Multi-Population Selective Genotyping to Identify Soybean [Glycine max (L.) Merr.] Seed Protein and Oil QTLs.

Science.gov (United States)

Phansak, Piyaporn; Soonsuwon, Watcharin; Hyten, David L; Song, Qijian; Cregan, Perry B; Graef, George L; Specht, James E

2016-06-01

Plant breeders continually generate ever-higher yielding cultivars, but also want to improve seed constituent value, which is mainly protein and oil, in soybean [Glycine max (L.) Merr.]. Identification of genetic loci governing those two traits would facilitate that effort. Though genome-wide association offers one such approach, selective genotyping of multiple biparental populations offers a complementary alternative, and was evaluated here, using 48 F2:3 populations (n = ∼224 plants) created by mating 48 high protein germplasm accessions to cultivars of similar maturity, but with normal seed protein content. All F2:3 progeny were phenotyped for seed protein and oil, but only 22 high and 22 low extreme progeny in each F2:3 phenotypic distribution were genotyped with a 1536-SNP chip (ca 450 bimorphic SNPs detected per mating). A significant quantitative trait locus (QTL) on one or more chromosomes was detected for protein in 35 (73%), and for oil in 25 (52%), of the 48 matings, and these QTL exhibited additive effects of ≥ 4 g kg(-1) and R(2) values of 0.07 or more. These results demonstrated that a multiple-population selective genotyping strategy, when focused on matings between parental phenotype extremes, can be used successfully to identify germplasm accessions possessing large-effect QTL alleles. Such accessions would be of interest to breeders to serve as parental donors of those alleles in cultivar development programs, though 17 of the 48 accessions were not unique in terms of SNP genotype, indicating that diversity among high protein accessions in the germplasm collection is less than what might ordinarily be assumed. Copyright © 2016 Phansak et al.

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.

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

Science.gov (United States)

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

2006-02-01

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

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

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.

Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high-density linkage mapping.

Science.gov (United States)

Patil, Gunvant; Vuong, Tri D; Kale, Sandip; Valliyodan, Babu; Deshmukh, Rupesh; Zhu, Chengsong; Wu, Xiaolei; Bai, Yonghe; Yungbluth, Dennis; Lu, Fang; Kumpatla, Siva; Grover Shannon, J; Varshney, Rajeev K; Nguyen, Henry T

2018-04-04

The cultivated [Glycine max (L) Merr.] and wild [Glycine soja Siebold & Zucc.] soybean species comprise wide variation in seed composition traits. Compared to wild soybean, cultivated soybean contains low protein, high oil and high sucrose. In this study, an inter-specific population was derived from a cross between G. max (Williams 82) and G. soja (PI 483460B). This recombinant inbred line (RIL) population of 188 lines was sequenced at 0.3x depth. Based on 91,342 single nucleotide polymorphisms (SNPs), recombination events in RILs were defined, and a high-resolution bin map was developed (4,070 bins). In addition to bin mapping, QTL analysis for protein, oil and sucrose was performed using 3,343 polymorphic SNPs (3K-SNP), derived from Illumina Infinium BeadChip sequencing platform. The QTL regions from both platforms were compared and a significant concordance was observed between bin and 3K-SNP markers. Importantly, the bin map derived from next generation sequencing technology enhanced mapping resolution (from 1325 Kb to 50 Kb). A total of 5, 9 and 4 QTLs were identified for protein, oil and sucrose content, respectively and some of the QTLs coincided with soybean domestication related genomic loci. The major QTL for protein and oil was mapped on Chr. 20 (qPro_20) and suggested negative correlation between oil and protein. In terms of sucrose content, a novel and major QTL was identified on Chr. 8 (qSuc_08) and harbors putative genes involved in sugar transport. In addition, genome-wide association (GWAS) using 91,342 SNPs confirmed the genomic loci derived from QTL mapping. A QTL based haplotype using whole genome resequencing of 106 diverse soybean lines identified unique allelic variation in wild soybean that could be utilized to widen the genetic base in cultivated soybean. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

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.

Mitogen-Activated Protein Kinase Kinase 3 Regulates Seed Dormancy in Barley.

Science.gov (United States)

Nakamura, Shingo; Pourkheirandish, Mohammad; Morishige, Hiromi; Kubo, Yuta; Nakamura, Masako; Ichimura, Kazuya; Seo, Shigemi; Kanamori, Hiroyuki; Wu, Jianzhong; Ando, Tsuyu; Hensel, Goetz; Sameri, Mohammad; Stein, Nils; Sato, Kazuhiro; Matsumoto, Takashi; Yano, Masahiro; Komatsuda, Takao

2016-03-21

Seed dormancy has fundamental importance in plant survival and crop production; however, the mechanisms regulating dormancy remain unclear [1-3]. Seed dormancy levels generally decrease during domestication to ensure that crops successfully germinate in the field. However, reduction of seed dormancy can cause devastating losses in cereals like wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) due to pre-harvest sprouting, the germination of mature seed (grain) on the mother plant when rain occurs before harvest. Understanding the mechanisms of dormancy can facilitate breeding of crop varieties with the appropriate levels of seed dormancy [4-8]. Barley is a model crop [9, 10] and has two major seed dormancy quantitative trait loci (QTLs), SD1 and SD2, on chromosome 5H [11-19]. We detected a QTL designated Qsd2-AK at SD2 as the single major determinant explaining the difference in seed dormancy between the dormant cultivar "Azumamugi" (Az) and the non-dormant cultivar "Kanto Nakate Gold" (KNG). Using map-based cloning, we identified the causal gene for Qsd2-AK as Mitogen-activated Protein Kinase Kinase 3 (MKK3). The dormant Az allele of MKK3 is recessive; the N260T substitution in this allele decreases MKK3 kinase activity and appears to be causal for Qsd2-AK. The N260T substitution occurred in the immediate ancestor allele of the dormant allele, and the established dormant allele became prevalent in barley cultivars grown in East Asia, where the rainy season and harvest season often overlap. Our findings show fine-tuning of seed dormancy during domestication and provide key information for improving pre-harvest sprouting tolerance in barley and wheat. Copyright © 2016 Elsevier Ltd. All rights reserved.

Seed Dormancy in Arabidopsis Requires Self-Binding Ability of DOG1 Protein and the Presence of Multiple Isoforms Generated by Alternative Splicing.

Directory of Open Access Journals (Sweden)

Kazumi Nakabayashi

2015-12-01

Full Text Available The Arabidopsis protein DELAY OF GERMINATION 1 (DOG1 is a key regulator of seed dormancy, which is a life history trait that determines the timing of seedling emergence. The amount of DOG1 protein in freshly harvested seeds determines their dormancy level. DOG1 has been identified as a major dormancy QTL and variation in DOG1 transcript levels between accessions contributes to natural variation for seed dormancy. The DOG1 gene is alternatively spliced. Alternative splicing increases the transcriptome and proteome diversity in higher eukaryotes by producing transcripts that encode for proteins with altered or lost function. It can also generate tissue specific transcripts or affect mRNA stability. Here we suggest a different role for alternative splicing of the DOG1 gene. DOG1 produces five transcript variants encoding three protein isoforms. Transgenic dog1 mutant seeds expressing single DOG1 transcript variants from the endogenous DOG1 promoter did not complement because they were non-dormant and lacked DOG1 protein. However, transgenic plants overexpressing single DOG1 variants from the 35S promoter could accumulate protein and showed complementation. Simultaneous expression of two or more DOG1 transcript variants from the endogenous DOG1 promoter also led to increased dormancy levels and accumulation of DOG1 protein. This suggests that single isoforms are functional, but require the presence of additional isoforms to prevent protein degradation. Subsequently, we found that the DOG1 protein can bind to itself and that this binding is required for DOG1 function but not for protein accumulation. Natural variation for DOG1 binding efficiency was observed among Arabidopsis accessions and contributes to variation in seed dormancy.

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

Science.gov (United States)

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

2005-11-01

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

Identification QTLs Controlling Genes for Se Uptake in Lentil Seeds.

Directory of Open Access Journals (Sweden)

Duygu Ates

Full Text Available Lentil (Lens culinaris Medik. is an excellent source of protein and carbohydrates and is also rich in essential trace elements for the human diet. Selenium (Se is an essential micronutrient for human health and nutrition, providing protection against several diseases and regulating important biological systems. Dietary intake of 55 μg of Se per day is recommended for adults, with inadequate Se intake causing significant health problems. The objective of this study was to identify and map quantitative trait loci (QTL of genes controlling Se accumulation in lentil seeds using a population of 96 recombinant inbred lines (RILs developed from the cross "PI 320937" × "Eston" grown in three different environments for two years (2012 and 2013. Se concentration in seed varied between 119 and 883 μg/kg. A linkage map consisting of 1,784 markers (4 SSRs, and 1,780 SNPs was developed. The map spanned a total length of 4,060.6 cM, consisting of 7 linkage groups (LGs with an average distance of 2.3 cM between adjacent markers. Four QTL regions and 36 putative QTL markers, with LOD scores ranging from 3.00 to 4.97, distributed across two linkage groups (LG2 and LG5 were associated with seed Se concentration, explaining 6.3-16.9% of the phenotypic variation.

QTL Analysis of Major Agronomic Traits in Soybean

Institute of Scientific and Technical Information of China (English)

CHEN Qing-shan; ZHANG Zhong-chen; LIU Chun-yan; XIN Da-wei; QIU Hong-mei; SHAN Da-peng; SHAN Cai-yun; HU Guo-hua

2007-01-01

Soybean is a main crop, and most agronomic traits of soybean are quantitative; therefore, there is very important studying and applying value to locating these traits. A F2:10 RIL population containing 154 lines, derived from the cross between Charleston as female and Dongnong 594 as male parent, were used in this experiment. A genetic linkage map was constructed with 164 SSR primers, which were screened with the two parents and amplified on the 154 lines. 12 agronomic traits different between the two parents were investigated, and QTLs of all the traits were analyzed using the software Windows QTL Cartographer V2.0. The agronomic traits included quality traits: protein content, oil content, and content of protein and oil; yield traits: pods per plant, seed weight per plant, arnd 100 seeds weight; and other agronomic traits: plant height, days to maturity, branches, nod number in main stem, average leaf length, and average leaf width. The results showed that 68 QTLs in total were found for the 12 agronomic traits. The number of QTLs per trait varied from 3 for the average leaf width to 11 for 100 seeds weight and plant height, and was 5.8 on average. Good accordance was seen in many QTLs between the results of this study and the results obtained by other similar studies; therefore, these QTLs may be valuable for molecular marker assistant selection in soybean. In this study, 68 major QTLs of 12 important traits of soybean were analyzed.

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.

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

Directory of Open Access Journals (Sweden)

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.

Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea.

Science.gov (United States)

Bajaj, Deepak; Saxena, Maneesha S; Kujur, Alice; Das, Shouvik; Badoni, Saurabh; Tripathi, Shailesh; Upadhyaya, Hari D; Gowda, C L L; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K; Parida, Swarup K

2015-03-01

Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5'-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Effects of gamma irradiation on chickpea seeds vis-a-vis total seed storage proteins, antioxidant activity and protein profiling.

Science.gov (United States)

Bhagyawant, S S; Gupta, N; Shrivastava, N

2015-10-23

The present work describes radiation—induced effects on seed composition vis—à—vis total seed proteins, antioxidant levels and protein profiling employing two dimensional gel electrophoresis (2D—GE) in kabuli and desi chickpea varities. Seeds were exposed to the radiation doses of 1,2,3,4 and 5 kGy. The total protein concentrations decreased and antioxidant levels were increased with increasing dose compared to control seed samples. Radiation induced effects were dose dependent to these seed parameters while it showed tolerance to 1 kGy dose. Increase in the dose was complimented with increase in antioxidant levels, like 5 kGy enhanced % scavenging activities in all the seed extracts. Precisely, the investigations reflected that the dose range from 2 to 5 kGy was effective for total seed storage proteins, as depicted quantitatively and qualitative 2D—GE means enhance antioxidant activities in vitro.

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

Directory of Open Access Journals (Sweden)

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

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.

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

Directory of Open Access Journals (Sweden)

Michael J. Fedoruk

2013-11-01

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

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....

Identification of loci governing eight agronomic traits using a GBS-GWAS approach and validation by QTL mapping in soya bean.

Science.gov (United States)

Sonah, Humira; O'Donoughue, Louise; Cober, Elroy; Rajcan, Istvan; Belzile, François

2015-02-01

Soya bean is a major source of edible oil and protein for human consumption as well as animal feed. Understanding the genetic basis of different traits in soya bean will provide important insights for improving breeding strategies for this crop. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of agronomic traits in soya bean. A genotyping-by-sequencing (GBS) approach was used to provide dense genome-wide marker coverage (>47,000 SNPs) for a panel of 304 short-season soya bean lines. A subset of 139 lines, representative of the diversity among these, was characterized phenotypically for eight traits under six environments (3 sites × 2 years). Marker coverage proved sufficient to ensure highly significant associations between the genes known to control simple traits (flower, hilum and pubescence colour) and flanking SNPs. Between one and eight genomic loci associated with more complex traits (maturity, plant height, seed weight, seed oil and protein) were also identified. Importantly, most of these GWAS loci were located within genomic regions identified by previously reported quantitative trait locus (QTL) for these traits. In some cases, the reported QTLs were also successfully validated by additional QTL mapping in a biparental population. This study demonstrates that integrating GBS and GWAS can be used as a powerful complementary approach to classical biparental mapping for dissecting complex traits in soya bean. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Electrophoretic studies on rape seed proteins

International Nuclear Information System (INIS)

Chaudry, M.A.; Starr, A.; Bibi, N.

1992-07-01

Electrophoresis is a technique which separates biological molecules on the basis of charge and mass properties. The technique is used for separation, purification, characterization and identification of molecules/ compounds. Two major objectives for applications of electrophoresis have been studied in this report i.e. characterization of rape seed proteins and enzymes and identification of rape seed cultivars by polyacrylamide gel electrophoresis (PAGE). Gamma irradiation is being successfully used to create genetic variability and germination which brought about definite changes in the rape seed proteins reflected in different bands. These differences could be used to study variability in crop plants. (A.B.)

