals (Sweden)

    Mehul S. Bhakta

    2017-12-01

    Full Text Available The common bean is a tropical facultative short-day legume that is now grown in tropical and temperate zones. This observation underscores how domestication and modern breeding can change the adaptive phenology of a species. A key adaptive trait is the optimal timing of the transition from the vegetative to the reproductive stage. This trait is responsive to genetically controlled signal transduction pathways and local climatic cues. A comprehensive characterization of this trait can be started by assessing the quantitative contribution of the genetic and environmental factors, and their interactions. This study aimed to locate significant QTL (G and environmental (E factors controlling time-to-flower in the common bean, and to identify and measure G × E interactions. Phenotypic data were collected from a biparental [Andean × Mesoamerican] recombinant inbred population (F11:14, 188 genotypes grown at five environmentally distinct sites. QTL analysis using a dense linkage map revealed 12 QTL, five of which showed significant interactions with the environment. Dissection of G × E interactions using a linear mixed-effect model revealed that temperature, solar radiation, and photoperiod play major roles in controlling common bean flowering time directly, and indirectly by modifying the effect of certain QTL. The model predicts flowering time across five sites with an adjusted r-square of 0.89 and root-mean square error of 2.52 d. The model provides the means to disentangle the environmental dependencies of complex traits, and presents an opportunity to identify in silico QTL allele combinations that could yield desired phenotypes under different climatic conditions.

  3. Study on the Occurrence and Epidemic Model of Rape Sclerotinia Stem Rot of ‘Zheyou 50’

    OpenAIRE

    Xu Sen-fu; Wang Hui-fu; Yu Shanhong; Wang En-guo

    2013-01-01

    In order to investigate invading and epidemic rules of rape sclerotinia stem rot of ‘Zheyou 50’ and promote the development of brassica campestris industry, this paper studied the outbreak regularity and epidemic model of rape sclerotinia stem rot according to field investigation and infection. The result showed that machinery direct seeding rape was good for the occurrence of sclerotinia stem rot for the reason of late seeding and high density. The period from water damage appeared to wiltin...

  4. Simultaneous Improvement and Genetic Dissection of Salt Tolerance of Rice (Oryza sativa L. by Designed QTL Pyramiding

    Directory of Open Access Journals (Sweden)

    Yunlong Pang

    2017-07-01

    Full Text Available Breeding of multi-stress tolerant rice varieties with higher grain yields is the best option to enhance the rice productivity of abiotic stresses prone areas. It also poses the greatest challenge to plant breeders to breed rice varieties for such stress prone conditions. Here, we carried out a designed QTL pyramiding experiment to develop high yielding “Green Super Rice” varieties with significantly improved tolerance to salt stress and grain yield. Using the F4 population derived from a cross between two selected introgression lines, we were able to develop six mostly homozygous promising high yielding lines with significantly improved salt tolerance and grain yield under optimal and/or saline conditions in 3 years. Simultaneous mapping using the same breeding population and tunable genotyping-by-sequencing technology, we identified three QTL affecting salt injury score and leaf chlorophyll content. By analyzing 32M SNP data of the grandparents and graphical genotypes of the parents, we discovered 87 positional candidate genes for salt tolerant QTL. According to their functional annotation, we inferred the most likely candidate genes. We demonstrated that designed QTL pyramiding is a powerful strategy for simultaneous improvement and genetic dissection of complex traits in rice.

  5. Pathological and rhizospherical studies on root-rot disease of ...

    African Journals Online (AJOL)

    AJB SERVER

    2007-02-05

    Feb 5, 2007 ... Rhizoctonia solani root-rot aggressive pathogens to squash on media containing culture of Trichoderma ..... The bacteriology of root region of cat ... (2004): Comparison of the behavior of a transformed hygromycin resistant ...

  6. Database Description - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ... QTL list, Plant DB link & Genome analysis methods Alternative name - DOI 10.18908/lsdba.nbdc01194-01-000 Cr...ers and QTLs are curated manually from the published literature. The marker information includes marker sequences, genotyping methods... Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  7. 大豆籽粒维生素E含量的QTL分析%Identification of QTL Associated with Vitamin E Content in Soybean Seeds

    Institute of Scientific and Technical Information of China (English)

    张红梅; 李海朝; 自翔; 顾和平; 袁星星; 陈华涛; 崔晓艳; 陈新; 卢为国

    2015-01-01

    Vitamin E has effects on human immunity, anti-cancer and prevention of cardiovascular disease. Vitamin E from soy-bean has the advantages of higher security and higher human body absorption rate. The objective of the present study was to map the additive, additive × additive (epistasis), additive × year and epistasis × year QTLs for vitamin E and relative tocopherol con-tents with the RIL population BIEX (Essex×ZDD2315) using HPLC (high performance liquid chromatography) method and soft-ware QTLNetwork 2.1. Eight additive QTLs and twelve additive × additive (epistasis) QTLs were detected for vitamin E and relative tocopherol contents. The contributions to the phenotypic variances of additive QTL and epistatic QTL pairs were 8.68%(two QTLs) and 15.57% (four pairs) for α-tocopherol, 8.59% (two QTL) and 11.57% (two pairs) for γ-tocopherol, 5.44% (one QTL) and 17.61% (three pairs) for δ-tocopherol and 11.39% (three QTL) and 9.48% (three pairs) for total vitamin E contents, respectively. Those of additive and epistatic QTLs by year interaction were not found. The accumulated contribution of the un-mapped minor QTLs was 66.16%–75.32%, indicating the variance of unmapped minor QTLs accounting for more than two thirds. In genetic composition, undetected minor QTLs accounted for a considerably large part additive QTLs and epistatic QTLs were nearly equal in α-tocopherol, γ-tocopherol, δ-tocopherol and total vitamin E contents. Accordingly, in breeding for vitamin E con-tents, the strategy of pyramiding multiple QTLs, both additive and epistatic, by using marker-assisted selection combined with accumulating minor effect QTLs through conversional procedures should be considered.%维生素 E (VE)具有提高人体免疫力、抗癌、预防心血管疾病等保健作用,从大豆中提取的 VE 安全性更高。本研究采用高效液相色谱技术(HPLC)检测大豆 BIEX 群体(Essex×ZDD2315)维生素 E

  8. Fungicides reduce Rhododendron root rot and mortality caused by Phytophthora cinnamomi, but not by P. plurivora

    Science.gov (United States)

    Rhododendron root rot, caused by several Phytophthora species, can cause devastating losses in nursery-grown plants. Most research on chemical control of root rot has focused on Phytophthora cinnamomi. However, it is unknown whether treatments recommended for P. cinnamomi are also effective for othe...

  9. A fast algorithm for estimating transmission probabilities in QTL detection designs with dense maps

    Directory of Open Access Journals (Sweden)

    Gilbert Hélène

    2009-11-01

    Full Text Available Abstract Background In the case of an autosomal locus, four transmission events from the parents to progeny are possible, specified by the grand parental origin of the alleles inherited by this individual. Computing the probabilities of these transmission events is essential to perform QTL detection methods. Results A fast algorithm for the estimation of these probabilities conditional to parental phases has been developed. It is adapted to classical QTL detection designs applied to outbred populations, in particular to designs composed of half and/or full sib families. It assumes the absence of interference. Conclusion The theory is fully developed and an example is given.

  10. Occurrence of Root Rot and Vascular Wilt Diseases in Roselle (Hibiscus sabdariffa L.) in Upper Egypt.

    Science.gov (United States)

    Hassan, Naglaa; Shimizu, Masafumi; Hyakumachi, Mitsuro

    2014-03-01

    Roselle (Hibiscus sabdariffa L.) family Malvaceae is an important crop used in food, cosmetics and pharmaceutics industries. Roselle is cultivated mainly in Upper Egypt (Qena and Aswan governorates) producing 94% of total production. Root rot disease of roselle is one of the most important diseases that attack both seedlings and adult plants causing serious losses in crop productivity and quality. The main objective of the present study is to identify and characterize pathogens associated with root rot and wilt symptoms of roselle in Qena, Upper Egypt and evaluate their pathogenicity under greenhouse and field condition. Fusarium oxysporum, Macrophomina phaseolina, Fusarium solani, Fusarium equiseti and Fusarium semitectum were isolated from the natural root rot diseases in roselle. All isolated fungi were morphologically characterized and varied in their pathogenic potentialities. They could attack roselle plants causing damping-off and root rot/wilt diseases in different pathogenicity tests. The highest pathogenicity was caused by F. oxysporum and M. phaseolina followed by F. solani. The least pathogenic fungi were F. equiseti followed by F. semitectum. It obviously noted that Baladi roselle cultivar was more susceptible to infection with all tested fungi than Sobhia 17 under greenhouse and field conditions. This is the first report of fungal pathogens causing root rot and vascular wilt in roselle in Upper Egypt.

  11. The association of Tarsonemus mites (Acari: Heterostigmata) with different apple developmental stages and apple core rot diseases

    OpenAIRE

    Ueckermann, Edward Albert; Van der Walt, Lené; Spotts, Robert A.; Smit, Francois J.; Jensen, Tamaryn; McLeod, Adéle

    2011-01-01

    Information on the role of mites in the genus Tarsonemus Canestrini and Fanzago, 1876 in the epidemiology of apple core rots (wet and dry) is limited. The aims of this study were to (1) assess the effect of different apple developmental stages (buds, blossoms, 4-cm diameter fruit, mature fruit and mummies) on the relative abundance of Tasonemus mites, (2) determine if there is a tendency of Tarsonemus mites to be associated with wet core rot (WCR) and dry core rot (DCR) apples, and (3) evalua...

  12. Behavior of hybrid corn crop as second rot incidence in West Region Paraná

    Directory of Open Access Journals (Sweden)

    Jean Sérgio Rosset

    2013-09-01

    Full Text Available The objective of this study was to evaluate the incidence and influence of stalk rot and ear in cultivation of hybrid corn second crop in west region Paraná. The experiment was conducted in randomized block design with six transgenic corn hybrids (DKB 330PRO, P4285HX, P3646HX, 30F53HX, P3340HX and P3161HX with four replications at spacing of 0.90 m between rows and 0.20 m between plants. The characteristics evaluated were: number of healthy and symptomatic plants, number of ears healthy and symptomatic and total number of spikes. After harvest, we assessed the length of ears healthy and symptomatic, bulk grain ears healthy and symptomatic, thousand grain weight of ears healthy and symptomatic, and grain mass per spike weighted, thousand grain weight and weighted productivity. The hybrid P3646HX showed 100% of plants with stem base rot (Colletotrichum graminicola and soft rot cob (Erwinia chrysanthemi pv. Zeae and 100% of ears with symptoms of soft rot, followed by hybrid 30F53HX, DKB 330PRO with 34.9 and 29.1% of ears with symptoms of soft rot respectively. The hybrid DKB330PRO showed healthy spikes and patients with superior size, resulting in less interference in the grain yield. The hybrid P3340 productivity was higher, with 7952 kg ha-1 , followed by hybrid 30F53HX and DKB330PRO. A positive correlation between agronomic characteristics and grain yield.

  13. QTL analysis of citrus tristeza virus-citradia interaction.

    Science.gov (United States)

    Asins, M J; Bernet, G P; Ruiz, C; Cambra, M; Guerri, J; Carbonell, E A

    2004-02-01

    Citrus tristeza virus (CTV) has caused the death of millions of trees grafted on sour orange ( Citrus aurantium). However, this rootstock is very well adapted to the Mediterranean, semi-arid conditions. The aim of the present research is to genetically analyze the accumulation of CTV in a progeny derived from the cross between C. aurantium and Poncirus trifoliata, both resistant to CTV isolate T-346. Graft propagation of 104 hybrids was done on healthy sweet orange as a rootstock. Three months later, each rootstock was graft inoculated with two patches of infected tissue (isolate T-346). One, 2, and sometimes, 3 and 4 years after inoculation, hybrids and infected patches were tested for CTV by tissue-blot immuno-assay. Additionally, CTV multiplication was evaluated every year as the optical density of double-antibody sandwich enzyme-linked immuno-sorbent assay reactions. Linkage maps for P. trifoliata based on 63 markers, and for C. aurantium based on 157 markers, were used. Most molecular markers were microsatellites and IRAP (inter-retrotransposon amplified polymorphisms). Some analogues of resistance and expressed sequences were also included for candidate gene analysis. Resistance against CTV was analyzed as a quantitative trait (CTV accumulation) by QTL (quantitative trait loci) analysis to avoid the assumption of monogenic control. Three major resistance QTLs were detected where the P. trifoliata resistance gene, Ctv-R, had been previously located in other progenies. Up to five minor QTLs were detected ( Ctv-A(1) to Ctv-A(5)). A significant epistatic interaction involving Ctv-R(1) and Ctv-A(1) was also found. An analogue of a resistance gene is a candidate for Ctv-A(3), and two expressed sequences are candidates for Ctv-A(1) and Ctv-A(5). Single-strand conformational polymorphism analysis of CTV genes QTL P20 and P25 (coat protein) in susceptible hybrids, was carried out to test whether or not any QTL accumulation was a defeated resistance gene. Since the

  14. The use of genome-wide eQTL associations in lymphoblastoid cell lines to identify novel genetic pathways involved in complex traits.

    Directory of Open Access Journals (Sweden)

    Josine L Min

    Full Text Available The integrated analysis of genotypic and expression data for association with complex traits could identify novel genetic pathways involved in complex traits. We profiled 19,573 expression probes in Epstein-Barr virus-transformed lymphoblastoid cell lines (LCLs from 299 twins and correlated these with 44 quantitative traits (QTs. For 939 expressed probes correlating with more than one QT, we investigated the presence of eQTL associations in three datasets of 57 CEU HapMap founders and 86 unrelated twins. Genome-wide association analysis of these probes with 2.2 m SNPs revealed 131 potential eQTLs (1,989 eQTL SNPs overlapping between the HapMap datasets, five of which were in cis (58 eQTL SNPs. We then tested 535 SNPs tagging the eQTL SNPs, for association with the relevant QT in 2,905 twins. We identified nine potential SNP-QT associations (P<0.01 but none significantly replicated in five large consortia of 1,097-16,129 subjects. We also failed to replicate previous reported eQTL associations with body mass index, plasma low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides levels derived from lymphocytes, adipose and liver tissue. Our results and additional power calculations suggest that proponents may have been overoptimistic in the power of LCLs in eQTL approaches to elucidate regulatory genetic effects on complex traits using the small datasets generated to date. Nevertheless, larger tissue-specific expression data sets relevant to specific traits are becoming available, and should enable the adoption of similar integrated analyses in the near future.

  15. The persistence of Gliocephalotrichum bulbilium and G. simplex causing fruit rot of rambutan in Puerto Rico

    Science.gov (United States)

    Fruit rot of rambutan (Nephelium lappaceum L.) is a pre and post-harvest disease problem that affects fruit quality. Significant post-harvest losses have occurred worldwide and several pathogens have been identified in Malaysia, Costa Rica, Hawaii, Thailand, and Puerto Rico. In 2011, fruit rot was o...

  16. Hendersonia Creberrima, the cause of soft brown rot of mango in South Africa

    International Nuclear Information System (INIS)

    Brodrick, H.T.; Van der westhuizen, G.C.A.

    1976-01-01

    A soft brown rot of mangoes in South Africa, is especially severe in export fruit kept in cold storage for prolonged periods. At present mangoes can be exported most economically by sea. This involves storage at 11 0 C for approximately 21 days. Unfortunately, these appear to be ideal conditions for the development of soft brown rot. Losses as high as 80% were recorded. The South African fungus agrees in morphology and cultural characters with Hendersonia Creberrima

  17. Aroma compounds and characteristics of noble-rot wines of Chardonnay grapes artificially botrytized in the vineyard.

    Science.gov (United States)

    Wang, Xing-Jie; Tao, Yong-Sheng; Wu, Yun; An, Rong-Yan; Yue, Zhuo-Ya

    2017-07-01

    Aroma characteristics and their impact volatile components of noble-rot wines elaborated from artificial botrytized Chardonnay grapes, obtained by spraying Botrytis cinerea suspension in Yuquan vineyard, Ningxia, China, were explored in this work. Dry white wine made from normal-harvested grapes and sweet wine produced from delay-harvested grapes were compared. Wine aromas were analysed by trained sensory panelists, and aroma compounds were determined by SPME-GC-MS. Results indicated that esters, fatty acids, thiols, lactones, volatile phenols and 2-nonanone increased markedly in noble-rot wines. In addition to typical aromas of noble-rot wines, artificial noble-rot wines were found to contain significant cream and dry apricot attributes. Partial Least-Squares Regression models of aroma characteristics against aroma components revealed that non-fermentative odorants were the primary contributor to dry apricot attribute, especially, thiols, C13-norisoprenoids, lactones, terpenols and phenolic acid derivatives, while cream attribute was dependent on both fermentative and non-fermentative volatile components. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Combined analysis of data from two granddaughter designs: A simple strategy for QTL confirmation and increasing experimental power in dairy cattle

    Directory of Open Access Journals (Sweden)

    Blümel Jürgen

    2003-05-01

    Full Text Available Abstract A joint analysis of five paternal half-sib Holstein families that were part of two different granddaughter designs (ADR- or Inra-design was carried out for five milk production traits and somatic cell score in order to conduct a QTL confirmation study and to increase the experimental power. Data were exchanged in a coded and standardised form. The combined data set (JOINT-design consisted of on average 231 sires per grandsire. Genetic maps were calculated for 133 markers distributed over nine chromosomes. QTL analyses were performed separately for each design and each trait. The results revealed QTL for milk production on chromosome 14, for milk yield on chromosome 5, and for fat content on chromosome 19 in both the ADR- and the Inra-design (confirmed within this study. Some QTL could only be mapped in either the ADR- or in the Inra-design (not confirmed within this study. Additional QTL previously undetected in the single designs were mapped in the JOINT-design for fat yield (chromosome 19 and 26, protein yield (chromosome 26, protein content (chromosome 5, and somatic cell score (chromosome 2 and 19 with genomewide significance. This study demonstrated the potential benefits of a combined analysis of data from different granddaughter designs.

  19. Identification of QTL Associated with Nitrogen Uptake and Nitrogen Use Efficiency Using High Throughput Genotyped CSSLs in Rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    Yong Zhou

    2017-07-01

    Full Text Available Nitrogen (N availability is a major factor limiting crop growth and development. Identification of quantitative trait loci (QTL for N uptake (NUP and N use efficiency (NUE can provide useful information regarding the genetic basis of these traits and their associated effects on yield production. In this study, a set of high throughput genotyped chromosome segment substitution lines (CSSLs derived from a cross between recipient 9311 and donor Nipponbare were used to identify QTL for rice NUP and NUE. Using high throughput sequencing, each CSSL were genotyped and an ultra-high-quality physical map was constructed. A total of 13 QTL, seven for NUP and six for NUE, were identified in plants under hydroponic culture with all nutrients supplied in sufficient quantities. The proportion of phenotypic variation explained by these QTL for NUP and NUE ranged from 3.16–13.99% and 3.76–12.34%, respectively. We also identified several QTL for biomass yield (BY and grain yield (GY, which were responsible for 3.21–45.54% and 6.28–7.31%, respectively, of observed phenotypic variation. GY were significantly positively correlated with NUP and NUE, with NUP more closely correlated than NUE. Our results contribute information to NUP and NUE improvement in rice.

  20. Relationship between QTL for grain shape, grain weight, test weight, milling yield, and plant height in the spring wheat cross RL4452/‘AC Domain’

    Science.gov (United States)

    Cabral, Adrian L.; Jordan, Mark C.; Larson, Gary; Somers, Daryl J.; Humphreys, D. Gavin

    2018-01-01

    Kernel morphology characteristics of wheat are complex and quantitatively inherited. A doubled haploid (DH) population of the cross RL4452/‘AC Domain’ was used to study the genetic basis of seed shape. Quantitative trait loci (QTL) analyses were conducted on a total of 18 traits: 14 grain shape traits, flour yield (Fyd), and three agronomic traits (Plant height [Plht], 1000 Grain weight [Gwt], Test weight [Twt]), using data from trial locations at Glenlea, Brandon, and Morden in Manitoba, Canada, between 1999 and 2004. Kernel shape was studied through digital image analysis with an Acurum® grain analyzer. Plht, Gwt, Twt, Fyd, and grain shape QTL were correlated with each other and QTL analysis revealed that QTL for these traits often mapped to the same genetic locations. The most significant QTL for the grain shape traits were located on chromosomes 4B and 4D, each accounting for up to 24.4% and 53.3% of the total phenotypic variation, respectively. In addition, the most significant QTL for Plht, Gwt, and Twt were all detected on chromosome 4D at the Rht-D1 locus. Rht-D1b decreased Plht, Gwt, Twt, and kernel width relative to the Rht-D1a allele. A narrow genetic interval on chromosome 4B contained significant QTL for grain shape, Gwt, and Plht. The ‘AC Domain’ allele reduced Plht, Gwt, kernel length and width traits, but had no detectable effect on Twt. The data indicated that this variation was inconsistent with segregation at Rht-B1. Numerous QTL were identified that control these traits in this population. PMID:29357369

  1. A major QTL controls susceptibility to spinal curvature in the curveback guppy

    Directory of Open Access Journals (Sweden)

    Dreyer Christine

    2011-01-01

    Full Text Available Abstract Background Understanding the genetic basis of heritable spinal curvature would benefit medicine and aquaculture. Heritable spinal curvature among otherwise healthy children (i.e. Idiopathic Scoliosis and Scheuermann kyphosis accounts for more than 80% of all spinal curvatures and imposes a substantial healthcare cost through bracing, hospitalizations, surgery, and chronic back pain. In aquaculture, the prevalence of heritable spinal curvature can reach as high as 80% of a stock, and thus imposes a substantial cost through production losses. The genetic basis of heritable spinal curvature is unknown and so the objective of this work is to identify quantitative trait loci (QTL affecting heritable spinal curvature in the curveback guppy. Prior work with curveback has demonstrated phenotypic parallels to human idiopathic-type scoliosis, suggesting shared biological pathways for the deformity. Results A major effect QTL that acts in a recessive manner and accounts for curve susceptibility was detected in an initial mapping cross on LG 14. In a second cross, we confirmed this susceptibility locus and fine mapped it to a 5 cM region that explains 82.6% of the total phenotypic variance. Conclusions We identify a major QTL that controls susceptibility to curvature. This locus contains over 100 genes, including MTNR1B, a candidate gene for human idiopathic scoliosis. The identification of genes associated with heritable spinal curvature in the curveback guppy has the potential to elucidate the biological basis of spinal curvature among humans and economically important teleosts.

  2. A major QTL affects temperature sensitive adult lethality and inbreeding depression in life span in Drosophila melanogaster.

    DEFF Research Database (Denmark)

    Vermeulen, Corneel J.; Bijlsma, R.; Loeschcke, Volker

    2008-01-01

    of inbreeding effects in specific traits, such as age-specific mortality and life span, provide a good starting point, as a limited set of genes is expected to be involved. Results Here we report on a QTL mapping study on inbreeding related and temperature sensitive lethality in male Drosophila melanogaster...... and the molecular properties of genes that give rise to or modulate its deleterious effects is lacking. These questions warrant the detailed study of genetic loci giving rise to inbreeding depression. However, the complex and polygenic nature of general inbreeding depression makes this a daunting task. Study...... simple, being due mainly to a single recessive QTL on the left arm of chromosome 2. This locus colocalised with a QTL that conditioned variation in female life span, acting as an overdominant locus for this trait. Male life span was additionally affected by variation at the X-chromosome. Conclusion...

  3. 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.

  4. Association of Pectolytic Fluorescent PSeudomonas with Postharvest Rots of Onion

    Directory of Open Access Journals (Sweden)

    H.H. El-Hendawy

    2004-12-01

    Full Text Available Five isolates of pectolytic fluorescent pseudomonads were obtained from a rotted onion bulb and identified as Pseudomonas marginalis. At both 4 and 25oC, all isolates caused soft rot to detached plant parts of onion and to carrot, celery, cucumber, pepper, spinach, tomato and turnip (but not garlic. They did not however cause any symptoms in living plants of these same species. These results suggest that the onion isolates are a postharvest pathogen which is not destructive in the field but becomes a threat to fresh vegetables stored at low-temperature. Analysis of cellulosolytic and pectic enzymes revealed that pectic lyases, but not polygalacturonases, pectin methyl esterases and cellulases were produced in culture by each isolate.

  5. Control of Root Rot and Wilt Diseases of Roselle under Field Conditions

    Science.gov (United States)

    Hassan, Naglaa; Elsharkawy, Mohsen Mohamed; Shimizu, Masafumi

    2014-01-01

    Roselle (Hibiscus sabdariffa L.) is one of the most important medicinal crops in many parts of the world. In this study, the effects of microelements, antioxidants, and bioagents on Fusarium oxysporum, F. solani, and Macrophomina phaseolina, the causal pathogens of root rot and wilt diseases in roselle, were examined under field conditions. Preliminary studies were carried out in vitro in order to select the most effective members to be used in field control trials. Our results showed that microelements (copper and manganese), antioxidants (salicylic acid, ascorbic acid, and EDTA), a fungicide (Dithane M45) and biological control agents (Trichoderma harzianum and Bacillus subtilis) were significantly reduced the linear growth of the causal pathogens. Additionally, application of the previous microelements, antioxidants, a fungicide and biological control agents significantly reduced disease incidence of root rot and wilt diseases under field conditions. Copper, salicylic acid, and T. harzianum showed the best results in this respect. In conclusion, microelements, antioxidants, and biocontrol agents could be used as alternative strategies to fungicides for controlling root rot and wilt diseases in roselle. PMID:25606010

  6. QTL Analysis and Nested Association Mapping for Adult Plant Resistance to Powdery Mildew in Two Bread Wheat Populations

    Directory of Open Access Journals (Sweden)

    Yan Ren

    2017-07-01

    Full Text Available CIMMYT wheat (Triticum aestivum L. lines Francolin#1 and Quaiu#3 displayed effective and stable adult plant resistance (APR to Chinese Blumeria graminis f. sp. tritici isolates in the field. To elucidate their genetic basis of resistance, two recombinant inbred line (RIL populations of their crosses with Avocet, the susceptible parent, were phenotyped in Zhengzhou and Shangqiu in the 2014–2015 and 2015–2016 cropping seasons. These populations were also genotyped with SSR (simple sequence repeat markers and DArT (diversity arrays technology markers. Two common significant quantitative trait loci (QTL on wheat chromosomes 1BL and 4BL were detected in both populations by joint and individual inclusive composite interval mapping, explaining 20.3–28.7% and 9.6–15.9% of the phenotypic variance in Avocet × Francolin#1 and 4.8–11.5% and 10.8–18.9% in Avocet × Quaiu#3, respectively. Additional QTL were mapped on chromosomes 1DL and 5BL in Avocet × Francolin#1 and on 2DL and 6BS in Avocet × Quaiu#3. Among these, QPm.heau-1DL is probably a novel APR gene contributing 6.1–8.5% of total phenotypic variance. The QTL on 1BL corresponds to the pleiotropic multi-pathogen resistance gene Yr29/Lr46/Pm39, whereas the QTL on 2DL maps to a similar region where stripe rust resistance gene Yr54 is located. The QTL identified can potentially be used for the improvement of powdery mildew and rust resistance in wheat breeding.

  7. Investigation of QTL regions on Chromosome 17 for genes associated with meat color in the pig.

    Science.gov (United States)

    Fan, B; Glenn, K L; Geiger, B; Mileham, A; Rothschild, M F

    2008-08-01

    Previous studies have uncovered several significant quantitative trait loci (QTL) relevant to meat colour traits mapped at the end of SSC17 in the pig. Furthermore, results released from the porcine genome sequencing project have identified genes underlying the entire QTL regions and can further contribute to mining the region for likely causative genes. Ten protein coding genes or novel transcripts located within the QTL regions were screened for single nucleotide polymorphisms (SNPs). Linkage mapping and association studies were carried out in the ISU Berkshire x Yorkshire (B x Y) pig resource family. The total length of the new SSC17 linkage map was 126.6 cM and additional markers including endothelin 3 (EDN3) and phosphatase and actin regulator 3 (PHACTR3) genes were assigned at positions 119.4 cM and 122.9 cM, respectively. A new QTL peak was noted at approximately 120 cM, close to the EDN3 gene, and for some colour traits QTL exceeded the 5% chromosome-wise significance threshold. The association analyses in the B x Y family showed that the EDN3 BslI and PHACTR3 PstI polymorphisms were strongly associated with the subjective colour score and objective colour reflectance measures in the loin, as well as average drip loss percentage and pH value. The RNPC1 DpnII and CTCFL HpyCH4III polymorphisms were associated with some meat colour traits. No significant association between CBLN4, TFAP2C, and four novel transcripts and meat colour traits were detected. The association analyses conducted in one commercial pig line found that both EDN3 BslI and PHACTR3 PstI polymorphisms were associated with meat colour reflectance traits such as centre loin hue angle and Minolta Lightness score. The present findings suggested that the EDN3 and PHACTR3 genes might have potential effects on meat colour in pigs, and molecular mechanisms of their functions are worth exploring.

  8. Toward positional cloning of Fhb1, a major QTL for Fusarium head blight resistance in wheat

    Czech Academy of Sciences Publication Activity Database

    Liu, S. X.; Pumphrey, M. O.; Gill, B. S.; Trick, H. N.; Zhang, J. X.; Doležel, Jaroslav; Chalhoub, B.; Anderson, J. A.

    2008-01-01

    Roč. 36, suppl. B (2008), s. 195-201 ISSN 0133-3720 Institutional research plan: CEZ:AV0Z50380511 Keywords : map-based cloning * Fusarium head blight * Fhb1 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.190, year: 2007

  9. Effects of Fungicides, Essential Oils and Gamma Irradiated Bioagents on Chickpea Root Rot Caused by Sclerotium rolfsii

    International Nuclear Information System (INIS)

    El-Batal, A.I.; Fathy, R.M.; Ismail, A.A.; Mubark, H.M.; Mahmoud, Y.A.

    2011-01-01

    Sclerotium rolfsii (S. rolfsii) causes root rot disease in several crops including Cicer arietinum (chickpea) that results in low yield. In vitro experiments on fungicides, vitavax and monceren T, and essential oils, clove and mint oils, were conducted to control root rot disease of chickpea caused by S. rolfsii. The treatments resulted in 80 % suppression of root rot disease. Gliocladium virens (G. virens) and Gliocladium deliquescens (G. deliquescens) were effective as biocontrol agents against S. rolfsii. The results showed that these treatments greatly reduced the root rot disease in chickpea. In this study, the effect of gamma irradiation at doses 0, 0.25, 0.5, 1.0, 1.5, 2.0, 2.5 and 3.0 kGy on the pathogenecity of G. virens and G. deliquescens against S. rolfsii were investigated. The results revealed that gamma irradiation increased the pathogenecity of G. virens and G. deliquescens against S. rolfsii

  10. Occurrence of Root Rot and Vascular Wilt Diseases in Roselle (Hibiscus sabdariffa L.) in Upper Egypt

    Science.gov (United States)

    Hassan, Naglaa; Shimizu, Masafumi

    2014-01-01

    Roselle (Hibiscus sabdariffa L.) family Malvaceae is an important crop used in food, cosmetics and pharmaceutics industries. Roselle is cultivated mainly in Upper Egypt (Qena and Aswan governorates) producing 94% of total production. Root rot disease of roselle is one of the most important diseases that attack both seedlings and adult plants causing serious losses in crop productivity and quality. The main objective of the present study is to identify and characterize pathogens associated with root rot and wilt symptoms of roselle in Qena, Upper Egypt and evaluate their pathogenicity under greenhouse and field condition. Fusarium oxysporum, Macrophomina phaseolina, Fusarium solani, Fusarium equiseti and Fusarium semitectum were isolated from the natural root rot diseases in roselle. All isolated fungi were morphologically characterized and varied in their pathogenic potentialities. They could attack roselle plants causing damping-off and root rot/wilt diseases in different pathogenicity tests. The highest pathogenicity was caused by F. oxysporum and M. phaseolina followed by F. solani. The least pathogenic fungi were F. equiseti followed by F. semitectum. It obviously noted that Baladi roselle cultivar was more susceptible to infection with all tested fungi than Sobhia 17 under greenhouse and field conditions. This is the first report of fungal pathogens causing root rot and vascular wilt in roselle in Upper Egypt. PMID:24808737

  11. CONTROL OF POSTHARVEST TOMATO ROT BY SPORE SUSPENSION AND ANTIFUNGAL METABOLITES OF TRICHODERMA HARZIANUM

    Directory of Open Access Journals (Sweden)

    Momein H. El-Katatny

    2012-06-01

    Full Text Available Rot of cherry tomato (Lycopersicon esculentum fruits caused by several fungal pathogens is a detrimental disease leading to substantial yield loses worldwide. Alternaria isolates were the most common fungal species isolated from healthy or rotten fruits. Trichoderma harzianum spore suspension and culture filtrate were tested for their antagonistic activity on controlling tomato fruit rot. T. harzianum isolates suppressed or interfered with the growth of different postharvest tomato fungal pathogens albeit at different degrees. Their culture filtrate inhibited pathogen spore germination possibly due to the released extracellular diffusible metabolite(s. Besides, aberrant morphology of conidia was observed with deformation of hyphal tips. Furthermore, the resulting mycelia appeared desiccated with coagulated protoplasm leading to complete collapse of protoplasm in presence of T. harzianum culture filtrate. Application of T. harzianum spores to tomato fruits decreased disease severity significantly with the most profound effect at higher spore concentrations (108 cells per ml. Similarly, culture filtrate of T. harzianum prevented pathogen spore germination on the surface of tomato fruits leading to decreased incidence of rot symptoms at high culture filtrate concentrations. This work provides strong evidence that T. harzianum is a competent antagonist and its spore suspension and culture filtrate can be used efficiently to control postharvest tomato rot.