A role for seed storage proteins in Arabidopsis seed longevity

NARCIS (Netherlands)

Nguyen, Thu-Phuong|info:eu-repo/dai/nl/328228818; Cueff, Gwendal; Hegedus, Dwayne D; Rajjou, Loïc; Bentsink, Leónie|info:eu-repo/dai/nl/241338735

2015-01-01

Proteomics approaches have been a useful tool for determining the biological roles and functions of individual proteins and identifying the molecular mechanisms that govern seed germination, vigour and viability in response to ageing. In this work the dry seed proteome of four Arabidopsis thaliana

Seed protein improvement in cereals and grain legumes

International Nuclear Information System (INIS)

1979-01-01

Based upon the recommendations of a panel of experts in 1968, the Joint FAO/IAEA Division of Atomic Energy in Food and Agriculture established an international programme to improve the protein content and quality in seed crops of importance to developing countries. Reports of previous meetings held under this programme have been published by the IAEA. The meeting on Seed Protein Improvement in Cereals and Grain Legumes, held in September 1978, marked the formal end of the FAO/IAEA/GSF Co-ordinated Research Programme on Seed Protein Improvement. It reviewed the progress achieved. Volume I covers 27 papers. Following a review of the world protein and nutritional situation, the contributions are grouped under the main headings of the need for and use of variability in protein characteristics; genetics, biochemistry and physiology of seed storage proteins; analytical and nutritional techniques; and coordinated research programmes under a joint FAO/IAEA/GSF programme on grain protein improvement. Individual papers of direct relevance are cited as separate entries in INIS

Association mapping of seed quality traits using the Canadian flax (Linum usitatissimum L.) core collection.

Science.gov (United States)

Soto-Cerda, Braulio J; Duguid, Scott; Booker, Helen; Rowland, Gordon; Diederichsen, Axel; Cloutier, Sylvie

2014-04-01

The identification of stable QTL for seed quality traits by association mapping of a diverse panel of linseed accessions establishes the foundation for assisted breeding and future fine mapping in linseed. Linseed oil is valued for its food and non-food applications. Modifying its oil content and fatty acid (FA) profiles to meet market needs in a timely manner requires clear understanding of their quantitative trait loci (QTL) architectures, which have received little attention to date. Association mapping is an efficient approach to identify QTL in germplasm collections. In this study, we explored the quantitative nature of seed quality traits including oil content (OIL), palmitic acid, stearic acid, oleic acid, linoleic acid (LIO) linolenic acid (LIN) and iodine value in a flax core collection of 390 accessions assayed with 460 microsatellite markers. The core collection was grown in a modified augmented design at two locations over 3 years and phenotypic data for all seven traits were obtained from all six environments. Significant phenotypic diversity and moderate to high heritability for each trait (0.73-0.99) were observed. Most of the candidate QTL were stable as revealed by multivariate analyses. Nine candidate QTL were identified, varying from one for OIL to three for LIO and LIN. Candidate QTL for LIO and LIN co-localized with QTL previously identified in bi-parental populations and some mapped nearby genes known to be involved in the FA biosynthesis pathway. Fifty-eight percent of the QTL alleles were absent (private) in the Canadian cultivars suggesting that the core collection possesses QTL alleles potentially useful to improve seed quality traits. The candidate QTL identified herein will establish the foundation for future marker-assisted breeding in linseed.

Genetic variation and inheritance of phytosterol and oil content in a doubled haploid population derived from the winter oilseed rape Sansibar × Oase cross.

Science.gov (United States)

Teh, Lishia; Möllers, Christian

2016-01-01

Identification of QTL for phytosterol content, oil content, fatty acids content, protein content of defatted meal, and seed weight by multiple interval mapping in a Brassica napus DH population. Phytosterols are minor seed constituents in oilseed rape which have recently drawn wide-interest from the food and nutrition industry due to their health benefit in lowering LDL cholesterol in humans. To understand the genetic basis of phytosterol content and its relationship with other seed quality traits in oilseed rape, QTL mapping was performed in a segregating DH population derived from the cross of two winter oilseed rape varieties, Sansibar and Oase, termed SODH population. Both parental lines are of canola quality which differ in phytosterol and oil content in seed. A genetic map was constructed for SODH population based on a total of 1638 markers organized in 23 linkage groups and covering a map length of 2350 cM with a mean marker interval of 2.0 cM. The SODH population and the parental lines were cultivated at six environments in Europe and were phenotyped for phytosterol content, oil content, fatty acids content, protein content of the defatted meal, and seed weight. Multiple interval mapping identified between one and six QTL for nine phytosterol traits, between two and six QTL for four fatty acids, five QTL for oil content, four QTL for protein content of defatted meal, and three QTL for seed weight. Colocalizations of QTL for different traits were more frequently observed than individual isolated QTL. Major QTL (R (2) ≥ 25%) were all located in the A genome, and the possible candidate genes were investigated by physical localization of the QTL to the reference genome sequence of Brassica rapa.

QTL mapping and molecular characterization of the classical D locus controlling seed and flower color in Linum usitatissimum (flax).

Science.gov (United States)

Sudarshan, Gurudatt Pavagada; Kulkarni, Manoj; Akhov, Leonid; Ashe, Paula; Shaterian, Hamid; Cloutier, Sylvie; Rowland, Gordon; Wei, Yangdou; Selvaraj, Gopalan

2017-11-16

The flowers of flax (linseed) are blue-hued, ephemeral and self-pollinating, and the seeds are typically brown. A century-old interest in natural yellow seed variants and a historical model point to recessive alleles in B1, D and G loci being responsible, but the functional aspects had remained unknown. Here, we characterized the "D" locus by quantitative trait loci (QTL) mapping and identified a FLAVONOID 3'5' HYDROXYLASE (F3'5'H) gene therein. It does not belong to the F3'5'H clade, but resembles biochemically characterized F3'Hs (flavonoid 3' hydroxylase) but without F3'H activity. The genome lacks other F3'H or F3'H-like genes. The apparent neo-functionalization from F3'H is associated with a Thr 498  → Ser 498 substitution in a substrate recognition site (SRS). The yellow seed and white flower phenotypes of the classical d mutation was found to be due to one nucleotide deletion that would truncate the deduced product and remove three of the six potential SRS, negatively impacting delphinidin synthesis. Delphinidin is sporadic in angiosperms, and flax has no known pollination syndrome(s) with functional pollinator group(s) that are attracted to blue flowers, raising questions on the acquisition of F3'5'H. The appearance of d allele is suggestive of the beginning of the loss of F3'5'H in this species.

大豆籽粒蛋白质含量相关QTL定位研究进展%Quantitative Trait Locus Mapping of Seed Protein Content in Soybean: Progress

Institute of Scientific and Technical Information of China (English)

齐波; 杨加银

2017-01-01

籽粒蛋白质含量是大豆品质性状改良的主要目标之一.笔者介绍了大豆遗传图谱的构建与基因组测序发展历程,从基于分离群体的连锁分析和基于自然群体的关联分析两方面阐述了大豆籽粒蛋白质含量QTL定位研究进展,进而讨论了大豆蛋白质含量MAS育种存在的问题,最后展望了大豆蛋白质含量分子遗传改良的研究趋势.以期为大豆高蛋白育种提供参考.%Seed protein content is one of the main objectives of soybean quality improvement.In this paper,the authors summarized the development of soybean genetic map construction and genome sequencing,and clarified the progress of QTL mapping of soybean seed protein content from linkage analysis based on the segregating population and association analysis based on the natural population.Furthermore,the authors discussed the existing problem of marker-assisted selection (MAS) breeding for seed protein content in soybean.Finally,the future research trend of molecular genetic improvement of seed protein content in soybean was discussed.It is expected that this paper will provide a reference for the selection of new soybean varieties with high protein content.

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.

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

Directory of Open Access Journals (Sweden)

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.

Maternal environment affects the genetic basis of seed dormancy in Arabidopsis thaliana.

Science.gov (United States)

Postma, Froukje M; Ågren, Jon

2015-02-01

The genetic basis of seed dormancy, a key life history trait important for adaptive evolution in plant populations, has yet been studied only using seeds produced under controlled conditions in greenhouse environments. However, dormancy is strongly affected by maternal environmental conditions, and interactions between seed genotype and maternal environment have been reported. Consequently, the genetic basis of dormancy of seeds produced under natural field conditions remains unclear. We examined the effect of maternal environment on the genetic architecture of seed dormancy using a recombinant inbred line (RIL) population derived from a cross between two locally adapted populations of Arabidopsis thaliana from Italy and Sweden. We mapped quantitative trait loci (QTL) for dormancy of seeds produced in the greenhouse and at the native field sites of the parental genotypes. The Italian genotype produced seeds with stronger dormancy at fruit maturation than did the Swedish genotype in all three environments, and the maternal field environments induced higher dormancy levels compared to the greenhouse environment in both genotypes. Across the three maternal environments, a total of nine dormancy QTL were detected, three of which were only detected among seeds matured in the field, and six of which showed significant QTL × maternal environment interactions. One QTL had a large effect on dormancy across all three environments and colocalized with the candidate gene DOG1. Our results demonstrate the importance of studying the genetic basis of putatively adaptive traits under relevant conditions. © 2015 John Wiley & Sons Ltd.

Identification of QTLs for seed germination capability after various storage periods using two RIL populations in rice.

Science.gov (United States)

Jiang, Wenzhu; Lee, Joohyun; Jin, Yong-Mei; Qiao, Yongli; Piao, Rihua; Jang, Sun Mi; Woo, Mi-Ok; Kwon, Soon-Wook; Liu, Xianhu; Pan, Hong-Yu; Du, Xinglin; Koh, Hee-Jong

2011-04-01

Seed germination capability of rice is one of the important traits in the production and storage of seeds. Quantitative trait loci (QTL) associated with seed germination capability in various storage periods was identified using two sets of recombinant inbred lines (RILs) which derived from crosses between Milyang 23 and Tong 88-7 (MT-RILs) and between Dasanbyeo and TR22183 (DT-RILs). A total of five and three main additive effects (QTLs) associated with seed germination capability were identified in MT-RILs and DT-RILs, respectively. Among them, six QTLs were identified repeatedly in various seed storage periods designated as qMT-SGC5.1, qMT-SGC7.2, and qMT-SGC9.1 on chromosomes 5, 7, and 9 in MT-RILs, and qDT-SGC2.1, qDT-SGC3.1, and qDT-SGC9.1 on chromosomes 2, 3, and 9 in DT-RILs, respectively. The QTL on chromosome 9 was identified in both RIL populations under all three storage periods, explaining up to 40% of the phenotypic variation. Eight and eighteen pairs additive × additive epistatic effect (epistatic QTL) were identified in MT-RILs and DT-RILs, respectively. In addition, several near isogenic lines (NILs) were developed to confirm six repeatable QTL effects using controlled deterioration test (CDT). The identified QTLs will be further studied to elucidate the mechanisms controlling seed germination capability, which have important implications for long-term seed storage.

Seed protein improvement in cereals and grain legumes

International Nuclear Information System (INIS)

1979-01-01

Plant breeders, molecular biologists, analytical chemists and nutritionists report on progress and achievements to date. High-lysine genotypes of maize, barley and sorghum have been produced. One high-protein variety of wheat is reported available for commercial use. Grain legumes already have high seed protein content but, compared to cereals, less of the total biological yield is available as seed, and intensive efforts are being made to produce genotypes with higher seed yield. Genetic variability is available from world germplasm collections and from induced-mutation programmes. In the basic sciences considerable advances are reported. Putative structural genes determining protein quality and quantity have been located on various chromosomes. In vitro synthesis of legume and cereal storage proteins and the isolation of some mRNA and the preparation and cloning of cDNA have been reported. Uptake and incorporation of N into amino acids, their synthesis into proteins, and interaction between protein and carbohydrate biosynthesis during seed development are discussed. Future prospects are considered including potential selection at the cellular rather than the whole plant level. In only a minority of the 64 papers is the use of nuclear techniques indicated specifically enough to justify individual entries in INIS

QTL that underlie seed protein, oil, fatty and amino acids content in the ‘Hamilton’ by ‘Spencer’ recombinant inbred line population of soybean [Glycine max (L.) Merr.

Science.gov (United States)

Improving seed composition and quality, including protein, oil, fatty acids, and amino acids content is an important goal of soybean farmers and breeders. Our previous research identified novel QTLs associated with seed isoflavones. The aim of this study was to use the ‘Hamilton’ by ‘Spencer’ recomb...

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

Directory of Open Access Journals (Sweden)

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

Identifying Hierarchical and Overlapping Protein Complexes Based on Essential Protein-Protein Interactions and “Seed-Expanding” Method

Directory of Open Access Journals (Sweden)

Jun Ren

2014-01-01

Full Text Available Many evidences have demonstrated that protein complexes are overlapping and hierarchically organized in PPI networks. Meanwhile, the large size of PPI network wants complex detection methods have low time complexity. Up to now, few methods can identify overlapping and hierarchical protein complexes in a PPI network quickly. In this paper, a novel method, called MCSE, is proposed based on λ-module and “seed-expanding.” First, it chooses seeds as essential PPIs or edges with high edge clustering values. Then, it identifies protein complexes by expanding each seed to a λ-module. MCSE is suitable for large PPI networks because of its low time complexity. MCSE can identify overlapping protein complexes naturally because a protein can be visited by different seeds. MCSE uses the parameter λ_th to control the range of seed expanding and can detect a hierarchical organization of protein complexes by tuning the value of λ_th. Experimental results of S. cerevisiae show that this hierarchical organization is similar to that of known complexes in MIPS database. The experimental results also show that MCSE outperforms other previous competing algorithms, such as CPM, CMC, Core-Attachment, Dpclus, HC-PIN, MCL, and NFC, in terms of the functional enrichment and matching with known protein complexes.

Identification of seed-related QTL in Brassica rapa

NARCIS (Netherlands)

Bagheri, H.; Pino del Carpio, D.; Hanhart, C.J.; Bonnema, A.B.; Keurentjes, J.J.B.; Aarts, M.G.M.

2013-01-01

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

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...

Metabolic profiling of a mapping population exposes new insights in the regulation of seed metabolism and seed, fruit, and plant relations.

Directory of Open Access Journals (Sweden)

David Toubiana

Full Text Available To investigate the regulation of seed metabolism and to estimate the degree of metabolic natural variability, metabolite profiling and network analysis were applied to a collection of 76 different homozygous tomato introgression lines (ILs grown in the field in two consecutive harvest seasons. Factorial ANOVA confirmed the presence of 30 metabolite quantitative trait loci (mQTL. Amino acid contents displayed a high degree of variability across the population, with similar patterns across the two seasons, while sugars exhibited significant seasonal fluctuations. Upon integration of data for tomato pericarp metabolite profiling, factorial ANOVA identified the main factor for metabolic polymorphism to be the genotypic background rather than the environment or the tissue. Analysis of the coefficient of variance indicated greater phenotypic plasticity in the ILs than in the M82 tomato cultivar. Broad-sense estimate of heritability suggested that the mode of inheritance of metabolite traits in the seed differed from that in the fruit. Correlation-based metabolic network analysis comparing metabolite data for the seed with that for the pericarp showed that the seed network displayed tighter interdependence of metabolic processes than the fruit. Amino acids in the seed metabolic network were shown to play a central hub-like role in the topology of the network, maintaining high interactions with other metabolite categories, i.e., sugars and organic acids. Network analysis identified six exceptionally highly co-regulated amino acids, Gly, Ser, Thr, Ile, Val, and Pro. The strong interdependence of this group was confirmed by the mQTL mapping. Taken together these results (i reflect the extensive redundancy of the regulation underlying seed metabolism, (ii demonstrate the tight co-ordination of seed metabolism with respect to fruit metabolism, and (iii emphasize the centrality of the amino acid module in the seed metabolic network. Finally, the study

Lack of Globulin Synthesis during Seed Development Alters Accumulation of Seed Storage Proteins in Rice

Directory of Open Access Journals (Sweden)

Hye-Jung Lee

2015-06-01

Full Text Available The major seed storage proteins (SSPs in rice seeds have been classified into three types, glutelins, prolamins, and globulin, and the proportion of each SSP varies. It has been shown in rice mutants that when either glutelins or prolamins are defective, the expression of another type of SSP is promoted to counterbalance the deficit. However, we observed reduced abundances of glutelins and prolamins in dry seeds of a globulin-deficient rice mutant (Glb-RNAi, which was generated with RNA interference (RNAi-induced suppression of globulin expression. The expression of the prolamin and glutelin subfamily genes was reduced in the immature seeds of Glb-RNAi lines compared with those in wild type. A proteomic analysis of Glb-RNAi seeds showed that the reductions in glutelin and prolamin were conserved at the protein level. The decreased pattern in glutelin was also significant in the presence of a reductant, suggesting that the polymerization of the glutelin proteins via intramolecular disulfide bonds could be interrupted in Glb-RNAi seeds. We also observed aberrant and loosely packed structures in the storage organelles of Glb-RNAi seeds, which may be attributable to the reductions in SSPs. In this study, we evaluated the role of rice globulin in seed development, showing that a deficiency in globulin could comprehensively reduce the expression of other SSPs.

Protein disulfide isomerase-like protein 1-1 controls endosperm development through regulation of the amount and composition of seed proteins in rice.

Directory of Open Access Journals (Sweden)

Yeon Jeong Kim

Full Text Available Protein disulfide isomerase (PDI is a chaperone protein involved in oxidative protein folding by acting as a catalyst and assisting folding in the endoplasmic reticulum (ER. A genome database search showed that rice contains 19 PDI-like genes. However, their functions are not clearly identified. This paper shows possible functions of rice PDI-like protein 1-1 (PDIL1-1 during seed development. Seeds of the T-DNA insertion PDIL1-1 mutant, PDIL1-1Δ, identified by genomic DNA PCR and western blot analysis, display a chalky phenotype and a thick aleurone layer. Protein content per seed was significantly lower and free sugar content higher in PDIL1-1Δ mutant seeds than in the wild type. Proteomic analysis of PDIL1-1Δ mutant seeds showed that PDIL1-1 is post-translationally regulated, and its loss causes accumulation of many types of seed proteins including glucose/starch metabolism- and ROS (reactive oxygen species scavenging-related proteins. In addition, PDIL1-1 strongly interacts with the cysteine protease OsCP1. Our data indicate that the opaque phenotype of PDIL1-1Δ mutant seeds results from production of irregular starch granules and protein body through loss of regulatory activity for various proteins involved in the synthesis of seed components.

Cellular recycling of proteins in seed dormancy alleviation and germination

Directory of Open Access Journals (Sweden)

Krystyna Oracz

2016-07-01

Full Text Available Each step of the seed-to-seed cycle of plant development including seed germination is characterized by a specific set of proteins. The continual renewal and/or replacement of these biomolecules are crucial for optimal plant adaptation. As proteins are the main effectors inside the cells, their levels need to be tightly regulated. This is partially achieved by specific proteolytic pathways via multicatalytic protease complexes defined as 20S and 26S proteasomes. In plants, the 20S proteasome is responsible for degradation of carbonylated proteins, while the 26S being a part of ubiquitin-proteasome pathway (UPP is known to be involved in proteolysis of phytohormone signaling regulators. On the other hand, the role of translational control of plant development is also well documented, especially in the context of pollen tube growth and light signaling. Despite the current progress that has been made in seed biology, the sequence of cellular events that determine if the seed can germinate or not are still far from complete understanding. The role and mechanisms of regulation of proteome composition during processes occurring in the plant’s photosynthetic tissues have been well characterized since many years, but in nonphotosynthetic seeds it has emerged as a tempting research task only since the last decade. This review discusses the recent discoveries providing insights into the role of protein turnover in seed dormancy alleviation, and germination, with a focus on the control of translation and proteasomal proteolysis. The presented novel data of translatome profiling in seeds highlighted that post-transcriptional regulation of germination results from a timely regulated initiation of translation. In addition, the importance of 26S proteasome in the degradation of regulatory elements of cellular signaling and that of the 20S complex in proteolysis of specific carbonylated proteins in hormonal- and light-dependent processes occurring in seeds is

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 ...

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 ...

Photoinhibition influences protein utilisation during seed ...

African Journals Online (AJOL)

STORAGESEVER

2008-05-16

May 16, 2008 ... Seed storage proteins are mobilised during germination, especially at ... of this study was to examine changes in protein expression during ... MATERIALS AND METHODS ... System (Pharmacia) were 500V for 4.5 h in Phase I and II and 2000 .... characterisation of photoinhibition and recovery during cold.

Proteins induced by salt stress in tomato germinating seeds

International Nuclear Information System (INIS)

Torres-Shumann, S.; Godoy, J.A.; del Pozo, O.; Pintor-Toro, J.A.

1989-01-01

Salt effects on protein synthesis in tomato germinating seeds were investigated by two-dimensional polyacrilamide gel electrophoresis of proteins labeled in vivo with ( 35 S)-Methionine. Seeds germinating in NaCl were analyzed at three germination stages (4mm long radicals, 15mm long radicles and expanding cotyledons) and compared to those germinating in water. At the first germination stage several basic proteins of M.W. 13Kd, 16Kd, 17Kd and 18Kd were detected in only salt germinating seeds. Other basic proteins of M.W. 12Kd, 50Kd and 54Kd were salt-induced at the second and third stage of germination. One 14Kd acid protein is observed in every assayed stage and shows several phosphorylated forms. The levels of expression of these proteins are directly correlated to assayed NaCl concentrations. All of these proteins, except 17Kd, are also induced by abscisic acid (ABA) in the same germination stages. A cooperative effect on the synthesis of these proteins is observed when both ABA and NaCl are present

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.

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

Anticariogenic and Hemolytic Activity of Selected Seed Protein Extracts In vitro conditions.

Directory of Open Access Journals (Sweden)

Kalpesh B Ishnava

2014-10-01

Full Text Available This study aimed to assess the anticariogenic and hemolytic activity of crude plant seed protein extracts against tooth decaying bacteria.The proteins from seeds of 12 different plants were extracted and used for antimicrobial assay against six different organisms. The extraction was carried out in 10mM of sodium phosphate buffer (pH 7.0. Protein concentrations were determined as described by Bradford method. Anticariogenic activity was studied by agar well diffusion method and Minimum Inhibitory Concentration (MIC was evaluated by the two-fold serial broth dilution method. Hemolytic activity, treatment of proteinase K and Kinetic study in Mimusops elengi crude seed protein extract.The anticariogenic assay demonstrated the activity of Mimusops elengi against Staphylococcus aureus and Streptococcus pyogenes. A minor activity of Glycine wightii against Streptococcus mutans was also found. The protein content of Mimusops elengi seed protein extract was 5.84mg/ml. The MIC values for Staphylococcus aureus and Streptococcus pyogenes against Mimusops elengi seed protein extract were 364.36μg/ml and 182.19μg/ml, respectively. Kinetic study further elucidated the mode of inhibition in the presence of the Mimusops elengi plant seed protein with respect to time. The concentration of crude extract which gave 50% hemolysis compared to Triton X-100 treatment (HC50 value was 1.58 mg/ml; which is more than five times larger than that of the MIC. Treatment with proteinase K of the Mimusops elengi seed protein resulted in absence of the inhibition zone; which clearly indicates that the activity was only due to protein.Our results showed the prominence of Mimusops elengi plant seed protein extract as an effective herbal medication against tooth decaying bacteria.

Genetic dissection of seed vigour traits in maize (Zea mays L.) under ...

Indian Academy of Sciences (India)

YONG SHI

measurements, the seeds of each genotype were divided into three portions, each consisting of 50 seeds, ... ance (ANOVA) using the general linear model procedure of the statistical software SPSS 12.0. Descriptive ... the phenotypic variation, with five QTL accounting for more than 10% of the total phenotypic variation.

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

Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison

DEFF Research Database (Denmark)

Li, Chengdao; Ni, Peixiang; Francki, Michael

2004-01-01

Pre-harvest sprouting results in significant economic loss for the grain industry around the world. Lack of adequate seed dormancy is the major reason for pre-harvest sprouting in the field under wet weather conditions. Although this trait is governed by multiple genes it is also highly heritable....... A major QTL controlling both pre-harvest sprouting and seed dormancy has been identified on the long arm of barley chromosome 5H, and it explains over 70% of the phenotypic variation. Comparative genomics approaches among barley, wheat and rice were used to identify candidate gene(s) controlling seed...... dormancy and hence one aspect of pre-harvest sprouting. The barley seed dormancy/pre-harvest sprouting QTL was located in a region that showed good synteny with the terminal end of the long arm of rice chromosome 3. The rice DNA sequences were annotated and a gene encoding GA20-oxidase was identified...

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....

Some physicochemical and nutritional studies on Karkade (Hibiscus sabdariffa) seed proteins

International Nuclear Information System (INIS)

Ahmed, Saif Aldein Bashir

1998-01-01

Seeds of Karkade (Al-Rahad variety) were obtained from western Sudan, and investigated perliminary for their chemical composition, the oil of the seed also was investigated. The factors affecting protein extractability such as PH, salt type and concentration and solvent to flour ratio, were studied. The anti nutritional factors investigated were protease inhibitors, gossypol, phytates and tanins, means of inactivation such as heat treatment for trypsin inhibitor and differential solubility for phytates were proposed. Protein fractionation due to solubility was carried out. Other physiochemical properties included polyacrylamide gel electrophersis, ultra violet absorption spectrum and gel filtration pattern. The functional properties investigated were bulk density, solubility, water and oil absorption, emulsifying activity and viscosity. Karkade seed was found to be rich in protein, oil and mineral matter. The amino acid profile of karkade seed proteins indicated the presence of most of essential amino acids in adequate amounts. The relative net protein ratio (RNPR) was found to be 0.75. Protein digestibility-corrected amino acid score of karkade seed protein was found to be 0.63 ( compared to casein in 1.0). The molecular weights of the protein fractions investigated by SDS- PAGE were in the range of 12-82 kDa. UV absorption spectra reflects changes in the molecular structure (native proteins absorb at 280 nm and also interaction with other components e.g. nucleic acids, poly phenols.....etc). Gel filtration pattern reflect changes in molecular size

Some physicochemical and nutritional studies on Karkade (Hibiscus sabdariffa) seed proteins

Energy Technology Data Exchange (ETDEWEB)

Ahmed, Saif Aldein Bashir [Department of Food Science and Technology, Faculty of Agriculture, University of Khartoum, Khatroum (Sudan)

1998-01-01

Seeds of Karkade (Al-Rahad variety) were obtained from western Sudan, and investigated perliminary for their chemical composition, the oil of the seed also was investigated. The factors affecting protein extractability such as PH, salt type and concentration and solvent to flour ratio, were studied. The anti nutritional factors investigated were protease inhibitors, gossypol, phytates and tanins, means of inactivation such as heat treatment for trypsin inhibitor and differential solubility for phytates were proposed. Protein fractionation due to solubility was carried out. Other physiochemical properties included polyacrylamide gel electrophersis, ultra violet absorption spectrum and gel filtration pattern. The functional properties investigated were bulk density, solubility, water and oil absorption, emulsifying activity and viscosity. Karkade seed was found to be rich in protein, oil and mineral matter. The amino acid profile of karkade seed proteins indicated the presence of most of essential amino acids in adequate amounts. The relative net protein ratio (RNPR) was found to be 0.75. Protein digestibility-corrected amino acid score of karkade seed protein was found to be 0.63 ( compared to casein in 1.0). The molecular weights of the protein fractions investigated by SDS- PAGE were in the range of 12-82 kDa. UV absorption spectra reflects changes in the molecular structure (native proteins absorb at 280 nm and also interaction with other components e.g. nucleic acids, poly phenols.....etc). Gel filtration pattern reflect changes in molecular size. 204 refs. , 35 tabs. , 8 figs.