  12. FOOT ROT DISEASE IDENTIFICATION FOR VELLAIKODI VARIETY OF BETELVINE PLANTS USING DIGITAL IMAGE PROCESSING

    Directory of Open Access Journals (Sweden)

    J. Vijayakumar

    2012-11-01

    Full Text Available Betelvine plants are infected variety of diseases in the complete plantation without any premature warning of the diseases. The aim of this paper is to detection of foot rot disease in the vellaikodi variety of betelvine plants using digital image processing techniques. The digital images of the uninfected or normal betelvine leaves and the digital images of the infected in foot rot diseased betelvine leaves at different stages are collected from different Betelvine plants using a high resolution digital camera and collected betelvine images are stored with JPEG format. The digital images of the betelvine leaves analyses are done using the image processing toolbox in MATLAB which gives the normal patterns of the digital images. Using RGB encoding process, the RGB components of the betelvine leaves are separated. The mean and median values for all sample leaves are computed and calculated values are stored in the system. The mean and median values of test leaves are computed and compared with the stored values. As the result of this comparison, it is identified whether test leaves are affected by foot rot disease or not. Finally this analysis helps to recognize the foot rot disease can be identified before it spreads to entire crop.

  13. Assessing the value of phenotypic information from non-genotyped animals for QTL mapping of complex traits in real and simulated populations.

    Science.gov (United States)

    Melo, Thaise P; Takada, Luciana; Baldi, Fernando; Oliveira, Henrique N; Dias, Marina M; Neves, Haroldo H R; Schenkel, Flavio S; Albuquerque, Lucia G; Carvalheiro, Roberto

    2016-06-21

    QTL mapping through genome-wide association studies (GWAS) is challenging, especially in the case of low heritability complex traits and when few animals possess genotypic and phenotypic information. When most of the phenotypic information is from non-genotyped animals, GWAS can be performed using the weighted single-step GBLUP (WssGBLUP) method, which permits to combine all available information, even that of non-genotyped animals. However, it is not clear to what extent phenotypic information from non-genotyped animals increases the power of QTL detection, and whether factors such as the extent of linkage disequilibrium (LD) in the population and weighting SNPs in WssGBLUP affect the importance of using information from non-genotyped animals in GWAS. These questions were investigated in this study using real and simulated data. Analysis of real data showed that the use of phenotypes of non-genotyped animals affected SNP effect estimates and, consequently, QTL mapping. Despite some coincidence, the most important genomic regions identified by the analyses, either using or ignoring phenotypes of non-genotyped animals, were not the same. The simulation results indicated that the inclusion of all available phenotypic information, even that of non-genotyped animals, tends to improve QTL detection for low heritability complex traits. For populations with low levels of LD, this trend of improvement was less pronounced. Stronger shrinkage on SNPs explaining lower variance was not necessarily associated with better QTL mapping. The use of phenotypic information from non-genotyped animals in GWAS may improve the ability to detect QTL for low heritability complex traits, especially in populations in which the level of LD is high.

  14. Associations of planting date, drought stress, and insects with Fusarium ear rot and fumonisin B1 contamination in California maize.

    Science.gov (United States)

    Parsons, M W; Munkvold, G P

    2010-05-01

    Fusarium ear rot, caused by Fusarium verticillioides, is one of the most common diseases of maize, causing yield and quality reductions and contamination of grain by fumonisins and other mycotoxins. Drought stress and various insects have been implicated as factors affecting disease severity. Field studies were conducted to evaluate the interactions and relative influences of drought stress, insect infestation, and planting date upon Fusarium ear rot severity and fumonisin B1 contamination. Three hybrids varying in partial resistance to Fusarium ear rot were sown on three planting dates and subjected to four irrigation regimes to induce differing levels of drought stress. A foliar-spray insecticide treatment was imposed to induce differing levels of insect injury. Populations of thrips (Frankliniella spp.), damage by corn earworm (Helicoverpa zeae), Fusarium ear rot symptoms, and fumonisin B1 levels were assessed. There were significant effects of hybrid, planting date, insecticide treatment, and drought stress on Fusarium ear rot symptoms and fumonisin B1 contamination, and these factors also had significant interacting effects. The most influential factors were hybrid and insecticide treatment, but their effects were influenced by planting date and drought stress. The more resistant hybrids and the insecticide-treated plots consistently had lower Fusarium ear rot severity and fumonisin B1 contamination. Later planting dates typically had higher thrips populations, more Fusarium ear rot, and higher levels of fumonisin B1. Insect activity was significantly correlated with disease severity and fumonisin contamination, and the correlations were strongest for thrips. The results of this study confirm the influence of thrips on Fusarium ear rot severity in California, USA, and also establish a strong association between thrips and fumonisin B1 levels.

  15. Bioconversion of dieldrin by wood-rotting fungi and metabolite detection.

    Science.gov (United States)

    Kamei, Ichiro; Takagi, Kazuhiro; Kondo, Ryuichiro

    2010-08-01

    Dieldrin is one of the most persistent organochlorine pesticides, listed as one of the 12 persistent organic pollutants in the Stockholm Convention. Although microbial degradation is an effective way to remediate environmental pollutants, reports on aerobic microbial degradation of dieldrin are limited. Wood-rotting fungi can degrade a wide spectrum of recalcitrant organopollutants, and an attempt has been made to select wood-rotting fungi that can degrade dieldrin, and to identify the metabolite. Thirty-four isolates of wood-rotting fungi were investigated for their ability to degrade dieldrin. Strain YK543 degraded 39.1 +/- 8.8% of dieldrin during 30 days of incubation. Phylogenetic analysis demonstrated that strain YK543 was closely related to the fungus Phlebia brevispora Nakasone TMIC33929, which has been reported as a fungus that can degrade chlorinated dioxins and polychlorinated biphenyls. 9-Hydroxydieldrin was detected as a metabolite in the cultures of strain YK543. It is important to select the microorganisms that degrade organic pollutants, and to identify the metabolic pathway for the development of bioremediation methods. Strain YK543 was selected as a fungus capable of degrading dieldrin. The metabolic pathway includes 9-hydroxylation reported in rat's metabolism catalysed by liver microsomal monooxygenase. This is the first report of transformation of dieldrin to 9-hydroxydieldrin by a microorganism. Copyright (c) 2010 Society of Chemical Industry.

  16. First report of Colletotrichum fructicola and C. queenslandicum causing fruit rot of rambutan (Nephelium lappaceum L.)

    Science.gov (United States)

    In rambutan production, fruit rot is the main pre- and post-harvest disease of concern. In a 2008-2013 fruit disease survey, fruit rot was observed in eight orchards in Puerto Rico. Infected fruit were collected and 1 mm2 tissue sections were surface disinfested with 70% ethanol followed by 0.5% sod...

  17. 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

    Comparing QTL analyses of multiple pair-mating families can provide a better understanding of important allelic variations and distributions. However, most QTL mapping studies in common carp have been based on analyses of individual families. In order to improve our understanding of heredity and variation of QTLs in different families and identify important QTLs, we performed QTL analysis of growth-related traits in multiple segregating families. We completed a genome scan for QTLs that affect body weight (BW), total length (TL), and body thickness (BT) of 522 individuals from eight full-sib families using 250 microsatellites evenly distributed across 50 chromosomes. Sib-pair and half-sib model mapping identified 165 QTLs on 30 linkage groups. Among them, 10 (genome-wide P <0.01 or P < 0.05) and 28 (chromosome-wide P < 0.01) QTLs exhibited significant evidence of linkage, while the remaining 127 exhibited a suggestive effect on the above three traits at a chromosome-wide (P < 0.05) level. Multiple QTLs obtained from different families affect BW, TL, and BT and locate at close or identical positions. It suggests that same genetic factors may control variability in these traits. Furthermore, the results of the comparative QTL analysis of multiple families showed that one QTL was common in four of the eight families, nine QTLs were detected in three of the eight families, and 26 QTLs were found common to two of the eight families. These common QTLs are valuable candidates in marker-assisted selection. A large number of QTLs were detected in the common carp genome and associated with growth-related traits. Some of the QTLs of different growth-related traits were identified at similar chromosomal regions, suggesting a role for pleiotropy and/or tight linkage and demonstrating a common genetic basis of growth trait variations. The results have set up an example for comparing QTLs in common carp and provided insights into variations in the identified QTLs

  18. QTL analysis for early yield in a pseudo F2 population of cassava

    African Journals Online (AJOL)

    SERVER

    2008-01-18

    Jan 18, 2008 ... Full Length Research Paper ... sive and labour intensive, genetic analysis with simple ..... Individual QTL loci are named by trait (abbreviation indicated in titles) and linkage groups. .... Past research in quantitative genetics.

  19. Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses

    Directory of Open Access Journals (Sweden)

    Lionikas Arimantas

    2012-11-01

    Full Text Available Abstract Background We have recently identified a number of Quantitative Trait Loci (QTL contributing to the 2-fold muscle weight difference between the LG/J and SM/J mouse strains and refined their confidence intervals. To facilitate nomination of the candidate genes responsible for these differences we examined the transcriptome of the tibialis anterior (TA muscle of each strain by RNA-Seq. Results 13,726 genes were expressed in mouse skeletal muscle. Intersection of a set of 1061 differentially expressed transcripts with a mouse muscle Bayesian Network identified a coherent set of differentially expressed genes that we term the LG/J and SM/J Regulatory Network (LSRN. The integration of the QTL, transcriptome and the network analyses identified eight key drivers of the LSRN (Kdr, Plbd1, Mgp, Fah, Prss23, 2310014F06Rik, Grtp1, Stk10 residing within five QTL regions, which were either polymorphic or differentially expressed between the two strains and are strong candidates for quantitative trait genes (QTGs underlying muscle mass. The insight gained from network analysis including the ability to make testable predictions is illustrated by annotating the LSRN with knowledge-based signatures and showing that the SM/J state of the network corresponds to a more oxidative state. We validated this prediction by NADH tetrazolium reductase staining in the TA muscle revealing higher oxidative potential of the SM/J compared to the LG/J strain (p Conclusion Thus, integration of fine resolution QTL mapping, RNA-Seq transcriptome information and mouse muscle Bayesian Network analysis provides a novel and unbiased strategy for nomination of muscle QTGs.

  20. A high density genetic map and QTL for agronomic and yield traits in Foxtail millet [Setaria italica (L.) P. Beauv].

    Science.gov (United States)

    Fang, Xiaomei; Dong, Kongjun; Wang, Xiaoqin; Liu, Tianpeng; He, Jihong; Ren, Ruiyu; Zhang, Lei; Liu, Rui; Liu, Xueying; Li, Man; Huang, Mengzhu; Zhang, Zhengsheng; Yang, Tianyu

    2016-05-04

    Foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China, has been adopted as a model crop for studying C-4 photosynthesis, stress biology and biofuel traits. Construction of a high density genetic map and identification of stable quantitative trait loci (QTL) lay the foundation for marker-assisted selection for agronomic traits and yield improvement. A total of 10598 SSR markers were developed according to the reference genome sequence of foxtail millet cultivar 'Yugu1'. A total of 1013 SSR markers showing polymorphism between Yugu1 and Longgu7 were used to genotype 167 individuals from a Yugu1 × Longgu7 F2 population, and a high density genetic map was constructed. The genetic map contained 1035 loci and spanned 1318.8 cM with an average distance of 1.27 cM between adjacent markers. Based on agronomic and yield traits identified in 2 years, 29 QTL were identified for 11 traits with combined analysis and single environment analysis. These QTL explained from 7.0 to 14.3 % of phenotypic variation. Favorable QTL alleles for peduncle length originated from Longgu7 whereas favorable alleles for the other traits originated from Yugu1 except for qLMS6.1. New SSR markers, a high density genetic map and QTL identified for agronomic and yield traits lay the ground work for functional gene mapping, map-based cloning and marker-assisted selection in foxtail millet.

  1. Following basal stem rot in young oil palm plantings.

    Science.gov (United States)

    Panchal, G; Bridge, P D

    2005-01-01

    The PCR primer GanET has previously been shown to be suitable for the specific amplification of DNA from Ganoderma boninense. A DNA extraction and PCR method has been developed that allows for the amplification of the G. boninense DNA from environmental samples of oil palm tissue. The GanET primer reaction was used in conjunction with a palm-sampling programme to investigate the possible infection of young palms through cut frond base surfaces. Ganoderma DNA was detected in frond base material at a greater frequency than would be expected by comparison with current infection levels. Comparisons are made between the height of the frond base infected, the number of frond bases infected, and subsequent development of basal stem rot. The preliminary results suggest that the development of basal stem rot may be more likely to occur when young lower frond bases are infected.

  2. Fusarium rot of onion and possible use of bioproduct

    Directory of Open Access Journals (Sweden)

    Klokočar-Šmit Zlata

    2008-01-01

    Full Text Available Several species of Fusarium are causal agents of onion rot in field and storage. Most prevalent are F. oxysporum f. sp. cepae and F. solani, and recently F. proliferatum, a toxigenic species. Most frequently isolated fungi in our field experiments were F. solani and F. proliferatum with different pathogenicity. Certain differences in antagonistic activity of Trichoderma asperellum on different isolates of F. proliferatum and F. solani have been found in in vitro study in dual culture, expressed as a slower inhibition of growth of the former, and faster of the latter pathogen. Antagonistic abilities of species from genus Trichoderma (T. asperellum are important, and have already been exploited in formulated biocontrol products in organic and conventional production, in order to prevent soil borne pathogens inducing fusarium wilt and rot. The importance of preventing onion infection by Fusarium spp., possible mycotoxin producers, has been underlined.

  3. Molecular characterization of a novel thermostable laccase PPLCC2 from the brown rot fungus Postia placenta MAD-698-R

    Directory of Open Access Journals (Sweden)

    Hongde An

    2015-11-01

    Conclusions: This is the first identified thermo activated and thermostable laccase in brown rot fungi. This investigation will contribute to understanding the roles played by laccases in brown rot fungi.

  4. rDNA-based characterization of a new binucleate Rhizoctonia spp. causing root rot on kale in Brazil

    NARCIS (Netherlands)

    Kuramae, E.E.; Buzeto, A.L.; Nakatani, A.K.; Souza, N.L.

    2007-01-01

    In this paper we present the first report of the occurrence of a binucleate Rhizoctonia spp. causing hypocotyl and root rot in kale in Brazil. Rhizoctonia spp. were isolated from kale (Brassica oleracea var. acephala) with symptoms of hypocotyl and root rot. The isolates, characterized as binucleate

  5. A system for predicting the amount of Phellinus (Fomes) igniarius rot in trembling aspen stands

    Science.gov (United States)

    Robert L. Anderson; Arthur L. Jr. Schipper

    1978-01-01

    The occurrence of Phellinus (Fomes) igniarius white trunk rot in 45- to 50-year-old trembling aspen stands can be predicted by applying a constant to the stand basal area with P. igniarius conks to estimate the total basal area with P. igniarius rot. Future decay projections can be made by reapplying the basal area of hidden decay for each 6 years projected. This paper...

  6. Interaction between N-fertilizer and water availability on borer-rot complex in sugarcane

    Directory of Open Access Journals (Sweden)

    Luiz Eduardo da Rocha Pannuti

    2015-03-01

    Full Text Available This study aimed to evaluate the effects of nitrogen availability in fertigation and rainfed management, as well as their interactions with the incidence of and damage caused by D. saccharalis and red rot in sugarcane. The experiment consisted of four treatments (0 and 150 kg ha–1 of N-fertilizer with irrigation; 0 and 150 kg ha–1 of N-fertilizer in rainfed management in a randomized complete block design with four replications. The evaluated parameters were the number of holes and internodes with red rot per meter of cultivation, stalk yield and sugar content. In the laboratory (T = 25 ± 2 °C; R.H. = 70 ± 10%: 12:12-L:D, we evaluated the attractiveness and consumption of fragments of stalks from the different treatments for fourth instar larvae through choice and no-choice tests in a randomized complete block design with ten replications. Nitrogen fertilization via irrigation has favorable effects on borer-rot complex and leads to higher gains in stalk and sugar yields when compared to rainfed management. The increments of stalk and sugar yields due to nitrogen fertilization compensates for the increase in borer-rot complex infestation. In laboratory tests, D. saccharalis larvae were similarly attracted to all treatments regardless of the doses of N-fertilizer or the water regimes evaluated. However, fragments of sugarcane stalks produced with nitrogen fertilization were consumed more by D. saccharalis in both water regimes.

  7. QTL-Kartierung und funktionelle Kandidatengenanalyse für das Merkmal Totgeburt in einer fortgeschrittenen Fleckvieh- x Red-Holstein-Rückkreuzungspopulation

    OpenAIRE

    Gomeringer, Verena

    2007-01-01

    Das Ziel dieser Arbeit war die Kartierung eines QTL mit Effekt auf paternalen Kalbeverlauf und paternale Totgeburt auf Bos Taurus Autosom 9 (BTA09) in einer fortgeschrittenen Fleckvieh x Red-Holstein Rückkreuzungspopulation mit positioneller und funktioneller Kandidatengenanalyse. Dazu wurden Untersuchungen mit verschiedenen Kartierungsdesigns in Granddaughter und Daughter Designs durchgeführt. Intervallkartierung und Linkage / Linkage-Disequilibrium-Kartierung wurden verwendet um den QTL ...

  8. Detecção de locos de características quantitativas (QTL afetando o crescimento e a carcaça de suínos: um enfoque Bayesiano com o uso de diferentes prioris Detection of quantitative trait loci (QTL affecting growth and carcass traits in swine: a Bayesian approach using differents priors

    Directory of Open Access Journals (Sweden)

    Tarcisio de Moraes Gonçalves

    2008-02-01

    Full Text Available Foram utilizados 1.129 animais, 298 F1 e 831 F2 para gordura intramuscular (GIM, % e ganho de peso (GP, g/dia e 324 F1 e 805 F2 para espessura de toucinho (ET, mm, obtidos por meio do cruzamento de suínos machos da raça Meishan e fêmeas Large White e Landrace. Os animais foram genotipados para marcadores moleculares cobrindo todo o genoma. Foram estudados os cromossomos 1, 2, 4, 5, 6, 7, 13, 14 e19 para ET e GIM e os cromossomos 1, 2, 4, 6, 7, 8, 13, 17 e19 para GP entre 25 e 90 kg de peso vivo (PV. Análises de QTL usando metodologia Bayesiana foram aplicadas mediante o modelo genético estatístico combinando os efeitos Poligênico Infinito (MPI, Poligênico Finito (MPF e de QTL. Os sumários dos parâmetros estimados foram baseados nas distribuições marginais a posteriori obtidas por Cadeia de Markov, algoritmo de Monte Carlo (MCMC. De modo geral, por meio dos resultados, foi possível evidenciar um QTL para ET, independentemente da priori estudada. Não foi possível detectar QTL para as características GIM e GP com a aplicação desta metodologia, o que pode estar relacionado aos marcadores não-informativos ou à ausência de QTL segregando nos cromossomos estudados. Há vantagens em analisar dados experimentais ajustando modelos genéticos combinados e não considerando unicamente o modelo poligênico ou o oligogênico. As análises ilustraram a utilidade e aplicabilidade do método Bayesiano no qual foram utilizados modelos finitos.Genome scan was used to identify chromosomal regions and genes that control quantitative trait loci (QTL of economic importance using 1129 animals from F1 and F2 populations obtained from crosses between Meishan and commercial Dutch breeds (Large White and Landrace. Animals were genotyped for molecular markers covering the entire genome. The chromosomes 1, 2, 4, 5, 6, 7, 13, 14 and 19 were studied for intramuscular fat (IMF, % and backfat thickness (BT, mm and the chromosomes 1, 2, 4, 6, 7, 8, 13, 17 and

  9. The influence of root rot incidence on cassava genotype on ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-11-16

    Nov 16, 2009 ... model statistical procedures with the SAS system for windows. Comparisons ... significantly different at probability 0.05%. The results of this ... Due to inefficient harvesting, packaging ... from rot for gari processing. Where there ...

  10. Biodegrading effects of some rot fungi on Pinus caribaea wood ...

    African Journals Online (AJOL)

    morelet) in Ijaiye Forest Reserve, 38 km northwest of Ibadan, Nigeria. The wood samples were inoculated separately with two species of white-rot fungi; Corioliopsis polyzona and Pleurotus squarrosulus, and two species of brownrot fungi; ...

  11. Management of chili pepper root rot and wilt (caused by Phytophthora nicotianae by grafting onto resistant rootstock

    Directory of Open Access Journals (Sweden)

    Mourad SAADOUN

    2013-05-01

    Full Text Available Root rot and plant wilting caused by Phytophthora nicotianae is a severe disease of chili pepper (Capsicum annuum L. in open fields and under greenhouse production in Tunisia. Chili pepper grafting for disease manage- ment is attracting increased interest in recent years. Using the tube grafting technique, different compatible scion/rootstock combinations were obtained with the wild-type pepper SCM334 and the local chili pepper cultivars ‘Beldi’ and ‘Baker’. SCM334 was resistant to P. nicotianae, while the cultivars Beldi and Baker were susceptible. Plant inoculations were performed with P. nicotianae zoospores, and severity of root rot was rated 30 days post- inoculation using a 0 (healthy plant to 5 (dead plant severity score. On SCM334 rootstock and with ‘Beldi’ or ‘Baker’ scions, the intensity of root rot was very low (mean score 0.1–0.2 and plants were healthy. However, with Baker or Beldi rootstocks and SCM334 scions, root rot was severe (mean score 3.1–4.6, leading to high numbers of wilting and dead plants. This severe root rot was similar to that observed on non-grafted plants of ‘Baker’ and ‘Beldi’ inoculated with the pathogen. Under greenhouse conditions, measurements of agronomic characters indicated non-consistent improvement of these features on the scion cultivar when SCM334 was the rootstock. Since plant foliage is not attacked by this pathogen, these results show that susceptible chili pepper scions grafted onto SCM334 rootstocks could be used for root rot management and improvement of pepper yields in P. nicotianae infested soils.

  12. Variation and inheritance of iron reductase activity in the roots of common bean (Phaseolus vulgaris L.) and association with seed iron accumulation QTL.

    Science.gov (United States)

    Blair, Matthew W; Knewtson, Sharon Jb; Astudillo, Carolina; Li, Chee-Ming; Fernandez, Andrea C; Grusak, Michael A

    2010-10-05

    Iron deficiency anemia is a global problem which often affects women and children of developing countries. Strategy I plants, such as common bean (Phaseolus vulgaris L.) take up iron through a process that involves an iron reduction mechanism in their roots; this reduction is required to convert ferric iron to ferrous iron. Root absorbed iron is critical for the iron nutrition of the plant, and for the delivery of iron to the shoot and ultimately the seeds. The objectives of this study were to determine the variability and inheritance for iron reductase activity in a range of genotypes and in a low × high seed iron cross (DOR364 x G19833), to identify quantitative trait loci (QTL) for this trait, and to assess possible associations with seed iron levels. The experiments were carried out with hydroponically grown plants provided different amounts of iron varying between 0 and 20 μM Fe(III)-EDDHA. The parents, DOR364 and G19833, plus 13 other cultivated or wild beans, were found to differ in iron reductase activity. Based on these initial experiments, two growth conditions (iron limited and iron sufficient) were selected as treatments for evaluating the DOR364 × G19833 recombinant inbred lines. A single major QTL was found for iron reductase activity under iron-limited conditions (1 μM Fe) on linkage group b02 and another major QTL was found under iron sufficient conditions (15 μM Fe) on linkage group b11. Associations between the b11 QTL were found with several QTL for seed iron. Genes conditioning iron reductase activity in iron sufficient bean plants appear to be associated with genes contributing to seed iron accumulation. Markers for bean iron reductase (FRO) homologues were found with in silico mapping based on common bean synteny with soybean and Medicago truncatula on b06 and b07; however, neither locus aligned with the QTL for iron reductase activity. In summary, the QTL for iron reductase activity under iron limited conditions may be useful in

  13. Variation and inheritance of iron reductase activity in the roots of common bean (Phaseolus vulgaris L. and association with seed iron accumulation QTL

    Directory of Open Access Journals (Sweden)

    Fernandez Andrea C

    2010-10-01

    Full Text Available Abstract Background Iron deficiency anemia is a global problem which often affects women and children of developing countries. Strategy I plants, such as common bean (Phaseolus vulgaris L. take up iron through a process that involves an iron reduction mechanism in their roots; this reduction is required to convert ferric iron to ferrous iron. Root absorbed iron is critical for the iron nutrition of the plant, and for the delivery of iron to the shoot and ultimately the seeds. The objectives of this study were to determine the variability and inheritance for iron reductase activity in a range of genotypes and in a low × high seed iron cross (DOR364 × G19833, to identify quantitative trait loci (QTL for this trait, and to assess possible associations with seed iron levels. Results The experiments were carried out with hydroponically grown plants provided different amounts of iron varying between 0 and 20 μM Fe(III-EDDHA. The parents, DOR364 and G19833, plus 13 other cultivated or wild beans, were found to differ in iron reductase activity. Based on these initial experiments, two growth conditions (iron limited and iron sufficient were selected as treatments for evaluating the DOR364 × G19833 recombinant inbred lines. A single major QTL was found for iron reductase activity under iron-limited conditions (1 μM Fe on linkage group b02 and another major QTL was found under iron sufficient conditions (15 μM Fe on linkage group b11. Associations between the b11 QTL were found with several QTL for seed iron. Conclusions Genes conditioning iron reductase activity in iron sufficient bean plants appear to be associated with genes contributing to seed iron accumulation. Markers for bean iron reductase (FRO homologues were found with in silico mapping based on common bean synteny with soybean and Medicago truncatula on b06 and b07; however, neither locus aligned with the QTL for iron reductase activity. In summary, the QTL for iron reductase activity

  14. Mapping of Ppd-B1, a Major Candidate Gene for Late Heading on Wild Emmer Chromosome Arm 2BS and Assessment of Its Interactions with Early Heading QTLs on 3AL.

    Science.gov (United States)

    Zhou, Wei; Wu, Shasha; Ding, Mingquan; Li, Jingjuan; Shi, Zhaobin; Wei, Wei; Guo, Jialian; Zhang, Hua; Jiang, Yurong; Rong, Junkang

    2016-01-01

    Wheat heading date is an important agronomic trait determining maturation time and yield. A set of common wheat (Triticum aestivum var. Chinese Spring; CS)-wild emmer (T. turgidum L. subsp. dicoccoides (TDIC)) chromosome arm substitution lines (CASLs) was used to identify and allocate QTLs conferring late or early spike emergence by examining heading date. Genetic loci accelerating heading were found on TDIC chromosome arms 3AL and 7BS, while loci delaying heading were located on 4AL and 2BS. To map QTLs conferring late heading on 2BS, F2 populations derived from two cross combinations of CASL2BS × CS and CASL3AL × CASL2BS were developed and each planted at two times, constituting four F2 mapping populations. Heading date varied continuously among individuals of these four populations, suggesting quantitative characteristics. A genetic map of 2BS, consisting of 23 SSR and one single-stranded conformation polymorphism (SSCP) marker(s), was constructed using these F2 populations. This map spanned a genetic length of 53.2 cM with average marker density of 2.3 cM. The photoperiod-sensitivity gene Ppd-B1 was mapped to chromosome arm 2BS as a SSCP molecular marker, and was validated as tightly linked to a major QTL governing late heading of CASL2BS in all mapping populations. A significant dominance by additive effect of Ppd-B1 with the LUX gene located on 3AL was also detected. CS had more copies of Ppd-B1 than CASL2BS, implying that increased copy number could elevate the expression of Ppd-1 in CS, also increasing expression of LUX and FT genes and causing CS to have an earlier heading date than CASL2BS in long days.

  15. Marker list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...Database Site Policy | Contact Us Marker list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  16. QTL replication and targeted association highlight the nerve growth factor gene for nonverbal communication deficits in autism spectrum disorders.

    Science.gov (United States)

    Lu, A T-H; Yoon, J; Geschwind, D H; Cantor, R M

    2013-02-01

    Autism Spectrum Disorder (ASD) has a heterogeneous etiology that is genetically complex. It is defined by deficits in communication and social skills and the presence of restricted and repetitive behaviors. Genetic analyses of heritable quantitative traits that correlate with ASD may reduce heterogeneity. With this in mind, deficits in nonverbal communication (NVC) were quantified based on items from the Autism Diagnostic Interview Revised. Our previous analysis of 228 families from the Autism Genetics Research Exchange (AGRE) repository reported 5 potential quantitative trait loci (QTL). Here we report an NVC QTL replication study in an independent sample of 213 AGRE families. One QTL was replicated (Panalysis of 476 haplotype blocks with 708 AGRE families using the Family Based Association Test (FBAT). Blocks in two QTL genes were associated with NVC with a P-value of 0.001. Three associated haplotype blocks were intronic to the Nerve Growth Factor (NGF) gene (P=0.001, 0.001, 0.002), and one was intronic to KCND3 (P=0.001). Individual haplotypes within the associated blocks drove the associations (0.003, 0.0004 and 0.0002) for NGF and 0.0001 for KCND3. Using the same methods, these genes were tested for association with NVC in an independent sample of 1517 families from an Autism Genome Project (AGP). NVC was associated with a haplotype in an adjacent NGF block (P=0.0005) and one 46 kb away from the associated block in KCND3 (0.008). These analyses illustrate the value of QTL and targeted association studies for genetically complex disorders such as ASD. NGF is a promising risk gene for NVC deficits.

  17. Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs

    DEFF Research Database (Denmark)

    Jouffe, Vincent; Rowe, Suzanne; Liaubet, Laurence

    2009-01-01

    this with information on published QTL. The starting point is a set of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH) Results: Different approaches to localize the differentially expressed (DE) genes to the pig genome....... Different approaches to localize the differentially expressed (DE) genes to the pig genome showed different levels of success and a clear lack of concordance for some genes between the various approaches. For a focused analysis on 12 genes, overlapping QTL from the public domain were presented. Also...

  18. Suppression of Rhizome Rot in Organically Cultivated Ginger Using Integrated Pest Management

    Directory of Open Access Journals (Sweden)

    Chang-Ki Shim

    2015-09-01

    Full Text Available This study was conducted to control ginger rhizome rot treated with the combined treatment, the hairy vetch, carbonized rice husk and eggshell calcium in organic ginger farm. Early symptoms of leaf yellowing and plant wilt began in the chemical fertilizer treatment on July 1. Ginger rhizome rot was more progressed on October 2, and stem browning and dead plant showed a high disease incidence with from 36.7% to 43.0%. On the other hand, the combined treatment did not occur at all until July 1 and delayed the disease incidence to October 2. It showed a low disease incidence of 1.3% to 1.7%. In the combined treatment, the content of soil Na, Fe, Cu was decreased and organic matter was increased twice with 31.6% than previous. Population density of Pythium sp. is lower in the combined treatment (0.3-2.0×103 cfu/g than the chemical fertilizer treatments (12.0-12.3×103 cfu/g. The combined treatment, hairy vetch, carbonized rice husk and the eggshell calcium is able to control the ginger rhizome rot in organically cultivated ginger field.

  19. High-Q Fabry–Pérot Micro-Cavities for High-Sensitivity Volume Refractometry

    Directory of Open Access Journals (Sweden)

    Noha Gaber

    2018-01-01

    Full Text Available This work reports a novel structure for a Fabry–Pérot micro cavity that combines the highest reported quality factor for an on-chip Fabry–Pérot resonator that exceeds 9800, and a very high sensitivity for an on-chip volume refractometer based on a Fabry–Pérot cavity that is about 1000 nm/refractive index unit (RIU. The structure consists of two cylindrical Bragg micromirrors that achieve confinement of the Gaussian beam in the plan parallel to the chip substrate, while for the perpendicular plan, external fiber rod lenses (FRLs are placed in the optical path of the input and the output of the cavity. This novel structure overcomes number of the drawbacks presented in previous designs. The analyte is passed between the mirrors, enabling its detection from the resonance peak wavelengths of the transmission spectra. Mixtures of ethanol and deionized (DI-water with different ratios are used as analytes with different refractive indices to exploit the device as a micro-opto-fluidic refractometer. The design criteria are detailed and the modeling is based on Gaussian-optics equations, which depicts a scenario closer to reality than the usually used ray-optics modeling.

  20. Lettuce genotype resistance to "soft rot" caused by Pectobacterium carotovorum subsp. carotovorum

    Directory of Open Access Journals (Sweden)

    Kátia Cilene da Silva Felix

    2014-08-01

    Full Text Available Soft rot, caused by Pectobacterium carotovorum subsp. carotovorum (Pcc, is the main bacterial disease affecting lettuce (Lactuca sativa L. crops in Brazil and leads to significant yield losses. This study aimed to assess the reaction of lettuce genotypes to soft rot induced by a virulent isolate and the stability of the resistance to three isolates varying in virulence. Using a descriptive ordinal scale ranging from 1 to 9 a classification system was defined: class 1 = resistant (R: severity (Sev 3.5. Of the 41 tested genotypes, 14 were classified as MR and 27 as S when inoculated with a Pcc isolate of intermediate virulence. Eleven of these genotypes (four S and seven MR were selected to test their resistance stability against three other isolates with an increasing degree of virulence (Pcc36 < Pcc-A1.1 < Pcc-23. Out of the 11 genotypes eight retained the original classification and three moved from S to MR resistant class when challenged with the least virulent isolate. Vitória de Santo Antão was the only genotype classified as MR for all tested isolates and is a promising candidate for durable soft rot resistance breeding.

  1. Maize kernel antioxidants and their potential involvement in Fusarium ear rot resistance.

    Science.gov (United States)

    Picot, Adeline; Atanasova-Pénichon, Vessela; Pons, Sebastien; Marchegay, Gisèle; Barreau, Christian; Pinson-Gadais, Laëtitia; Roucolle, Joël; Daveau, Florie; Caron, Daniel; Richard-Forget, Florence

    2013-04-10

    The potential involvement of antioxidants (α-tocopherol, lutein, zeaxanthin, β-carotene, and ferulic acid) in the resistance of maize varieties to Fusarium ear rot was the focus of this study. These antioxidants were present in all maize kernel stages, indicating that the fumonisin-producing fungi (mainly Fusarium verticillioides and Fusarium proliferatum ) are likely to face them during ear colonization. The effect of these compounds on fumonisin biosynthesis was studied in F. verticillioides liquid cultures. In carotenoid-treated cultures, no inhibitory effect of fumonisin accumulation was observed while a potent inhibitory activity was obtained for sublethal doses of α-tocopherol (0.1 mM) and ferulic acid (1 mM). Using a set of genotypes with moderate to high susceptibility to Fusarium ear rot, ferulic acid was significantly lower in immature kernels of the very susceptible group. Such a relation was nonexistent for tocopherols and carotenoids. Also, ferulic acid in immature kernels ranged from 3 to 8.5 mg/g, i.e., at levels consistent with the in vitro inhibitory concentration. Overall, our data support the fact that ferulic acid may contribute to resistance to Fusarium ear rot and/or fumonisin accumulation.

  2. Detection, identification and differentiation of Pectobacterium and Dickeya species causing potato blackleg and tuber soft rot: a review

    NARCIS (Netherlands)

    Czajkowski, R.L.; Pérombelon, M.C.M.; Jafra, S.; Lojkowska, E.; Potrykus, M.; Wolf, van der J.M.; Sledz, W.

    2015-01-01

    The soft rot Enterobacteriaceae (SRE) Pectobacterium and Dickeya species (formerly classified as pectinolytic Erwinia spp.) cause important diseases on potato and other arable and horticultural crops. They may affect the growing potato plant causing blackleg and are responsible for tuber soft rot in

  3. Genetic Architecture of Main Effect QTL for Heading Date in European Winter Wheat

    Directory of Open Access Journals (Sweden)

    Christine eZanke

    2014-05-01

    Full Text Available A genome-wide association study (GWAS for heading date (HD was performed with a panel of 358 European winter wheat (Triticum aestivum L. varieties and 14 spring wheat varieties through the phenotypic evaluation of HD in field tests in eight environments. Genotyping data consisted of 770 mapped microsatellite loci and 7934 mapped SNP markers derived from the 90K iSelect wheat chip. Best linear unbiased estimations (BLUEs were calculated across all trials and ranged from 142.5 to 159.6 days after the 1st of January with an average value of 151.4 days. Considering only associations with a –log10 (P-value ≥3.0, a total of 340 SSR and 2983 SNP marker-trait associations (MTAs were detected. After Bonferroni correction for multiple testing, a total of 72 SSR and 438 SNP marker-trait associations remained significant. Highly significant MTAs were detected for the photoperiodism gene Ppd-D1, which was genotyped in all varieties. Consistent associations were found on all chromosomes with the highest number of MTAs on chromosome 5B. Linear regression showed a clear dependence of the HD score BLUEs on the number of favourable alleles (decreasing HD and unfavourable alleles (increasing HD per variety meaning that genotypes with a higher number of favourable or a low number of unfavourable alleles showed lower HD and therefore flowered earlier. For the vernalization gene Vrn-A2 co-locating MTAs on chromosome 5A, as well as for the photoperiodism genes Ppd-A1 and Ppd-B1 on chromosomes 2A and 2B were detected. After the construction of an integrated map of the SSR and SNP markers and by exploiting the synteny to sequenced species, such as rice and Brachypodium distachyon, we were able to demonstrate that a marker locus on wheat chromosome 5BL with homology to the rice photoperiodism gene Hd6 played a significant role in the determination of the heading date in wheat.

  4. Meta-analysis of sequence-based association studies across three cattle breeds reveals 25 QTL for fat and protein percentages in milk at nucleotide resolution.

    Science.gov (United States)

    Pausch, Hubert; Emmerling, Reiner; Gredler-Grandl, Birgit; Fries, Ruedi; Daetwyler, Hans D; Goddard, Michael E

    2017-11-09

    Genotyping and whole-genome sequencing data have been generated for hundreds of thousands of cattle. International consortia used these data to compile imputation reference panels that facilitate the imputation of sequence variant genotypes for animals that have been genotyped using dense microarrays. Association studies with imputed sequence variant genotypes allow for the characterization of quantitative trait loci (QTL) at nucleotide resolution particularly when individuals from several breeds are included in the mapping populations. We imputed genotypes for 28 million sequence variants in 17,229 cattle of the Braunvieh, Fleckvieh and Holstein breeds in order to compile large mapping populations that provide high power to identify QTL for milk production traits. Association tests between imputed sequence variant genotypes and fat and protein percentages in milk uncovered between six and thirteen QTL (P < 1e-8) per breed. Eight of the detected QTL were significant in more than one breed. We combined the results across breeds using meta-analysis and identified a total of 25 QTL including six that were not significant in the within-breed association studies. Two missense mutations in the ABCG2 (p.Y581S, rs43702337, P = 4.3e-34) and GHR (p.F279Y, rs385640152, P = 1.6e-74) genes were the top variants at QTL on chromosomes 6 and 20. Another known causal missense mutation in the DGAT1 gene (p.A232K, rs109326954, P = 8.4e-1436) was the second top variant at a QTL on chromosome 14 but its allelic substitution effects were inconsistent across breeds. It turned out that the conflicting allelic substitution effects resulted from flaws in the imputed genotypes due to the use of a multi-breed reference population for genotype imputation. Many QTL for milk production traits segregate across breeds and across-breed meta-analysis has greater power to detect such QTL than within-breed association testing. Association testing between imputed sequence variant genotypes and

  5. QTL Mapping of Genome Regions Controlling Manganese Uptake in Lentil Seed

    Directory of Open Access Journals (Sweden)

    Duygu Ates

    2018-05-01

    Full Text Available This study evaluated Mn concentration in the seeds of 120 RILs of lentil developed from the cross “CDC Redberry” × “ILL7502”. Micronutrient analysis using atomic absorption spectrometry indicated mean seed manganese (Mn concentrations ranging from 8.5 to 26.8 mg/kg, based on replicated field trials grown at three locations in Turkey in 2012 and 2013. A linkage map of lentil was constructed and consisted of seven linkage groups with 5,385 DNA markers. The total map length was 973.1 cM, with an average distance between markers of 0.18 cM. A total of 6 QTL for Mn concentration were identified using composite interval mapping (CIM. All QTL were statistically significant and explained 15.3–24.1% of the phenotypic variation, with LOD scores ranging from 3.00 to 4.42. The high-density genetic map reported in this study will increase fundamental knowledge of the genome structure of lentil, and will be the basis for the development of micronutrient-enriched lentil genotypes to support biofortification efforts.

  6. QTL Mapping of Genome Regions Controlling Manganese Uptake in Lentil Seed.

    Science.gov (United States)

    Ates, Duygu; Aldemir, Secil; Yagmur, Bulent; Kahraman, Abdullah; Ozkan, Hakan; Vandenberg, Albert; Tanyolac, Muhammed Bahattin

    2018-05-04

    This study evaluated Mn concentration in the seeds of 120 RILs of lentil developed from the cross "CDC Redberry" × "ILL7502". Micronutrient analysis using atomic absorption spectrometry indicated mean seed manganese (Mn) concentrations ranging from 8.5 to 26.8 mg/kg, based on replicated field trials grown at three locations in Turkey in 2012 and 2013. A linkage map of lentil was constructed and consisted of seven linkage groups with 5,385 DNA markers. The total map length was 973.1 cM, with an average distance between markers of 0.18 cM. A total of 6 QTL for Mn concentration were identified using composite interval mapping (CIM). All QTL were statistically significant and explained 15.3-24.1% of the phenotypic variation, with LOD scores ranging from 3.00 to 4.42. The high-density genetic map reported in this study will increase fundamental knowledge of the genome structure of lentil, and will be the basis for the development of micronutrient-enriched lentil genotypes to support biofortification efforts. Copyright © 2018 Ates et al.

  7. Identifying QTL for fur quality traits in mink (Neovison vison)

    DEFF Research Database (Denmark)

    Thirstrup, Janne Pia; Anistoroaei, Razvan Marian; Guldbrandtsen, Bernt

    2012-01-01

    Mapping of quantitative trait loci (QTL) affecting fur quality traits (guard hair length, guard hair thikness, and density of woll) was performed in a 3-generation population (F2-design). In the parental generation, Nordic wild mink were crossed reciprocally with American short nap mink. Twenty o...

  8. Development of a QTL-environment-based predictive model for node addition rate in common bean.

    Science.gov (United States)

    Zhang, Li; Gezan, Salvador A; Eduardo Vallejos, C; Jones, James W; Boote, Kenneth J; Clavijo-Michelangeli, Jose A; Bhakta, Mehul; Osorno, Juan M; Rao, Idupulapati; Beebe, Stephen; Roman-Paoli, Elvin; Gonzalez, Abiezer; Beaver, James; Ricaurte, Jaumer; Colbert, Raphael; Correll, Melanie J

    2017-05-01

    This work reports the effects of the genetic makeup, the environment and the genotype by environment interactions for node addition rate in an RIL population of common bean. This information was used to build a predictive model for node addition rate. To select a plant genotype that will thrive in targeted environments it is critical to understand the genotype by environment interaction (GEI). In this study, multi-environment QTL analysis was used to characterize node addition rate (NAR, node day - 1 ) on the main stem of the common bean (Phaseolus vulgaris L). This analysis was carried out with field data of 171 recombinant inbred lines that were grown at five sites (Florida, Puerto Rico, 2 sites in Colombia, and North Dakota). Four QTLs (Nar1, Nar2, Nar3 and Nar4) were identified, one of which had significant QTL by environment interactions (QEI), that is, Nar2 with temperature. Temperature was identified as the main environmental factor affecting NAR while day length and solar radiation played a minor role. Integration of sites as covariates into a QTL mixed site-effect model, and further replacing the site component with explanatory environmental covariates (i.e., temperature, day length and solar radiation) yielded a model that explained 73% of the phenotypic variation for NAR with root mean square error of 16.25% of the mean. The QTL consistency and stability was examined through a tenfold cross validation with different sets of genotypes and these four QTLs were always detected with 50-90% probability. The final model was evaluated using leave-one-site-out method to assess the influence of site on node addition rate. These analyses provided a quantitative measure of the effects on NAR of common beans exerted by the genetic makeup, the environment and their interactions.

  9. Dissection of two soybean QTL conferring partial resistance to Phytophthora sojae through sequence and gene expression analysis

    Directory of Open Access Journals (Sweden)

    Wang Hehe

    2012-08-01

    Full Text Available Abstract Background Phytophthora sojae is the primary pathogen of soybeans that are grown on poorly drained soils. Race-specific resistance to P. sojae in soybean is gene-for-gene, although in many areas of the US and worldwide there are populations that have adapted to the most commonly deployed resistance to P. sojae ( Rps genes. Hence, this system has received increased attention towards identifying mechanisms and molecular markers associated with partial resistance to this pathogen. Several quantitative trait loci (QTL have been identified in the soybean cultivar ‘Conrad’ that contributes to the expression of partial resistance to multiple P. sojae isolates. Results In this study, two of the Conrad QTL on chromosome 19 were dissected through sequence and expression analysis of genes in both resistant (Conrad and susceptible (‘Sloan’ genotypes. There were 1025 single nucleotide polymorphisms (SNPs in 87 of 153 genes sequenced from Conrad and Sloan. There were 304 SNPs in 54 genes sequenced from Conrad compared to those from both Sloan and Williams 82, of which 11 genes had SNPs unique to Conrad. Eleven of 19 genes in these regions analyzed with qRT-PCR had significant differences in fold change of transcript abundance in response to infection with P. sojae in lines with QTL haplotype from the resistant parent compared to those with the susceptible parent haplotype. From these, 8 of the 11 genes had SNPs in the upstream, untranslated region, exon, intron, and/or downstream region. These 11 candidate genes encode proteins potentially involved in signal transduction, hormone-mediated pathways, plant cell structural modification, ubiquitination, and basal resistance. Conclusions These findings may indicate a complex defense network with multiple mechanisms underlying these two soybean QTL conferring resistance to P. sojae. SNP markers derived from these candidate genes can contribute to fine mapping of QTL and marker assisted breeding for

  10. Salmonella enterica suppresses Pectobacterium carotovorum subsp. carotovorum population and soft rot progression by acidifying the microaerophilic environment.

    Science.gov (United States)

    Kwan, Grace; Charkowski, Amy O; Barak, Jeri D

    2013-02-12

    Although enteric human pathogens are usually studied in the context of their animal hosts, a significant portion of their life cycle occurs on plants. Plant disease alters the phyllosphere, leading to enhanced growth of human pathogens; however, the impact of human pathogens on phytopathogen biology and plant health is largely unknown. To characterize the interaction between human pathogens and phytobacterial pathogens in the phyllosphere, we examined the interactions between Pectobacterium carotovorum subsp. carotovorum and Salmonella enterica or Escherichia coli O157:H7 with regard to bacterial populations, soft rot progression, and changes in local pH. The presence of P. carotovorum subsp. carotovorum enhanced the growth of both S. enterica and E. coli O157:H7 on leaves. However, in a microaerophilic environment, S. enterica reduced P. carotovorum subsp. carotovorum populations and soft rot progression by moderating local environmental pH. Reduced soft rot was not due to S. enterica proteolytic activity. Limitations on P. carotovorum subsp. carotovorum growth, disease progression, and pH elevation were not observed on leaves coinoculated with E. coli O157:H7 or when leaves were coinoculated with S. enterica in an aerobic environment. S. enterica also severely undermined the relationship between the phytobacterial population and disease progression of a P. carotovorum subsp. carotovorum budB mutant defective in the 2,3-butanediol pathway for acid neutralization. Our results show that S. enterica and E. coli O157:H7 interact differently with the enteric phytobacterial pathogen P. carotovorum subsp. carotovorum. S. enterica inhibition of soft rot progression may conceal a rapidly growing human pathogen population. Whereas soft rotted produce can alert consumers to the possibility of food-borne pathogens, healthy-looking produce may entice consumption of contaminated vegetables. Salmonella enterica and Escherichia coli O157:H7 may use plants to move between animal

  11. Occurrence, characterization and management of fruit rot of immature cucumber fruits under arid greenhouse conditions

    Directory of Open Access Journals (Sweden)

    ABDULLAH M AL-SADI

    2012-01-01

    Full Text Available A study was undertaken to characterize and manage pathogens associated with fruit rot of immature cucumber fruits in greenhouses in Oman. A survey over 5 growing seasons from 2008 to 2010 in 99 different greenhouses in Oman showed that the disease is prevalent in 91 (92% greenhouses and results in losses of 10 to 60% (avg. 33% of immature fruits per plant. Incidence of the disease was not found to be affected by growing seasons, which could be attributed to the limited fluctuations in ambient temperatures in greenhouses. Isolations from diseased cucumber fruits yielded Alternaria alternata (isolation frequency = 52%, Fusarium equiseti (40%, Cladosporium tenuissium (27%, Botrytis cinerea (6%, Fusarium solani (6%, Corynespora cassiicola (3%, Aspergillus spp. (2%, Curvularia sp. (1% and Bipolaris sp. (1%. With the exception of Curvularia and Bipolaris species, all other fungi were pathogenic on cucumber fruits, with Fusarium equiseti being the most aggressive, followed by Corynespora cassiicola, Botrytis cinerea and Alternaria alternata. Cladosporium and Aspergillus spp. were found to be weakly pathogenic. Comparing the efficacy of foliar and soil applications of carbendazim fungicide on fruit rot of cucumber showed that foliar applications significantly reduced fruit rot and increased cucumber yield when compared to soil application or to control (P < 0.01. This appears to be the first report of the association of Corynespora cassiicola and Fusarium equiseti with fruit rot of immature greenhouse cucumbers. This is also the first report in Oman for the association of Cladosporium tenuissimum with fruit rot of immature cucumbers. Findings are discussed in terms of factors affecting disease control in greenhouses using carbendazim.

  12. Genetic control of soybean seed oil: I. QTL and genes associated with seed oil concentration in RIL populations derived from crossing moderately high-oil parents.

    Science.gov (United States)

    Eskandari, Mehrzad; Cober, Elroy R; Rajcan, Istvan

    2013-02-01

    Soybean seed is a major source of oil for human consumption worldwide and the main renewable feedstock for biodiesel production in North America. Increasing seed oil concentration in soybean [Glycine max (L.) Merrill] with no or minimal impact on protein concentration could be accelerated by exploiting quantitative trait loci (QTL) or gene-specific markers. Oil concentration in soybean is a polygenic trait regulated by many genes with mostly small effects and which is negatively associated with protein concentration. The objectives of this study were to discover and validate oil QTL in two recombinant inbred line (RIL) populations derived from crosses between three moderately high-oil soybean cultivars, OAC Wallace, OAC Glencoe, and RCAT Angora. The RIL populations were grown across several environments over 2 years in Ontario, Canada. In a population of 203 F(3:6) RILs from a cross of OAC Wallace and OAC Glencoe, a total of 11 genomic regions on nine different chromosomes were identified as associated with oil concentration using multiple QTL mapping and single-factor ANOVA. The percentage of the phenotypic variation accounted for by each QTL ranged from 4 to 11 %. Of the five QTL that were tested in a population of 211 F(3:5) RILs from the cross RCAT Angora × OAC Wallace, a "trait-based" bidirectional selective genotyping analysis validated four QTL (80 %). In addition, a total of seven two-way epistatic interactions were identified for oil concentration in this study. The QTL and epistatic interactions identified in this study could be used in marker-assisted introgression aimed at pyramiding high-oil alleles in soybean cultivars to increase oil concentration for biodiesel as well as edible oil applications.

  13. Microbial detoxification of waste rubber material by wood-rotting fungi.

    Science.gov (United States)

    Bredberg, Katarina; Andersson, B Erik; Landfors, Eva; Holst, Olle

    2002-07-01

    The extensive use of rubber products, mainly tires, and the difficulties to recycle those products, has resulted in world wide environmental problems. Microbial devulcanisation is a promising way to increase the recycling of rubber materials. One obstacle is that several microorganisms tested for devulcanisation are sensitive to rubber additives. A way to overcome this might be to detoxify the rubber material with fungi prior to the devulcanisation. In this study, 15 species of white-rot and brown-rot fungi have been screened with regard to their capacity to degrade an aromatic model compound in the presence of ground waste tire rubber. The most effective fungus, Resinicium bicolor, was used for detoxification of rubber material. Increase in growth of the desulfurising bacterium Thiobacillus ferrooxidans in presence of the rubber treated with Resinicium bicolor compared to untreated rubber demonstrated that detoxification with fungi is possible.

  14. First report of root rot of cowpea caused by Fusarium equiseti in Georgia in the United States

    Science.gov (United States)

    Root rot was observed on cowpea in Tift County, Georgia, in May of 2015. The disease occurred on approximately 10% of cowpea plants in 2 fields (2 ha). Symptoms appeared as sunken reddish brown lesions on roots and stems under the soil line, secondary roots became dark brown and rotted, and infected...

  15. Chitosan and oligochitosan enhance ginger (Zingiber officinale Roscoe) resistance to rhizome rot caused by Fusarium oxysporum in storage

    Science.gov (United States)

    The ability of chitosan and oligochitosan to enhance the resistance of ginger (Zingiber officinale) to rhizome rot, caused by Fusarium oxysporum, in storage was investigated. Both chitosan and oligochitosan at 1 and 5 g/L significantly inhibited rhizome rot, relative to the untreated control, with...

  16. Update History of This Database - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...B link & Genome analysis methods English archive site is opened. 2012/08/08 PGDBj... Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods is opened. About This...ate History of This Database - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  17. Huanglongbing increases Diplodia Stem End Rot in Citrus sinensis

    Science.gov (United States)

    Huanglongbing (HLB), one of the most devastating diseases of citrus is caused by the a-Proteobacteria Candidatus Liberibacter. Diplodia natalensis Pole-Evans is a fungal pathogen which has been known to cause a postharvest stem-end rot of citrus, the pathogen infects citrus fruit under the calyx, an...

  18. Comprehensive QTL mapping survey dissects the complex fruit texture physiology in apple (Malus x domestica Borkh.).

    Science.gov (United States)

    Longhi, Sara; Moretto, Marco; Viola, Roberto; Velasco, Riccardo; Costa, Fabrizio

    2012-02-01

    Fruit ripening is a complex physiological process in plants whereby cell wall programmed changes occur mainly to promote seed dispersal. Cell wall modification also directly regulates the textural properties, a fundamental aspect of fruit quality. In this study, two full-sib populations of apple, with 'Fuji' as the common maternal parent, crossed with 'Delearly' and 'Pink Lady', were used to understand the control of fruit texture by QTL mapping and in silico gene mining. Texture was dissected with a novel high resolution phenomics strategy, simultaneously profiling both mechanical and acoustic fruit texture components. In 'Fuji × Delearly' nine linkage groups were associated with QTLs accounting from 15.6% to 49% of the total variance, and a highly significant QTL cluster for both textural components was mapped on chromosome 10 and co-located with Md-PG1, a polygalacturonase gene that, in apple, is known to be involved in cell wall metabolism processes. In addition, other candidate genes related to Md-NOR and Md-RIN transcription factors, Md-Pel (pectate lyase), and Md-ACS1 were mapped within statistical intervals. In 'Fuji × Pink Lady', a smaller set of linkage groups associated with the QTLs identified for fruit texture (15.9-34.6% variance) was observed. The analysis of the phenotypic variance over a two-dimensional PCA plot highlighted a transgressive segregation for this progeny, revealing two QTL sets distinctively related to both mechanical and acoustic texture components. The mining of the apple genome allowed the discovery of the gene inventory underlying each QTL, and functional profile assessment unravelled specific gene expression patterns of these candidate genes.

  19. Lignin as a facilitator, not a barrier, during saccharification by brown rot fungi

    Energy Technology Data Exchange (ETDEWEB)

    Schilling, Jonathan S. [Univ. of Minnesota, Minneapolis, MN (United States); Tschirner, Ulrike [Univ. of Minnesota, Minneapolis, MN (United States); Blanchette, Robert A [Univ. of Minnesota, Minneapolis, MN (United States); Filley, Timothy [Purdue Univ., West Lafayette, IN (United States)

    2012-11-28

    This research focused on the biology of a group of wood-degrading fungi that cause brown rot in wood, with particular attention to the potential to mimic this biological approach ex situ for bioprocessing lignocellulosic biomass. Supported by the long-standing theory that these fungi use a two-step oxidative/enzymatic approach during brown rot, our team’s objectives were as follows: 1) to determine the discrete timing of lignin modifications, 2) to correlate these alterations with biocatalyst efficiency and ingress into plant cell walls, and 3) to reproduce modifications prior to saccharification for efficient bioprocessing. The core findings of our research were that 1) lignin modifications occur nearly coincident with enzyme secretion during brown rot and 2) there is no specificity to the benefit that a brown rot pretreatment has on the efficacy of cellulases – it is a general enhancement best predicted by chemical changes to lignin and side-chain hemicellulose sugars. In our work, this meant we could attain and predict broad improvements in saccharification using commercial cellulase cocktails, in some cases more than three-fold of that in untreated biomass. This project was completed with minimal variance from the original project management plan (PMP), resulting in fourteen presentations and posters, four peer-reviewed publications, and one additional publication now in review. The publications have been valuable to other scientists working toward similar goals and have been cited in thirteen peer-reviewed publications written by others since 2010. We are working with ADM to advance application options for industry, building on the lessons learned during this DOE award period.

  20. Introgression of Black Rot Resistance from Brassica carinata to Cauliflower (Brassica oleracea botrytis Group) through Embryo Rescue.

    Science.gov (United States)

    Sharma, Brij B; Kalia, Pritam; Singh, Dinesh; Sharma, Tilak R

    2017-01-01

    Black rot caused by Xanthomonas campestris pv. campestris ( Xcc ) is a very important disease of cauliflower ( Brassica oleracea botrytis group) resulting into 10-50% yield losses every year. Since there is a dearth of availability of resistance to black rot disease in B. oleracea (C genome), therefore exploration of A and B genomes was inevitable as they have been reported to be potential reservoirs of gene(s) for resistance to black rot. To utilize these sources, interspecific hybrid and backcross progeny (B 1 ) were generated between cauliflower "Pusa Sharad" and Ethiopian mustard "NPC-9" employing in vitro embryo rescue technique. Direct ovule culture method was better than siliqua culture under different temperature regime periods. Hybridity testing of F 1 inter-specific plants was carried out using co-dominant SSR marker and Brassica B and C genome-specific (DB and DC) primers. Meiosis in the di-genomic (BCC) interspecific hybrid of B. oleracea botrytis group (2 n = 18, CC) × B. carinata (2 n = 4x = 34, BBCC) was higly disorganized and cytological analysis of pollen mother cells revealed chromosomes 2 n = 26 at metaphase-I. Fertile giant pollen grain formation was observed frequently in interspecific F 1 hybrid and BC 1 plants. The F 1 inter-specific plants were found to be resistant to Xcc race 1. Segregation distortion was observed in BC 1 generation for black rot resistance and different morphological traits. The At1g70610 marker analysis confirmed successful introgression of black rot resistance in interspecific BC 1 population. This effort will go a long way in pyramiding gene(s) for resistance against black rot in Cole crops, especially cauliflower and cabbage for developing durable resistance, thus minimize dependency on bactericides.

  1. Introgression of Black Rot Resistance from Brassica carinata to Cauliflower (Brassica oleracea botrytis Group) through Embryo Rescue

    Science.gov (United States)

    Sharma, Brij B.; Kalia, Pritam; Singh, Dinesh; Sharma, Tilak R.

    2017-01-01

    Black rot caused by Xanthomonas campestris pv. campestris (Xcc) is a very important disease of cauliflower (Brassica oleracea botrytis group) resulting into 10–50% yield losses every year. Since there is a dearth of availability of resistance to black rot disease in B. oleracea (C genome), therefore exploration of A and B genomes was inevitable as they have been reported to be potential reservoirs of gene(s) for resistance to black rot. To utilize these sources, interspecific hybrid and backcross progeny (B1) were generated between cauliflower “Pusa Sharad” and Ethiopian mustard “NPC-9” employing in vitro embryo rescue technique. Direct ovule culture method was better than siliqua culture under different temperature regime periods. Hybridity testing of F1 inter-specific plants was carried out using co-dominant SSR marker and Brassica B and C genome-specific (DB and DC) primers. Meiosis in the di-genomic (BCC) interspecific hybrid of B. oleracea botrytis group (2n = 18, CC) × B. carinata (2n = 4x = 34, BBCC) was higly disorganized and cytological analysis of pollen mother cells revealed chromosomes 2n = 26 at metaphase-I. Fertile giant pollen grain formation was observed frequently in interspecific F1 hybrid and BC1 plants. The F1 inter-specific plants were found to be resistant to Xcc race 1. Segregation distortion was observed in BC1 generation for black rot resistance and different morphological traits. The At1g70610 marker analysis confirmed successful introgression of black rot resistance in interspecific BC1 population. This effort will go a long way in pyramiding gene(s) for resistance against black rot in Cole crops, especially cauliflower and cabbage for developing durable resistance, thus minimize dependency on bactericides. PMID:28769959

  2. Introgression of Black Rot Resistance from Brassica carinata to Cauliflower (Brassica oleracea botrytis Group through Embryo Rescue

    Directory of Open Access Journals (Sweden)

    Brij B. Sharma

    2017-07-01

    Full Text Available Black rot caused by Xanthomonas campestris pv. campestris (Xcc is a very important disease of cauliflower (Brassica oleracea botrytis group resulting into 10–50% yield losses every year. Since there is a dearth of availability of resistance to black rot disease in B. oleracea (C genome, therefore exploration of A and B genomes was inevitable as they have been reported to be potential reservoirs of gene(s for resistance to black rot. To utilize these sources, interspecific hybrid and backcross progeny (B1 were generated between cauliflower “Pusa Sharad” and Ethiopian mustard “NPC-9” employing in vitro embryo rescue technique. Direct ovule culture method was better than siliqua culture under different temperature regime periods. Hybridity testing of F1 inter-specific plants was carried out using co-dominant SSR marker and Brassica B and C genome-specific (DB and DC primers. Meiosis in the di-genomic (BCC interspecific hybrid of B. oleracea botrytis group (2n = 18, CC × B. carinata (2n = 4x = 34, BBCC was higly disorganized and cytological analysis of pollen mother cells revealed chromosomes 2n = 26 at metaphase-I. Fertile giant pollen grain formation was observed frequently in interspecific F1 hybrid and BC1 plants. The F1 inter-specific plants were found to be resistant to Xcc race 1. Segregation distortion was observed in BC1 generation for black rot resistance and different morphological traits. The At1g70610 marker analysis confirmed successful introgression of black rot resistance in interspecific BC1 population. This effort will go a long way in pyramiding gene(s for resistance against black rot in Cole crops, especially cauliflower and cabbage for developing durable resistance, thus minimize dependency on bactericides.

  3. Mapping of Novel QTL Regulating Grain Shattering Using Doubled Haploid Population in Rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    Gyu-Ho Lee

    2016-01-01

    Full Text Available The critical evolutionary step during domestication of major cereals was elimination of seed shattering because the easy-to-shatter trait in wild relatives results in a severe reduction in yield. In this study, we analyzed the QTLs associated with shattering employing a high-density genetic map in doubled haploid (DH population of rice (Oryza sativa L.. A genetic linkage map was generated with 217 microsatellite markers spanning 2082.4 cM and covering 12 rice chromosomes with an average interval of 9.6 cM between markers based on 120 DHLs derived from a cross between Cheongcheong indica type cultivar and Nagdong japonica type cultivar. In the QTL analysis, five QTLs pertaining to the breaking tensile strength (BTS were detected in 2013 and 2015. Two regions of the QTLs related to BTS on chromosome 1 and chromosome 6 were detected. Several important genes are distributed in 1 Mbp region of the QTL on chromosome 6 and they are related to the formation of abscission layer. We decide to name this QTL qSh6 and the candidate genes in the qSh6 region can be employed usefully in further research for cloning.

  4. Molecular systematics of the cotton root rot pathogen, Phymatotrichopsis omnivora

    NARCIS (Netherlands)

    Marek, S.M.; Hansen, K.; Romanish, M.; Thorn, R.G.