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 �

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

Directory of Open Access Journals (Sweden)

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.

Rapid analysis of seed size in Arabidopsis for mutant and QTL discovery

Directory of Open Access Journals (Sweden)

Baldwin Samantha

2011-02-01

Full Text Available Abstract Background Arabidopsis thaliana is a useful model organism for deciphering the genetic determinants of seed size; however the small size of its seeds makes measurements difficult. Bulk seed weights are often used as an indicator of average seed size, but details of individual seed is obscured. Analysis of seed images is possible but issues arise from variations in seed pigmentation and shadowing making analysis laborious. We therefore investigated the use of a consumer level scanner to facilitate seed size measurements in conjunction with open source image-processing software. Results By using the transmitted light from the slide scanning function of a flatbed scanner and particle analysis of the resulting images, we have developed a method for the rapid and high throughput analysis of seed size and seed size distribution. The technical variation due to the approach was negligible enabling us to identify aspects of maternal plant growth that contribute to biological variation in seed size. By controlling for these factors, differences in seed size caused by altered parental genome dosage and mutation were easily detected. The method has high reproducibility and sensitivity, such that a mutant with a 10% reduction in seed size was identified in a screen of endosperm-expressed genes. Our study also generated average seed size data for 91 Arabidopsis accessions and identified a number of quantitative trait loci from two recombinant inbred line populations, generated from Cape Verde Islands and Burren accessions crossed with Columbia. Conclusions This study describes a sensitive, high-throughput approach for measuring seed size and seed size distribution. The method provides a low cost and robust solution that can be easily implemented into the workflow of studies relating to various aspects of seed development.

Characterization of pea (Pisum sativum) seed protein fractions.

Science.gov (United States)

Rubio, Luis A; Pérez, Alicia; Ruiz, Raquel; Guzmán, M Ángeles; Aranda-Olmedo, Isabel; Clemente, Alfonso

2014-01-30

Legume seed proteins have to be chemically characterized in order to properly link their nutritional effects with their chemical structure. Vicilin and albumin fractions devoid of cross-contamination, as assessed by mass peptide fingerprinting analysis, were obtained from defatted pea (Pisum sativum cv. Bilbo) meal. The extracted protein fractions contained 56.7-67.7 g non-starch polysaccharides kg⁻¹. The vicilin fraction was higher than legumins in arginine, isoleucine, leucine, phenylalanine and lysine. The most abundant amino acids in the albumin fraction were aspartic acid, glutamic acid, lysine and arginine, and the amounts of methionine were more than double than those in legumins and vicilins. The pea albumin fraction showed a clear enrichment of protease inhibitory activity when compared with the seed meal. In vitro digestibility values for pea proteins were 0.63 ±  0.04, 0.88 ±  0.04 and 0.41 ±  0.23 for legumins, vicilins and albumins respectively. Vicilin and albumin fractions devoid of cross-contamination with other proteins were obtained from pea seed meal. The vicilin fraction also contained low amounts of soluble non-starch polysaccharides and was enriched in isoleucine, leucine, phenylalanine and lysine. In vitro digestibility values for pea proteins were similar or even numerically higher than those for control proteins. © 2013 Society of Chemical Industry.

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.

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.

Identification and characterisation of seed storage protein transcripts from Lupinus angustifolius

Directory of Open Access Journals (Sweden)

Goggin Danica E

2011-04-01

Full Text Available Abstract Background In legumes, seed storage proteins are important for the developing seedling and are an important source of protein for humans and animals. Lupinus angustifolius (L., also known as narrow-leaf lupin (NLL is a grain legume crop that is gaining recognition as a potential human health food as the grain is high in protein and dietary fibre, gluten-free and low in fat and starch. Results Genes encoding the seed storage proteins of NLL were characterised by sequencing cDNA clones derived from developing seeds. Four families of seed storage proteins were identified and comprised three unique α, seven β, two γ and four δ conglutins. This study added eleven new expressed storage protein genes for the species. A comparison of the deduced amino acid sequences of NLL conglutins with those available for the storage proteins of Lupinus albus (L., Pisum sativum (L., Medicago truncatula (L., Arachis hypogaea (L. and Glycine max (L. permitted the analysis of a phylogenetic relationships between proteins and demonstrated, in general, that the strongest conservation occurred within species. In the case of 7S globulin (β conglutins and 2S sulphur-rich albumin (δ conglutins, the analysis suggests that gene duplication occurred after legume speciation. This contrasted with 11S globulin (α conglutin and basic 7S (γ conglutin sequences where some of these sequences appear to have diverged prior to speciation. The most abundant NLL conglutin family was β (56%, followed by α (24%, δ (15% and γ (6% and the transcript levels of these genes increased 103 to 106 fold during seed development. We used the 16 NLL conglutin sequences identified here to determine that for individuals specifically allergic to lupin, all seven members of the β conglutin family were potential allergens. Conclusion This study has characterised 16 seed storage protein genes in NLL including 11 newly-identified members. It has helped lay the foundation for efforts to use

Protein-free cress seed (Lepidium sativum) gum: Physicochemical characterization and rheological properties

DEFF Research Database (Denmark)

Razmkhah, Somayeh; Razavi, Seyed Mohammad Ali; Mohammadifar, Mohammad Amin

2016-01-01

Protein-free cress seed gum (PFCSG) was obtained by precipitation of crude cress seed gum (CSG) withethanol followed by treatment with protease. Molecular weight, moisture, ash and uronic acids contentdecreased after elimination of protein. Elimination of protein improved significantly rheologica...

Characterisation and functional properties of watermelon (Citrullus lanatus) seed proteins.

Science.gov (United States)

Wani, Ali Abas; Sogi, Dalbir Singh; Singh, Preeti; Wani, Idrees Ahmed; Shivhare, Uma S

2011-01-15

People in developing countries depend largely on non-conventional protein sources to augment the availability of proteins in their diets. Watermelon seed meal is reported to contain an adequate amount of nutritional proteins that could be extracted for use as nutritional ingredients in food products. Osborne classification showed that globulin was the major protein (≥500 g kg (-1)) present in watermelon seed meal, followed by albumin and glutelin. Sodium dodecyl sulfate polyacrylamide gel electrophoresis indicated that the polypeptides had low molecular weights ranging from 35 to 47 kDa. Isoelectric focusing revealed that the isoelectric point of most proteins was in the acidic range 4-6. These proteins are rich in aspartic acid, glutamic acid and serine. An increase in pH (5-9) significantly (P watermelon protein fractions respectively, while surface hydrophobicity ranged from 126.4 to 173.2 and from 125.8 to 169.3 respectively. The foaming and emulsifying properties of albumin were better than those of the other proteins studied. The good nutritional and functional properties of watermelon seed meal proteins suggest their potential use in food formulations. Copyright © 2010 Society of Chemical Industry.

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.

Study on proteins of bean plants originating from gamma-treated seeds

International Nuclear Information System (INIS)

Tsonev, D.; Chalykova, M.

1975-01-01

Dry seeds of bean variety Stella were radiated with gamma rays using 60 C as a source of radiation. The dose applied was 30 kR at an intensity 9.6 R/s. Irradiation caused disturbances at synthesis and properties of proteins of bean plants originating from gamma treated seeds. Some protein components showed changes in relative content and electrophoretic mobility. New more mobile protein components appeared. Protein complex of overground parts were more radioresistant than protein complex of the roots. (M.Ts.)

Improvement of Protein Digestibility in Jatropha curcas Seed Cakes by Gamma Irradiation

International Nuclear Information System (INIS)

Sudprasert, Wanwisa; Pakkong, Pannee; Thiengtham, Jamroen; Chandang, Pipatpong

2011-06-01

Full text: The effect of gamma radiation on protein digestibility of Jatropha curcas press cake was investigated using in vitro digestibility technique. Six varieties of Jatropha curcas seeds were subjected to cobalt-60 gamma radiation at doses of 10-100 kGy. All treated seeds were defatted by screw press. In vitro protein digest abilities in defatted seeds were assayed using trinitrobenzene sulphonic acid (TNBS) method, by which the contents of alpha amino induced from the function of enzymes were determined using L-alanine as a reference standard. It was found that irradiation treatment at 60 kGy significantly increased the protein digestibility by 15-92%. Also, the results showed that moisture, crude protein, fat and ash contents were unchanged by irradiation, whereas fiber was significantly decreased (p < 0.05). Therefore, irradiation could serve as a possible processing method for protein utilization improvement in defatted Jatropha curcas seeds before using as a protein supplement in animal feed

Pumpkin (Cucurbita maxima) seed proteins: sequential extraction processing and fraction characterization.

Science.gov (United States)

Rezig, Leila; Chibani, Farhat; Chouaibi, Moncef; Dalgalarrondo, Michèle; Hessini, Kamel; Guéguen, Jacques; Hamdi, Salem

2013-08-14

Seed proteins extracted from Tunisian pumpkin seeds ( Cucurbita maxima ) were investigated for their solubility properties and sequentially extracted according to the Osborne procedure. The solubility of pumpkin proteins from seed flour was greatly influenced by pH changes and ionic strength, with higher values in the alkaline pH regions. It also depends on the seed defatting solvent. Protein solubility was decreased by using chloroform/methanol (CM) for lipid extraction instead of pentane (P). On the basis of differential solubility fractionation and depending on the defatting method, the alkali extract (AE) was the major fraction (42.1 (P), 22.3% (CM)) compared to the salt extract (8.6 (P), 7.5% (CM)). In salt, alkali, and isopropanol extracts, all essential amino acids with the exceptions of threonine and lysine met the minimum requirements for preschool children (FAO/WHO/UNU). The denaturation temperatures were 96.6 and 93.4 °C for salt and alkali extracts, respectively. Pumpkin protein extracts with unique protein profiles and higher denaturation temperatures could impart novel characteristics when used as food ingredients.

The role of seed coat phenolics on water uptake and early protein synthesis during germination of dimorphic seeds of halopyrum mucronatum (L.) staph

International Nuclear Information System (INIS)

Siddiqui, Z. S.; Khan, M.A.

2010-01-01

Role of seed coat phenolics on water uptake and early protein synthesis of Halopyrum mucronatum dimorphic seeds during germination were tested. Scanning electron micrographs (SEM) showed seed texture with differential deposition of secondary metabolites in both morphs. Ability of both seed morphs to retain secondary deposition was dependent on exposure to either saline or non-saline conditions. More phenols leached from the brown seed during the initial hours of soaking when compared to black seeds. Water uptake pattern was slightly different in both seed type particularly during initial hours when imbibition in black seeds showed little water uptake while in brown seeds absorption was quick in the first hour under both saline and non saline condition. Change in total protein was somewhat similar in both seeds morphs showing early increase (4 and 8 h), reaching to the maximum (12 h) and decreasing (24 and 48 h) afterward. The results are discussed in relation to seed coat phenolics, water uptake and early protein synthesis during germination. (author)

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

Proteomic analysis of lettuce seed germination and thermoinhibition by sampling of individual seeds at germination and removal of storage proteins by polyethylene glycol fractionation.

Science.gov (United States)

Wang, Wei-Qing; Song, Bin-Yan; Deng, Zhi-Jun; Wang, Yue; Liu, Shu-Jun; Møller, Ian Max; Song, Song-Quan

2015-04-01

Germination and thermoinhibition in lettuce (Lactuca sativa 'Jianyexianfeng No. 1') seeds were investigated by a proteomic comparison among dry seeds, germinated seeds at 15°C, at 15°C after imbibition at 25°C for 48 h, or at 25°C in KNO3 (all sampled individually at germination), and ungerminated seeds at 25°C, a thermoinhibitory temperature. Before two-dimensional gel electrophoresis analysis, storage proteins (greater than 50% of total extractable protein) were removed by polyethylene glycol precipitation, which significantly improved the detection of less abundant proteins on two-dimensional gels. A total of 108 protein spots were identified to change more than 2-fold (Pseeds than in ungerminated 25°C seeds. Gene expression of 12 of those proteins correlated well with the protein accumulation. Methionine metabolism, ethylene production, lipid mobilization, cell elongation, and detoxification of aldehydes were revealed to be potentially related to lettuce seed germination and thermoinhibition. Accumulation of three proteins and expression of five genes participating in the mevalonate (MVA) pathway of isoprenoid biosynthesis correlated positively with seed germinability. Inhibition of this pathway by lovastatin delayed seed germination and increased the sensitivity of germination to abscisic acid. MVA pathway-derived products, cytokinins, partially reversed the lovastatin inhibition of germination and released seed thermoinhibition at 25°C. We conclude that the MVA pathway for isoprenoid biosynthesis is involved in lettuce seed germination and thermoinhibition. © 2015 American Society of Plant Biologists. All Rights Reserved.

Proteomic analysis reveals differential accumulation of small heat shock proteins and late embryogenesis abundant proteins between ABA-deficient mutant vp5 seeds and wild-type Vp5 seeds in maize

Directory of Open Access Journals (Sweden)

Xiaolin eWu

2015-01-01

Full Text Available ABA is a major plant hormone that plays important roles during many phases of plant life cycle, including seed development, maturity and dormancy, and especially the acquisition of desiccation tolerance. Understanding of the molecular basis of ABA-mediated plant response to stress is of interest not only in basic research on plant adaptation but also in applied research on plant productivity. Maize mutant viviparous-5 (vp5, deficient in ABA biosynthesis in seeds, is a useful material for studying ABA-mediated response in maize. Due to carotenoid deficiency, vp5 endosperm is white, compared to yellow Vp5 endosperm. However, the background difference at proteome level between vp5 and Vp5 seeds is unclear. This study aimed to characterize proteome alterations of maize vp5 seeds and to identify ABA-dependent proteins during seed maturation. We compared the embryo and endosperm proteomes of vp5 and Vp5 seeds by gel-based proteomics. Up to 46 protein spots, most in embryos, were found to be differentially accumulated between vp5 and Vp5. The identified proteins included small heat shock proteins (sHSPs, late embryogenesis abundant (LEA proteins, stress proteins, storage proteins and enzymes among others. However, EMB564, the most abundant LEA protein in maize embryo, accumulated in comparable levels between vp5 and Vp5 embryos, which contrasted to previously characterized, greatly lowered expression of emb564 mRNA in vp5 embryos. Moreover, LEA proteins and sHSPs displayed differential accumulations in vp5 embryos: six out of eight identified LEA proteins decreased while nine sHSPs increased in abundance. Finally, we discussed the possible causes of global proteome alterations, especially the observed differential accumulation of identified LEA proteins and sHSPs in vp5 embryos. The data derived from this study provides new insight into ABA-dependent proteins and ABA-mediated response during maize seed maturation.