    2009-01-01

    Cotton root rot is an important soilborne disease of cotton and numerous dicot plants in the south-western United States and Mexico. The causal organism, Phymatotrichopsis omnivora (= Phymatotrichum omnivorum), is known only as an asexual, holoanamorphic (mitosporic) fungus, and produces conidia

  5. A survey of pre-harvest ear rot diseases of maize and associated mycotoxins in south and central Zambia.

    Science.gov (United States)

    Mukanga, Mweshi; Derera, John; Tongoona, Pangirayi; Laing, Mark D

    2010-07-15

    Maize ear rots reduce grain yield and quality with implication on food security and health. Some of the pathogenic fungi produce mycotoxins in maize grain posing a health risk to humans and livestock. Unfortunately, the levels of ear rot and mycotoxin infection in grain produced by subsistence farmers in sub-Saharan countries are not known. A survey was thus conducted to determine the prevalence of the ear rot problem and levels of mycotoxins in maize grain. A total of 114 farmsteads were randomly sampled from 11 districts in Lusaka and southern provinces in Zambia during 2006. Ten randomly picked cobs were examined per farmstead and the ear rot disease incidence and severity were estimated on site. This was followed by the standard seed health testing procedures for fungal isolation in the laboratory. Results indicated that the dominant ear rots were caused by Fusarium and Stenocarpella. Incidence of Fusarium verticillioides ranged from 2 to 21%, whereas that of Stenocarpella maydis reached 37% on ear rot diseased maize grain. In addition, 2-7% F. verticillioides, and 3-18% Aspergillus flavus, respectively, were recovered from seemingly healthy maize grain. The mean rank of fungal species, from highest to lowest, was F. verticillioides, S. maydis, A. flavus, Fusarium graminearum, Aspergillus niger, Penicillium spp., Botrydiplodia spp., and Cladosporium spp. The direct competitive ELISA-test indicated higher levels of fumonisins than aflatoxins in pre-harvest maize grain samples. The concentration of fumonisins from six districts, and aflatoxin from two districts, was 10-fold higher than 2 ppm and far higher than 2 ppb maximum daily intake recommended by the FAO/WHO. The study therefore suggested that subsistence farmers and consumers in this part of Zambia, and maybe also in similar environments in sub-Saharan Africa, might be exposed to dangerous levels of mycotoxins due to the high levels of ear rot infections in maize grain. 2010 Elsevier B.V. All rights

  6. Gene cloning and heterologous expression of pyranose 2-oxidase from the brown-rot fungus, Gloeophyllum trabeum

    Science.gov (United States)

    Diane Dietrich; Casey Crooks

    2009-01-01

    A pyranose 2-oxidase gene from the brown-rot basidiomycete Gloeophyllum trabeum was isolated using homology-based degenerate PCR. The gene structure was determined and compared to that of several pyranose 2-oxidases cloned from white-rot fungi. The G. trabeum pyranose 2-oxidase gene consists of 16 coding exons with canonical promoter CAAT and TATA elements in the 5’UTR...

  7. Identification of sources of resistance to anthracnose stalk rot in maize

    Directory of Open Access Journals (Sweden)

    Alessandro Nicoli

    Full Text Available ABSTRACT: Adoption of resistant cultivars is the primary measure used to control anthracnose stalk rot. The goal of this study was to identify maize-resistant genotypes to anthracnose stalk rot, which are similar to the hybrid 2B710. Experiments were performed at Embrapa Maize and Sorghum experimental fields in Brazil. The first experimental trial evaluated 234 maize lines as well as two commercials hybrids, BRS1010 (susceptible and 2B710 (resistant. Artificial inoculations were performed with a strain at the blister (R2 phase, and evaluation of disease severity was performed after 30 days. The second experimental trial evaluated 48 maize lines and hybrids, inoculated with two Colletotrichum graminicola strains. In the first trial, eight resistance groups were formed, and the last lines were more resistant, as was the hybrid 2B710, with values between 11.50% and 23.0% of severity. In the second trial, there was an interaction between the two factors, lines and isolates, and the lines often showed the same reaction features as those obtained in the first trial. However, the disease severity was higher for most lines, even when using other isolates. These lines with effective levels of resistance could be used in future studies of inheritance, in programs to develop hybrids, and to identify molecular markers associated with resistance to anthracnose stalk rot in maize.

  8. A genomics-informed, SNP association study reveals FBLN1 and FABP4 as contributing to resistance to fleece rot in Australian Merino sheep

    Directory of Open Access Journals (Sweden)

    Norris Belinda J

    2010-05-01

    Full Text Available Abstract Background Fleece rot (FR and body-strike of Merino sheep by the sheep blowfly Lucilia cuprina are major problems for the Australian wool industry, causing significant losses as a result of increased management costs coupled with reduced wool productivity and quality. In addition to direct effects on fleece quality, fleece rot is a major predisposing factor to blowfly strike on the body of sheep. In order to investigate the genetic drivers of resistance to fleece rot, we constructed a combined ovine-bovine cDNA microarray of almost 12,000 probes including 6,125 skin expressed sequence tags and 5,760 anonymous clones obtained from skin subtracted libraries derived from fleece rot resistant and susceptible animals. This microarray platform was used to profile the gene expression changes between skin samples of six resistant and six susceptible animals taken immediately before, during and after FR induction. Mixed-model equations were employed to normalize the data and 155 genes were found to be differentially expressed (DE. Ten DE genes were selected for validation using real-time PCR on independent skin samples. The genomic regions of a further 5 DE genes were surveyed to identify single nucleotide polymorphisms (SNP that were genotyped across three populations for their associations with fleece rot resistance. Results The majority of the DE genes originated from the fleece rot subtracted libraries and over-representing gene ontology terms included defense response to bacterium and epidermis development, indicating a role of these processes in modulating the sheep's response to fleece rot. We focused on genes that contribute to the physical barrier function of skin, including keratins, collagens, fibulin and lipid proteins, to identify SNPs that were associated to fleece rot scores. Conclusions We identified FBLN1 (fibulin and FABP4 (fatty acid binding protein 4 as key factors in sheep's resistance to fleece rot. Validation of these

  9. Characterizing forest root‐ and butt‐rot fungi in Yap, Palau, Pohnpei, Kosrae, Guam and Saipan [Chapter III

    Science.gov (United States)

    Phil Cannon; Ned B. Klopfenstein; Mee-Sook Kim; Yuko Ota; Norio Sahashi; Robert L. Schlub; Roger Brown; Sara M. Ashiglar; Amy L. Ross-Davis; John W. Hanna

    2014-01-01

    Ganoderma and Phellinus are two common fungal genera causing butt-rot on trees growing on USA-affiliated islands of the western Pacific. Although these fungi can be quite prevalent, especially in some older mangrove stands, it appears that the majority of infections caused by these fungi leads to severe rotting of the heartwood but do not kill the living...

  10. Simultaneous Detection of Brown Rot- and Soft Rot-Causing Bacterial Pathogens from Potato Tubers Through Multiplex PCR.

    Science.gov (United States)

    Ranjan, R K; Singh, Dinesh; Baranwal, V K

    2016-11-01

    Ralstonia solanacearum (Smith) Yabuuchi et al. and Erwinia carotovora subsp. carotovora (Jones) Bergey et al. (Pectobacterium carotovorum subsp. carotovorum) are the two major bacterial pathogens of potato causing brown rot (wilt) and soft rot diseases, respectively, in the field and during storage. Reliable and early detection of these pathogens are keys to avoid occurrence of these diseases in potato crops and reduce yield loss. In the present study, multiplex polymerase chain reaction (PCR) protocol was developed for simultaneous detection of R. solanacearum and E. carotovora subsp. carotovora from potato tubers. A set of oligos targeting the pectatelyase (pel) gene of E. carotovora subsp. carotovora and the universal primers based on 16S r RNA gene of R. solanacearum were used. The standardized multiplex PCR protocol could detect R. solanacearum and E. carotovora subsp. carotovora up to 0.01 and 1.0 ng of genomic DNA, respectively. The protocol was further validated on 96 stored potato tuber samples, collected from different potato-growing states of India, viz. Uttarakhand, Odisha, Meghalaya and Delhi. 53.1 % tuber samples were positive for R. solanacearum, and 15.1 % of samples were positive for E. carotovora subsp. carotovora, and both the pathogens were positive in 26.0 % samples when BIO-PCR was used. This method offers sensitive, specific, reliable and fast detection of two major bacterial pathogens from potato tubers simultaneously, particularly pathogen-free seed certification in large scale.

  11. Mapping of a major QTL for salt tolerance of mature field-grown maize plants based on SNP markers.

    Science.gov (United States)

    Luo, Meijie; Zhao, Yanxin; Zhang, Ruyang; Xing, Jinfeng; Duan, Minxiao; Li, Jingna; Wang, Naishun; Wang, Wenguang; Zhang, Shasha; Chen, Zhihui; Zhang, Huasheng; Shi, Zi; Song, Wei; Zhao, Jiuran

    2017-08-15

    Salt stress significantly restricts plant growth and production. Maize is an important food and economic crop but is also a salt sensitive crop. Identification of the genetic architecture controlling salt tolerance facilitates breeders to select salt tolerant lines. However, the critical quantitative trait loci (QTLs) responsible for the salt tolerance of field-grown maize plants are still unknown. To map the main genetic factors contributing to salt tolerance in mature maize, a double haploid population (240 individuals) and 1317 single nucleotide polymorphism (SNP) markers were employed to produce a genetic linkage map covering 1462.05 cM. Plant height of mature maize cultivated in the saline field (SPH) and plant height-based salt tolerance index (ratio of plant height between saline and control fields, PHI) were used to evaluate salt tolerance of mature maize plants. A major QTL for SPH was detected on Chromosome 1 with the LOD score of 22.4, which explained 31.2% of the phenotypic variation. In addition, the major QTL conditioning PHI was also mapped at the same position on Chromosome 1, and two candidate genes involving in ion homeostasis were identified within the confidence interval of this QTL. The detection of the major QTL in adult maize plant establishes the basis for the map-based cloning of genes associated with salt tolerance and provides a potential target for marker assisted selection in developing maize varieties with salt tolerance.

  12. 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.

  13. Identification of QTL conferring resistance to stripe rust (Puccinia striiformis f. sp. hordei) and leaf rust (Puccinia hordei) in barley using nested association mapping (NAM).

    Science.gov (United States)

    Vatter, Thomas; Maurer, Andreas; Perovic, Dragan; Kopahnke, Doris; Pillen, Klaus; Ordon, Frank

    2018-01-01

    The biotrophic rust fungi Puccinia hordei and Puccinia striiformis are important barley pathogens with the potential to cause high yield losses through an epidemic spread. The identification of QTL conferring resistance to these pathogens is the basis for targeted breeding approaches aiming to improve stripe rust and leaf rust resistance of modern cultivars. Exploiting the allelic richness of wild barley accessions proved to be a valuable tool to broaden the genetic base of resistance of barley cultivars. In this study, SNP-based nested association mapping (NAM) was performed to map stripe rust and leaf rust resistance QTL in the barley NAM population HEB-25, comprising 1,420 lines derived from BC1S3 generation. By scoring the percentage of infected leaf area, followed by calculation of the area under the disease progress curve and the average ordinate during a two-year field trial, a large variability of resistance across and within HEB-25 families was observed. NAM based on 5,715 informative SNPs resulted in the identification of twelve and eleven robust QTL for resistance against stripe rust and leaf rust, respectively. Out of these, eight QTL for stripe rust and two QTL for leaf rust are considered novel showing no overlap with previously reported resistance QTL. Overall, resistance to both pathogens in HEB-25 is most likely due to the accumulation of numerous small effect loci. In addition, the NAM results indicate that the 25 wild donor QTL alleles present in HEB-25 strongly differ in regard to their individual effect on rust resistance. In future, the NAM concept will allow to select and combine individual wild barley alleles from different HEB parents to increase rust resistance in barley. The HEB-25 results will support to unravel the genetic basis of rust resistance in barley, and to improve resistance against stripe rust and leaf rust of modern barley cultivars.

  14. Temporal changes in wood crystalline cellulose during degradation by brown rot fungi

    DEFF Research Database (Denmark)

    Howell, Caitlin; Hastrup, Anne Christine Steenkjær; Goodell, Barry

    2009-01-01

    The degradation of wood by brown rot fungi has been studied intensely for many years in order to facilitate the preservation of in-service wood. In this work we used X-ray diffraction to examine changes in wood cellulose crystallinity caused by the brown rot fungi Gloeophyllum trabeum, Coniophora...... planes in all degraded samples after roughly 20% weight loss, as well as a decrease in the average observed relative peak width at 2¿ = 22.2°. These results may indicate a disruption of the outer most semi-crystalline cellulose chains comprising the wood microfibril. X-ray diffraction analysis of wood...... subjected to biological attack by fungi may provide insight into degradative processes and wood cellulose structure....

  15. Report of postharvest rot of kiwifruit in Korea caused by Sclerotinia sclerotiorum.

    Science.gov (United States)

    Lee, Jung Han; Kwon, Young Ho; Kwack, Yong-Bum; Kwak, Youn-Sig

    2015-08-03

    In May 2014, sclerotinia rot symptoms caused by Sclerotinia sclerotiorum were observed on stored kiwifruit in Jinju, South Korea. The symptoms appeared as soft, water-soaked lesions on fruit covered with a white mycelium. The morphological characteristics and the internal transcribed spacer sequences of rRNA of the pathogen isolated from the sclerotinia rot showed it to be S. sclerotiorum. This was confirmed by performing a pathogenicity test with pure cultures of S. sclerotiorum and by reisolating S. sclerotiorum from artificially inoculated kiwifruits. Our results should help promote a better understanding of the diseases that affect kiwifruit and improve practices for postharvest disease control in the kiwifruit industry. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Plant DB link - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...e Site Policy | Contact Us Plant DB link - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  17. Genetic analysis and QTL mapping for fruit skin anthocyanidin in grape (vitis vinifera)

    International Nuclear Information System (INIS)

    Guo, Y.; Xue, R.; Lin, H.; Su, K.; Zhao, Y.; Zhendong, L.; Shi, G.; Niu, Z.; Li, K.; Guo, X.

    2015-01-01

    In this study, an F1 population was created by the cross 87-1*9-22. The female parent 87-1 was a black purple cultivar and the male parent was an excellent breeding line with green pericarp. the skin color separation of population and distribution, and determined the content of each individual fruit peel pigment. On the basis of the genetic map of Vitis vinifera L. We carried out the grape skin pigment content quantitative trait locus (QTL) analyses. The results show that the fruit color performance for continuous variation and the inheritance of fruit skin anthocyanidin content was a quantitative inheritance. The color of offspring ranges from green and black-blue and existing distribution. Using SSR and SRAP molecular markers to construct 188 female parent maps,175 male parent maps and 251 consensus maps, and the total map distance is 1047.5 cM,1100.2 cM and 1264.2 cM respectively. The result of QTL showed that there were more QTLs exist in the linkage group of 1, 2, 3, 4, 9, 13, 14, 16 and 19 and in the linkage group of 3, 4, 13 and 14, we detected QTLs in the similar position with the result of the study in the year of 2011 and 2012, and based on this we will conduct the fine QTL location in the future, this result will lay a good foundation for the grape in the department of molecular assistant breeding in the future. (author)

  18. High-density genetic mapping of a major QTL for resistance to multiple races of loose smut in a tetraploid wheat cross

    Science.gov (United States)

    Kumar, Sachin; Knox, Ron E.; Singh, Asheesh K.; DePauw, Ron M.; Campbell, Heather L.; Isidro-Sanchez, Julio; Clarke, Fran R.; Pozniak, Curtis J.; N’Daye, Amidou; Meyer, Brad; Sharpe, Andrew; Ruan, Yuefeng; Cuthbert, Richard D.; Somers, Daryl; Fedak, George

    2018-01-01

    Loose smut, caused by Ustilago tritici (Pers.) Rostr., is a systemic disease of tetraploid durum wheat (Triticum turgidum L.). Loose smut can be economically controlled by growing resistant varieties, making it important to find and deploy new sources of resistance. Blackbird, a variety of T. turgidum L. subsp. carthlicum (Nevski) A. Love & D. Love, carries a high level of resistance to loose smut. Blackbird was crossed with the loose smut susceptible durum cultivar Strongfield to produce a doubled haploid (DH) mapping population. The parents and progenies were inoculated with U. tritici races T26, T32 and T33 individually and as a mixture at Swift Current, Canada in 2011 and 2012 and loose smut incidence (LSI) was assessed. Genotyping of the DH population and parents using an Infinium iSelect 90K single nucleotide polymorphism (SNP) array identified 12,952 polymorphic SNPs. The SNPs and 426 SSRs (previously genotyped in the same population) were mapped to 16 linkage groups spanning 3008.4 cM at an average inter-marker space of 0.2 cM in a high-density genetic map. Composite interval mapping analysis revealed three significant quantitative trait loci (QTL) for loose smut resistance on chromosomes 3A, 6B and 7A. The loose smut resistance QTL on 6B (QUt.spa-6B.2) and 7A (QUt.spa-7A.2) were derived from Blackbird. Strongfield contributed the minor QTL on 3A (QUt.spa-3A.2). The resistance on 6B was a stable major QTL effective against all individual races and the mixture of the three races; it explained up to 74% of the phenotypic variation. This study is the first attempt in durum wheat to identify and map loose smut resistance QTL using a high-density genetic map. The QTL QUt.spa-6B.2 would be an effective source for breeding resistance to multiple races of the loose smut pathogen because it provides near-complete broad resistance to the predominant virulence on the Canadian prairies. PMID:29485999

  19. High-density genetic mapping of a major QTL for resistance to multiple races of loose smut in a tetraploid wheat cross.

    Directory of Open Access Journals (Sweden)

    Sachin Kumar

    Full Text Available Loose smut, caused by Ustilago tritici (Pers. Rostr., is a systemic disease of tetraploid durum wheat (Triticum turgidum L.. Loose smut can be economically controlled by growing resistant varieties, making it important to find and deploy new sources of resistance. Blackbird, a variety of T. turgidum L. subsp. carthlicum (Nevski A. Love & D. Love, carries a high level of resistance to loose smut. Blackbird was crossed with the loose smut susceptible durum cultivar Strongfield to produce a doubled haploid (DH mapping population. The parents and progenies were inoculated with U. tritici races T26, T32 and T33 individually and as a mixture at Swift Current, Canada in 2011 and 2012 and loose smut incidence (LSI was assessed. Genotyping of the DH population and parents using an Infinium iSelect 90K single nucleotide polymorphism (SNP array identified 12,952 polymorphic SNPs. The SNPs and 426 SSRs (previously genotyped in the same population were mapped to 16 linkage groups spanning 3008.4 cM at an average inter-marker space of 0.2 cM in a high-density genetic map. Composite interval mapping analysis revealed three significant quantitative trait loci (QTL for loose smut resistance on chromosomes 3A, 6B and 7A. The loose smut resistance QTL on 6B (QUt.spa-6B.2 and 7A (QUt.spa-7A.2 were derived from Blackbird. Strongfield contributed the minor QTL on 3A (QUt.spa-3A.2. The resistance on 6B was a stable major QTL effective against all individual races and the mixture of the three races; it explained up to 74% of the phenotypic variation. This study is the first attempt in durum wheat to identify and map loose smut resistance QTL using a high-density genetic map. The QTL QUt.spa-6B.2 would be an effective source for breeding resistance to multiple races of the loose smut pathogen because it provides near-complete broad resistance to the predominant virulence on the Canadian prairies.

  20. Status of maize stalk rot complex in western belts of Nepal and its integrated management

    Directory of Open Access Journals (Sweden)

    Subash Subedi

    2016-12-01

    Full Text Available Maize stalk rot complex is becoming a serious threat for maize growing areas of Nepal. A field monitoring for maize stalk rot complex was done during crop season (August, 2016 covering 10 farmers field each of Surkhet, Banke, Dang, Chitwan and Nawalparasi districts. Maize crop showed highly susceptible reaction to the disease at western belts of Dang and susceptible reaction was marked in Chitwan and Nawalparasi districts while the disease effect was mild at Banke and Surkhet district. Most of the plant diseases managed successfully through the application of bio-control agents, host resistance, chemicals and other different cultural control methods. The result of field experiment conducted at Dang showed that all the treatments had significant (P≤0.05 effect on percent disease index (PDI and crop yield over farmers practice to control maize stalk rot. The higher percent disease control (52.36% and yield increase (40.29% were recorded from the plot sprayed with streptocyclin @ 2 g L-1 and insecticide (cypermethrin + chloropyrifos @ 2.5 ml L-1 of water during knee height and subsequent spray after 15 days interval as compared to farmers practice. Out of 30 genotypes, Rampur composit, Arun 2, Rampur 34, RamS03F08, TLBRS07F16 and Rampur 24 were found resistant against stalk rot complex with higher yield at Rampur Chitwan.

  1. QTL for phytosterol and sinapate ester content in Brassica napus L. collocate with the two erucic acid genes

    Science.gov (United States)

    Amar, Samija; Ecke, Wolfgang; Becker, Heiko C.

    2008-01-01

    Improving oil and protein quality for food and feed purposes is an important goal in rapeseed (Brassica napus L.) breeding programs. Rapeseed contains phytosterols, used to enrich food products, and sinapate esters, which are limiting the utilization of rapeseed proteins in the feed industry. Increasing the phytosterol content of oil and lowering sinapate ester content of meal could increase the value of the oilseed rape crop. The objective of the present study was to identify quantitative trait loci (QTL) for phytosterol and sinapate ester content in a winter rapeseed population of 148 doubled haploid lines, previously found to have a large variation for these two traits. This population also segregated for the two erucic acid genes. A close negative correlation was found between erucic acid and phytosterol content (Spearman’s rank correlation, rs = −0.80**). For total phytosterol content, three QTL were detected, explaining 60% of the genetic variance. The two QTL with the strongest additive effects were mapped on linkage groups N8 and N13 within the confidence intervals of the two erucic acid genes. For sinapate ester content four QTL were detected, explaining 53% of the genetic variance. Again, a close negative correlation was found between erucic acid and sinapate ester content (rs = −0.66**) and the QTL with the strongest additive effects mapped on linkage groups N8 and N13 within the confidence intervals of the two erucic acid genes. The results suggests, that there is a pleiotropic effect of the two erucic acid genes on phytosterol and sinapate ester content; the effect of the alleles for low erucic acid content is to increase phytosterol and sinapate ester content. Possible reasons for this are discussed based on known biosynthetic pathways. Electronic supplementary material The online version of this article (doi:10.1007/s00122-008-0734-2) contains supplementary material, which is available to authorized users. PMID:18335203

  2. QTL Mapping of Agronomic Waterlogging Tolerance Using Recombinant Inbred Lines Derived from Tropical Maize (Zea mays L) Germplasm

    Science.gov (United States)

    Zaidi, Pervez Haider; Rashid, Zerka; Vinayan, Madhumal Thayil; Almeida, Gustavo Dias; Phagna, Ramesh Kumar; Babu, Raman

    2015-01-01

    Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate

  3. Fungal hydroquinones contribute to brown rot of wood

    Science.gov (United States)

    Melissa R. Suzuki; Christopher G. Hunt; Carl J. Houtman; Zachary D. Dalebroux; Kenneth E. Hammel

    2006-01-01

    The fungi that cause brown rot of wood initiate lignocellulose breakdown with an extracellular Fenton system in which Fe2+ and H2O2 react to produce hydroxyl radicals (•OH), which then oxidize and cleave the wood holocellulose. One such fungus, Gloeophyllum trabeum, drives Fenton chemistry on defined media by reducing Fe3+ and O2 with two extracellular hydroquinones,...

  4. Mucor rot - An emerging postharvest disease of mandarin fruit caused by Mucor piriformis and other Mucor spp. in California

    Science.gov (United States)

    In recent years, an emerging, undescribed postharvest fruit rot disease was observed on mandarin fruit after extended storage in California. We collected decayed mandarin fruit from three citrus packinghouses in the Central Valley of California in 2015 and identified this disease as Mucor rot caused...

  5. Fungi associated with base rot disease of aloe vera ( Aloe ...

    African Journals Online (AJOL)

    Fungi associated with base rot disease of Aloe vera (syn. Aloe barbadensis) were investigated in Niger Delta Area of Nigeria. Fungi and their percentage frequency were Aspergillus verocosa 28.03%, Fusarium oxysporium 24.24%, Plectosphaerella cucumerina 16.67%, Mammeria ehinobotryoides 15.91% and Torula ...

  6. Soybean Resistance to White Mold: Evaluation of Soybean Germplasm Under Different Conditions and Validation of QTL

    Science.gov (United States)

    Kandel, Ramkrishna; Chen, Charles Y.; Grau, Craig R.; Dorrance, Ann E.; Liu, Jean Q.; Wang, Yang; Wang, Dechun

    2018-01-01

    Soybean (Glycine max L. Merr.) white mold (SWM), caused by Sclerotinia sclerotiorum (Lib) de Barry), is a devastating fungal disease in the Upper Midwest of the United States and southern Canada. Various methods exist to evaluate for SWM resistance and many quantitative trait loci (QTL) with minor effect governing SWM resistance have been identified in prior studies. This study aimed to predict field resistance to SWM using low-cost and efficient greenhouse inoculation methods and to confirm the QTL reported in previous studies. Three related but independent studies were conducted in the field, greenhouse, and laboratory to evaluate for SWM resistance. The first study evaluated 66 soybean plant introductions (PIs) with known field resistance to SWM using the greenhouse drop-mycelium inoculation method. These 66 PIs were significantly (P greenhouse inoculation methods with disease severity index (DSI) in field evaluations. Moderate correlation (r) between PM under drop-mycelium method and DSI in field trials (r = 0.65, p greenhouse inoculation methods and DSI across field trials. These findings suggest that greenhouse inoculation methods could predict the field resistance to SWM. The third study attempted to validate 33 QTL reported in prior studies using seven populations that comprised a total of 392 F4 : 6 lines derived from crosses involving a partially resistant cultivar “Skylla,” five partially resistant PIs, and a known susceptible cultivar “E00290.” The estimates of broad-sense heritability (h2) ranged from 0.39 to 0.66 in the populations. Of the seven populations, four had h2 estimates that were significantly different from zero (p < 0.05). Single marker analysis across populations and inoculation methods identified 11 significant SSRs (p < 0.05) corresponding to 10 QTL identified by prior studies. Thus, these five new PIs could be used as new sources of resistant alleles to develop SWM resistant commercial cultivars. PMID:29731761

  7. The Use of Antioxidants to Control Root Rot and Wilt Diseases of Pepper

    Directory of Open Access Journals (Sweden)

    Montaser Fawzy ABDEL-MONAIM

    2010-06-01

    Full Text Available Ten isolates of Fusarium spp were isolated from pepper plants collected from different locations in New Valley Governorate, Egypt. Fusarium solani isolate FP2 and F. oxysporum isolate FP4 were highly pathogenic isolates but the other isolates moderate or less pathogenic to pepper plants (cv. Anaheim-M. The four antioxidant compounds (coumaric acid, citric acid, propylgalate and salicylic acid each at 100 and 200 ppm were evaluated for their in vitro and in vivo agonist to Fusarium pathogenic isolates caused root rot and wilt diseases in pepper plants. All tested antioxidant compounds reduced damping-off, root rot/wilt and area under root rot/wilt progress curve when used as seed soaking, seedling soaking, and soil drench especially at 200 ppm under greenhouse and field conditions compared with untreated plants. All chemicals increased fresh and dry weight of seedling grown in soil drenching or seed treatment with any antioxidants. At the same time, all tested chemicals significantly increase plant growth parameters i.e plant length, plant branching, and total yield per plant in case of seedling soaking or soil drench. In general, propylgalate at 200 ppm was more efficient in reducing infection with damping-off, root rot and wilt diseases as well as increasing the seedling fresh weight, dry weight, plant length, plant branching, number of pod plant-1 and pod yield plant-1. On the other hand, all tested antioxidants had less or no effect on mycelial dry weight and mycelial leaner growth. On the contrary, all chemicals much reduced spore formation in both Fusarium species at 100 or 200 ppm and the inhibitory effect of antioxidants increased with increasing their concentrations.

  8. Detection of a Cis [corrected] eQTL controlling BCMO1 gene expression leads to the identification of a QTG for chicken breast meat color.

    Science.gov (United States)

    Le Bihan-Duval, Elisabeth; Nadaf, Javad; Berri, Cécile; Pitel, Frédérique; Graulet, Benoît; Godet, Estelle; Leroux, Sophie Y; Demeure, Olivier; Lagarrigue, Sandrine; Duby, Cécile; Cogburn, Larry A; Beaumont, Catherine M; Duclos, Michel J

    2011-01-01

    Classical quantitative trait loci (QTL) analysis and gene expression QTL (eQTL) were combined to identify the causal gene (or QTG) underlying a highly significant QTL controlling the variation of breast meat color in a F2 cross between divergent high-growth (HG) and low-growth (LG) chicken lines. Within this meat quality QTL, BCMO1 (Accession number GenBank: AJ271386), encoding the β-carotene 15, 15'-monooxygenase, a key enzyme in the conversion of β-carotene into colorless retinal, was a good functional candidate. Analysis of the abundance of BCMO1 mRNA in breast muscle of the HG x LG F2 population allowed for the identification of a strong cis eQTL. Moreover, reevaluation of the color QTL taking BCMO1 mRNA levels as a covariate indicated that BCMO1 mRNA levels entirely explained the variations in meat color. Two fully-linked single nucleotide polymorphisms (SNP) located within the proximal promoter of BCMO1 gene were identified. Haplotype substitution resulted in a marked difference in BCMO1 promoter activity in vitro. The association study in the F2 population revealed a three-fold difference in BCMO1 expression leading to a difference of 1 standard deviation in yellow color between the homozygous birds at this haplotype. This difference in meat yellow color was fully consistent with the difference in carotenoid content (i.e. lutein and zeaxanthin) evidenced between the two alternative haplotypes. A significant association between the haplotype, the level of BCMO1 expression and the yellow color of the meat was also recovered in an unrelated commercial broiler population. The mutation could be of economic importance for poultry production by making possible a gene-assisted selection for color, a determining aspect of meat quality. Moreover, this natural genetic diversity constitutes a new model for the study of β-carotene metabolism which may act upon diverse biological processes as precursor of the vitamin A.

  9. Detection of a Cis [corrected] eQTL controlling BCMO1 gene expression leads to the identification of a QTG for chicken breast meat color.

    Directory of Open Access Journals (Sweden)

    Elisabeth Le Bihan-Duval

    Full Text Available Classical quantitative trait loci (QTL analysis and gene expression QTL (eQTL were combined to identify the causal gene (or QTG underlying a highly significant QTL controlling the variation of breast meat color in a F2 cross between divergent high-growth (HG and low-growth (LG chicken lines. Within this meat quality QTL, BCMO1 (Accession number GenBank: AJ271386, encoding the β-carotene 15, 15'-monooxygenase, a key enzyme in the conversion of β-carotene into colorless retinal, was a good functional candidate. Analysis of the abundance of BCMO1 mRNA in breast muscle of the HG x LG F2 population allowed for the identification of a strong cis eQTL. Moreover, reevaluation of the color QTL taking BCMO1 mRNA levels as a covariate indicated that BCMO1 mRNA levels entirely explained the variations in meat color. Two fully-linked single nucleotide polymorphisms (SNP located within the proximal promoter of BCMO1 gene were identified. Haplotype substitution resulted in a marked difference in BCMO1 promoter activity in vitro. The association study in the F2 population revealed a three-fold difference in BCMO1 expression leading to a difference of 1 standard deviation in yellow color between the homozygous birds at this haplotype. This difference in meat yellow color was fully consistent with the difference in carotenoid content (i.e. lutein and zeaxanthin evidenced between the two alternative haplotypes. A significant association between the haplotype, the level of BCMO1 expression and the yellow color of the meat was also recovered in an unrelated commercial broiler population. The mutation could be of economic importance for poultry production by making possible a gene-assisted selection for color, a determining aspect of meat quality. Moreover, this natural genetic diversity constitutes a new model for the study of β-carotene metabolism which may act upon diverse biological processes as precursor of the vitamin A.