Unraveling the genetic basis of seed tocopherol content and composition in rapeseed (Brassica napus L.).

Science.gov (United States)

Wang, Xingxing; Zhang, Chunyu; Li, Lingjuan; Fritsche, Steffi; Endrigkeit, Jessica; Zhang, Wenying; Long, Yan; Jung, Christian; Meng, Jinling

2012-01-01

Tocopherols are important antioxidants in vegetable oils; when present as vitamin E, tocopherols are an essential nutrient for humans and livestock. Rapeseed (Brassica napus L, AACC, 2 n = 38) is one of the most important oil crops and a major source of tocopherols. Although the tocopherol biosynthetic pathway has been well elucidated in the model photosynthetic organisms Arabidopsis thaliana and Synechocystis sp. PCC6803, knowledge about the genetic basis of tocopherol biosynthesis in seeds of rapeseed is scant. This project was carried out to dissect the genetic basis of seed tocopherol content and composition in rapeseed through quantitative trait loci (QTL) detection, genome-wide association analysis, and homologous gene mapping. We used a segregating Tapidor × Ningyou7 doubled haploid (TNDH) population, its reconstructed F(2) (RC-F(2)) population, and a panel of 142 rapeseed accessions (association panel). Genetic effects mainly contributed to phenotypic variations in tocopherol content and composition; environmental effects were also identified. Thirty-three unique QTL were detected for tocopherol content and composition in TNDH and RC-F(2) populations. Of these, seven QTL co-localized with candidate sequences associated with tocopherol biosynthesis through in silico and linkage mapping. Several near-isogenic lines carrying introgressions from the parent with higher tocopherol content showed highly increased tocopherol content compared with the recurrent parent. Genome-wide association analysis was performed with 142 B. napus accessions. Sixty-one loci were significantly associated with tocopherol content and composition, 11 of which were localized within the confidence intervals of tocopherol QTL. This joint QTL, candidate gene, and association mapping study sheds light on the genetic basis of seed tocopherol biosynthesis in rapeseed. The sequences presented here may be used for marker-assisted selection of oilseed rape lines with superior tocopherol

Unraveling the genetic basis of seed tocopherol content and composition in rapeseed (Brassica napus L..

Directory of Open Access Journals (Sweden)

Xingxing Wang

Full Text Available BACKGROUND: Tocopherols are important antioxidants in vegetable oils; when present as vitamin E, tocopherols are an essential nutrient for humans and livestock. Rapeseed (Brassica napus L, AACC, 2 n = 38 is one of the most important oil crops and a major source of tocopherols. Although the tocopherol biosynthetic pathway has been well elucidated in the model photosynthetic organisms Arabidopsis thaliana and Synechocystis sp. PCC6803, knowledge about the genetic basis of tocopherol biosynthesis in seeds of rapeseed is scant. This project was carried out to dissect the genetic basis of seed tocopherol content and composition in rapeseed through quantitative trait loci (QTL detection, genome-wide association analysis, and homologous gene mapping. METHODOLOGY/PRINCIPAL FINDINGS: We used a segregating Tapidor × Ningyou7 doubled haploid (TNDH population, its reconstructed F(2 (RC-F(2 population, and a panel of 142 rapeseed accessions (association panel. Genetic effects mainly contributed to phenotypic variations in tocopherol content and composition; environmental effects were also identified. Thirty-three unique QTL were detected for tocopherol content and composition in TNDH and RC-F(2 populations. Of these, seven QTL co-localized with candidate sequences associated with tocopherol biosynthesis through in silico and linkage mapping. Several near-isogenic lines carrying introgressions from the parent with higher tocopherol content showed highly increased tocopherol content compared with the recurrent parent. Genome-wide association analysis was performed with 142 B. napus accessions. Sixty-one loci were significantly associated with tocopherol content and composition, 11 of which were localized within the confidence intervals of tocopherol QTL. CONCLUSIONS/SIGNIFICANCE: This joint QTL, candidate gene, and association mapping study sheds light on the genetic basis of seed tocopherol biosynthesis in rapeseed. The sequences presented here may be used

Jatropha seed protein functional properties for technical applications

NARCIS (Netherlands)

Lestari, D.; Mulder, W.J.; Sanders, J.P.M.

2011-01-01

Jatropha press cake, by-product after oil expression from Jatropha seeds, contains 24–28% protein on dry basis. Objectives of this research were to investigate functional properties, such as solubility, emulsifying, foaming, film forming, and adhesive properties, of Jatropha press cake proteins and

Rapid evaluation of seed vigor by the absolute content of protein in seed within the same crop.

Science.gov (United States)

Wen, Daxing; Hou, Hongcun; Meng, Aiju; Meng, Jie; Xie, Liuyong; Zhang, Chunqing

2018-04-03

Seed vigor, an important index of seed quality, determines the potential for rapid and uniform emergence of plants. The objective of this study was to explore a rapid method for evaluating seed vigor. To analyze the correlation of seed traits and seedling traits related to seed vigor, we designed five experiments including nitrogen fertilizer, irrigation and seed sorting treatments in wheat. The results showed that only the absolute content of protein (ACP) in wheat seed was significantly correlated with plant dry weight in five experiments. Subsequently, another experiment including 30 wheat seed lots was used to validate the above results. Although 100-grain weight was also correlated with plant dry weight (R = 0.799, p vigor and could potentially be used for processing and screening high vigor seeds.

Small heat shock proteins can release light dependence of tobacco seed during germination.

Science.gov (United States)

Koo, Hyun Jo; Park, Soo Min; Kim, Keun Pill; Suh, Mi Chung; Lee, Mi Ok; Lee, Seong-Kon; Xinli, Xia; Hong, Choo Bong

2015-03-01

Small heat shock proteins (sHSPs) function as ATP-independent molecular chaperones, and although the production and function of sHSPs have often been described under heat stress, the expression and function of sHSPs in fundamental developmental processes, such as pollen and seed development, have also been confirmed. Seed germination involves the breaking of dormancy and the resumption of embryo growth that accompany global changes in transcription, translation, and metabolism. In many plants, germination is triggered simply by imbibition of water; however, different seeds require different conditions in addition to water. For small-seeded plants, like Arabidopsis (Arabidopsis thaliana), lettuce (Lactuca sativa), tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum), light is an important regulator of seed germination. The facts that sHSPs accumulate during seed development, sHSPs interact with various client proteins, and seed germination accompanies synthesis and/or activation of diverse proteins led us to investigate the role of sHSPs in seed germination, especially in the context of light dependence. In this study, we have built transgenic tobacco plants that ectopically express sHSP, and the effect was germination of the seeds in the dark. Administering heat shock to the seeds also resulted in the alleviation of light dependence during seed germination. Subcellular localization of ectopically expressed sHSP was mainly observed in the cytoplasm, whereas heat shock-induced sHSPs were transported to the nucleus. We hypothesize that ectopically expressed sHSPs in the cytoplasm led the status of cytoplasmic proteins involved in seed germination to function during germination without additional stimulus and that heat shock can be another signal that induces seed germination. © 2015 American Society of Plant Biologists. All Rights Reserved.

Genetic similarity of soybean genotypes revealed by seed protein

Directory of Open Access Journals (Sweden)

Nikolić Ana

2005-01-01

Full Text Available More accurate and complete descriptions of genotypes could help determinate future breeding strategies and facilitate introgression of new genotypes in current soybean genetic pool. The objective of this study was to characterize 20 soybean genotypes from the Maize Research Institute "Zemun Polje" collection, which have good agronomic performances, high yield, lodging and drought resistance, and low shuttering by seed proteins as biochemical markers. Seed proteins were isolated and separated by PAA electrophoresis. On the basis of the presence/absence of protein fractions coefficients of similarity were calculated as Dice and Roger and Tanamoto coefficient between pairs of genotypes. The similarity matrix was submitted for hierarchical cluster analysis of un weighted pair group using arithmetic average (UPGMA method and necessary computation were performed using NTSYS-pc program. Protein seed analysis confirmed low level of genetic diversity in soybean. The highest genetic similarity was between genotypes P9272 and Kador. According to obtained results, soybean genotypes were assigned in two larger groups and coefficients of similarity showed similar results. Because of the lack of pedigree data for analyzed genotypes, correspondence with marker data could not be determined. In plant with a narrow genetic base in their gene pool, such as soybean, protein markers may not be sufficient for characterization and study of genetic diversity.

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.

Seed storage protein components are associated with curled ...

African Journals Online (AJOL)

PRECIOUS

2009-11-16

Nov 16, 2009 ... analysis suggests that the two increased protein spots in mutants were ... The main objective of this work was to gain further understanding of the influence of curled cotyledon on the seed storage protein components in soybean by com- .... cotyledon formation during Arabidopsis embryogenesis: interaction.

Fractionation of hairless canary seed (Phalaris canariensis) into starch, protein, and oil.

Science.gov (United States)

Abdel-Aal, El-Sayed M; Hucl, Pierre; Patterson, Carol Ann; Gray, Danielle

2010-06-09

Canary seed is an important specialty crop in Canada. The current market for this true cereal (i.e., belonging to the family Poaceae as wheat) is limited to feed for caged birds. However, canary seed holds a promise for many food and industrial applications based on its composition. Three wet milling procedures based on ethanol (E), water (W), and alkaline (A) extractions used in different order were investigated to determine extraction efficiency and purity of starch, protein, oil, and fiber separated from hairless canary seed, a variety developed for human consumption. Highest extraction efficiencies were obtained when canary seed was defatted with ethanol and then extracted with alkali and water (EAW process). Using this process, approximately 92% pure starch, 75% pure protein, and oil were recovered from canary seed groats. The highest purity of protein, however, was obtained when canary seed was fractionated by the EWA process, that is, defatted and then extracted with water followed by alkali. Fiber component separated prior to alkaline extraction contained high amounts of nonfiber components as indicated by its yield. The EAW extraction process seems to be more promising in canary seed fractionation based on recovery and purity of components.

Proteomic Analysis of Lettuce Seed Germination and Thermoinhibition by Sampling of Individual Seeds at Germination and Removal of Storage Proteins by Polyethylene Glycol Fractionation1

Science.gov (United States)

Song, Bin-Yan; Deng, Zhi-Jun; Wang, Yue; Liu, Shu-Jun; Møller, Ian Max; Song, Song-Quan

2015-01-01

Germination and thermoinhibition in lettuce (Lactuca sativa ‘Jianyexianfeng No. 1’) seeds were investigated by a proteomic comparison among dry seeds, germinated seeds at 15°C, at 15°C after imbibition at 25°C for 48 h, or at 25°C in KNO3 (all sampled individually at germination), and ungerminated seeds at 25°C, a thermoinhibitory temperature. Before two-dimensional gel electrophoresis analysis, storage proteins (greater than 50% of total extractable protein) were removed by polyethylene glycol precipitation, which significantly improved the detection of less abundant proteins on two-dimensional gels. A total of 108 protein spots were identified to change more than 2-fold (P lettuce seed germination and thermoinhibition. Accumulation of three proteins and expression of five genes participating in the mevalonate (MVA) pathway of isoprenoid biosynthesis correlated positively with seed germinability. Inhibition of this pathway by lovastatin delayed seed germination and increased the sensitivity of germination to abscisic acid. MVA pathway-derived products, cytokinins, partially reversed the lovastatin inhibition of germination and released seed thermoinhibition at 25°C. We conclude that the MVA pathway for isoprenoid biosynthesis is involved in lettuce seed germination and thermoinhibition. PMID:25736209

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...

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.

Identification of differentially expressed genes between developing seeds of different soybean cultivars

Directory of Open Access Journals (Sweden)

Rongshuang Lin

2015-12-01

Full Text Available Soybean is a major source of protein and oil and a primary feedstock for biodiesel production. Research on soybean seed composition and yield has revealed that protein, oil and yield are controlled quantitatively and quantitative trait loci (QTL have been identified for each of these traits. However, very limited information is available regarding the genetic mechanisms controlling seed composition and yield. To help address this deficiency, we used Affymetrix Soybean GeneChips® to identify genes that are differentially expressed between developing seeds of the Minsoy and Archer soybean cultivars, which differ in seed weight, yield, protein content and oil content. A total of 700 probe sets were found to be expressed at significantly different (defined as having an adjusted p-value below or equal to 0.05 and an at least 2-fold difference levels between the two cultivars at one or more of the three developmental stages and in at least one of the two years assayed. Comparison of data from soybeans collected in two different years revealed that 97 probe sets were expressed at significantly different levels in both years. Functional annotations were assigned to 78% of these 97 probe sets based on the SoyBase Affymetrix™ GeneChip® Soybean Genome Array Annotation. Genes involved in receptor binding/activity and protein binding are overrepresented among the group of 97 probe sets that were differentially expressed in both years assayed. Probe sets involved in growth/development, signal transduction, transcription, defense/stress response and protein and lipid metabolism were also identified among the 97 probe sets and their possible implications in the regulation of agronomic traits are discussed. As the Minsoy and Archer soybean cultivars differ with respect to seed size, yield, protein content and lipid content, some of the differentially expressed probe sets identified in this study may thus play important roles in controlling these traits

Genotypic variability and mutant identification in cicer arietinum L. by seed storage protein profiling

International Nuclear Information System (INIS)

Hameed, A.; Iqbal, N.; Shah, T.M.

2012-01-01

A collection of thirty-four chickpea genotypes, including five kabuli and twenty-nine desi, were analyzed by SDS-PAGE for seed storage protein profiling. Total soluble seed proteins were resolved on 12% gels. A low level of variability was observed in desi as compared to kabuli genotypes. Dendrogram based on electrophoretic data clustered the thirty-four genotypes in four major groups. As large number of desi genotypes illustrated identical profiles, therefore could not be differentiated on the basis of seed storage protein profiles. One kabuli genotype ILC-195 found to be the most divergent showing 86% similarity with all other genotypes. ILC-195 can be distinguished from its mutant i.e., CM-2000 and other kabuli genotypes on the basis of three peptides i.e. SSP-66, SSP-43 and SSP-39. Some proteins peptides were found to be genotype specific like SSP-26 for ICCV-92311. Uniprot and NCBI protein databases were searched for already reported and characterized seed storage proteins in chickpea. Among 33 observed peptides, only six seed storages proteins from chickpea source were available in databases. On the basis of molecular weight similarity, identified peptides were SSP-64 as Serine/Threonine dehydratase, SSP-56 as Alpha-amylase inhibitor, SSP-50 as Provicillin, SSP-39 as seed imbibition protein, SSP-35 as Isoflavane reductase and SSP-19 as lipid transport protein. Highest variability was observed in vicillin subunits and beta subunits of legumins and its polymorphic forms. In conclusion, seed storage profiling can be economically used to asses the genetic variation, phylogenetic relationship and as markers to differentiate mutants from their parents. (author)

Barley seed ageing: genetics behind the dry elevated pressure of oxygen ageing and moist controlled deterioration

Directory of Open Access Journals (Sweden)

Manuela eNagel

2016-03-01

Full Text Available Experimental seed ageing approaches intend to mimic seed deterioration processes to achieve a storage interval reduction. Common methods apply higher seed moisture levels and temperatures. In contrast, the elevated partial pressure of oxygen (EPPO approach treats dry seed stored at ambient temperatures with high oxygen pressure. To analyse the genetic background of seed longevity and the effects of seed ageing under dry conditions, the EPPO approach was applied to the progeny of the Oregon Wolfe Barley (OWB mapping population. In comparison to a non-treated control and a control high-pressure nitrogen treatment, EPPO stored seeds showed typical symptoms of ageing with a significant reduction of normal seedlings, slower germination, and less total germination. Thereby, the parent Dom (OWB-D, carrying dominant alleles, is more sensitive to ageing in comparison to the population mean and in most cases to the parent Rec (OWB-R, carrying recessive alleles. Quantitative trait locus (QTL analyses using 2,832 markers revealed 65 QTLs, including two major loci for seed vigor on 2H and 7H. QTLs for EPPO tolerance were detected on 3H, 4H, and 5H. An applied controlled deterioration (CD treatment (aged at higher moisture level and temperature revealed a tolerance QTL on 5H, indicating that the mechanism of seed deterioration differs in part between EPPO or CD conditions.

A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea.

Science.gov (United States)

Bajaj, Deepak; Das, Shouvik; Upadhyaya, Hari D; Ranjan, Rajeev; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C L Laxmipathi; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K; Parida, Swarup K

2015-01-01

The study identified 9045 high-quality SNPs employing both genome-wide GBS- and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci exhibiting significant association with seed coat color. Five seed color-associated major genomic loci underlying robust QTLs mapped on a high-density intra-specific genetic linkage map were validated by QTL mapping. The integration of association and QTL mapping with gene haplotype-specific LD mapping and transcript profiling identified novel allelic variants (non-synonymous SNPs) and haplotypes in a MATE secondary transporter gene regulating light/yellow brown and beige seed coat color differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat color-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed colored desi and kabuli accessions for their coloration/pigmentation. This seed color-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed colored desi and wild Cicer reticulatum accessions compared with the BE seed colored kabuli accessions. The functionally relevant molecular tags identified have potential to decipher the complex transcriptional regulatory gene function of seed coat coloration and for understanding the selective sweep-based seed color trait evolutionary pattern in cultivated and wild accessions during chickpea domestication. The genome-wide integrated approach employed will expedite marker-assisted genetic enhancement for developing cultivars with desirable seed coat color types in chickpea.

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

Science.gov (United States)

Schwember, Andrés R; Bradford, Kent J

2010-10-01

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

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.

Improving persistence in red clover: Insights from QTL analysis and comparative phenotypic evaluation

DEFF Research Database (Denmark)

Herrmann, Dorris; Boller, Beat; Studer, Bruno

2008-01-01

, persistence is difficult to improve. The objectives of this study were to optimize the phenotypic evaluation of persistence, to identify quantitative trait loci (QTLs) for this important trait, and to investigate the association of persistence with other important traits. A weighted average of vigor scores...... assessed during two winters and three growing seasons was identified as the optimal method to phenotype persistence. For this index, one QTL explaining 12.2% of the total phenotypic variation was identified. While there was no negative correlation between persistence and seed yield, persistence...

Seed yield and protein content in sunflower depending on stand density

Directory of Open Access Journals (Sweden)

Balalić Igor M.

2016-01-01

Full Text Available The aim of this research was to investigate the effect of stand density on seed yield and protein content in sunflower hybrids. The field experiment was carried out at Rimski Šančevi location. Six NS sunflower hybrids were examined. Five hybrids are confectionery (NS Goliat, NS Slatki, NS Gricko, Vranac and Cepko, and one is used for bird food (NS-H-6485. The trial was arranged as randomized complete block design (RCBD with four replications. Sowing was done with six different densities (from 20,000 to 70,000 plants per hectare, with an increment of 10,000 plants per hectare. Analysis of variance (ANOVA showed that the effect of hybrid, stand density and hybrid × stand density interation were highly significant for seed yield and protein content. The highest seed yield, on the basis of average for all densities, was found in NS-H-6485 (4.77 t ha-1 and in NS Gricko (4.43 t ha-1. Average seed yield of hybrids significantly increased up to 50,000 plants per ha-1, when it reached the value of 4.50 t ha-1, and then decreased. Significantly higher protein content, taking into account all stand densities, showed hybrid Cepko (16.94%. Protein content, above the overall average value, was achieved in hybrid Vranac (16.11%. The high­est protein content in the average for all six hybrids was at the lowest stand density (20,000 plants per ha-1, and then decreased up to higher densities. The results showed that stand density had significant effect on seed yield and protein content in sunflower hybrids. [Projekat Ministarstva nauke Republike Srbije, br. TR31025: The development of new cultivars and improving the technology of producing oil plant species for different purposes

PROTEIN L-ISOASPARTYL METHYLTRANSFERASE2 is differentially expressed in chickpea and enhances seed vigor and longevity by reducing abnormal isoaspartyl accumulation predominantly in seed nuclear proteins.

Science.gov (United States)

Verma, Pooja; Kaur, Harmeet; Petla, Bhanu Prakash; Rao, Venkateswara; Saxena, Saurabh C; Majee, Manoj

2013-03-01

PROTEIN l-ISOASPARTYL METHYLTRANSFERASE (PIMT) is a widely distributed protein-repairing enzyme that catalyzes the conversion of abnormal l-isoaspartyl residues in spontaneously damaged proteins to normal aspartyl residues. This enzyme is encoded by two divergent genes (PIMT1 and PIMT2) in plants, unlike many other organisms. While the biological role of PIMT1 has been elucidated, the role and significance of the PIMT2 gene in plants is not well defined. Here, we isolated the PIMT2 gene (CaPIMT2) from chickpea (Cicer arietinum), which exhibits a significant increase in isoaspartyl residues in seed proteins coupled with reduced germination vigor under artificial aging conditions. The CaPIMT2 gene is found to be highly divergent and encodes two possible isoforms (CaPIMT2 and CaPIMT2') differing by two amino acids in the region I catalytic domain through alternative splicing. Unlike CaPIMT1, both isoforms possess a unique 56-amino acid amino terminus and exhibit similar yet distinct enzymatic properties. Expression analysis revealed that CaPIMT2 is differentially regulated by stresses and abscisic acid. Confocal visualization of stably expressed green fluorescent protein-fused PIMT proteins and cell fractionation-immunoblot analysis revealed that apart from the plasma membrane, both CaPIMT2 isoforms localize predominantly in the nucleus, while CaPIMT1 localizes in the cytosol. Remarkably, CaPIMT2 enhances seed vigor and longevity by repairing abnormal isoaspartyl residues predominantly in nuclear proteins upon seed-specific expression in Arabidopsis (Arabidopsis thaliana), while CaPIMT1 enhances seed vigor and longevity by repairing such abnormal proteins mainly in the cytosolic fraction. Together, our data suggest that CaPIMT2 has most likely evolved through gene duplication, followed by subfunctionalization to specialize in repairing the nuclear proteome.

Eliminating anti-nutritional plant food proteins: the case of seed protease inhibitors in pea.

Science.gov (United States)

Clemente, Alfonso; Arques, Maria C; Dalmais, Marion; Le Signor, Christine; Chinoy, Catherine; Olias, Raquel; Rayner, Tracey; Isaac, Peter G; Lawson, David M; Bendahmane, Abdelhafid; Domoney, Claire

2015-01-01

Several classes of seed proteins limit the utilisation of plant proteins in human and farm animal diets, while plant foods have much to offer to the sustainable intensification of food/feed production and to human health. Reduction or removal of these proteins could greatly enhance seed protein quality and various strategies have been used to try to achieve this with limited success. We investigated whether seed protease inhibitor mutations could be exploited to enhance seed quality, availing of induced mutant and natural Pisum germplasm collections to identify mutants, whilst acquiring an understanding of the impact of mutations on activity. A mutant (TILLING) resource developed in Pisum sativum L. (pea) and a large germplasm collection representing Pisum diversity were investigated as sources of mutations that reduce or abolish the activity of the major protease inhibitor (Bowman-Birk) class of seed protein. Of three missense mutations, predicted to affect activity of the mature trypsin / chymotrypsin inhibitor TI1 protein, a C77Y substitution in the mature mutant inhibitor abolished inhibitor activity, consistent with an absolute requirement for the disulphide bond C77-C92 for function in the native inhibitor. Two further classes of mutation (S85F, E109K) resulted in less dramatic changes to isoform or overall inhibitory activity. The alternative strategy to reduce anti-nutrients, by targeted screening of Pisum germplasm, successfully identified a single accession (Pisum elatius) as a double null mutant for the two closely linked genes encoding the TI1 and TI2 seed protease inhibitors. The P. elatius mutant has extremely low seed protease inhibitory activity and introgression of the mutation into cultivated germplasm has been achieved. The study provides new insights into structure-function relationships for protease inhibitors which impact on pea seed quality. The induced and natural germplasm variants identified provide immediate potential for either halving

Seed protein improvement in cereals and grain legumes. Proceedings series

Energy Technology Data Exchange (ETDEWEB)

1979-01-01

The following topics were discussed in the five sections of the conference: the world protein and nutritional situation; the need for and use of variability in protein characteristics; genetics, biochemistry, and physiology of seed storage proteins; analytical and nutritional techniques; and coordinated research programs. (HLW)

Isolation of nuclear proteins from flax (Linum usitatissimum L. seed coats for gene expression regulation studies

Directory of Open Access Journals (Sweden)

Renouard Sullivan

2012-01-01

Full Text Available Abstract Background While seed biology is well characterized and numerous studies have focused on this subject over the past years, the regulation of seed coat development and metabolism is for the most part still non-elucidated. It is well known that the seed coat has an essential role in seed development and its features are associated with important agronomical traits. It also constitutes a rich source of valuable compounds such as pharmaceuticals. Most of the cell genetic material is contained in the nucleus; therefore nuclear proteins constitute a major actor for gene expression regulation. Isolation of nuclear proteins responsible for specific seed coat expression is an important prerequisite for understanding seed coat metabolism and development. The extraction of nuclear proteins may be problematic due to the presence of specific components that can interfere with the extraction process. The seed coat is a rich source of mucilage and phenolics, which are good examples of these hindering compounds. Findings In the present study, we propose an optimized nuclear protein extraction protocol able to provide nuclear proteins from flax seed coat without contaminants and sufficient yield and quality for their use in transcriptional gene expression regulation by gel shift experiments. Conclusions Routinely, around 250 μg of nuclear proteins per gram of fresh weight were extracted from immature flax seed coats. The isolation protocol described hereafter may serve as an effective tool for gene expression regulation and seed coat-focused proteomics studies.

Effect of thermal processing on estimated metabolizable protein supply to dairy cattle from camelina seeds: relationship with protein molecular structural changes.

Science.gov (United States)

Peng, Quanhui; Khan, Nazir A; Wang, Zhisheng; Zhang, Xuewei; Yu, Peiqiang

2014-08-20

This study evaluated the effect of thermal processing on the estimated metabolizable protein (MP) supply to dairy cattle from camelina seeds (Camelina sativa L. Crantz) and determined the relationship between heat-induced changes in protein molecular structural characteristics and the MP supply. Seeds from two camelina varieties were sampled in two consecutive years and were either kept raw or were heated in an autoclave (moist heating) or in an air-draft oven (dry heating) at 120 °C for 1 h. The MP supply to dairy cattle was modeled by three commonly used protein evaluation systems. The protein molecular structures were analyzed by Fourier transform/infrared-attenuated total reflectance molecular spectroscopy. The results showed that both the dry and moist heating increased the contents of truly absorbable rumen-undegraded protein (ARUP) and total MP and decreased the degraded protein balance (DPB). However, the moist-heated camelina seeds had a significantly higher (P seeds. The regression equations showed that intensities of the protein molecular structural bands can be used to estimate the contents of ARUP, MP, and DPB with high accuracy (R(2) > 0.70). These results show that protein molecular structural characteristics can be used to rapidly assess the MP supply to dairy cattle from raw and heat-treated camelina seeds.