  10. Effects of bunch rot (Botrytis cinerea) and powdery mildew (Erysiphe necator) fungal diseases on wine aroma

    Science.gov (United States)

    Lopez Pinar, Angela; Rauhut, Doris; Ruehl, Ernst; Buettner, Andrea

    2017-03-01

    This study aimed to characterize the effects of bunch rot and powdery mildew on the primary quality parameter of wine, the aroma. The influence of these fungal diseases was studied by comparative Aroma Extract Dilution Analyses (AEDA) and sensory tests. The effect of bunch rot was investigated on three grape varieties, namely White Riesling, Red Riesling and Gewürztraminer and that of powdery mildew on the hybrid Gm 8622-3; thereby, samples were selected that showed pronounced cases of infection to elaborate potential currently unknown effects. Both infections revealed aromatic differences induced by these fungi. The sensory changes were not associated with one specific compound only, but were due to quantitative variations of diverse substances. Bunch rot predominantly induced an increase in the intensities of peach-like/fruity, floral and liquor-like/toasty aroma notes. These effects were found to be related to variations in aroma substance composition as monitored via AEDA, mainly an increase in the FD factors of lactones and a general moderate increase of esters and alcohols. On the other hand, powdery mildew decreased the vanilla-like character of the wine while the remaining sensory attributes were rather unaffected. Correspondingly, FD factors of the main aroma constituents were either the same or only slightly modified by this disease. Moreover, bunch rot influenced the aroma profiles of the three varieties studied to a different degree. In hedonic evaluation, bunch rot-affected samples were rated as being more pleasant in comparison to their healthy controls in all three varieties while the powdery mildew-affected sample was rated as being less pleasant than its healthy control.

  11. Teamwork: improved eQTL mapping using combinations of machine learning methods.

    Directory of Open Access Journals (Sweden)

    Marit Ackermann

    Full Text Available Expression quantitative trait loci (eQTL mapping is a widely used technique to uncover regulatory relationships between genes. A range of methodologies have been developed to map links between expression traits and genotypes. The DREAM (Dialogue on Reverse Engineering Assessments and Methods initiative is a community project to objectively assess the relative performance of different computational approaches for solving specific systems biology problems. The goal of one of the DREAM5 challenges was to reverse-engineer genetic interaction networks from synthetic genetic variation and gene expression data, which simulates the problem of eQTL mapping. In this framework, we proposed an approach whose originality resides in the use of a combination of existing machine learning algorithms (committee. Although it was not the best performer, this method was by far the most precise on average. After the competition, we continued in this direction by evaluating other committees using the DREAM5 data and developed a method that relies on Random Forests and LASSO. It achieved a much higher average precision than the DREAM best performer at the cost of slightly lower average sensitivity.

  12. Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.).

    Science.gov (United States)

    Pandit, Awadhesh; Rai, Vandna; Bal, Subhashis; Sinha, Shikha; Kumar, Vinod; Chauhan, Mahesh; Gautam, Raj K; Singh, Rakesh; Sharma, Prakash C; Singh, Ashok K; Gaikwad, Kishor; Sharma, Tilak R; Mohapatra, Trilochan; Singh, Nagendra K

    2010-08-01

    Identification of genes for quantitative traits is difficult using any single approach due to complex inheritance of the traits and limited resolving power of the individual techniques. Here a combination of genetic mapping and bulked transcriptome profiling was used to narrow down the number of differentially expressed salt-responsive genes in rice in order to identify functional polymorphism of genes underlying the quantitative trait loci (QTL). A population of recombinant inbred lines (RILs) derived from cross between salt-tolerant variety CSR 27 and salt-sensitive variety MI 48 was used to map QTL for salt ion concentrations in different tissues and salt stress susceptibility index (SSI) for spikelet fertility, grain weight, and grain yield. Eight significant QTL intervals were mapped on chromosomes 1, 8, and 12 for the salt ion concentrations and a QTL controlling SSI for spikelet fertility was co-located in one of these intervals on chromosome 8. However, there were total 2,681 genes in these QTL intervals, making it difficult to pinpoint the genes responsible for the functional differences for the traits. Similarly, transcriptome profiling of the seedlings of tolerant and sensitive parents grown under control and salt-stress conditions showed 798 and 2,407 differentially expressed gene probes, respectively. By analyzing pools of RNA extracted from ten each of extremely tolerant and extremely sensitive RILs to normalize the background noise, the number of differentially expressed genes under salt stress was drastically reduced to 30 only. Two of these genes, an integral transmembrane protein DUF6 and a cation chloride cotransporter, were not only co-located in the QTL intervals but also showed the expected distortion of allele frequencies in the extreme tolerant and sensitive RILs, and therefore are suitable for future validation studies and development of functional markers for salt tolerance in rice to facilitate marker-assisted breeding.

  13. Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values

    NARCIS (Netherlands)

    Calus, M.P.L.; Meuwissen, T.H.E.; Windig, J.J.; Knol, E.F.; Schrooten, C.; Vereijken, A.L.J.; Veerkamp, R.F.

    2009-01-01

    The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD) probabilities between haplotypes, various haplotype definitions were tested i.e.

  14. Brown rot fungal early stage decay mechanism as a biological pretreatment for softwood biomass in biofuel production

    Energy Technology Data Exchange (ETDEWEB)

    Ray, Michael J.; Leak, David J.; Spanu, Pietro D.; Murphy, Richard J. [Division of Biology, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ (United Kingdom); Porter Alliance, Imperial College London, London SW7 2AZ (United Kingdom)

    2010-08-15

    A current barrier to the large-scale production of lignocellulosic biofuels is the cost associated with the energy and chemical inputs required for feedstock pretreatment and hydrolysis. The use of controlled partial biological degradation to replace elements of the current pretreatment technologies would offer tangible energy and cost benefits to the whole biofuel process. It has been known for some time from studies of wood decay that, in the early stages of growth in wood, brown rot fungi utilise a mechanism that causes rapid and extensive depolymerisation of the carbohydrate polymers of the wood cell wall. The brown rot hyphae act as delivery vectors to the plant cell wall for what is thought to be a combination of a localised acid pretreatment and a hydroxyl radical based depolymerisation of the cell wall carbohydrate polymers. It is this quality that we have exploited in the present work to enhance the saccharification potential of softwood forest residues for biofuel production. Here we show that after restricted exposure of pine sapwood to brown rot fungi, glucose yields following enzymatic saccharification are significantly increased. Our results demonstrate the potential of using brown rot fungi as a biological pretreatment for biofuel production. (author)

  15. PATHOLOGICAL AND MOLECULAR GENETIC STUDIES ON SOME SOYBEAN MUTANTS INDUCED BY GAMMA RAYS IN RELATION TO CHARCOAL ROT DISEASE

    International Nuclear Information System (INIS)

    ASHRY, N.A.; EL-DEMERDASH, H.M.; ABD EL-RAHMAN, S.S.

    2008-01-01

    The Egyptian soybean cultivar Giza-22 was used to induce resistant mutants for charcoal rot disease using gamma rays. Sixteen mutants and their parental cultivar were evaluated in M3 generation for their agronomic traits and for resistance to charcoal rot disease. Four mutants showed superiority in their agronomic traits as compared with their parental cultivar. Three mutants were significantly resistant to the disease than their parental cultivar (Giza-22). These three resistant mutants showed non-significant improvement in their agronomic traits as compared with Giza-22 cultivar. DNA extractions from the three resistant mutants and their parent were used to test the differences on the molecular level. Seven random amplified polymorphic DNA (RAPD) primers were used to detect RAPD markers related to charcoal rot resistance in soybean, and to differentiate these mutants. Six RAPD-primers showed molecular markers associated with resistance to charcoal rot in soybean, where five RAPD-primers could differentiate each of the three mutants from each other and from their parental cultivar

  16. Effect of essential oil of Satureja hortensis against Bacillus pumilus, which cause of soft rot on some plants

    Science.gov (United States)

    Dadaşoǧlu, Fatih

    2017-04-01

    In this study, it is aimmed to be determined the antimicrobial effects of the essential oil in vitro conditions, extracted from wild forms of plant which is known as Satureja hortensis around the world and grows naturally at Erzurum province of Turkey against Bacillus pumilus isolates, which are the agent of Soft Rot for some fruits and vegetables. For this purpose, 18 isolates of B. pumilus which have been determined as the agent of Soft Rot in previous studies performed in plants such as potatos, onions, strawberries, melons and watermelons. As the positive control, Streptomycin antibiotics sold as ready produce were used. According to the obtained results, the essential oil have the antibactericidal effect of 19-29 mm against 18 isolates of B. pumilus. It has been observed that the antibiotics used as the positive control has the antibacterial effect of 16-22 mm. In conclusion, the essential oil has the lethal effect against 18 B. pumilus isolates which are agents of Soft Rot. It is assesed that these essential oil extracted from Satureja hortensis can be used against these Soft Rot pathogens.

  17. Biochemical response and host-pathogen relation of stalk rot fungi ...

    African Journals Online (AJOL)

    Stalk rot is a destructive disease in maize caused by Fusarium and Macrophomina species. A study was carried out to understand the mode of infection, host biochemical response and comparison of inoculation techniques in Fusarium verticillioides and Macrophomina phaseolina in maize. In seed inoculation experiment, ...

  18. Cis-eQTL analysis and functional validation of candidate susceptibility genes for high-grade serous ovarian cancer.

    Science.gov (United States)

    Lawrenson, Kate; Li, Qiyuan; Kar, Siddhartha; Seo, Ji-Heui; Tyrer, Jonathan; Spindler, Tassja J; Lee, Janet; Chen, Yibu; Karst, Alison; Drapkin, Ronny; Aben, Katja K H; Anton-Culver, Hoda; Antonenkova, Natalia; Baker, Helen; Bandera, Elisa V; Bean, Yukie; Beckmann, Matthias W; Berchuck, Andrew; Bisogna, Maria; Bjorge, Line; Bogdanova, Natalia; Brinton, Louise A; Brooks-Wilson, Angela; Bruinsma, Fiona; Butzow, Ralf; Campbell, Ian G; Carty, Karen; Chang-Claude, Jenny; Chenevix-Trench, Georgia; Chen, Anne; Chen, Zhihua; Cook, Linda S; Cramer, Daniel W; Cunningham, Julie M; Cybulski, Cezary; Dansonka-Mieszkowska, Agnieszka; Dennis, Joe; Dicks, Ed; Doherty, Jennifer A; Dörk, Thilo; du Bois, Andreas; Dürst, Matthias; Eccles, Diana; Easton, Douglas T; Edwards, Robert P; Eilber, Ursula; Ekici, Arif B; Fasching, Peter A; Fridley, Brooke L; Gao, Yu-Tang; Gentry-Maharaj, Aleksandra; Giles, Graham G; Glasspool, Rosalind; Goode, Ellen L; Goodman, Marc T; Grownwald, Jacek; Harrington, Patricia; Harter, Philipp; Hasmad, Hanis Nazihah; Hein, Alexander; Heitz, Florian; Hildebrandt, Michelle A T; Hillemanns, Peter; Hogdall, Estrid; Hogdall, Claus; Hosono, Satoyo; Iversen, Edwin S; Jakubowska, Anna; James, Paul; Jensen, Allan; Ji, Bu-Tian; Karlan, Beth Y; Kruger Kjaer, Susanne; Kelemen, Linda E; Kellar, Melissa; Kelley, Joseph L; Kiemeney, Lambertus A; Krakstad, Camilla; Kupryjanczyk, Jolanta; Lambrechts, Diether; Lambrechts, Sandrina; Le, Nhu D; Lee, Alice W; Lele, Shashi; Leminen, Arto; Lester, Jenny; Levine, Douglas A; Liang, Dong; Lissowska, Jolanta; Lu, Karen; Lubinski, Jan; Lundvall, Lene; Massuger, Leon F A G; Matsuo, Keitaro; McGuire, Valerie; McLaughlin, John R; Nevanlinna, Heli; McNeish, Ian; Menon, Usha; Modugno, Francesmary; Moysich, Kirsten B; Narod, Steven A; Nedergaard, Lotte; Ness, Roberta B; Azmi, Mat Adenan Noor; Odunsi, Kunle; Olson, Sara H; Orlow, Irene; Orsulic, Sandra; Weber, Rachel Palmieri; Pearce, Celeste L; Pejovic, Tanja; Pelttari, Liisa M; Permuth-Wey, Jennifer; Phelan, Catherine M; Pike, Malcolm C; Poole, Elizabeth M; Ramus, Susan J; Risch, Harvey A; Rosen, Barry; Rossing, Mary Anne; Rothstein, Joseph H; Rudolph, Anja; Runnebaum, Ingo B; Rzepecka, Iwona K; Salvesen, Helga B; Schildkraut, Joellen M; Schwaab, Ira; Sellers, Thomas A; Shu, Xiao-Ou; Shvetsov, Yurii B; Siddiqui, Nadeem; Sieh, Weiva; Song, Honglin; Southey, Melissa C; Sucheston, Lara; Tangen, Ingvild L; Teo, Soo-Hwang; Terry, Kathryn L; Thompson, Pamela J; Timorek, Agnieszka; Tsai, Ya-Yu; Tworoger, Shelley S; van Altena, Anne M; Van Nieuwenhuysen, Els; Vergote, Ignace; Vierkant, Robert A; Wang-Gohrke, Shan; Walsh, Christine; Wentzensen, Nicolas; Whittemore, Alice S; Wicklund, Kristine G; Wilkens, Lynne R; Woo, Yin-Ling; Wu, Xifeng; Wu, Anna H; Yang, Hannah; Zheng, Wei; Ziogas, Argyrios; Monteiro, Alvaro; Pharoah, Paul D; Gayther, Simon A; Freedman, Matthew L

    2015-09-22

    Genome-wide association studies have reported 11 regions conferring risk of high-grade serous epithelial ovarian cancer (HGSOC). Expression quantitative trait locus (eQTL) analyses can identify candidate susceptibility genes at risk loci. Here we evaluate cis-eQTL associations at 47 regions associated with HGSOC risk (P≤10(-5)). For three cis-eQTL associations (P<1.4 × 10(-3), FDR<0.05) at 1p36 (CDC42), 1p34 (CDCA8) and 2q31 (HOXD9), we evaluate the functional role of each candidate by perturbing expression of each gene in HGSOC precursor cells. Overexpression of HOXD9 increases anchorage-independent growth, shortens population-doubling time and reduces contact inhibition. Chromosome conformation capture identifies an interaction between rs2857532 and the HOXD9 promoter, suggesting this SNP is a leading causal variant. Transcriptomic profiling after HOXD9 overexpression reveals enrichment of HGSOC risk variants within HOXD9 target genes (P=6 × 10(-10) for risk variants (P<10(-4)) within 10 kb of a HOXD9 target gene in ovarian cells), suggesting a broader role for this network in genetic susceptibility to HGSOC.

  19. A major and stable QTL associated with seed weight in soybean across multiple environments and genetic backgrounds.

    Science.gov (United States)

    Kato, Shin; Sayama, Takashi; Fujii, Kenichiro; Yumoto, Setsuzo; Kono, Yuhi; Hwang, Tae-Young; Kikuchi, Akio; Takada, Yoshitake; Tanaka, Yu; Shiraiwa, Tatsuhiko; Ishimoto, Masao

    2014-06-01

    We detected a QTL for single seed weight in soybean that was stable across multiple environments and genetic backgrounds with the use of two recombinant inbred line populations. Single seed weight (SSW) in soybean is a key determinant of both seed yield and the quality of soy food products, and it exhibits wide variation. SSW is under genetic control, but the molecular mechanisms of such control remain unclear. We have now investigated quantitative trait loci (QTLs) for SSW in soybean and have identified such a QTL that is stable across multiple environments and genetic backgrounds. Two populations of 225 and 250 recombinant inbred lines were developed from crosses between Japanese and US cultivars of soybean that differ in SSW by a factor of ~2, and these populations were grown in at least three different environments. A whole-genome panel comprising 304 simple sequence repeat (SSR) loci was applied to mapping in each population. We identified 15 significant QTLs for SSW dispersed among 11 chromosomes in the two populations. One QTL located between Sat_284 and Sat_292 on chromosome 17 was detected (3.6 soybean.

  20. A genome-wide association study to detect QTL for commercially important traits in Swiss Large White boars.

    Directory of Open Access Journals (Sweden)

    Doreen Becker

    Full Text Available The improvement of meat quality and production traits has high priority in the pork industry. Many of these traits show a low to moderate heritability and are difficult and expensive to measure. Their improvement by targeted breeding programs is challenging and requires knowledge of the genetic and molecular background. For this study we genotyped 192 artificial insemination boars of a commercial line derived from the Swiss Large White breed using the PorcineSNP60 BeadChip with 62,163 evenly spaced SNPs across the pig genome. We obtained 26 estimated breeding values (EBVs for various traits including exterior, meat quality, reproduction, and production. The subsequent genome-wide association analysis allowed us to identify four QTL with suggestive significance for three of these traits (p-values ranging from 4.99×10⁻⁶ to 2.73×10⁻⁵. Single QTL for the EBVs pH one hour post mortem (pH1 and carcass length were on pig chromosome (SSC 14 and SSC 2, respectively. Two QTL for the EBV rear view hind legs were on SSC 10 and SSC 16.

  1. Inflorescence rot disease of date palm caused by Fusarium ...

    African Journals Online (AJOL)

    Date palm is one of the important income sources for many farmers in different parts of several countries, including Iraq, Iran, Saudi Arabia, North Africa etc. Inflorescence rot is a serious disease of date palm which limits its yield. The identification of the causal organism is a key step to tackling this disease, and such studies ...

  2. Diagnostic of dry rot in living trees

    International Nuclear Information System (INIS)

    Schaetzler, H.P.

    1978-01-01

    The γ-desorption method has been used in the early diagnosis of dry rot in trees. The attenuation of a 60 keV γ-beam ( 241 Am) has been measured on eleven healthy spruce disks. It is seen that early diagnostic of rotten trees is limited by natural density variation of the wood itself, but for a 95% confidence level that the wood is diseased, a tree must have an average of less than 0.59 g./cm 3 . (Auth/C.F.)

  3. Biological Control Of The Egyptian Brown Rot In Potato (Solanum Tuberosum L.)

    International Nuclear Information System (INIS)

    Salem, E.A.; Askora, A. M.

    2012-01-01

    Pseudomonas fluorescence, P. aeruginosa, Bacillus subtillus and streptomyces spp. Were used in control of Ralstonia solanacearum, the casual agent of brown rot in potato. In vitro, antagonistic activities showed that streptomyces spp. was the most antagonistic followed by P. fluorescence, Bacillus subtilus and P. aeruginosa respectively. Also, in vivo, biological control of R. solanacearum showed that Streptomyces spp. was found to reduce the percentage of brown rot infection to 5% followed by P. fluorescence, Bacillus subtilus and P. aeruginosa reducing the percentage of infection to 15 , 25 and 40%, respectively. Also, the disease severity when using Streptomyces spp. and P. fluorescence was reduced from 5 to 1 and reduced from 5 to 2 when using Bacillus subtilus and P. aeruginosa.

  4. Effect of combinations of gamma irradiation, hot water, Sodium chloride, and Acetic acid treatments on potato-dry rot

    International Nuclear Information System (INIS)

    El-Zayat, M.M.; Farahat, A.A.; Saad, N.H.; Shaarawy, N.S.M.

    1992-01-01

    Gamma irradiation increased the severity of dry rot in potato tubers when they were inoculated with any of 4 species of Fusarium, previously isolated either from irradiated or unirradiated tubers. Treating either irradiated or unirradiated tubers with warm water or sodium chloride solutions following inoculation with F. roseum also increased the severity of dry rot to some extent

  5. 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.

  6. The Induction of Noble Rot (Botrytis cinerea Infection during Postharvest Withering Changes the Metabolome of Grapevine Berries (Vitis vinifera L., cv. Garganega

    Directory of Open Access Journals (Sweden)

    Stefano Negri

    2017-06-01

    Full Text Available The natural or induced development of noble rot caused by the fungus Botrytis cinerea during the late stages of grapevine (Vitis vinifera L. berry ripening is used in some traditional viticulture areas to produce high-quality wines such as Sauternes and Tokaji. In this research, we wanted to verify if by changing the environmental conditions during post-harvest withering we could induce the noble rot development on harvested berries in order to positively change the wine produced from withered Garganega berries. Therefore, we exposed the berries to postharvest withering under normal or artificially humid conditions, the latter to induce noble rot. The presence of noble rot symptoms was associated with the development of B. cinerea in the berries maintained under humid conditions. The composition of infected and non-infected berries was investigated by untargeted metabolomics using liquid chromatography/mass spectrometry. We also explored the effects of the two withering methods on the abundance of volatile organic compounds in wine by yeast-inoculated micro-fermentation followed by targeted gas chromatography/mass spectrometry. These experiments revealed significant metabolic differences between berries withered under normal and humid conditions, indicating that noble rot affects berry metabolism and composition. As well as well-known botrytization markers, we detected two novel lipids that have not been observed before in berries infected with noble rot. Unraveling the specific metabolic profile of berries infected with noble rot may help to determine the compounds responsible for the organoleptic quality traits of botrytized Garganega wines.

  7. [Studies of marker screening efficiency and corresponding influencing factors in QTL composite interval mapping].

    Science.gov (United States)

    Gao, Yong-Ming; Wan, Ping

    2002-06-01

    Screening markers efficiently is the foundation of mapping QTLs by composite interval mapping. Main and interaction markers distinguished, besides using background control for genetic variation, could also be used to construct intervals of two-way searching for mapping QTLs with epistasis, which can save a lot of calculation time. Therefore, the efficiency of marker screening would affect power and precision of QTL mapping. A doubled haploid population with 200 individuals and 5 chromosomes was constructed, with 50 markers evenly distributed at 10 cM space. Among a total of 6 QTLs, one was placed on chromosome I, two linked on chromosome II, and the other three linked on chromosome IV. QTL setting included additive effects and epistatic effects of additive x additive, the corresponding QTL interaction effects were set if data were collected under multiple environments. The heritability was assumed to be 0.5 if no special declaration. The power of marker screening by stepwise regression, forward regression, and three methods for random effect prediction, e.g. best linear unbiased prediction (BLUP), linear unbiased prediction (LUP) and adjusted unbiased prediction (AUP), was studied and compared through 100 Monte Carlo simulations. The results indicated that the marker screening power by stepwise regression at 0.1, 0.05 and 0.01 significant level changed from 2% to 68%, the power changed from 2% to 72% by forward regression. The larger the QTL effects, the higher the marker screening power. While the power of marker screening by three random effect prediction was very low, the maximum was only 13%. That suggested that regression methods were much better than those by using the approaches of random effect prediction to identify efficient markers flanking QTLs, and forward selection method was more simple and efficient. The results of simulation study on heritability showed that heightening of both general heritability and interaction heritability of genotype x

  8. Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values

    Directory of Open Access Journals (Sweden)

    Schrooten Chris

    2009-01-01

    Full Text Available Abstract The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD probabilities between haplotypes, various haplotype definitions were tested i.e. including 2, 6, 12 or 20 marker alleles and clustering base haplotypes related with an IBD probability of > 0.55, 0.75 or 0.95. Simulated data contained 1100 animals with known genotypes and phenotypes and 1000 animals with known genotypes and unknown phenotypes. Genomes comprising 3 Morgan were simulated and contained 74 polymorphic QTL and 383 polymorphic SNP markers with an average r2 value of 0.14 between adjacent markers. The total number of haplotypes decreased up to 50% when the window size was increased from two to 20 markers and decreased by at least 50% when haplotypes related with an IBD probability of > 0.55 instead of > 0.95 were clustered. An intermediate window size led to more precise QTL mapping. Window size and clustering had a limited effect on the accuracy of predicted total breeding values, ranging from 0.79 to 0.81. Our conclusion is that different optimal window sizes should be used in QTL-mapping versus genome-wide breeding value prediction.

  9. Download - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...t_db_link_en.zip (36.3 KB) - 6 Genome analysis methods pgdbj_dna_marker_linkage_map_genome_analysis_methods_... of This Database Site Policy | Contact Us Download - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  10. Lignin-modifying enzymes of the white rot basidiomycete Ganoderma lucidum

    Energy Technology Data Exchange (ETDEWEB)

    D/Souza, T.M.; Merritt, C.S.; Reddy, C.A.

    1999-12-01

    Ganoderma lucidum, a white rot basidiomycete widely distributed worldwide, was studied for the production of the lignin-modifying enzymes laccase, manganese-dependent peroxidase (MnP), and lignin peroxidase (LiP). Laccase levels observed in high-nitrogen shaken cultures were much greater than those seen in low-nitrogen, malt extract, or wool-grown cultures and those reported for most other white rot fungi to date. Laccase production was readily seen in cultures grown with pine or poplar as the sole carbon and energy source. Cultures containing both pine and poplar showed 5- to 10-fold-higher levels of laccase than cultures containing pine or poplar alone. Since syringyl units are structural components important in poplar lignin and other hardwoods but much less so in pine lignin and other softwoods, pine cultures were supplemented with syringic acid, and this resulted in laccase levels comparable to those seen in pine-plus-poplar cultures. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of concentrated extracellular culture fluid from HM cultures showed two laccase activity bands, where as isoelectric focusing revealed five major laccase activity bands with estimated pIs of 3.0, 4.25, 4.5, and 5.1. Low levels of MnP activity were detected in poplar-grown cultures but not in cultures grown with pine, with pine plus syringic acid, or in HN medium. No LiP activity was seen in any of the media tested; however, probing the genomic DNA with the LiP cDNA (CLG4) from the white rot fungus Phanerochaete chrysosporium showed distinct hybridization bands suggesting the presence of lip-like sequences in G. lucidum.

  11. Genetic control of soybean seed oil: II. QTL and genes that increase oil concentration without decreasing protein or with increased seed yield.

    Science.gov (United States)

    Eskandari, Mehrzad; Cober, Elroy R; Rajcan, Istvan

    2013-06-01

    Soybean [Glycine max (L.) Merrill] seed oil is the primary global source of edible oil and a major renewable and sustainable feedstock for biodiesel production. Therefore, increasing the relative oil concentration in soybean is desirable; however, that goal is complex due to the quantitative nature of the oil concentration trait and possible effects on major agronomic traits such as seed yield or protein concentration. The objectives of the present study were to study the relationship between seed oil concentration and important agronomic and seed quality traits, including seed yield, 100-seed weight, protein concentration, plant height, and days to maturity, and to identify oil quantitative trait loci (QTL) that are co-localized with the traits evaluated. A population of 203 F4:6 recombinant inbred lines, derived from a cross between moderately high oil soybean genotypes OAC Wallace and OAC Glencoe, was developed and grown across multiple environments in Ontario, Canada, in 2009 and 2010. Among the 11 QTL associated with seed oil concentration in the population, which were detected using either single-factor ANOVA or multiple QTL mapping methods, the number of QTL that were co-localized with other important traits QTL were six for protein concentration, four for seed yield, two for 100-seed weight, one for days to maturity, and one for plant height. The oil-beneficial allele of the QTL tagged by marker Sat_020 was positively associated with seed protein concentration. The oil favorable alleles of markers Satt001 and GmDGAT2B were positively correlated with seed yield. In addition, significant two-way epistatic interactions, where one of the interacting markers was solely associated with seed oil concentration, were identified for the selected traits in this study. The number of significant epistatic interactions was seven for yield, four for days to maturity, two for 100-seed weight, one for protein concentration, and one for plant height. The identified molecular

  12. Control of Fusarium verticillioides, cause of ear rot of maize, by Pseudomonas fluorescens.

    Science.gov (United States)

    Nayaka, Siddaiah Chandra; Shankar, Arakere C Udaya; Reddy, Munagala S; Niranjana, Siddapura R; Prakash, Harishchandra S; Shetty, Hunthrike S; Mortensen, Carmen N

    2009-07-01

    Maize is one of the staple food crops grown in India. Fusarium verticillioides (Sacc.) Nirenberg is the most important fungal pathogen of maize, associated with diseases such as ear rot and kernel rot. Apart from the disease, it is capable of producing fumonisins, which have elicited considerable attention over the past decade owing to their association with animal disease syndromes. Hence, the present study was conducted to evaluate ecofriendly approaches by using a maize rhizosphere isolate of Pseudomonas fluorescens (Trev.) Mig. and its formulation to control ear rot disease and fumonisin accumulation, and also to study the capacity to promote growth and yield of maize. In vitro assays were conducted to test the efficacy of P. fluorescens as a seed treatment on seed germination, seedling vigour and also the incidence of F. verticillioides in different maize cultivars. The field trials included both seed treatment and foliar spray. For all the experiments, P. fluorescens was formulated using corn starch, wheat bran and talc powder. In each case there were three different treatments of P. fluorescens, a non-treated control and chemical control. Pure culture and the formulations, in comparison with the control, increased plant growth and vigour as measured by seed germination, seedling vigour, plant height, 1000 seed weight and yield. P. fluorescens pure culture used as seed treatment and as spray treatment enhanced the growth parameters and reduced the incidence of F. verticillioides and the level of fumonisins to a maximum extent compared with the other treatments. The study demonstrates the potential role of P. fluorescens and its formulations in ear rot disease management. The biocontrol potential of this isolate is more suited for fumonisin reduction in maize kernels intended for human and animal feed. (c) 2009 Society of Chemical Industry.

  13. Identification of QTL conferring resistance to stripe rust (Puccinia striiformis f. sp. hordei) and leaf rust (Puccinia hordei) in barley using nested association mapping (NAM)

    Science.gov (United States)

    Vatter, Thomas; Maurer, Andreas; Perovic, Dragan; Kopahnke, Doris; Pillen, Klaus

    2018-01-01

    The biotrophic rust fungi Puccinia hordei and Puccinia striiformis are important barley pathogens with the potential to cause high yield losses through an epidemic spread. The identification of QTL conferring resistance to these pathogens is the basis for targeted breeding approaches aiming to improve stripe rust and leaf rust resistance of modern cultivars. Exploiting the allelic richness of wild barley accessions proved to be a valuable tool to broaden the genetic base of resistance of barley cultivars. In this study, SNP-based nested association mapping (NAM) was performed to map stripe rust and leaf rust resistance QTL in the barley NAM population HEB-25, comprising 1,420 lines derived from BC1S3 generation. By scoring the percentage of infected leaf area, followed by calculation of the area under the disease progress curve and the average ordinate during a two-year field trial, a large variability of resistance across and within HEB-25 families was observed. NAM based on 5,715 informative SNPs resulted in the identification of twelve and eleven robust QTL for resistance against stripe rust and leaf rust, respectively. Out of these, eight QTL for stripe rust and two QTL for leaf rust are considered novel showing no overlap with previously reported resistance QTL. Overall, resistance to both pathogens in HEB-25 is most likely due to the accumulation of numerous small effect loci. In addition, the NAM results indicate that the 25 wild donor QTL alleles present in HEB-25 strongly differ in regard to their individual effect on rust resistance. In future, the NAM concept will allow to select and combine individual wild barley alleles from different HEB parents to increase rust resistance in barley. The HEB-25 results will support to unravel the genetic basis of rust resistance in barley, and to improve resistance against stripe rust and leaf rust of modern barley cultivars. PMID:29370232

  14. Identification of QTL conferring resistance to stripe rust (Puccinia striiformis f. sp. hordei and leaf rust (Puccinia hordei in barley using nested association mapping (NAM.

    Directory of Open Access Journals (Sweden)

    Thomas Vatter

    Full Text Available The biotrophic rust fungi Puccinia hordei and Puccinia striiformis are important barley pathogens with the potential to cause high yield losses through an epidemic spread. The identification of QTL conferring resistance to these pathogens is the basis for targeted breeding approaches aiming to improve stripe rust and leaf rust resistance of modern cultivars. Exploiting the allelic richness of wild barley accessions proved to be a valuable tool to broaden the genetic base of resistance of barley cultivars. In this study, SNP-based nested association mapping (NAM was performed to map stripe rust and leaf rust resistance QTL in the barley NAM population HEB-25, comprising 1,420 lines derived from BC1S3 generation. By scoring the percentage of infected leaf area, followed by calculation of the area under the disease progress curve and the average ordinate during a two-year field trial, a large variability of resistance across and within HEB-25 families was observed. NAM based on 5,715 informative SNPs resulted in the identification of twelve and eleven robust QTL for resistance against stripe rust and leaf rust, respectively. Out of these, eight QTL for stripe rust and two QTL for leaf rust are considered novel showing no overlap with previously reported resistance QTL. Overall, resistance to both pathogens in HEB-25 is most likely due to the accumulation of numerous small effect loci. In addition, the NAM results indicate that the 25 wild donor QTL alleles present in HEB-25 strongly differ in regard to their individual effect on rust resistance. In future, the NAM concept will allow to select and combine individual wild barley alleles from different HEB parents to increase rust resistance in barley. The HEB-25 results will support to unravel the genetic basis of rust resistance in barley, and to improve resistance against stripe rust and leaf rust of modern barley cultivars.

  15. Root rots of common and tepary beans in Puerto Rico

    Science.gov (United States)

    Root rots are a disease complex affecting common bean and can be severe in bean growing areas in the tropics and subtropics. The presence of several pathogens makes it difficult to breed for resistance because of the synergistic effect of the pathogens in the host and the interaction of soil factors...