Antioxidative effects of pumpkin seed (Cucurbita pepo) protein isolate in CCl4-induced liver injury in low-protein fed rats.

Science.gov (United States)

Nkosi, C Z; Opoku, A R; Terblanche, S E

2006-11-01

The effects of pumpkin seed (Cucurbita pepo) protein isolate on the plasma activity levels of catalase (CA), superoxide dismutase (SOD), glutathione peroxidase (GSHpx) and total antioxidant capacity (TAC) as well as glucose-6-phosphatase (G6Pase) in liver homogenates and lipid peroxidation (LPO-malondialdehyde-MDA) levels in liver homogenates and liver microsomal fractions against carbon tetrachloride (CCl(4))-induced acute liver injury in low-protein fed Sprague-Dawley rats (Rattus norvegicus) were investigated. A group of male Sprague-Dawley rats maintained on a low-protein diet for 5 days were divided into three subgroups. Two subgroups were injected with carbon tetrachloride and the other group with an equivalent amount of olive oil. Two hours after CCl(4) intoxication one of the two subgroups was administered with pumpkin seed protein isolate and thereafter switched onto a 20% pumpkin seed protein isolate diet. The other two groups of rats were maintained on the low-protein diet for the duration of the investigation. Groups of rats from the different subgroups were killed at 24, 48 and 72 h after their respective treatments. After 5 days on the low-protein diet the activity levels of all the enzymes as well as antioxidant levels were significantly lower than their counterparts on a normal balanced diet. However, a low-protein diet resulted in significantly increased levels of lipid peroxidation. The CCl(4) intoxicated rats responded in a similar way, regarding all the variables investigated, to their counterparts on a low-protein diet. The administration of pumpkin seed protein isolate after CCl(4) intoxication resulted in significantly increased levels of all the variables investigated, with the exception of the lipid peroxidation levels which were significantly decreased. From the results of the present study it is concluded that pumpkin seed protein isolate administration was effective in alleviating the detrimental effects associated with protein

Protein synthesis in the embryo of Pinus thunbergii seed, 2

International Nuclear Information System (INIS)

Yamamoto, Naoaki; Sasaki, Satohiko.

1977-01-01

14 C-Amino acid incorporating activity in the absence of exogenous mRNA was found in a cell-free system from embryos of light-germinated Pinus thunbergii seeds, but not in that from dark-imbibed seed embryos. Template activity in the cell-free system from the light-germinated seed embryos was observed in the ribosome fraction, especially the polyribosome fraction, but not in the 100,000 x g supernatant fraction (s100). These facts suggest that the nature of the block in protein synthesis during the imbibition of seeds in the dark is due to the lack or inactivity of mRNA. The s100 from light-germinated seed embryos was found to be less active in amino acid incorporation than that from dark-imbibed seed embryos. (auth.)

Regulatory-associated protein of TOR (RAPTOR) alters the hormonal and metabolic composition of Arabidopsis seeds, controlling seed morphology, viability and germination potential.

Science.gov (United States)

Salem, Mohamed A; Li, Yan; Wiszniewski, Andrew; Giavalisco, Patrick

2017-11-01

Target of Rapamycin (TOR) is a positive regulator of growth and development in all eukaryotes, which positively regulates anabolic processes like protein synthesis, while repressing catabolic processes, including autophagy. To better understand TOR function we decided to analyze its role in seed development and germination. We therefore performed a detailed phenotypic analysis using mutants of the REGULATORY-ASSOCIATED PROTEIN OF TOR 1B (RAPTOR1B), a conserved TOR interactor, acting as a scaffold protein, which recruits substrates for the TOR kinase. Our results show that raptor1b plants produced seeds that were delayed in germination and less resistant to stresses, leading to decreased viability. These physiological phenotypes were accompanied by morphological changes including decreased seed-coat pigmentation and reduced production of seed-coat mucilage. A detailed molecular analysis revealed that many of these morphological changes were associated with significant changes of the metabolic content of raptor1b seeds, including elevated levels of free amino acids, as well as reduced levels of protective secondary metabolites and storage proteins. Most of these observed changes were accompanied by significantly altered phytohormone levels in the raptor1b seeds, with increases in abscisic acid, auxin and jasmonic acid, which are known to inhibit germination. Delayed germination and seedling growth, observed in the raptor1b seeds, could be partially restored by the exogenous supply of gibberellic acid, indicating that TOR is at the center of a regulatory hub controlling seed metabolism, maturation and germination. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

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

[Analysis of total proteins in the seed of almond (Prunus dulcis) by two-dimensional electrophoresis].

Science.gov (United States)

Li, Dong-dong; He, Shao-heng

2004-07-01

To analyse the total proteins in the seeds of almond (Prunus dulcis), one of the popular ingestent allergens in China, by two-dimensional electrophoresis. The total proteins of the seeds were extracted by trichloracetic acid (TCA) method, and then separated by isoelectric focusing as first dimension and SDS-PAGE as the second dimension. The spots of proteins were visualized by staining with Coomassie Brilliant Blue R-250. After analysis with software (ImageMaster 2D), 188 different proteins were detected. The isoelectric points (pI) for approximately 28% of total proteins were between 4.5-5.5, and the relative molecular mass (M(r)) of approximately 62% total proteins were between (20-25)x10(3). This was the first high-resolution, two-dimensional protein map of the seed of almond (Prunus dulcis) in China. Our finding has laid a solid foundation for further identification, characterization, gene cloning and standardization of allergenic proteins in the seed of almond (Prunus dulcis).

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.

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 ...

Role of protein and mRNA oxidation in seed dormancy and germination

Directory of Open Access Journals (Sweden)

hayat eel-maarouf-bouteau

2013-04-01

Full Text Available Reactive oxygen species (ROS are key players in the regulation of seed germination and dormancy. Although their regulated accumulation is a prerequisite for germination, the cellular basis of their action remains unknown, but very challenging to elucidate due to the lack of specificity of these compounds that can potentially react with all biomolecules. Among these, nucleic acids and proteins are very prone to oxidative damage. RNA is highly sensitive to oxidation because of its single-stranded structure and the absence of a repair system. Oxidation of mRNAs induces their decay through processing bodies or results in the synthesis of aberrant proteins through altered translation. Depending on the oxidized amino acid, ROS damage of proteins can be irreversible (i.e. carbonylation thus triggering the degradation of the oxidized proteins by the cytosolic 20S proteasome or can be reversed through the action of thioredoxins, peroxiredoxins or glutaredoxins (cysteine oxidation or by methionine sulfoxide reductase (methionine oxidation. Seed dormancy alleviation in the dry state, referred to as after-ripening, requires both selective mRNA oxidation and protein carbonylation. Similarly, seed imbibition of non-dormant seeds is associated with targeted oxidation of a subset of proteins. Altogether, these specific features testify that such oxidative modifications play important role in commitment of the cellular functioning toward germination completion.

Biorefinery methods for separation of protein and oil fractions from rubber seed kernel

NARCIS (Netherlands)

Widyarani, R.; Ratnaningsih, E.; Sanders, J.P.M.; Bruins, M.E.

2014-01-01

Biorefinery of rubber seeds can generate additional income for farmers, who already grow rubber trees for latex production. The aim of this study was to find the best method for protein and oil production from rubber seed kernel, with focus on protein recovery. Different pre-treatments and oil

Analysis of natural allelic variation of Arabidopsis seed germination and seed longevity traits between the accessions Landberg erecta and Shakdara, using a new recombinant inbred line population

NARCIS (Netherlands)

Clerkx, E.J.M.; El-Lithy, M.E.M.; Vierling, E.; Ruijs, G.J.; Vries, de M.H.C.; Groot, S.P.C.; Vreugdenhil, D.; Koornneef, M.

2004-01-01

Quantitative trait loci (QTL) mapping was used to identify loci controlling various aspects of seed longevity during storage and germination. Similar locations for QTLs controlling different traits might be an indication for a common genetic control of such traits. For this analysis we used a new

Effect of Stirring and Seeding on Whey Protein Fibril Formation

NARCIS (Netherlands)

Bolder, S.G.; Sagis, L.M.C.; Venema, P.; Linden, van der E.

2007-01-01

The effect of stirring and seeding on the formation of fibrils in whey protein isolate (WPI) solutions was studied. More fibrils of a similar length are formed when WPI is stirred during heating at pH 2 and 80 C compared to samples that were heated at rest. Addition of seeds did not show an

Genetic improvement of soybean seed proteins by γ-ray irradiation

International Nuclear Information System (INIS)

Kitamura, Keisuke

1998-01-01

Although soybeans have the highest protein content among seed crops, the protein quality is poor due to the low content of the sulfur-containing amino acids, cysteine and methionine. Soybean 7S globulin and 11S globulin are the two major protein components, accounting for about 70% of the total seed protein. The 11S globulin contains three to four times more methionine and cysteine per unit protein than that of the 7S globulin. Furthermore, the two globulins show considerable differences in food processing properties such as gel-making ability and emulsifying capacity. The 7S globulin is composed of three kinds of polypeptides, designated as α, α' and β subunits. A variety of soybean cv. Keburi, which lacks α' subunit was identified in a germplasm collection. An induced mutant line which lacks both α and α' subunits, was recently identified in the progeny of γ-ray-irradiated seeds from a line lacking α' subunit. On the other hand, the 11S globulin is composed of the A 1a B 2 , A 1b B 1b , A 2 B 1a , A 3 B 4 and A 4 A 5 B 3 subunits. It has become possible to breed soybeans with markedly modified protein composition from extremely high to extremely low 7S : 11S ratios using mutant genes for the subunits of the two globulins. Lipoxygenase catalyzes the hydroperoxydation of unsaturated fatty acids and polyunsaturated lipids. Soybean seeds contain three lipoxygenase isozymes, called L-1, L-2 and L-3, which are responsible for the generation of grassy-beany and bitter tastes, limiting the use of whole soybeans and soy proteins in certain food products. In the early 1980s, three types of spontaneous mutant soybean varieties lacking L-1, L-2 or L-3 were detected. Soybean cultivars having the lipoxygenase-null traits could become economically valuable for the manufacture of soy products such as soy milk due to their low levels of beany taste and their enhanced storage stability. (J.P.N.)

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.

Small Heat Shock Proteins Can Release Light Dependence of Tobacco Seed during Germination1[OPEN

Science.gov (United States)

Koo, Hyun Jo; Park, Soo Min; Kim, Keun Pill; Suh, Mi Chung; Lee, Mi Ok; Lee, Seong-Kon; Xinli, Xia

2015-01-01

Small heat shock proteins (sHSPs) function as ATP-independent molecular chaperones, and although the production and function of sHSPs have often been described under heat stress, the expression and function of sHSPs in fundamental developmental processes, such as pollen and seed development, have also been confirmed. Seed germination involves the breaking of dormancy and the resumption of embryo growth that accompany global changes in transcription, translation, and metabolism. In many plants, germination is triggered simply by imbibition of water; however, different seeds require different conditions in addition to water. For small-seeded plants, like Arabidopsis (Arabidopsis thaliana), lettuce (Lactuca sativa), tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum), light is an important regulator of seed germination. The facts that sHSPs accumulate during seed development, sHSPs interact with various client proteins, and seed germination accompanies synthesis and/or activation of diverse proteins led us to investigate the role of sHSPs in seed germination, especially in the context of light dependence. In this study, we have built transgenic tobacco plants that ectopically express sHSP, and the effect was germination of the seeds in the dark. Administering heat shock to the seeds also resulted in the alleviation of light dependence during seed germination. Subcellular localization of ectopically expressed sHSP was mainly observed in the cytoplasm, whereas heat shock-induced sHSPs were transported to the nucleus. We hypothesize that ectopically expressed sHSPs in the cytoplasm led the status of cytoplasmic proteins involved in seed germination to function during germination without additional stimulus and that heat shock can be another signal that induces seed germination. PMID:25604531

Proteomic and transcriptomic analysis of Arabidopsis seeds: molecular evidence for successive processing of seed proteins and its implication in the stress response to sulfur nutrition.

Science.gov (United States)

Higashi, Yasuhiro; Hirai, Masami Yokota; Fujiwara, Toru; Naito, Satoshi; Noji, Masaaki; Saito, Kazuki

2006-11-01

Seed storage proteins are synthesized as sources of carbon, nitrogen and sulfur for the next generation of plants. Their composition changes according to nutritional conditions. Here, we report the precise molecular identification of seed proteins by proteomic analysis of wild-type Arabidopsis thaliana and methionine-over-accumulating mutant mto1-1 plants. The identities of 50 protein spots were determined in the protein extract of mature Arabidopsis seeds by two-dimensional (2D) gel electrophoresis and subsequent mass spectrometric analysis. Of these protein spots, 42 were identified as derived from 12S globulins or 2S albumins. These results indicate that approximately 84% of protein species in Arabidopsis seeds are derived from a few genes coding for 12S globulins and 2S albumins. Extensive mass spectrometric analysis of the 42 spots revealed that successive C-terminal degradation occurred on the 12S globulins. The feasibility of this C-terminal processing was rationalized by molecular modeling of the three-dimensional structure of 12S globulins. The C-terminal degradation at glutamic acid residues of the 12S globulin subunits was repressed under sulfur-deficient conditions. Transcriptome analysis was combined with proteomic analysis to elucidate the mechanism of changes in seed protein composition in response to sulfur deficiency. The results suggest that seed storage proteins in Arabidopsis undergo multi-layer regulation, with emphasis on post-translational modifications that enable the plant to respond to sulfur deficiency.

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.

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.

Differentiation of Vitis vinifera varieties by MALDI-MS analysis of the grape seed proteins.