  16. Organics and mineral fertilizers and biological control on the incidence of stalk rot and corn yield

    Directory of Open Access Journals (Sweden)

    Elena Blume

    2014-06-01

    Full Text Available The expansion of area under maize (Zea mays L. and the use of no tillage have favored the incidence of stalk rot on this crop. The study aimed to evaluate the organic fertilizers and the treatment of corn seeds with Trichoderma spp. on the production of dry matter (DM of shoot, incidence of stalk rot and corn yield. The experiment consisted in a factorial with split-plot in strips, on the randomized block design with four replicates, and the fertilization treatments (pig slurry; swine deep bedding; cattle slurry; mineral fertilizer; control treatment were applied to the plots and the seeds treatment (with and without Trichoderma spp. in the subplots. At the flowering stage, three corn plants per subplot were collected for the assessment of DM production. At physiological maturity stage, the incidence of stalk rot was assessed, and the ears of corn harvested for productivity assessment. The organic and mineral fertilizers increased the production of DM and productivity of corn. Trichoderma spp. increased the production of DM of corn, but had no reflection on productivity. The incidence of stalk rot in corn was higher in treatments with organic and mineral fertilization. Organic fertilizers increase dry matter production of shoot and corn yield, and Trichoderma spp. provides an increase in dry matter production of shoot.

  17. 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.

  18. A first linkage map and downy mildew resistance QTL discovery for sweet basil (Ocimum basilicum) facilitated by double digestion restriction site associated DNA sequencing (ddRADseq).

    Science.gov (United States)

    Pyne, Robert; Honig, Josh; Vaiciunas, Jennifer; Koroch, Adolfina; Wyenandt, Christian; Bonos, Stacy; Simon, James

    2017-01-01

    Limited understanding of sweet basil (Ocimum basilicum L.) genetics and genome structure has reduced efficiency of breeding strategies. This is evidenced by the rapid, worldwide dissemination of basil downy mildew (Peronospora belbahrii) in the absence of resistant cultivars. In an effort to improve available genetic resources, expressed sequence tag simple sequence repeat (EST-SSR) and single nucleotide polymorphism (SNP) markers were developed and used to genotype the MRI x SB22 F2 mapping population, which segregates for response to downy mildew. SNP markers were generated from genomic sequences derived from double digestion restriction site associated DNA sequencing (ddRADseq). Disomic segregation was observed in both SNP and EST-SSR markers providing evidence of an O. basilicum allotetraploid genome structure and allowing for subsequent analysis of the mapping population as a diploid intercross. A dense linkage map was constructed using 42 EST-SSR and 1,847 SNP markers spanning 3,030.9 cM. Multiple quantitative trait loci (QTL) model (MQM) analysis identified three QTL that explained 37-55% of phenotypic variance associated with downy mildew response across three environments. A single major QTL, dm11.1 explained 21-28% of phenotypic variance and demonstrated dominant gene action. Two minor QTL dm9.1 and dm14.1 explained 5-16% and 4-18% of phenotypic variance, respectively. Evidence is provided for an additive effect between the two minor QTL and the major QTL dm11.1 increasing downy mildew susceptibility. Results indicate that ddRADseq-facilitated SNP and SSR marker genotyping is an effective approach for mapping the sweet basil genome.

  19. Joint High-Dimensional Bayesian Variable and Covariance Selection with an Application to eQTL Analysis

    KAUST Repository

    Bhadra, Anindya; Mallick, Bani K.

    2013-01-01

    our method to an expression quantitative trait loci (eQTL) analysis on publicly available single nucleotide polymorphism (SNP) and gene expression data for humans where the primary interest lies in finding the significant associations between the sets

  20. Preliminary study on antifungal effect of commercial essential oils against white rot fungi

    Science.gov (United States)

    Khalid, Nurul Izzaty; Baharum, Azizah; Daud, Fauzi

    2015-09-01

    Protecting and preserving wood plastic composite from deterioration caused by fungal attack is a high challenge issue to cater nowadays. The objective of this study was to carry out a screening test towards antifungal effect of essential oil and to investigate the potential of raw materials that will be used as basic material for manufacturing wood plastic composite against white rot fungi. Essential oils from four types of natural products comprising cinnamon, lemongrass, lavender and geranium have been screened for their ability to inhibit five types of white rot fungi species which are Lentinus squarrosulus, Pleuorotus pulmonarius, Lentinus sp., Pleuorotus sajor-caju and Lignosus rhinocerus. The antifungal evaluation showed that no inhibitory effect against tested white rot fungi since the mycelia completely filled the plates. From the observation, mycelia of L. squarrosulus, P. pulmonarius and Lentinus sp. were found to filled the surface of falcon tubes with rubber sawdust after 15 days. Mycelia of L. squarrosulus and P. pulmonarius also were found to completely covered the surface of media that contain polypropylene and maleic anhydride grafted polypropylene on it. Therefore, this report proved that the main materials that will be applicable in manufacturing of wood plastic composite had potential to be degraded by this type of fungal attack.

  1. An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis

    NARCIS (Netherlands)

    Geest, van Geert; Bourke, Peter M.; Voorrips, Roeland E.; Marasek-Ciolakowska, Agnieszka; Liao, Yanlin; Post, Aike; Meeteren, van Uulke; Visser, Richard G.F.; Maliepaard, Chris; Arens, Paul

    2017-01-01

    Key message: We constructed the first integrated genetic linkage map in a polysomic hexaploid. This enabled us to estimate inheritance of parental haplotypes in the offspring and detect multi-allelic QTL.Abstract: Construction and use of linkage maps are challenging in hexaploids with polysomic

  2. Control of Fusarium verticillioides, cause of ear rot of maize, by Pseudomonas fluorescens

    DEFF Research Database (Denmark)

    Nayaka, Siddaiah Chandra; Shankar, Akarere C. Udaya; Reddy, Munagala S.

    2009-01-01

    Abstract BACKGROUND: Maize is one of the staple food crops grown in India. Fusarium verticillioides (Sacc.) Nirenberg is the most important fungal pathogen of maize, associated with diseases such as ear rot and kernel rot. Apart from the disease, it is capable of producing fumonisins, which have...... disease and fumonisin accumulation, and also to study the capacity to promote growth and yield of maize. In vitro assays were conducted to test the efficacy of P. fluorescens as a seed treatment on seed germination, seedling vigour and also the incidence of F. verticillioides in different maize cultivars....... verticillioides and the level of fumonisins to a maximum extent compared with the other treatments. CONCLUSION: The study demonstrates the potential role of P. fluorescens and its formulations in ear rot disease management. The biocontrol potential of this isolate is more suited for fumonisin reduction in maize...

  3. Effect of the planting material on the incidence of dry rot in Colocasia esculenta (L. Schott and Xanthosoma spp.

    Directory of Open Access Journals (Sweden)

    Ernesto Espinosa

    2012-10-01

    Full Text Available The cocoyam (Xanthosoma spp. and Colocasia esculenta is a monocot plant with vegetative propagation. This work was developed with the aim of determining the effect of the planting material type on the incidence of dry rot in two cultivars of Colocasia and Xanthosoma genera. Primary and secondary rhizomes, crowns of primary rhizomes and in vitro plants were used. The plantation was maintained for twelve months and the plants were characterized morphologically in the growing stage. Besides, it was determined the incidence of dry rot per treatment at growing and harvest stage. Finally, the yield was determined. When in vitro plants were used the percentage of incidence and intensity of the damage of dry rot was less in both cultivars. The yield in primary rhizomes and overall was significantly higher. The results indicated the superiority of in vitro plants as initial plantation material over the traditional seed used in taro culture. Furthermore, it allows the designing a seed production program by biotechnological methods. Key words: clone, cocoyam, dry rot, in vitro plants.

  4. Genetic control of functional traits related to photosynthesis and water use efficiency in Pinus pinaster Ait. drought response: integration of genome annotation, allele association and QTL detection for candidate gene identification.

    Science.gov (United States)

    de Miguel, Marina; Cabezas, José-Antonio; de María, Nuria; Sánchez-Gómez, David; Guevara, María-Ángeles; Vélez, María-Dolores; Sáez-Laguna, Enrique; Díaz, Luis-Manuel; Mancha, Jose-Antonio; Barbero, María-Carmen; Collada, Carmen; Díaz-Sala, Carmen; Aranda, Ismael; Cervera, María-Teresa

    2014-06-12

    Understanding molecular mechanisms that control photosynthesis and water use efficiency in response to drought is crucial for plant species from dry areas. This study aimed to identify QTL for these traits in a Mediterranean conifer and tested their stability under drought. High density linkage maps for Pinus pinaster were used in the detection of QTL for photosynthesis and water use efficiency at three water irrigation regimes. A total of 28 significant and 27 suggestive QTL were found. QTL detected for photochemical traits accounted for the higher percentage of phenotypic variance. Functional annotation of genes within the QTL suggested 58 candidate genes for the analyzed traits. Allele association analysis in selected candidate genes showed three SNPs located in a MYB transcription factor that were significantly associated with efficiency of energy capture by open PSII reaction centers and specific leaf area. The integration of QTL mapping of functional traits, genome annotation and allele association yielded several candidate genes involved with molecular control of photosynthesis and water use efficiency in response to drought in a conifer species. The results obtained highlight the importance of maintaining the integrity of the photochemical machinery in P. pinaster drought response.

  5. Segregation of a QTL cluster for home-cage activity using a new mapping method based on regression analysis of congenic mouse strains

    Science.gov (United States)

    Kato, S; Ishii, A; Nishi, A; Kuriki, S; Koide, T

    2014-01-01

    Recent genetic studies have shown that genetic loci with significant effects in whole-genome quantitative trait loci (QTL) analyses were lost or weakened in congenic strains. Characterisation of the genetic basis of this attenuated QTL effect is important to our understanding of the genetic mechanisms of complex traits. We previously found that a consomic strain, B6-Chr6CMSM, which carries chromosome 6 of a wild-derived strain MSM/Ms on the genetic background of C57BL/6J, exhibited lower home-cage activity than C57BL/6J. In the present study, we conducted a composite interval QTL analysis using the F2 mice derived from a cross between C57BL/6J and B6-Chr6CMSM. We found one QTL peak that spans 17.6 Mbp of chromosome 6. A subconsomic strain that covers the entire QTL region also showed lower home-cage activity at the same level as the consomic strain. We developed 15 congenic strains, each of which carries a shorter MSM/Ms-derived chromosomal segment from the subconsomic strain. Given that the results of home-cage activity tests on the congenic strains cannot be explained by a simple single-gene model, we applied regression analysis to segregate the multiple genetic loci. The results revealed three loci (loci 1–3) that have the effect of reducing home-cage activity and one locus (locus 4) that increases activity. We also found that the combination of loci 3 and 4 cancels out the effects of the congenic strains, which indicates the existence of a genetic mechanism related to the loss of QTLs. PMID:24781804

  6. Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization.

    Directory of Open Access Journals (Sweden)

    Xiaoquan Wen

    2017-03-01

    Full Text Available We propose a novel statistical framework for integrating the result from molecular quantitative trait loci (QTL mapping into genome-wide genetic association analysis of complex traits, with the primary objectives of quantitatively assessing the enrichment of the molecular QTLs in complex trait-associated genetic variants and the colocalizations of the two types of association signals. We introduce a natural Bayesian hierarchical model that treats the latent association status of molecular QTLs as SNP-level annotations for candidate SNPs of complex traits. We detail a computational procedure to seamlessly perform enrichment, fine-mapping and colocalization analyses, which is a distinct feature compared to the existing colocalization analysis procedures in the literature. The proposed approach is computationally efficient and requires only summary-level statistics. We evaluate and demonstrate the proposed computational approach through extensive simulation studies and analyses of blood lipid data and the whole blood eQTL data from the GTEx project. In addition, a useful utility from our proposed method enables the computation of expected colocalization signals using simple characteristics of the association data. Using this utility, we further illustrate the importance of enrichment analysis on the ability to discover colocalized signals and the potential limitations of currently available molecular QTL data. The software pipeline that implements the proposed computation procedures, enloc, is freely available at https://github.com/xqwen/integrative.

  7. White-rot fungi in phenols, dyes and other xenobiotics treatment – a brief review

    Directory of Open Access Journals (Sweden)

    B. Zelić

    2010-01-01

    Full Text Available Bioremediation is an attractive technology that utilizes the metabolic potential of microorganisms in order to clean up the environmental pollutants to the less hazardous or non-hazardous forms with less input of chemicals, energy and time. White-rot fungi are unique organisms that show the capacities of degrading and mineralizing lignin as well as organic, highly toxic and recalcitrant compounds. The key enzymes of their metabolism are extracellular lignolytic enzymes that enable fungi to tolerate a relatively high concentration of toxic substrates. This paper gives a brief review of many aspects concerning the application of white-rot fungi with the purpose of the industrial contaminants removal.

  8. Reciprocal Genetics: Identifying QTL for General and Specific Combining Abilities in Hybrids Between Multiparental Populations from Two Maize (Zea mays L.) Heterotic Groups.

    Science.gov (United States)

    Giraud, Héloïse; Bauland, Cyril; Falque, Matthieu; Madur, Delphine; Combes, Valérie; Jamin, Philippe; Monteil, Cécile; Laborde, Jacques; Palaffre, Carine; Gaillard, Antoine; Blanchard, Philippe; Charcosset, Alain; Moreau, Laurence

    2017-11-01

    Several plant and animal species of agricultural importance are commercialized as hybrids to take advantage of the heterosis phenomenon. Understanding the genetic architecture of hybrid performances is therefore of key importance. We developed two multiparental maize ( Zea mays L.) populations, each corresponding to an important heterotic group (dent or flint) and comprised of six connected biparental segregating populations of inbred lines (802 and 822 lines for each group, respectively) issued from four founder lines. Instead of using "testers" to evaluate their hybrid values, segregating lines were crossed according to an incomplete factorial design to produce 951 dent-flint hybrids, evaluated for four biomass production traits in eight environments. QTL detection was carried out for the general-combining-ability (GCA) and specific-combining-ability (SCA) components of hybrid value, considering allelic effects transmitted from each founder line. In total, 42 QTL were detected across traits. We detected mostly QTL affecting GCA, 31% (41% for dry matter yield) of which also had mild effects on SCA. The small impact of dominant effects is consistent with the known differentiation between the dent and flint heterotic groups and the small percentage of hybrid variance due to SCA observed in our design (∼20% for the different traits). Furthermore, most (80%) of GCA QTL were segregating in only one of the two heterotic groups. Relative to tester-based designs, use of hybrids between two multiparental populations appears highly cost efficient to detect QTL in two heterotic groups simultaneously. This presents new prospects for selecting superior hybrid combinations with markers. Copyright © 2017 by the Genetics Society of America.

  9. A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic QTL

    Directory of Open Access Journals (Sweden)

    Bidanel Jean P

    2009-12-01

    Full Text Available Abstract Background Prolificacy is the most important trait influencing the reproductive efficiency of pig production systems. The low heritability and sex-limited expression of prolificacy have hindered to some extent the improvement of this trait through artificial selection. Moreover, the relative contributions of additive, dominant and epistatic QTL to the genetic variance of pig prolificacy remain to be defined. In this work, we have undertaken this issue by performing one-dimensional and bi-dimensional genome scans for number of piglets born alive (NBA and total number of piglets born (TNB in a three generation Iberian by Meishan F2 intercross. Results The one-dimensional genome scan for NBA and TNB revealed the existence of two genome-wide highly significant QTL located on SSC13 (P SSC17 (P P P P P Conclusions The complex inheritance of prolificacy traits in pigs has been evidenced by identifying multiple additive (SSC13 and SSC17, dominant and epistatic QTL in an Iberian × Meishan F2 intercross. Our results demonstrate that a significant fraction of the phenotypic variance of swine prolificacy traits can be attributed to first-order gene-by-gene interactions emphasizing that the phenotypic effects of alleles might be strongly modulated by the genetic background where they segregate.

  10. A major QTL corresponding to the Rk locus for resistance to root-knot nematodes in cowpea (Vigna unguiculata L. Walp.).

    Science.gov (United States)

    Huynh, Bao-Lam; Matthews, William C; Ehlers, Jeffrey D; Lucas, Mitchell R; Santos, Jansen R P; Ndeve, Arsenio; Close, Timothy J; Roberts, Philip A

    2016-01-01

    Genome resolution of a major QTL associated with the Rk locus in cowpea for resistance to root-knot nematodes has significance for plant breeding programs and R gene characterization. Cowpea (Vigna unguiculata L. Walp.) is a susceptible host of root-knot nematodes (Meloidogyne spp.) (RKN), major plant-parasitic pests in global agriculture. To date, breeding for host resistance in cowpea has relied on phenotypic selection which requires time-consuming and expensive controlled infection assays. To facilitate marker-based selection, we aimed to identify and map quantitative trait loci (QTL) conferring the resistance trait. One recombinant inbred line (RIL) and two F2:3 populations, each derived from a cross between a susceptible and a resistant parent, were genotyped with genome-wide single nucleotide polymorphism (SNP) markers. The populations were screened in the field for root-galling symptoms and/or under growth-chamber conditions for nematode reproduction levels using M. incognita and M. javanica biotypes. One major QTL was mapped consistently on linkage group VuLG11 of each population. By genotyping additional cowpea lines and near-isogenic lines derived from conventional backcrossing, we confirmed that the detected QTL co-localized with the genome region associated with the Rk locus for RKN resistance that has been used in conventional breeding for many decades. This chromosomal location defined with flanking markers will be a valuable target in marker-assisted breeding and for positional cloning of genes controlling RKN resistance.

  11. High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth.

    Science.gov (United States)

    Zhang, Xuehai; Huang, Chenglong; Wu, Di; Qiao, Feng; Li, Wenqiang; Duan, Lingfeng; Wang, Ke; Xiao, Yingjie; Chen, Guoxing; Liu, Qian; Xiong, Lizhong; Yang, Wanneng; Yan, Jianbing

    2017-03-01

    With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize ( Zea mays ) recombinant inbred line population ( n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction. © 2017 American Society of Plant Biologists. All Rights Reserved.

  12. Dinámica poblacional del rotífero Brachionus ibericus aislado de estanques para camarón, alimentado con diferentes dietas

    Directory of Open Access Journals (Sweden)

    José Cristóbal Román-Reyes

    2014-11-01

    Full Text Available La producción de microalgas vivas para cultivar rotíferos constituye uno de los mayores costos de operación en la larvicultura de peces, por lo que se están desarrollando sustitutos comerciales de microalgas para la alimentación y producción de rotíferos. Se desconoce el efecto que tienen las formulaciones comerciales sobre la dinámica poblacional de rotíferos nativos del noroeste de México y en este estudio se evaluó el efecto de cuatro dietas comerciales (Espirulina, RotiMac®, Nanno 3600®, RotiGrow-Plus® y la microalga viva Nannochloropsis sp., sobre el crecimiento poblacional y fecundidad del rotífero Brachionus ibericus (GenBank KJ949043, aislado de una granja de camarón blanco (Litopenaeus vannamei. Se realizaron cinco réplicas por tratamiento alimenticio utilizando recipientes con volumen de 12 L de agua, con temperatura de 29 ± 1°C y salinidad de 35 ± 1, respectivamente. Los resultados mostraron que durante los periodos experimentales, las dietas probadas resultaron adecuadas para alimentar a B. ibericus, con tasas de crecimiento, tiempos de duplicación, densidades máximas y fecundidades que fluctuaron entre 0.20 a 0.27 rotíferos día-1, 2.60 a 3.42 días, 215 a 344 rotíferos mL-1 y de 0.16 a 0.39 huevos hembra-1, respectivamente. Las diferencias entre tratamientos fueron significativas (P 0.05 a las obtenidas con Nanno 3600®.

  13. Moniliophthora roreri, causal agent of cacao frosty pod rot.

    Science.gov (United States)

    Bailey, Bryan A; Evans, Harry C; Phillips-Mora, Wilbert; Ali, Shahin S; Meinhardt, Lyndel W

    2017-12-01

    Taxonomy: Moniliophthora roreri (Cif.) H.C. Evans et al. ; Phylum Basidiomycota; Class Agaricomycetes; Order Agaricales; Family Marasmiaceae; Genus Moniliophthora. Biology: Moniliophthora roreri attacks Theobroma and Herrania species causing frosty pod rot. Theobroma cacao (cacao) is the host of major economic concern. Moniliophthora roreri is a hemibiotroph with a long biotrophic phase (45-90 days). Spore masses, of apparent asexual origin, are produced on the pod surface after initiation of the necrotrophic phase. Spores are spread by wind, rain and human activity. Symptoms of the biotrophic phase can include necrotic flecks and, in some cases, pod malformation, but pods otherwise remain asymptomatic. Relationship to Moniliophthora perniciosa: Moniliophthora roreri and Moniliophthora perniciosa, causal agent of witches' broom disease of cacao, are closely related. Their genomes are similar, including many of the genes they carry which are considered to be important in the disease process. Moniliophthora perniciosa, also a hemibiotroph, has a typical basidiomycete lifestyle and morphology, forming clamp connections and producing mushrooms. Basidiospores infect meristematic tissues including flower cushions, stem tips and pods. Moniliophthora roreri does not form clamp connections or mushrooms and infects pods only. Both pathogens are limited to the Western Hemisphere and are a threat to cacao production around the world. Agronomic importance: Disease losses caused by frosty pod rot can reach 90% and result in field abandonment. Moniliophthora roreri remains in the invasive phase in the Western Hemisphere, not having reached Brazil, some islands within the Caribbean and a few specific regions within otherwise invaded countries. The disease can be managed by a combination of cultural (for example, maintenance of tree height and removal of infected pods) and chemical methods. These methods benefit from regional application, but can be cost prohibitive. Breeding for

  14. Probing genetic diversity to characterize red rot resistance in sugarcane

    Energy Technology Data Exchange (ETDEWEB)

    Mumtaz, A S; Dure-e-Nayab,; Iqbal, M J; Shinwari, Z.K., E-mail: asmumtaz@qau.edu.pk

    2011-10-15

    Genetic diversity was assessed in a set of twelve sugarcane genotypes using Random Amplified Polymorphic DNA (RAPD). A total of thirty-two oligo-primers were employed, sixteen of them revealed amplification at 149 loci, out of which 136 were polymorphic. The genotype SPSG-26 showed the highest number of polymorphic loci, followed by CSSG-668 and HSF-242. Pairwise genetic similarity ranged from 67.2% to 83.3%. The UPGMA cluster analysis resolved most of the accessions in two groups. The clustering pattern did not place all resistant varieties in one or related group which depict diverse resistance source in the present set of sugarcane varieties. Ten primers revealed genotype specific bands among which four primers (K07, H02, K10 and F01) produced multiple genotype specific bands that aid genotype identification especially those with red rot resistance. The present study not only provided information on the genetic diversity among the genotypes but also revealed the potential of RAPD-PCR markers for genotype identification and therefore could be utilized in marker assisted selection for red rot resistance in sugarcane. (author)

  15. Sclerotinia Rot on Basil Caused by Sclerotinia sclerotiorum in Korea

    Directory of Open Access Journals (Sweden)

    Soo Sang Hahm

    2017-03-01

    Full Text Available During growing season of 2011 to 2013, Sclerotinia rot symptoms consistently have been observed on basil in Yesan-gun, Chungcheongnam-do in Korea. The typical symptom formed initially brownish spot on leaf and stem, and then advancing margins, wilting the whole plant and blighting, eventually died. On the surface of diseased lesions was observed cottony, white, dense mat of mycelial growth, and sclerotia (30–100 µm diameter formed on stem and leaf. Morphological and cultural characteristic on potato dextrose agar, color of colony was white and colorless chocolate, sclerotium of irregular shape of the oval was black and 5–50 µm diameter in size. In pathogenicity test, necrosis and wilt of the inoculated stem were observed in all plants and the pathogen was reisolated from stems. On the basis of mycological characteristics, pathogenicity, and internal transcribed spacer rDNA sequence analysis, this fungus was identified as Sclerotinia sclerotiorum. This is the first report of Sclerotinia rot on basil caused by S. sclerotiorum in Korea.

  16. Gibberella ear rot of maize (Zea mays) in Nepal: distribution of the mycotoxins nivalenol and deoxynivalenol in naturally and experimentally infected maize.

    Science.gov (United States)

    Desjardins, Anne E; Busman, Mark; Manandhar, Gyanu; Jarosz, Andrew M; Manandhar, Hira K; Proctor, Robert H

    2008-07-09

    The fungus Fusarium graminearum (sexual stage Gibberella zeae) causes ear rot of maize (Zea mays) and contamination with the 8-ketotrichothecenes nivalenol (1) or 4-deoxynivalenol (2), depending on diversity of the fungal population for the 4-oxygenase gene (TRI13). To determine the importance of 1 and 2 in maize ear rot, a survey of naturally contaminated maize in Nepal was combined with experiments in the field and in a plant growth room. In the survey, 1 contamination was 4-fold more frequent than 2 contamination and 1-producers (TRI13) were isolated more than twice as frequently as 2-producers (Psi TRI13). In maize ear rot experiments, genetically diverse 1-producers and 2-producers caused ear rot and trichothecene contamination. Among strains with the same genetic background, however, 1-producers caused less ear rot and trichothecene contamination than did 2-producers. The high frequency of 1 contamination and the high virulence of many 1-producers are of concern because maize is a staple food of rural populations in Nepal and because 1 has proven to be more toxic than 2 to animals.

  17. Potential of popcorn germplasm as a source of resistance to ear rot

    Directory of Open Access Journals (Sweden)

    Railan do Nascimento Ferreira Kurosawa

    Full Text Available ABSTRACT Because of its multi-purpose nature, popcorn has sparked the interest of the World Trade Organization as regards fungal contamination by mycotoxins. However, no investigations have been conducted on popcorn for resistance of genotypes to ear rot. The aim of this study was to evaluate the potential of popcorn genotypes as to resistance to ear rot and rotten kernels, as an initial step for the implementation of a breeding program with the popcorn crop in Northern Rio de Janeiro State, Brazil. Thirty-seven accessions from different ecogeographic regions of Latin America were evaluated in 2 cultivation periods, in a randomized block design with 4 replications. We evaluated the incidence of rotten ears, incidence of rotten ears caused by Fusarium spp., severity of ears with Fusarium spp. rot, and incidence of rotten kernels. The results were subjected to analysis of variance, and means were compared by the Scott-Knott clustering test (p < 0.05. A significant effect was observed for all evaluated variables, characterizing them as efficient in the discrimination of genotypic variability for reaction to fungal injuries in popcorn. The gene pool of the tropical and temperate Germplasm Collection evaluated here has the potential to generate superior segregants and provide hybrid combinations with alleles of resistance to diseases affecting ears and stored kernels. Based on the different variables and times, the experiment was conducted, and genotypes L65, L80, and IAC 125 showed the highest levels of resistance.

  18. Irpex lacteus, a white-rot fungus with biotechnological potential — review

    Czech Academy of Sciences Publication Activity Database

    Novotný, Čeněk; Cajthaml, Tomáš; Svobodová, Kateřina; Šušla, Martin; Šašek, Václav

    2009-01-01

    Roč. 5, č. 5 (2009), s. 375-390 ISSN 0015-5632 R&D Projects: GA AV ČR IAAX00200901 Institutional research plan: CEZ:AV0Z50200510 Keywords : White-rot fungi * degradation * irpex lacteus Subject RIV: EE - Microbiology, Virology Impact factor: 0.978, year: 2009

  19. Pathogen toxin-indiced electrolyte leakage and phytoalexin accumulation as indices of red-rot (Colletotrichum falcatum Went resistance in sugarcane

    Directory of Open Access Journals (Sweden)

    D. Mohanraj

    2003-08-01

    Full Text Available A phytotoxin produced by the sugarcane red-rot fungus Colletotrichum falcatum Went was partially purified. The phytotoxin caused increased electrolyte leakage in susceptible sugarcane varieties and higher levels of phytoalexins (3-deoxyanthocyanidins in resistant sugarcane varieties. This relationship between phytotoxin induced changes and disease reaction could possibly be used as an additional index to rapidly identify red-rot resistant varieties.

  20. Antagonistic Effect of Native Bacillus Isolates against Black Root Rot ...

    African Journals Online (AJOL)

    Faba bean (Vicia faba L.) is one of the most important pulse crops grown in eastern Africa. Black root rot (Fusarium solani) is known to cause great yield losses in faba bean, especially in the highlands of Ethiopia. The objective of this study was to evaluate the biological control ability of native Bacillus species on the basis of ...

  1. Contrasting results from GWAS and QTL mapping on wing length in great reed warblers.

    Science.gov (United States)

    Hansson, Bengt; Sigeman, Hanna; Stervander, Martin; Tarka, Maja; Ponnikas, Suvi; Strandh, Maria; Westerdahl, Helena; Hasselquist, Dennis

    2018-04-15

    A major goal in evolutionary biology is to understand the genetic basis of adaptive traits. In migratory birds, wing morphology is such a trait. Our previous work on the great reed warbler (Acrocephalus arundinaceus) shows that wing length is highly heritable and under sexually antagonistic selection. Moreover, a quantitative trait locus (QTL) mapping analysis detected a pronounced QTL for wing length on chromosome 2, suggesting that wing morphology is partly controlled by genes with large effects. Here, we re-evaluate the genetic basis of wing length in great reed warblers using a genomewide association study (GWAS) approach based on restriction site-associated DNA sequencing (RADseq) data. We use GWAS models that account for relatedness between individuals and include covariates (sex, age and tarsus length). The resulting association landscape was flat with no peaks on chromosome 2 or elsewhere, which is in line with expectations for polygenic traits. Analysis of the distribution of p-values did not reveal biases, and the inflation factor was low. Effect sizes were however not uniformly distributed on some chromosomes, and the Z chromosome had weaker associations than autosomes. The level of linkage disequilibrium (LD) in the population decayed to background levels within c. 1 kbp. There could be several reasons to why our QTL study and GWAS gave contrasting results including differences in how associations are modelled (cosegregation in pedigree vs. LD associations), how covariates are accounted for in the models, type of marker used (multi- vs. biallelic), difference in power or a combination of these. Our study highlights that the genetic architecture even of highly heritable traits is difficult to characterize in wild populations. © 2018 John Wiley & Sons Ltd.

  2. [Research progress in root rot diseases of Chinese herbal medicine and control strategy by antagonistic microorganisms].

    Science.gov (United States)

    Gao, Fen; Ren, Xiao-xia; Wang, Meng-liang; Qin, Xue-mei

    2015-11-01

    In recent years, root rot diseases of Chinese herbal medicine have been posing grave threat to the development of the traditional Chinese medicine industry. This article presents a review on the occurring situation of the root rot disease, including the occurrence of the disease, the diversity of the pathogens, the regional difference in dominant pathogens,and the complexity of symptoms and a survey of the progress in bio-control of the disease using antagonistic microorganisms. The paper also discusses the existing problems and future prospects in the research.

  3. A single dominant Ganoderma species is responsible for root rot of ...

    African Journals Online (AJOL)

    Ganoderma root rot is the most serious disease affecting commercially planted Acacia mangium in plantations in Indonesia. Numerous Ganoderma spp. have been recorded from diseased trees of this species and to a lesser extent Eucalyptus, causing confusion regarding the primary cause of the disease. In this study, a ...

  4. Control of yam tuber rot with leaf extracts of Xylopia aethiopica and ...

    African Journals Online (AJOL)

    JOHN

    Investigation was carried out to test the potency of some plant extracts for the control of yam tuber rot caused by Fusarium ... The extracts of suppressed the growth of these fungi in culture ..... Methodolgy for analysis of Vegetable drug. Practical.

  5. Quorum sensing signaling molecules produced by reference and emerging soft-rot bacteria (Dickeya and Pectobacterium spp..

    Directory of Open Access Journals (Sweden)

    Alexandre Crépin

    Full Text Available Several small diffusible molecules are involved in bacterial quorum sensing and virulence. The production of autoinducers-1 and -2, quinolone, indole and γ-amino butyrate signaling molecules was investigated in a set of soft-rot bacteria belonging to six Dickeya or Pectobacterium species including recent or emerging potato isolates.Using bacterial biosensors, immunoassay, and chromatographic analysis, we showed that soft-rot bacteria have the common ability to produce transiently during their exponential phase of growth the N-3-oxo-hexanoyl- or the N-3-oxo-octanoyl-l-homoserine lactones and a molecule of the autoinducer-2 family. Dickeya spp. produced in addition the indole-3-acetic acid in tryptophan-rich conditions. All these signaling molecules have been identified for the first time in the novel Dickeya solani species. In contrast, quinolone and γ-amino butyrate signals were not identified and the corresponding synthases are not present in the available genomes of soft-rot bacteria. To determine if the variations of signal production according to growth phase could result from expression modifications of the corresponding synthase gene, the respective mRNA levels were estimated by reverse transcriptase-PCR. While the N-acyl-homoserine lactone production is systematically correlated to the synthase expression, that of the autoinducer-2 follows the expression of an enzyme upstream in the activated methyl cycle and providing its precursor, rather than the expression of its own synthase.Despite sharing the S-adenosylmethionine precursor, no strong link was detected between the production kinetics or metabolic pathways of autoinducers-1 and -2. In contrast, the signaling pathway of autoinducer-2 seems to be switched off by the indole-3-acetic acid pathway under tryptophan control. It therefore appears that the two genera of soft-rot bacteria have similarities but also differences in the mechanisms of communication via the diffusible molecules

  6. Quorum Sensing Signaling Molecules Produced by Reference and Emerging Soft-Rot Bacteria (Dickeya and Pectobacterium spp.)

    Science.gov (United States)

    Crépin, Alexandre; Barbey, Corinne; Beury-Cirou, Amélie; Hélias, Valérie; Taupin, Laure; Reverchon, Sylvie; Nasser, William; Faure, Denis; Dufour, Alain; Orange, Nicole; Feuilloley, Marc; Heurlier, Karin; Burini, Jean-François; Latour, Xavier

    2012-01-01

    Background Several small diffusible molecules are involved in bacterial quorum sensing and virulence. The production of autoinducers-1 and -2, quinolone, indole and γ-amino butyrate signaling molecules was investigated in a set of soft-rot bacteria belonging to six Dickeya or Pectobacterium species including recent or emerging potato isolates. Methodology/Principal Findings Using bacterial biosensors, immunoassay, and chromatographic analysis, we showed that soft-rot bacteria have the common ability to produce transiently during their exponential phase of growth the N-3-oxo-hexanoyl- or the N-3-oxo-octanoyl-l-homoserine lactones and a molecule of the autoinducer-2 family. Dickeya spp. produced in addition the indole-3-acetic acid in tryptophan-rich conditions. All these signaling molecules have been identified for the first time in the novel Dickeya solani species. In contrast, quinolone and γ-amino butyrate signals were not identified and the corresponding synthases are not present in the available genomes of soft-rot bacteria. To determine if the variations of signal production according to growth phase could result from expression modifications of the corresponding synthase gene, the respective mRNA levels were estimated by reverse transcriptase-PCR. While the N-acyl-homoserine lactone production is systematically correlated to the synthase expression, that of the autoinducer-2 follows the expression of an enzyme upstream in the activated methyl cycle and providing its precursor, rather than the expression of its own synthase. Conclusions/Significance Despite sharing the S-adenosylmethionine precursor, no strong link was detected between the production kinetics or metabolic pathways of autoinducers-1 and -2. In contrast, the signaling pathway of autoinducer-2 seems to be switched off by the indole-3-acetic acid pathway under tryptophan control. It therefore appears that the two genera of soft-rot bacteria have similarities but also differences in the

  7. Candidate gene association mapping of Sclerotinia stalk rot resistance in sunflower (Helianthus annuus L.) uncovers the importance of COI1 homologs.

    Science.gov (United States)

    Talukder, Zahirul I; Hulke, Brent S; Qi, Lili; Scheffler, Brian E; Pegadaraju, Venkatramana; McPhee, Kevin; Gulya, Thomas J

    2014-01-01

    Functional markers for Sclerotinia basal stalk rot resistance in sunflower were obtained using gene-level information from the model species Arabidopsis thaliana. Sclerotinia stalk rot, caused by Sclerotinia sclerotiorum, is one of the most destructive diseases of sunflower (Helianthus annuus L.) worldwide. Markers for genes controlling resistance to S. sclerotiorum will enable efficient marker-assisted selection (MAS). We sequenced eight candidate genes homologous to Arabidopsis thaliana defense genes known to be associated with Sclerotinia disease resistance in a sunflower association mapping population evaluated for Sclerotinia stalk rot resistance. The total candidate gene sequence regions covered a concatenated length of 3,791 bp per individual. A total of 187 polymorphic sites were detected for all candidate gene sequences, 149 of which were single nucleotide polymorphisms (SNPs) and 38 were insertions/deletions. Eight SNPs in the coding regions led to changes in amino acid codons. Linkage disequilibrium decay throughout the candidate gene regions declined on average to an r (2) = 0.2 for genetic intervals of 120 bp, but extended up to 350 bp with r (2) = 0.1. A general linear model with modification to account for population structure was found the best fitting model for this population and was used for association mapping. Both HaCOI1-1 and HaCOI1-2 were found to be strongly associated with Sclerotinia stalk rot resistance and explained 7.4 % of phenotypic variation in this population. These SNP markers associated with Sclerotinia stalk rot resistance can potentially be applied to the selection of favorable genotypes, which will significantly improve the efficiency of MAS during the development of stalk rot resistant cultivars.

  8. QTL and candidate genes associated with common bacterial blight resistance in the common bean cultivar Longyundou 5 from China

    Institute of Scientific and Technical Information of China (English)

    Jifeng Zhu; Jing Wu; Lanfen Wang; Matthew W. Blair; Zhendong Zhu; Shumin Wang

    2016-01-01

    Common bacterial blight (CBB), caused by Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans (Xff), is a worldwide disease of common bean (Phaseolus vulgaris L.). Longyundou 5, a Chinese cultivar in the Mesoamerican gene pool of common bean, displays resistance to the Xff strain XSC3-1. To identify the genetic mechanisms behind this resistance, we crossed Long 5 with a susceptible genotype to develop a mapping population of F2 plants. Plant resistance to CBB was identified at 14 and 21 days after inoculation with Xff strain XSC3-1. A major QTL at 14 and 21 days after inoculation was mapped on chromosome Pv10 with LOD scores of 6.41 and 5.35, respectively. This locus was associated with SAP6, a previously-identified and much-used dominant marker, but in a 4.2 cM interval between new codominant markers BMp10s174 and BMp10s244. Ten candidate genes were found between markers BMp10s174 and BMp10s244 on chromosome Pv10 and could encode defense response proteins responding to CBB pathogens. Four pairs each of epistatic QTL for CBB resistance were detected at 14 and 21 days after inoculation. Phenotypic variation explained by the epistatic QTL ranged from 7.19%to 12.15%and 7.72%to 8.80%at 14 and 21 days after inoculation, respectively. These results confirmed the importance of epistasis in CBB resistance in common bean. The adjacent markers found may be more efficient for marker assisted selection in common bean breeding for CBB resistance owing to their closer linkage to the target QTL.

  9. QTL and candidate genes associated with common bacterial blight resistance in the common bean cultivar Longyundou 5 from China

    Institute of Scientific and Technical Information of China (English)

    Jifeng; Zhu; Jing; Wu; Lanfen; Wang; Matthew; W.Blair; Zhendong; Zhu; Shumin; Wang

    2016-01-01

    Common bacterial blight(CBB), caused by Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans(Xff), is a worldwide disease of common bean(Phaseolus vulgaris L.).Longyundou 5, a Chinese cultivar in the Mesoamerican gene pool of common bean, displays resistance to the Xff strain XSC3-1. To identify the genetic mechanisms behind this resistance,we crossed Long 5 with a susceptible genotype to develop a mapping population of F2 plants.Plant resistance to CBB was identified at 14 and 21 days after inoculation with Xff strain XSC3-1.A major QTL at 14 and 21 days after inoculation was mapped on chromosome Pv10 with LOD scores of 6.41 and 5.35, respectively. This locus was associated with SAP6, a previouslyidentified and much-used dominant marker, but in a 4.2 cM interval between new codominant markers BMp10s174 and BMp10s244. Ten candidate genes were found between markers BMp10s174 and BMp10s244 on chromosome Pv10 and could encode defense response proteins responding to CBB pathogens. Four pairs each of epistatic QTL for CBB resistance were detected at 14 and 21 days after inoculation. Phenotypic variation explained by the epistatic QTL ranged from 7.19% to 12.15% and 7.72% to 8.80% at 14 and 21 days after inoculation, respectively. These results confirmed the importance of epistasis in CBB resistance in common bean. The adjacent markers found may be more efficient for marker assisted selection in common bean breeding for CBB resistance owing to their closer linkage to the target QTL.

  10. The preventive Control of White Root Rot Disease in Small Holder Rubber Plantation Using Botanical, Biological and Chemical Agents

    Directory of Open Access Journals (Sweden)

    Joko Prasetyo

    2014-03-01

    Full Text Available The preventive control of white root rot disease in small holder plantation using botanical, biological, and chemical agents. A field and laboratory experiment were conducted from June 2008 to December 2009 in Panumangan, Tulang Bawang - Lampung. The  field experiment was intended to evaluate the effect of  botanical plants (Alpinia galanga, Sansiviera auranthii, and Marantha arundinacea, biological agents (organic matter and Trichoderma spp., and chemical agents (lime and natural sulphur on the incidence of white root rot disease and population of some soil microbes. The laboratory experiment was conducted  to observe the mechanism of botanical agents  in controlling white root rot disease. In the field experiment, the treatments were applied  in the experimental plot with cassava plant infection as the indicator. The variables  examined were the incidence of  white root rot and population of soil microbes. In the laboratory experiment, culture of R. microporus was grown in PDA containing root exudate of the antagonistic plant (botanical agent. The variable examined was colony diameter of R. microporus growing in the PDA plates. The results of the  field experiment  showed that planting of the botanical agents, and application of Trichoderma spp., as well as natural sulphur, decreased the incidence of white root rot disease. The effectiveness of M. arundinacea and Trichoderma spp. was comparable to natural  sulphur. The laboratory experiment showed only root exudate of  A. galanga and  S. auranthii that were significantly inhibit the growth of R. microporus.

  11. Apple ring rot-responsive putative microRNAs revealed by high-throughput sequencing in Malus × domestica Borkh.

    Science.gov (United States)

    Yu, Xin-Yi; Du, Bei-Bei; Gao, Zhi-Hong; Zhang, Shi-Jie; Tu, Xu-Tong; Chen, Xiao-Yun; Zhang, Zhen; Qu, Shen-Chun

    2014-08-01

    MicroRNAs (miRNAs) are small non-coding RNAs, which silence target mRNA via cleavage or translational inhibition to function in regulating gene expression. MiRNAs act as important regulators of plant development and stress response. For understanding the role of miRNAs responsive to apple ring rot stress, we identified disease-responsive miRNAs using high-throughput sequencing in Malus × domestica Borkh.. Four small RNA libraries were constructed from two control strains in M. domestica, crabapple (CKHu) and Fuji Naga-fu No. 6 (CKFu), and two disease stress strains, crabapple (DSHu) and Fuji Naga-fu No. 6 (DSFu). A total of 59 miRNA families were identified and five miRNAs might be responsive to apple ring rot infection and validated via qRT-PCR. Furthermore, we predicted 76 target genes which were regulated by conserved miRNAs potentially. Our study demonstrated that miRNAs was responsive to apple ring rot infection and may have important implications on apple disease resistance.

  12. Evaluation of the porcine Melanocortin 4 receptor (MC4R) gene as a positional candidate for a fatness QTL in a cross between Landrace and Hampshire

    DEFF Research Database (Denmark)

    Bruun, Camilla Vibeke; Jørgensen, Claus Bøttcher; Nielsen, V.H.

    2006-01-01

    . In a previously performed genome scan based on a Hampshire x Landrace cross, we detected one quantitative trait loci (QTL) affecting carcass fat/meat ratio and one QTL affecting the biceps femoris muscle, both close to the position of MC4R on porcine chromosome 1. In this study, the two lines were found...

  13. Root rot diseases of sugar beet

    Directory of Open Access Journals (Sweden)

    Jacobsen Barry J.

    2006-01-01

    Full Text Available Root rot diseases of sugar beet caused by Rhizoctonia solani (AG 2-2 IIIB and AG 2-2 IV, R. crocorum, Aphanomyces cochlioides, Phoma betae, Macrophomina phaeseolina, Fusarium oxysporum f.sp. radicis-betae, Pythium aphanidermatum Phytophthora drechsleri, Rhizopus stolonifer, R. arrhizus and Sclerotium rolfsii cause significant losses wherever sugar beets are grown. However, not all these soil-borne pathogens have been reported in all sugar beet production areas. Losses include reduced harvestable tonnage and reduced white sugar recovery. Many of these pathogens also cause post harvest losses in storage piles. Control for diseases caused by these pathogens include disease resistant cultivars, avoidance of stresses, cultural practices such as water management and the use of fungicides.

  14. Adult Plant Leaf Rust Resistance Derived from Toropi Wheat is Conditioned by Lr78 and Three Minor QTL.

    Science.gov (United States)

    Kolmer, J A; Bernardo, A; Bai, G; Hayden, M J; Chao, S

    2018-02-01

    Leaf rust caused by Puccinia triticina is an important disease of wheat in many regions worldwide. Durable or long-lasting leaf rust resistance has been difficult to achieve because populations of P. triticina are highly variable for virulence to race-specific resistance genes, and respond to selection by resistance genes in released wheat cultivars. The wheat cultivar Toropi, developed and grown in Brazil, was noted to have long-lasting leaf rust resistance that was effective only in adult plants. The objectives of this study were to determine the chromosome location of the leaf rust resistance genes derived from Toropi in two populations of recombinant inbred lines in a partial Thatcher wheat background. In the first population, a single gene with major effects on chromosome 5DS that mapped 2.2 centimorgans distal to IWA6289, strongly reduced leaf rust severity in all 3 years of field plot tests. This gene for adult plant leaf rust resistance was designated as Lr78. In the second population, quantitative trait loci (QTL) with small effects on chromosomes 1BL, 3BS, and 4BS were found. These QTL expressed inconsistently over 4 years of field plot tests. The adult plant leaf rust resistance derived from Toropi involved a complex combination of QTL with large and small effects.

  15. Potential of bulb-associated bacteria for biocontrol of hyacinth soft rot caused by Dickeya zeae.

    Science.gov (United States)

    Jafra, S; Przysowa, J; Gwizdek-Wiśniewska, A; van der Wolf, J M

    2009-01-01

    Dickeya zeae is a pectinolytic bacterium responsible for soft rot disease in flower bulb crops. In this study, the possibility of controlling soft rot disease in hyacinth by using antagonistic bacteria isolated from hyacinth bulbs was explored. Bacterial isolates with potential for biocontrol were selected on the basis of antibiosis against D. zeae, siderophore production, and the N-acyl homoserine lactones (AHLs)-inactivation. In in vitro assays, 35 out of 565 hyacinth-associated bacterial isolates produced antimicrobial substances against D. zeae, whereas 20 degraded AHLs, and 35 produced siderophores. Isolates of interest were identified by 16S rDNA sequence analysis and reaction in BIOLOG tests. Twenty-six isolates that differed in characteristics were selected for pathogenicity testing on hyacinth cultivars, Pink Pearl and Carnegie. Two strains identified as Rahnella aquatilis and one as Erwinia persicinus significantly reduced tissue maceration caused by D. zeae 2019 on hyacinth bulbs, but not on leaves. Hyacinth bulbs harbour bacteria belonging to different taxonomic groups that are antagonistic to D. zeae, and some can attenuate decay of bulb tissue. Selected hyacinth-associated bacterial isolates have potential for control of soft rot disease caused by D. zeae in hyacinth bulb production.

  16. Selection on crop-derived traits and QTL in sunflower (Helianthus annuus) crop-wild hybrids under water stress.

    Science.gov (United States)

    Owart, Birkin R; Corbi, Jonathan; Burke, John M; Dechaine, Jennifer M

    2014-01-01

    Locally relevant conditions, such as water stress in irrigated agricultural regions, should be considered when assessing the risk of crop allele introgression into wild populations following hybridization. Although research in cultivars has suggested that domestication traits may reduce fecundity under water stress as compared to wild-like phenotypes, this has not been investigated in crop-wild hybrids. In this study, we examine phenotypic selection acting on, as well as the genetic architecture of vegetative, reproductive, and physiological characteristics in an experimental population of sunflower crop-wild hybrids grown under wild-like low water conditions. Crop-derived petiole length and head diameter were favored in low and control water environments. The direction of selection differed between environments for leaf size and leaf pressure potential. Interestingly, the additive effect of the crop-derived allele was in the direction favored by selection for approximately half the QTL detected in the low water environment. Selection favoring crop-derived traits and alleles in the low water environment suggests that a subset of these alleles would be likely to spread into wild populations under water stress. Furthermore, differences in selection between environments support the view that risk assessments should be conducted under multiple locally relevant conditions.

  17. Biodiversity of Fusarium species causing ear rot of maize in Germany

    NARCIS (Netherlands)

    Görtz, A.; Oerke, E.C.; Steiner, U.; Waalwijk, C.; Vries, de P.M.; Dehne, H.W.

    2008-01-01

    In Germany, maize is one of the most important agriculture commodities, a major component in animal feed as well as an essential substrate producing biogas. Maize car rot poses a major impact worldwide as it is caused by several Fusarium spp., most of which have the ability to produce mycotoxins.

  18. Root Rot Disease of Five Fruit Tree Seedlings in the Nursery ...

    African Journals Online (AJOL)

    The incidence of root rot disease in the nursery of Chrysophyllum albidun Dacryodes edulis, persea Americana, Irvingia gabonensis and Annona muricala was assessed. Ten fungal pathogen were isolated using serial dilution and pathogenicity tests were carried out on the 5 fruit trees with the 10 isolated fungi. The 5 fruit ...

  19. Fine-mapping of qGW4.05, a major QTL for kernel weight and size in maize.

    Science.gov (United States)

    Chen, Lin; Li, Yong-xiang; Li, Chunhui; Wu, Xun; Qin, Weiwei; Li, Xin; Jiao, Fuchao; Zhang, Xiaojing; Zhang, Dengfeng; Shi, Yunsu; Song, Yanchun; Li, Yu; Wang, Tianyu

    2016-04-12

    Kernel weight and size are important components of grain yield in cereals. Although some information is available concerning the map positions of quantitative trait loci (QTL) for kernel weight and size in maize, little is known about the molecular mechanisms of these QTLs. qGW4.05 is a major QTL that is associated with kernel weight and size in maize. We combined linkage analysis and association mapping to fine-map and identify candidate gene(s) at qGW4.05. QTL qGW4.05 was fine-mapped to a 279.6-kb interval in a segregating population derived from a cross of Huangzaosi with LV28. By combining the results of regional association mapping and linkage analysis, we identified GRMZM2G039934 as a candidate gene responsible for qGW4.05. Candidate gene-based association mapping was conducted using a panel of 184 inbred lines with variable kernel weights and kernel sizes. Six polymorphic sites in the gene GRMZM2G039934 were significantly associated with kernel weight and kernel size. The results of linkage analysis and association mapping revealed that GRMZM2G039934 is the most likely candidate gene for qGW4.05. These results will improve our understanding of the genetic architecture and molecular mechanisms underlying kernel development in maize.

  20. QTL analysis of internode elongation in response to gibberellin in deepwater rice

    OpenAIRE

    Nagai, Keisuke; Kondo, Yuma; Kitaoka, Takuya; Noda, Tomonori; Kuroha, Takeshi; Angeles-Shim, Rosalyn B.; Yasui, Hideshi; Yoshimura, Atsushi; Ashikari, Motoyuki

    2014-01-01

    Gibberellin (GA) is a plant hormone that has important roles in numerous plant developmental phases. Rice plants known as deepwater rice respond to flooding by elongating their internodes to avoid anoxia. Previous studies reported that GA is essential for internode elongation in deepwater rice. Quantitative trait locus (QTL) analyses identified QTLs regulating internode elongation in response to deepwater conditions. However, the interaction between internode elongation and regulators of GA s...

  1. Genetic dissection of milk yield traits and mastitis resistance QTL on chromosome 20 in dairy cattle

    DEFF Research Database (Denmark)

    Kadri, Naveen Kumar; Guldbrandtsen, Bernt; Lund, Mogens Sandø

    2015-01-01

    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 (CM) and milk yield (MY) 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...... (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), which identifies 1,568 single...

  2. Producción artesanal del rotífero Philodina sp. y de algas para la alimentación de post-larvas de bocachico

    Directory of Open Access Journals (Sweden)

    Victoria Eugenia Quintero P

    2009-01-01

    Full Text Available El cultivo de algas mixtas se realizó en el Instituto de Piscicultura Tropical de la Corporación Autónoma Regional del Valle del Cauca (Buga 25 ºC y 969 m.s.n.m. utilizando fertilizantes inorgánicos en baldes plásticos, se produjeron en promedio 386 x 10³ células/ml de cultivo. En el cultivo de Philodina en frascos de vidrio alimentado con algas y levadura, se obtuvieron 410 rotíferos/ml de cultivo. Se evaluaron tres tratamientos: rotíferos enriquecidos con aceite de pescado; rotíferos más algas (Chlorella, Scenedesmus, Pediastrum, Spyrogira y Anabaena y Artemia salina + Spirulina, usando 100 post-larvas de bocachico/acuario, alimentadas dos veces al día según biomasa sembrada. El mayor porcentaje de sobrevivencia, peso y talla se obtuvo con el alimento constituido por rotíferos enriquecidos con aceite de pescado (93 %,3.2mg, 6.86mm, seguido de rotíferos + algas (80.67 %,2 mg, 6.1mm y Artemia+ Spirulina (60.6 %,1.6mg, 6.06mm respectivamente

  3. Confirming QTL for aflatoxin resistance from Mp313E in different genetic backgrounds

    Science.gov (United States)

    The fungus Aspergillus flavus (Link:Fr) causes ear rot of maize (Zea mays L.) and produces the toxic metabolic product aflatoxin. One particularly effective method to control the fungus is via host plant resistance, but while several resistant breeding lines have been identified, transferring the r...

  4. QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments

    Science.gov (United States)

    2011-01-01

    Background The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be validated from one experiment to another. The aim of our study was to overcome this limitation by basing QTL detection on the construction of genetic maps highly-enriched in gene markers, and by assessing QTLs across pedigrees, years, and environments. Results Four saturated individual linkage maps representing two unrelated mapping populations of 260 and 500 clonally replicated progeny were assembled from 471 to 570 markers, including from 283 to 451 gene SNPs obtained using a multiplexed genotyping assay. Thence, a composite linkage map was assembled with 836 gene markers. For individual linkage maps, a total of 33 distinct quantitative trait loci (QTLs) were observed for bud flush, 52 for bud set, and 52 for height growth. For the composite map, the corresponding numbers of QTL clusters were 11, 13, and 10. About 20% of QTLs were replicated between the two mapping populations and nearly 50% revealed spatial and/or temporal stability. Three to four occurrences of overlapping QTLs between characters were noted, indicating regions with potential pleiotropic effects. Moreover, some of the genes involved in the QTLs were also underlined by recent genome scans or expression profile studies. Overall, the proportion of phenotypic variance explained by each QTL ranged from 3.0 to 16.4% for bud flush, from 2.7 to 22.2% for bud set, and from 2.5 to 10.5% for height growth. Up to 70% of the total character variance could be accounted for by QTLs for bud flush or bud set, and up to 59% for height growth. Conclusions This study provides a basic understanding of the genomic architecture related to bud flush, bud set, and height growth in a conifer species, and a useful indicator to compare with Angiosperms. It will serve as a basic reference to functional and

  5. Identification and Verification of QTL Associated with Frost Tolerance Using Linkage Mapping and GWAS in Winter Faba Bean

    Science.gov (United States)

    Sallam, Ahmed; Arbaoui, Mustapha; El-Esawi, Mohamed; Abshire, Nathan; Martsch, Regina

    2016-01-01

    Frost stress is one of the abiotic stresses that causes a significant reduction in winter faba bean yield in Europe. The main objective of this work is to genetically improve frost tolerance in winter faba bean by identifying and validating QTL associated with frost tolerance to be used in marker-assisted selection (MAS). Two different genetic backgrounds were used: a biparental population (BPP) consisting of 101 inbred lines, and 189 genotypes from single seed descent (SSD) from the Gottingen Winter bean Population (GWBP). All experiments were conducted in a frost growth chamber under controlled conditions. Both populations were genotyped using the same set of 189 SNP markers. Visual scoring for frost stress symptoms was used to define frost tolerance in both populations. In addition, leaf fatty acid composition (FAC) and proline content were analyzed in BPP as physiological traits. QTL mapping (for BPP) and genome wide association studies (for GWBP) were performed to detect QTL associated with frost tolerance. High genetic variation between genotypes, and repeatability estimates, were found for all traits. QTL mapping and GWAS identified new putative QTL associated with promising frost tolerance and related traits. A set of 54 SNP markers common in both genetic backgrounds showed a high genetic diversity with polymorphic information content (PIC) ranging from 0.31 to 0.37 and gene diversity ranging from 0.39 to 0.50. This indicates that these markers may be polymorphic for many faba bean populations. Five SNP markers showed a significant marker-trait association with frost tolerance and related traits in both populations. Moreover, synteny analysis between Medicago truncatula (a model legume) and faba bean genomes was performed to identify candidate genes for these markers. Collinearity was evaluated between the faba bean genetic map constructed in this study and the faba bean consensus map, resulting in identifying possible genomic regions in faba bean which may

  6. Identification and Verification of QTL Associated with Frost Tolerance Using Linkage Mapping and GWAS in Winter Faba Bean.

    Science.gov (United States)

    Sallam, Ahmed; Arbaoui, Mustapha; El-Esawi, Mohamed; Abshire, Nathan; Martsch, Regina

    2016-01-01

    Frost stress is one of the abiotic stresses that causes a significant reduction in winter faba bean yield in Europe. The main objective of this work is to genetically improve frost tolerance in winter faba bean by identifying and validating QTL associated with frost tolerance to be used in marker-assisted selection (MAS). Two different genetic backgrounds were used: a biparental population (BPP) consisting of 101 inbred lines, and 189 genotypes from single seed descent (SSD) from the Gottingen Winter bean Population (GWBP). All experiments were conducted in a frost growth chamber under controlled conditions. Both populations were genotyped using the same set of 189 SNP markers. Visual scoring for frost stress symptoms was used to define frost tolerance in both populations. In addition, leaf fatty acid composition (FAC) and proline content were analyzed in BPP as physiological traits. QTL mapping (for BPP) and genome wide association studies (for GWBP) were performed to detect QTL associated with frost tolerance. High genetic variation between genotypes, and repeatability estimates, were found for all traits. QTL mapping and GWAS identified new putative QTL associated with promising frost tolerance and related traits. A set of 54 SNP markers common in both genetic backgrounds showed a high genetic diversity with polymorphic information content (PIC) ranging from 0.31 to 0.37 and gene diversity ranging from 0.39 to 0.50. This indicates that these markers may be polymorphic for many faba bean populations. Five SNP markers showed a significant marker-trait association with frost tolerance and related traits in both populations. Moreover, synteny analysis between Medicago truncatula (a model legume) and faba bean genomes was performed to identify candidate genes for these markers. Collinearity was evaluated between the faba bean genetic map constructed in this study and the faba bean consensus map, resulting in identifying possible genomic regions in faba bean which may

  7. LHD1, an allele of DTH8/Ghd8, controls late heading date in common wild rice (Oryza rufipogon).

    Science.gov (United States)

    Dai, Xiaodong; Ding, Younian; Tan, Lubin; Fu, Yongcai; Liu, Fengxia; Zhu, Zuofeng; Sun, Xianyou; Sun, Xuewen; Gu, Ping; Cai, Hongwei; Sun, Chuanqing

    2012-10-01

    Flowering at suitable time is very important for plants to adapt to complicated environments and produce their seeds successfully for reproduction. In rice (Oryza rufipogon Griff.) photoperiod regulation is one of the important factors for controlling heading date. Common wild rice, the ancestor of cultivated rice, exhibits a late heading date and a more sensitive photoperiodic response than cultivated rice. Here, through map-based cloning, we identified a major quantitative trait loci (QTL) LHD1 (Late Heading Date 1), an allele of DTH8/Ghd8, which controls the late heading date of wild rice and encodes a putative HAP3/NF-YB/CBF-A subunit of the CCAAT-box-binding transcription factor. Sequence analysis revealed that several variants in the coding region of LHD1 were correlated with a late heading date, and a further complementary study successfully rescued the phenotype. These results suggest that a functional site for LHD1 could be among those variants present in the coding region. We also found that LHD1 could down-regulate the expression of several floral transition activators such as Ehd1, Hd3a and RFT1 under long-day conditions, but not under short-day conditions. This indicates that LHD1 may delay flowering by repressing the expression of Ehd1, Hd3a and RFT1 under long-day conditions. © 2012 Institute of Botany, Chinese Academy of Sciences.

  8. Analysis of QTL for resistance to radiation in rice

    International Nuclear Information System (INIS)

    Zhao Fei; Zhou Yifeng; Ren Sanjuan; Fu Junjie; Zhuang Jieyun; Shen Shengquan

    2010-01-01

    The recombinant inbred line (RIL) population derived from rice variates Zhenshan 97B/Miyang 46 and their genetic linkage maps were used to map QTLs controlling resistant to radiation. The trait was measured by the relative germination rate (RGR) and the relative surviving plant rate (RSPR) after the seeds of each line treated with γ-rays irradiation at two 350 and 550 Gy. The results indicated that the lines treated with γ-irradiation showed different performance in resistance to radiation. Under the treatment of 350 Gy, two QTLs with additive effects were detected, of which qRR (g) 81 was only significant for relative germination rate, and it had the positive additive effects from the male parent, explaining 6.53% of the total phenotypic variations. The qRR(s)2-2 was another significant one for relative surviving plant rate, whose positive effects came from the female parent,explaining 12.81% of the total phenotypic variations. Similarly, 4 QTLs were detected under irradiation dose of 550 Gy, and qRR(g)1-2 and qRR(g)8-2 were detected for relative germination rate, with positive effects coming from female and male parent,respectively,explaining 14.38% of the total variations. qRR(s)5-2 and qRR(s)10 were detected for relative surviving plant rate, with positive effects coming from the male parent, explaining 19.65% of total variations. Under different irradiation dose, 9 pairs of double QTL epistasis effects could be identified in this population. The results suggested that the expression of QTL with resistance to radiation might have relation with the irradiation dose. (authors)

  9. A consensus microsatellite-based linkage map for the hermaphroditic bay scallop (Argopecten irradians and its application in size-related QTL analysis.

    Directory of Open Access Journals (Sweden)

    Hongjun Li

    Full Text Available Bay scallop (Argopecten irradians is one of the most economically important aquaculture species in China. In this study, we constructed a consensus microsatellite-based genetic linkage map with a mapping panel containing two hybrid backcross-like families involving two subspecies of bay scallop, A. i. irradians and A. i. concentricus. One hundred sixty-one microsatellite and one phenotypic (shell color markers were mapped to 16 linkage groups (LGs, which corresponds to the haploid chromosome number of bay scallop. The sex-specific map was 779.2 cM and 781.6 cM long in female and male, respectively, whereas the sex-averaged map spanned 849.3 cM. The average resolution of integrated map was 5.9 cM/locus and the estimated coverage was 81.3%. The proportion of distorted markers occurred more in the hybrid parents, suggesting that the segregation distortion was possibly resulted from heterospecific interaction between genomes of two subspecies of bay scallop. The overall female-to-male recombination rate was 1.13:1 across all linked markers in common to both parents, and considerable differences in recombination also existed among different parents in both families. Four size-related traits, including shell length (SL, shell height (SH, shell width (SW and total weight (TW were measured for quantitative trait loci (QTL analysis. Three significant and six suggestive QTL were detected on five LGs. Among the three significant QTL, two (qSW-10 and qTW-10, controlling SW and TW, respectively were mapped on the same region near marker AiAD121 on LG10 and explained 20.5% and 27.7% of the phenotypic variance, while the third (qSH-7, controlling SH was located on LG7 and accounted for 15.8% of the phenotypic variance. Six suggestive QTL were detected on four different LGs. The linkage map and size-related QTL obtained in this study may facilitate marker-assisted selection (MAS in bay scallop.

  10. Detection, identification and differentiation of Pectobacterium and Dickeya species causing potato blackleg and tuber soft rot: a review.

    Science.gov (United States)

    Czajkowski, R; Pérombelon, McM; Jafra, S; Lojkowska, E; Potrykus, M; van der Wolf, Jm; Sledz, W

    2015-01-01

    The soft rot Enterobacteriaceae (SRE) Pectobacterium and Dickeya species (formerly classified as pectinolytic Erwinia spp.) cause important diseases on potato and other arable and horticultural crops. They may affect the growing potato plant causing blackleg and are responsible for tuber soft rot in storage thereby reducing yield and quality. Efficient and cost-effective detection and identification methods are essential to investigate the ecology and pathogenesis of the SRE as well as in seed certification programmes. The aim of this review was to collect all existing information on methods available for SRE detection. The review reports on the sampling and preparation of plant material for testing and on over thirty methods to detect, identify and differentiate the soft rot and blackleg causing bacteria to species and subspecies level. These include methods based on biochemical characters, serology, molecular techniques which rely on DNA sequence amplification as well as several less-investigated ones.

  11. root rot disease of five fruit tree seedlings in the nursery

    African Journals Online (AJOL)

    KAMALDEEN

    on them. Our experience in the nursery in Port Harcourt had been that many tree species of the tropical region are susceptible to root rot diseases of fungal origin. The fungal invasion of the succulent root tissues causes the young tree seedlings to dieback; their leaves becomes discoloured, wilted and eventually dead.

  12. Multiple Breed Validation of Five QTL Affecting Mastitis Resistance

    DEFF Research Database (Denmark)

    Vilkki, Johanna; Dolezal, Marlies A; Sahana, Goutam

    to mastitis were identified by GWAS using high-density SNP array in the Finnish Ayrshire and Brown Swiss breeds. These targeted regions were analyzed for polymorphisms from 20X whole-genome sequences of 38 ancestral bulls of the two populations. A set of 384 SNPs were selected based on their ranking from...... (on BTA3, BTA6, BTA8, BTA19, and BTA27) agreed across the breeds, but no identical associated SNPs were detected. Higher power (imputation to bigger population samples) will be needed to confirm results. On BTA6 the results indicate several QTL within a 5 Mb region. The results provide a basis...

  13. Evaluation of some garlic (Allium Sativum L.) mutants resistant to white rot disease by RAPD analysis

    International Nuclear Information System (INIS)

    Nabulsi, I.; Al-Safadi, B.; Mir ali, N.; Arabi, M.I.E.

    2002-01-01

    Random amplified polymorphic DNA (RAPD) analysis was used to evaluate genetic diversity among eight garlic mutants resistant to white rot disease (Sclerotium cepivorum) and two controls. Twelve of 13 synthetic random primers were found to identify polymorphism in amplification products. Mutants characterised with moderate resistance to white rot were closely related to the control using cluster and correlation analyses. On the other hand, highly resistant mutants were quite distant from the control with low correlation coefficients. The banding patterns produced by primer OPB-15 (GGAAGGGTGTT) with highly resistant mutants may be used as genetic markers for early selection of resistant plants. (author)

  14. Mapping of quantitative adult plant field resistance to leaf rust and stripe rust in two European winter wheat populations reveals co-location of three QTL conferring resistance to both rust pathogens.

    Science.gov (United States)

    Buerstmayr, Maria; Matiasch, Lydia; Mascher, Fabio; Vida, Gyula; Ittu, Marianna; Robert, Olivier; Holdgate, Sarah; Flath, Kerstin; Neumayer, Anton; Buerstmayr, Hermann

    2014-09-01

    We detected several, most likely novel QTL for adult plant resistance to rusts. Notably three QTL improved resistance to leaf rust and stripe rust simultaneously indicating broad spectrum resistance QTL. The rusts of wheat (Puccinia spp.) are destructive fungal wheat diseases. The deployment of resistant cultivars plays a central role in integrated rust disease management. Durability of resistance would be preferred, but is difficult to analyse. The Austrian winter wheat cultivar Capo was released in the 1989 and grown on a large acreage during more than two decades and maintained a good level of quantitative leaf rust and stripe rust resistance. Two bi-parental mapping populations: Capo × Arina and Capo × Furore were tested in multiple environments for severity of leaf rust and stripe rust at the adult plant stage in replicated field experiments. Quantitative trait loci associated with leaf rust and stripe rust severity were mapped using DArT and SSR markers. Five QTL were detected in multiple environments associated with resistance to leaf rust designated as QLr.ifa-2AL, QLr.ifa-2BL, QLr.ifa-2BS, QLr.ifa-3BS, and QLr.ifa-5BL, and five for resistance to stripe rust QYr.ifa-2AL, QYr.ifa-2BL, QYr.ifa-3AS, QYr.ifa-3BS, and QYr.ifa-5A. For all QTL apart from two (QYr.ifa-3AS, QLr.ifa-5BL) Capo contributed the resistance improving allele. The leaf rust and stripe rust resistance QTL on 2AL, 2BL and 3BS mapped to the same chromosome positions, indicating either closely linked genes or pleiotropic gene action. These three multiple disease resistance QTL (QLr.ifa-2AL/QYr.ifa-2AL, QLr.ifa.2BL/QYr.ifa-2BL, QLr.ifa-3BS/QYr.ifa.3BS) potentially contribute novel resistance sources for stripe rust and leaf rust. The long-lasting resistance of Capo apparently rests upon a combination of several genes. The described germplasm, QTL and markers are applicable for simultaneous resistance improvement against leaf rust and stripe rust.

  15. A High-Density Genetic Linkage Map and QTL Fine Mapping for Body Weight in Crucian Carp (Carassius auratus Using 2b-RAD Sequencing

    Directory of Open Access Journals (Sweden)

    Haiyang Liu

    2017-08-01

    Full Text Available A high-resolution genetic linkage map is essential for a wide range of genetics and genomics studies such as comparative genomics analysis and QTL fine mapping. Crucian carp (Carassius auratus is widely distributed in Eurasia, and is an important aquaculture fish worldwide. In this study, a high-density genetic linkage map was constructed for crucian carp using 2b-RAD technology. The consensus map contains 8487 SNP markers, assigning to 50 linkage groups (LGs and spanning 3762.88 cM, with an average marker interval of 0.44 cM and genome coverage of 98.8%. The female map had 4410 SNPs, and spanned 3500.42 cM (0.79 cM/marker, while the male map had 4625 SNPs and spanned 3346.33 cM (0.72 cM/marker. The average recombination ratio of female to male was 2.13:1, and significant male-biased recombination suppressions were observed in LG47 and LG49. Comparative genomics analysis revealed a clear 2:1 syntenic relationship between crucian carp LGs and chromosomes of zebrafish and grass carp, and a 1:1 correspondence, but extensive chromosomal rearrangement, between crucian carp and common carp, providing evidence that crucian carp has experienced a fourth round of whole genome duplication (4R-WGD. Eight chromosome-wide QTL for body weight at 2 months after hatch were detected on five LGs, explaining 10.1–13.2% of the phenotypic variations. Potential candidate growth-related genes, such as an EGF-like domain and TGF-β, were identified within the QTL intervals. This high-density genetic map and QTL analysis supplies a basis for genome evolutionary studies in cyprinid fishes, genome assembly, and QTL fine mapping for complex traits in crucian carp.

  16. Evaluation of rhizobacterial indicators of tobacco black root rot suppressiveness in farmers' fields

    Czech Academy of Sciences Publication Activity Database

    Kyselková, Martina; Almario, J.; Kopecký, J.; Ságová-Marečková, M.; Haurat, J.; Muller, D.; Grundmann, G.L.; Moënne-Loccoz, Y.

    2014-01-01

    Roč. 6, č. 4 (2014), s. 346-353 ISSN 1758-2229 Institutional support: RVO:60077344 Keywords : rhizobacterial indicators * tobacco black root rot suppressiveness * farmers' fields Subject RIV: EH - Ecology, Behaviour Impact factor: 3.293, year: 2014

  17. Molecular Detection of Monilinia fructigena as Causal Agent of Brown Rot on Quince

    Directory of Open Access Journals (Sweden)

    Jovana Hrustić

    2012-01-01

    Full Text Available Species of the genus Monilinia are important causal agents of fruit rot on pome and stone fruits in Serbia. The pathogen is very harmful, especially on small properties and cottage plantations where intensive control measures are not applied. Quince is importanthost for the pathogens of this genus. During spring 2010, intensive occurrence of mummified fruits overwintering on branches of the quince was observed. The pathogen was isolated using standard phytopathological methods. Pathogenicity of eight obtained isolates was tested by artificial inoculation of injured apple fruits. Identification was performed according to pathogenic, morphological and ecological properties, and was confirmed by Multiplex polimeraze chain reaction, PCR. All the isolates studied caused brown rot on inoculated apple fruits. The isolates form light yellow colonies with lobate margins,with single-celled, transparent, elliptical or oval conidia in chains, regardless temperature or light presence. Sclerotia are observed in 14 days old cultures. The highest growth rate of most of the isolates is at 27°C and in dark. Based on studied pathogenic, morphological and ecological characteristics, it was found that the Monilinia fructigena is causal agent of brown rot of quince. Using specific primers (MO368-5, MO368-8R, MO368-10R, Laxa-R2for detection of Monilinia species in Multiplex PCR reaction, the expected fragment 402 bp in size was amplified, which confirmed that the studied isolates belonged to the speciesM. fructigena.

  18. Integrated management of foot rot of lentil using biocontrol agents under field condition.

    Science.gov (United States)

    Hannan, M A; Hasan, M M; Hossain, I; Rahman, S M E; Ismail, Alhazmi Mohammed; Oh, Deog-Hwan

    2012-07-01

    The efficacy of cowdung, Bangladesh Institute of Nuclear Agriculture (BINA)-biofertilizer, and Bangladesh Agricultural University (BAU)-biofungicide, alone or in combination, was evaluated for controlling foot rot disease of lentil. The results exhibited that BINA-biofertilizer and BAUbiofungicide (peat soil-based Rhizobium leguminosarum and black gram bran-based Trichoderma harzianum) are compatible and have combined effects in controlling the pathogenic fungi Fusarium oxysporum and Sclerotium rolfsii, which cause the root rot of lentil. Cowdung mixing with soil (at 5 t/ha) during final land preparation and seed coating with BINA-biofertilizer and BAU-biofungicide (at 2.5% of seed weight) before sowing recorded 81.50% field emergence of lentil, which showed up to 19.85% higher field emergence over the control. Post-emergence deaths of plants due to foot rot disease were significantly reduced after combined seed treatment with BINA-biofertilizer and BAU-biofungicide. Among the treatments used, only BAU-biofungicide as the seed treating agent resulted in higher plant stand (84.82%). Use of BINA-biofertilizer and BAU-biofungicide as seed treating biocontrol agents and application of cowdung in the soil as an organic source of nutrient resulted in higher shoot and root lengths, and dry shoot and root weights of lentil. BINA-biofertilizer significantly increased the number of nodules per plant and nodules weight of lentil. Seeds treating with BAUbiofungicide and BINA-biofertilizer and soil amendment with cowdung increased the biomass production of lentil up to 75.56% over the control.

  19. QTL mapping of combining ability and heterosis of agronomic traits in rice backcross recombinant inbred lines and hybrid crosses.

    Directory of Open Access Journals (Sweden)

    Zhen Qu

    Full Text Available BACKGROUND: Combining ability effects are very effective genetic parameters in deciding the next phase of breeding programs. Although some breeding strategies on the basis of evaluating combining ability have been utilized extensively in hybrid breeding, little is known about the genetic basis of combining ability. Combining ability is a complex trait that is controlled by polygenes. With the advent and development of molecular markers, it is feasible to evaluate the genetic bases of combining ability and heterosis of elite rice hybrids through QTL analysis. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we first developed a QTL-mapping method for dissecting combining ability and heterosis of agronomic traits. With three testcross populations and a BCRIL population in rice, biometric and QTL analyses were conducted for ten agronomic traits. The significance of general combining ability and special combining ability for most of the traits indicated the importance of both additive and non-additive effects on expression levels. A large number of additive effect QTLs associated with performance per se of BCRIL and general combining ability, and dominant effect QTLs associated with special combining ability and heterosis were identified for the ten traits. CONCLUSIONS/SIGNIFICANCE: The combining ability of agronomic traits could be analyzed by the QTL mapping method. The characteristics revealed by the QTLs for combining ability of agronomic traits were similar with those by multitudinous QTLs for agronomic traits with performance per se of BCRIL. Several QTLs (1-6 in this study were identified for each trait for combining ability. It demonstrated that some of the QTLs were pleiotropic or linked tightly with each other. The identification of QTLs responsible for combining ability and heterosis in the present study provides valuable information for dissecting genetic basis of combining ability.

  20. Registered plant list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...the Plant DB link list in simple search page) Genome analysis methods Presence or... absence of Genome analysis methods information in this DB (link to the Genome analysis methods information ...base Site Policy | Contact Us Registered plant list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  1. Response of cultivars of malanga (Xanthosoma sagittifolium (L. Schott to dry rot

    Directory of Open Access Journals (Sweden)

    Ernesto Espinosa Cuéllar

    2017-01-01

    Full Text Available Malanga (Xanthosoma sagittifolium (L. Schott is an important food crop for over 400 million people in the tropics and subtropics. In order to determine the response of different varieties of malanga Xanthosoma to dry rot, a series of experiments were conducted in the period between 2012 and 2014. The experiments were performed on loamy Soil at the National Research Institute in Tropical Crops and Roots (INIVIT. We determined the incidence and severity of damage, yields and percent of losses at harvest. The lowest values of incidence and the highest total return was achieved in clons ‘INIVIT MX-95-2’, ‘INIVIT MX-95-1’ and ‘INIVIT MX-2007’. Clones of malanga Xanthosoma belonging to the group purple, showed lower incidence that of white and yellow groups. These results will allow selecting cultivars of malanga with greater resistance to the dry rot and with this to diminish the losses in the harvest.

  2. Efficacy of four plant extracts in the control of root rot disease of ...

    African Journals Online (AJOL)

    Garcinia cola) and neem (Azadirachta indica) extracts in the control of root rot of cowpea caused by Pythium aphanidermatum was carried out in vitro and in the field (in vivo). They were evaluated for their antifungal activity over P.

  3. Isolation, Characterization, and Identification of Biological Control Agent for Potato Soft Rot in Bangladesh

    Science.gov (United States)

    Rahman, M. M.; Ali, M. E.; Khan, A. A.; Akanda, A. M.; Uddin, Md. Kamal; Hashim, U.; Abd Hamid, S. B.

    2012-01-01

    A total of 91 isolates of probable antagonistic bacteria of potato soft rot bacterium Erwinia carotovora subsp. carotovora (Ecc) were extracted from rhizospheres and endophytes of various crop plants, different soil varieties, and atmospheres in the potato farming areas of Bangladesh. Antibacterial activity of the isolated probable antagonistic bacteria was tested in vitro against the previously identified most common and most virulent soft rot causing bacterial strain Ecc P-138. Only two isolates E-45 and E-65 significantly inhibited the in vitro growth of Ecc P-138. Physiological, biochemical, and carbon source utilization tests identified isolate E-65 as a member of the genus Bacillus and the isolate E-45 as Lactobacillus sp. The stronger antagonistic activity against Ecc P-138 was found in E-65 in vitro screening and storage potatoes. E-65 reduced the soft rot infection to 22-week storage potatoes of different varieties by 32.5–62.5% in model experiment, demonstrating its strong potential to be used as an effective biological control agent for the major pectolytic bacteria Ecc. The highest (62.5%) antagonistic effect of E-65 was observed in the Granola and the lowest (32.7%) of that was found in the Cardinal varieties of the Bangladeshi potatoes. The findings suggest that isolate E-65 could be exploited as a biocontrol agent for potato tubers. PMID:22645446

  4. Isolation, Characterization, and Identification of Biological Control Agent for Potato Soft Rot in Bangladesh

    Directory of Open Access Journals (Sweden)

    M. M. Rahman

    2012-01-01

    Full Text Available A total of 91 isolates of probable antagonistic bacteria of potato soft rot bacterium Erwinia carotovora subsp. carotovora (Ecc were extracted from rhizospheres and endophytes of various crop plants, different soil varieties, and atmospheres in the potato farming areas of Bangladesh. Antibacterial activity of the isolated probable antagonistic bacteria was tested in vitro against the previously identified most common and most virulent soft rot causing bacterial strain Ecc P-138. Only two isolates E-45 and E-65 significantly inhibited the in vitro growth of Ecc P-138. Physiological, biochemical, and carbon source utilization tests identified isolate E-65 as a member of the genus Bacillus and the isolate E-45 as Lactobacillus sp. The stronger antagonistic activity against Ecc P-138 was found in E-65 in vitro screening and storage potatoes. E-65 reduced the soft rot infection to 22-week storage potatoes of different varieties by 32.5–62.5% in model experiment, demonstrating its strong potential to be used as an effective biological control agent for the major pectolytic bacteria Ecc. The highest (62.5% antagonistic effect of E-65 was observed in the Granola and the lowest (32.7% of that was found in the Cardinal varieties of the Bangladeshi potatoes. The findings suggest that isolate E-65 could be exploited as a biocontrol agent for potato tubers.

  5. Trichoderma spp. decrease Fusarium root rot in common bean

    Directory of Open Access Journals (Sweden)

    Hudson Teixeira

    2012-12-01

    Full Text Available The effectiveness of six Trichoderma-based commercial products (TCP in controlling Fusarium root rot (FRR in common bean was assessed under field conditions. Three TCP, used for seed treatment or applied in the furrow, increased seedling emergence as much as the fungicide fludioxonil. FRR incidence was not affected, but all TCP and fludioxonil reduced the disease severity, compared to control. Application of Trichoderma-based products was as effective as that of fludioxonil in FRR management.

  6. Chitosan and oligochitosan enhance ginger (Zingiber officinale Roscoe) resistance to rhizome rot caused by Fusarium oxysporum in storage.

    Science.gov (United States)

    Liu, Yiqing; Wisniewski, Michael; Kennedy, John F; Jiang, Yusong; Tang, Jianmin; Liu, Jia

    2016-10-20

    The ability of chitosan and oligochitosan to enhance ginger (Zingiber officinale) resistance to rhizome rot caused by Fusarium oxysporum in storage was investigated. Both chitosan and oligochitosan at 1 and 5g/L significantly inhibited rhizome rot, with the best control at 5g/L. Chitosan and oligochitosan applied at 5g/L also reduced weight loss, measured as a decrease in fresh weight, but did not affect soluble solids content or titratable acidity of rhizomes. The two compounds applied at 5g/L induced β-1,3-glucanase and phenylalanine ammonia-lyase enzyme activity and the transcript levels of their coding genes, as well as the total phenolic compounds in rhizome tissues. Therefore, the ability of chitosan and oligochitosan to reduce rot in stored rhizomes may be associated with their ability to induce defense responses in ginger. These results have practical implications for the application of chitosan and oligochitosan to harvested ginger rhizomes to reduce postharvest losses. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease.

    Directory of Open Access Journals (Sweden)

    James E Peters

    2016-03-01

    Full Text Available Genome-wide association studies (GWAS have transformed our understanding of the genetics of complex traits such as autoimmune diseases, but how risk variants contribute to pathogenesis remains largely unknown. Identifying genetic variants that affect gene expression (expression quantitative trait loci, or eQTLs is crucial to addressing this. eQTLs vary between tissues and following in vitro cellular activation, but have not been examined in the context of human inflammatory diseases. We performed eQTL mapping in five primary immune cell types from patients with active inflammatory bowel disease (n = 91, anti-neutrophil cytoplasmic antibody-associated vasculitis (n = 46 and healthy controls (n = 43, revealing eQTLs present only in the context of active inflammatory disease. Moreover, we show that following treatment a proportion of these eQTLs disappear. Through joint analysis of expression data from multiple cell types, we reveal that previous estimates of eQTL immune cell-type specificity are likely to have been exaggerated. Finally, by analysing gene expression data from multiple cell types, we find eQTLs not previously identified by database mining at 34 inflammatory bowel disease-associated loci. In summary, this parallel eQTL analysis in multiple leucocyte subsets from patients with active disease provides new insights into the genetic basis of immune-mediated diseases.

  8. Bacteriophages of Soft Rot Enterobacteriaceae-a minireview.

    Science.gov (United States)

    Czajkowski, Robert

    2016-01-01

    Soft rot Enterobacteriaceae (Pectobacterium spp. and Dickeya spp., formerly pectinolytic Erwinia spp.) are ubiquitous necrotrophic bacterial pathogens that infect a large number of different plant species worldwide, including economically important crops. Despite the fact that these bacteria have been studied for more than 50 years, little is known of their corresponding predators: bacteriophages, both lytic and lysogenic. The aim of this minireview is to critically summarize recent ecological, biological and molecular research on bacteriophages infecting Pectobacterium spp. and Dickeya spp. with the main focus on current and future perspectives in that field. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. Modification of wheat straw lignin by solid state fermentation with white-rot fungi

    NARCIS (Netherlands)

    Dinis, M.J.; Bezerra, R.M.F.; Nunes, F.; Dias, A.A.; Guedes, C.; Ferreira, L.M.M.; Cone, J.W.; Marques, G.S.M.; Barros, A.R.N.; Rodrigues, M.A.M.

    2009-01-01

    The potential of crude enzyme extracts, obtained from solid state cultivation of four white-rot fungi (Trametes versicolor, Bjerkandera adusta, Ganoderma applanatum and Phlebia rufa), was exploited to modify wheat straw cell wall. At different fermentation times, manganese-dependent peroxidase

  10. Draft Genome Sequences of Dickeya sp. Isolates B16 (NIB Z 2098) and S1 (NIB Z 2099) Causing Soft Rot of Phalaenopsis Orchids.

    Science.gov (United States)

    Alič, Špela; Naglič, Tina; Llop, Pablo; Toplak, Nataša; Koren, Simon; Ravnikar, Maja; Dreo, Tanja

    2015-09-10

    The genus Dickeya contains bacteria causing soft rot of economically important crops and ornamental plants. Here, we report the draft genome sequences of two Dickeya sp. isolates from rotted leaves of Phalaenopsis orchids. Copyright © 2015 Alič et al.

  11. Optimization of Laccase Production using White Rot Fungi and Agriculture Wastes in Solid State Fermentation

    Directory of Open Access Journals (Sweden)

    Hendro Risdianto

    2012-07-01

    Full Text Available Laccase has been produced in a solid state fermentation (SSF using white rot fungi and various lignocellulosic based substrates. White rot fungi used were Marasmius sp, Trametes hirsuta, Trametes versicolor and Phanerochaete crysosporium. The solid substrates employed in this research were collected from agriculture waste which were empty fruit bunches (EFB, rice straw, corn cob, and rice husk. The objective of this research was to determine the most promising fungus, the best solid substrate and the optimal conditions for the production of laccase. The results showed that Marasmius sp. on all solid substrates displayed higher laccase activity than that of any other strain of white rot fungi. Marasmius sp. and solid substrate of rice straw demonstrated the highest laccase activity of 1116.11 U/L on day 10. Three significant factors, i.e. pH, temperature and yeast extract concentration were studied by response surface method on laccase production using Marasmius sp and rice straw. The optimized conditions were pH, temperature and yeast extract concentration of 4.9, 31ºC and 0.36 g/L respectively. The fermentation of Marasmius sp. in SSF on agricultural waste shows a great potential for the production of laccase.

  12. Control of postharvest Botrytis fruit rot of strawberry by volatile organic compounds of Candida intermedia.

    Science.gov (United States)

    Huang, R; Li, G Q; Zhang, J; Yang, L; Che, H J; Jiang, D H; Huang, H C

    2011-07-01

    A study was conducted to identify volatile organic compounds or volatiles produced by Candida intermedia strain C410 using gas chromatography-mass spectrometry, and to determine efficacy of the volatiles of C. intermedia in suppression of conidial germination and mycelial growth of Botrytis cinerea and control of Botrytis fruit rot of strawberry. Results showed that, among 49 volatiles (esters, alcohols, alkenes, alkanes, alkynes, organic acids, ketones, and aldehydes) identified from C. intermedia cultures on yeast extract peptone dextrose agar, two compounds, 1,3,5,7-cyclooctatetraene and 3-methyl-1-butanol, were the most abundant. Synthetic chemicals of 1,3,5,7-cyclooctatetraene; 3-methyl-1-butanol; 2-nonanone; pentanoic acid, 4-methyl-, ethyl ester; 3-methyl-1-butanol, acetate; acetic acid, pentyl ester; and hexanoic acid, ethyl ester were highly inhibitory to conidial germination and mycelial growth of B. cinerea. Inhibition of conidial germination and mycelial growth of B. cinerea by volatiles of C. intermedia was also observed. Meanwhile, results showed that incidence and severity of Botrytis fruit rot of strawberry was significantly (P intermedia cultures or C. intermedia-infested strawberry fruit. These results suggest that the volatiles of C. intermedia C410 are promising biofumigants for control of Botrytis fruit rot of strawberry.

  13. Fourier Transform Infrared Radiation Spectroscopy Applied for Wood Rot Decay and Mould Fungi Growth Detection

    Directory of Open Access Journals (Sweden)

    Bjørn Petter Jelle

    2012-01-01

    Full Text Available Material characterization may be carried out by the attenuated total reflectance (ATR Fourier transform infrared (FTIR radiation spectroscopical technique, which represents a powerful experimental tool. The ATR technique may be applied on both solid state materials, liquids, and gases with none or only minor sample preparations, also including materials which are nontransparent to IR radiation. This facilitation is made possible by pressing the sample directly onto various crystals, for example, diamond, with high refractive indices, in a special reflectance setup. Thus ATR saves time and enables the study of materials in a pristine condition, that is, the comprehensive sample preparation by pressing thin KBr pellets in traditional FTIR transmittance spectroscopy is hence avoided. Materials and their ageing processes, both ageing by natural and accelerated climate exposure, decomposition and formation of chemical bonds and products, may be studied in an ATR-FTIR analysis. In this work, the ATR-FTIR technique is utilized to detect wood rot decay and mould fungi growth on various building material substrates. An experimental challenge and aim is to be able to detect the wood rot decay and mould fungi growth at early stages when it is barely visible to the naked eye. Another goal is to be able to distinguish between various species of fungi and wood rot.

  14. Characterization of calla Lily sot rot caused by Pectobacterium Carotovorum subsp. Carotovorum ZT0505 bacterial growth and pectate lyase activity under different conditions.

    NARCIS (Netherlands)

    Ni, L.; Guo, L.; Custers, J.B.M.; Zhang, L.

    2010-01-01

    Soft rot is a major disease of calla lily (Zantedeschia spp.) and other important crops worldwide. In this report, the bacterial isolate ZT0505 proved to be a soft rot pathogen of calla lily growing around Kunming (subtropical China) and was identified as Pectobacterium carotovorum subsp.

  15. Mechanisms of qualitative and quantitative resistance to Aphanomyces root rot in alfalfa

    Science.gov (United States)

    Aphanomyces root rot (ARR), caused by Aphanomyces euteiches, is one of the most important diseases of alfalfa (Medicago sativa) in the United States. Two races of the pathogen are currently recognized. Most modern alfalfa cultivars have high levels of resistance to race 1 but few cultivars have resi...

  16. Isolation and identification of bacteria causing blackleg and soft rot of potato

    Science.gov (United States)

    Both Dickeya and Pectobacterium spp. are important causal agents of blackleg and soft rot of potato. To understand the outbreak of blackleg in the Northeastern U.S. in 2015, samples were collected from symptomatic plants, dormant tubers, and surface water in 2016 and 2017. Diseased plant samples wer...

  17. Earwigs ( Labidura riparia) mimic rotting-flesh odor to deceive vertebrate predators

    Science.gov (United States)

    Byers, John A.

    2015-08-01

    Many insects repel predators with caustic chemicals, while insects mimicking odors of wastes/dead insects to fool predators have not been documented. We found that the shore earwig, Labidura riparia (Dermaptera: Labiduridae) when bitten by anole lizards, Anolis carolinenesus, spits a rotting-flesh odor that deceives these insectivores into rejecting prey. Once a lizard attacked and rejected an earwig, the lizard did not attack another earwig during several weeks despite consuming other prey, indicating associative learning after one trial. The fetid odor was found in the head-prothorax containing salivary glands of both male and female earwigs and was comprised of ˜100 ng dimethyl disulfide and ˜600 ng dimethyl trisulfide. Nymphs had odorous sulfides after prolonged attacks by harvester ants, Pogonomyrmex rugosus, who were only deterred by the earwig's forceps. Sulfides released by the earwig are similar to odors of carrion/feces, which may be innately repulsive to some vertebrate predators. The mean initial discharge percentage (IDP) of sulfides from a cohort of earwigs was 62 %; however, IDPs of individuals were highly variable (3-99 %; mean 57 %). The discharge refill time (DRT) to refill 50 % of the earwig's allomone reservoir was estimated at 13 h. A positive relationship in sulfide amounts with body weight was found only in females in 2009, suggesting metabolic cost tradeoffs were revealed when sulfide content was half that in 2010. This is the first report of insects releasing sulfur-containing compounds that may mimic carrion-fecal odors as a deceptive defense against vertebrate predators.

  18. Molecular identification and potential of an isolate of white rot fungi in bioremediation of petroleum contaminated soils

    Directory of Open Access Journals (Sweden)

    Maryam Mohammadi-sichani

    2017-06-01

    Full Text Available Introduction:Elimination or reduction of petroleum hydrocarbons from natural resources such as water and soil is a serious problem of countries, particularly oil-rich countries of the world. Using white rotting fungi compost for bioremediation of soils contaminated by petroleum hydrocarbons is effective. The aim of this study is molecular identification and potential of anisolate of white rot fungi in bioremediation of petroleum contaminated soils. Materials and methods: Spent compost of white rotting fungi was inoculated with petroleum contaminated soil into 3%, 5% and 10% (w/w. Treatments were incubated at 25-23 °C for 3 months. Reduction of petroleum hydrocarbons in treated soil was determined by gas chromatography. Ecotoxicity of soil was evaluated by seed germination test. Results: Based on the genome sequence of 18s rRNA, it is revealed that this isolate is Ganoderma lucidum and this isolate is deposited as accession KX525204 in the Gene Bank database. Reduction of petroleum hydrocarbons in soil treated with compost (3, 5 and 10% ranged from 42% to 71%. The germination index (% in ecotoxicity tests ranged from 20.8% to 70.8%. Gas chromatography results also showed a decrease in soil Hydrocarbons compounds. Discussion and conclusion: The compost of Ganoderma lucidum, a white rot fungus, has a potential ability to remove petroleum hydrocarbons in contaminated soil. Removal of hydrocarbons was increased with increase in compost mixed with contaminated soil. Petroleum contaminated soil amended with spent compost of G.lucidum 10% during three months is appropriate to remove this pollutant.

  19. Pseudomonas cichorii as the causal agent of midrib rot, an emerging disease of greenhouse-grown butterhead lettuce in Flanders.

    Science.gov (United States)

    Cottyn, Bart; Heylen, Kim; Heyrman, Jeroen; Vanhouteghem, Katrien; Pauwelyn, Ellen; Bleyaert, Peter; Van Vaerenbergh, Johan; Höfte, Monica; De Vos, Paul; Maes, Martine

    2009-05-01

    Bacterial midrib rot of greenhouse-grown butterhead lettuce (Lactuca sativa L. var. capitata) is an emerging disease in Flanders (Belgium) and fluorescent pseudomonads are suspected to play an important role in the disease. Isolations from infected lettuces, collected from 14 commercial greenhouses in Flanders, yielded 149 isolates that were characterized polyphasically, which included morphological characteristics, pigmentation, pathogenicity tests by both injection and spraying of lettuce, LOPAT characteristics, FAME analysis, BOX-PCR fingerprinting, 16S rRNA and rpoB gene sequencing, as well as DNA-DNA hybridization. Ninety-eight isolates (66%) exhibited a fluorescent pigmentation and were associated with the genus Pseudomonas. Fifty-five of them induced an HR+ (hypersensitive reaction in tobacco leaves) response. The other 43 fluorescent isolates were most probably saprophytic bacteria and about half of them were able to cause rot on potato tuber slices. BOX-PCR genomic fingerprinting was used to assess the genetic diversity of the Pseudomonas midrib rot isolates. The delineated BOX-PCR patterns matched quite well with Pseudomonas morphotypes defined on the basis of colony appearance and variation in fluorescent pigmentation. 16S rRNA and rpoB gene sequence analyses allowed most of the fluorescent isolates to be allocated to Pseudomonas, and they belonged to either the Pseudomonas fluorescens group, Pseudomonas putida group, or the Pseudomonas cichorii/syringae group. In particular, the isolates allocated to this latter group constituted the vast majority of HR+ isolates and were identified as P. cichorii by DNA-DNA hybridization. They were demonstrated by spray-inoculation tests on greenhouse-grown lettuce to induce the midrib rot disease and could be re-isolated from lesions of inoculated plants. Four HR+ non-fluorescent isolates associated with one sample that showed an atypical midrib rot were identified as Dickeya sp.

  20. Treatment of micropollutants in municipal wastewater using white-rot fungi

    OpenAIRE

    Margot, Jonas; Vargas, Micaela; Contijoch, Andreu; Barry, David Andrew; Holliger, Christof

    2014-01-01

    Treatment of micropollutants such as pharmaceuticals and pesticides in municipal wastewater is challenging due to their very low concentrations (ng/l to µg/l), their relatively low biodegradability, and their different physico-chemical characteristics. One potential way to improve micropollutant biodegradation in wastewater treatment plant (WWTP) effluent is by using microorganisms such as white-rot fungi that produce powerful unspecific oxidative exo-enzymes (laccase, peroxidase) that are ab...