Science.gov (United States)

Pesavento, Ivana Chiara; Bertazzo, Antonella; Flamini, Riccardo; Vedova, Antonio Dalla; De Rosso, Mirko; Seraglia, Roberta; Traldi, Pietro

2008-02-01

Until now the study of pathogenic related proteins in grape juice and wine, performed by ESI-MS, LC/ESI-MS, and MALDI/MS, has been proposed for differentiation of varieties. In fact, chitinases and thaumatin-like proteins persist through the vinification process and cause hazes and sediments in bottled wines. An additional instrument, potentially suitable for the grape varieties differentiation, has been developed by MALDI/MS for the grape seed protein analysis. The hydrosoluble protein profiles of seeds extract from three different Vitis vinifera grape (red and white) varieties were analyzed and compared. In order to evaluate the environmental conditions and harvest effects, the seed protein profiles of one grape variety from different locations and harvests were studied. (c) 2008 John Wiley & Sons, Ltd.

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

The Arabidopsis CROWDED NUCLEI genes regulate seed germination by modulating degradation of ABI5 protein.

Science.gov (United States)

Zhao, Wenming; Guan, Chunmei; Feng, Jian; Liang, Yan; Zhan, Ni; Zuo, Jianru; Ren, Bo

2016-07-01

In Arabidopsis, the phytohormone abscisic acid (ABA) plays a vital role in inhibiting seed germination and in post-germination seedling establishment. In the ABA signaling pathway, ABI5, a basic Leu zipper transcription factor, has important functions in the regulation of seed germination. ABI5 protein localizes in nuclear bodies, along with AFP, COP1, and SIZ1, and was degraded through the 26S proteasome pathway. However, the mechanisms of ABI5 nuclear body formation and ABI5 protein degradation remain obscure. In this study, we found that the Arabidopsis CROWDED NUCLEI (CRWN) proteins, predicted nuclear matrix proteins essential for maintenance of nuclear morphology, also participate in ABA-controlled seed germination by regulating the degradation of ABI5 protein. During seed germination, the crwn mutants are hypersensitive to ABA and have higher levels of ABI5 protein compared to wild type. Genetic analysis suggested that CRWNs act upstream of ABI5. The observation that CRWN3 colocalizes with ABI5 in nuclear bodies indicates that CRWNs might participate in ABI5 protein degradation in nuclear bodies. Moreover, we revealed that the extreme C-terminal of CRWN3 protein is necessary for its function in the response to ABA in germination. Our results suggested important roles of CRWNs in ABI5 nuclear body organization and ABI5 protein degradation during seed germination. © 2015 Institute of Botany, Chinese Academy of Sciences.

Selection for a Zinc-Finger Protein Contributes to Seed Oil Increase during Soybean Domestication.

Science.gov (United States)

Li, Qing-Tian; Lu, Xiang; Song, Qing-Xin; Chen, Hao-Wei; Wei, Wei; Tao, Jian-Jun; Bian, Xiao-Hua; Shen, Ming; Ma, Biao; Zhang, Wan-Ke; Bi, Ying-Dong; Li, Wei; Lai, Yong-Cai; Lam, Sin-Man; Shui, Guang-Hou; Chen, Shou-Yi; Zhang, Jin-Song

2017-04-01

Seed oil is a momentous agronomical trait of soybean ( Glycine max ) targeted by domestication in breeding. Although multiple oil-related genes have been uncovered, knowledge of the regulatory mechanism of seed oil biosynthesis is currently limited. We demonstrate that the seed-preferred gene GmZF351 , encoding a tandem CCCH zinc finger protein, is selected during domestication. Further analysis shows that GmZF351 facilitates oil accumulation by directly activating WRINKLED1 , BIOTIN CARBOXYL CARRIER PROTEIN2 , 3-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III , DIACYLGLYCEROL O-ACYLTRANSFERASE1 , and OLEOSIN2 in transgenic Arabidopsis ( Arabidopsis thaliana ) seeds. Overexpression of GmZF351 in transgenic soybean also activates lipid biosynthesis genes, thereby accelerating seed oil accumulation. The ZF351 haplotype from the cultivated soybean group and the wild soybean ( Glycine soja ) subgroup III correlates well with high gene expression level, seed oil contents and promoter activity, suggesting that selection of GmZF351 expression leads to increased seed oil content in cultivated soybean. Our study provides novel insights into the regulatory mechanism for seed oil accumulation, and the manipulation of GmZF351 may have great potential in the improvement of oil production in soybean and other related crops. © 2017 American Society of Plant Biologists. All Rights Reserved.

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.

Mobilization and Role of Starch, Protein, and Fat Reserves during Seed Germination of Six Wild Grassland Species.

Science.gov (United States)

Zhao, Ming; Zhang, Hongxiang; Yan, Hong; Qiu, Lu; Baskin, Carol C

2018-01-01

Since seed reserves can influence seed germination, the quantitative and qualitative differences in seed reserves may relate to the germination characteristics of species. The purpose of our study was to evaluate the correlation between germination and seed reserves, as well as their mobilization during germination of six grassland species ( Chloris virgata , Kochia scoparia , Lespedeza hedysaroides , Astragalus adsurgens , Leonurus artemisia , and Dracocephalum moldavica ) and compare the results with domesticated species. We measured starch, protein, and fat content in dry seeds and the initial absorption of water during imbibition. Starch, soluble protein, fat, and soluble sugar content also were determined at five stages during germination. Starch, protein, and fat reserves in dry seeds were not significantly correlated with germination percentage and rate (speed), but soluble sugar and soluble protein contents at different germination stages were positively significantly correlated with germination rate for the six species. Starch was mainly used during seed imbibition, and soluble protein was used from the imbibition stage to the highest germination stage. Fat content for all species remained relatively constant throughout germination for six species, regardless of the proportion of other seed reserves in the seeds. Our results for fat utilization differ from those obtained for cultivated grasses and legumes. These results provide new insight on the role of seed reserves as energy resources in germination for wild species.

Mobilization and Role of Starch, Protein, and Fat Reserves during Seed Germination of Six Wild Grassland Species

Directory of Open Access Journals (Sweden)

Ming Zhao

2018-02-01

Full Text Available Since seed reserves can influence seed germination, the quantitative and qualitative differences in seed reserves may relate to the germination characteristics of species. The purpose of our study was to evaluate the correlation between germination and seed reserves, as well as their mobilization during germination of six grassland species (Chloris virgata, Kochia scoparia, Lespedeza hedysaroides, Astragalus adsurgens, Leonurus artemisia, and Dracocephalum moldavica and compare the results with domesticated species. We measured starch, protein, and fat content in dry seeds and the initial absorption of water during imbibition. Starch, soluble protein, fat, and soluble sugar content also were determined at five stages during germination. Starch, protein, and fat reserves in dry seeds were not significantly correlated with germination percentage and rate (speed, but soluble sugar and soluble protein contents at different germination stages were positively significantly correlated with germination rate for the six species. Starch was mainly used during seed imbibition, and soluble protein was used from the imbibition stage to the highest germination stage. Fat content for all species remained relatively constant throughout germination for six species, regardless of the proportion of other seed reserves in the seeds. Our results for fat utilization differ from those obtained for cultivated grasses and legumes. These results provide new insight on the role of seed reserves as energy resources in germination for wild species.

Characterization of seed storage protein patterns of Heliotropium digynum.

Science.gov (United States)

Alwhibi, Mona Soliman

2017-09-01

Heliotropium digynum , is a shrub that has ecological importance. The height of the plant differs from one population to another and the difference in length of the inflorescence can be attributed to environmental factors, such as rainfall or type of soil and temperature. To date, no study has shed light on estimation in seed samples of H. digynum in Saudi Arabia. So, the aim is to evaluate and characterize the protein patterns of seed storage proteins of H. digynum to be used as fingerprint of this plant in Saudi Arabia. It is collected from different locations in the central region of Saudi Arabia and total protein extraction from plant was compared in SDS-PAGE. The genetic relationships among all cultivars were analyzed using UPGMA and NJ using Total Lab TL and in the same way using Jaccard Similarity Coefficient dendrogram using STATISTICA (ver.8) software. Results, our data show that amounts of protein are different, although they are of the same type or from the same geographical region. Amounts ranged between 22 and 1.5 mg/g of dry weight. Less amount of protein was obtained from the group of samples collected from Dir'iyah area, and the highest amount of protein was from the group of samples collected from Dyrab area in general.

Modeling Protein Structures in Feed and Seed Tissues Using Novel Synchrotron-Based Analytical Technique

International Nuclear Information System (INIS)

Yu, P.

2008-01-01

Traditional 'wet' chemical analyses usually looks for a specific known component (such as protein) through homogenization and separation of the components of interest from the complex tissue matrix. Traditional 'wet' chemical analyses rely heavily on the use of harsh chemicals and derivatization, therefore altering the native feed protein structures and possibly generating artifacts. The objective of this study was to introduce a novel and non-destructive method to estimate protein structures in feed and seeds within intact tissues using advanced synchrotron-based infrared microspectroscopy (SFTIRM). The experiments were performed at the National Synchrotron Light Source in Brookhaven National Laboratory (US Dept. of Energy, NY). The results show that with synchrotron-based SFTIRM, we are able to localize relatively 'pure' protein without destructions of the feed and seed tissues and qualify protein internal structures in terms of the proportions and ratios of a-helix, β-sheet, random coil and β-turns on a relative basis using multi-peak modeling procedures. These protein structure profile (a-helix, β-sheet, etc.) may influence protein quality and availability in animals. Several examples of feed and seeds were provided. The implications of this study are that we can use this new method to compare internal protein structures between feeds and between seed verities. We can also use this method to detect heat-induced the structural changes of protein in feeds.

Biogenesis of protein bodies during legumin accumulation in developing olive (Olea europaea L.) seed.

Science.gov (United States)

Jimenez-Lopez, Jose C; Zienkiewicz, Agnieszka; Zienkiewicz, Krzysztof; Alché, Juan D; Rodríguez-García, Maria I

2016-03-01

Much of our current knowledge about seed development and differentiation regarding reserves synthesis and accumulation come from monocot (cereals) plants. Studies in dicotyledonous seeds differentiation are limited to a few species and in oleaginous species are even scarcer despite their agronomic and economic importance. We examined the changes accompanying the differentiation of olive endosperm and cotyledon with a focus on protein bodies (PBs) biogenesis during legumin protein synthesis and accumulation, with the aim of getting insights and a better understanding of the PBs' formation process. Cotyledon and endosperm undergo differentiation during seed development, where an asynchronous time-course of protein synthesis, accumulation, and differential PB formation patterns was found in both tissues. At the end of seed maturation, a broad population of PBs, particularly in cotyledon cells, was distinguishable in terms of number per cell and morphometric and cytochemical features. Olive seed development is a tissue-dependent process characterized by differential rates of legumin accumulation and PB formation in the main tissues integrating seed. One of the main features of the impressive differentiation process is the specific formation of a broad group of PBs, particularly in cotyledon cells, which might depend on selective accumulation and packaging of proteins and specific polypeptides into PBs. The nature and availability of the major components detected in the PBs of olive seed are key parameters in order to consider the potential use of this material as a suitable source of carbon and nitrogen for animal or even human use.

Improving Jatropha curcas seed protein recovery by using counter current multistage extraction

NARCIS (Netherlands)

Lestari, D.; Mulder, W.J.; Sanders, J.P.M.

2010-01-01

Jatropha curcas seed press cake contains 23 wt% proteins (dry basis). Due to the toxic compounds in Jatropha, we will use the proteins for non-food applications. Related to non-food applications, an efficient protein extraction to obtain a high protein recovery and high protein concentration with

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.

Functional properties and Solubility of date seed proteins as ...

African Journals Online (AJOL)

Med ali

2013-03-06

Mar 6, 2013 ... Key words: Phoenix dactylifera L, date palm seed, fibre, protein, functional properties. INTRODUCTION. The date .... was employed to perform dynamic measurements. ... are likely to be composed of high-molecular weight.

Effects of seed preparation and oil pressing on milkweed (Asclepias spp.) protein functional properties

Science.gov (United States)

The effects of seed cooking and oil processing conditions on functional properties of milkweed seed proteins were determined to identify potential value-added uses for the meal. Milkweed seeds were flaked and then cooked in the seed conditioner at 82°C for 30, 60 or 90 min. Oil was extracted by scre...

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.

Identification of quantitative trait loci underlying seed protein content of soybean including main, epistatic, and QTL × environment effects in different regions of Northeast China.

Science.gov (United States)

Teng, Weili; Li, Wen; Zhang, Qi; Wu, Depeng; Zhao, Xue; Li, Haiyan; Han, Yingpeng; Li, Wenbin

2017-08-01

The objective here was to identify QTL underlying soybean protein content (PC), and to evaluate the additive and epistatic effects of the QTLs. A mapping population, consisting of 129 recombinant inbred lines (RILs), was created by crossing 'Dongnong 46' and 'L-100'. Phenotypic data of the parents and RILs were collected for 4 years in three locations of Heilongjiang Province of China. A total of 213 SSR markers were used to construct a genetic linkage map. Eight QTLs, located on seven chromosomes (Chr), were identified to be associated with PC among the 10 tested environments. Of the seven QTLs, five QTLs, qPR-2 (Satt710, on Chr9), qPR-3 (Sat_122, on Chr12), qPR-5 (Satt543, on Chr17), qPR-7 (Satt163, on Chr18), and qPR-8 (Satt614, on Chr20), were detected in six, seven, seven, six, and seven environments, respectively, implying relatively stable QTLs. qPR-3 could explain 3.33%-11.26% of the phenotypic variation across eight tested environments. qPR-5 and qPR-8 explained 3.64%-10.1% and 11.86%-18.40% of the phenotypic variation, respectively, across seven tested environments. Eight QTLs associated with PC exhibited additive and (or) additive × environment interaction effects. The results showed that environment-independent QTLs often had higher additive effects. Moreover, five epistatic pairwise QTLs were identified in the 10 environments.

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

The genotype-environment interaction variance in rice-seed protein determination

International Nuclear Information System (INIS)

Ismachin, M.

1976-01-01

Many environmental factors influence the protein content of cereal seed. This fact procured difficulties in breeding for protein. Yield is another example on which so many environmental factors are of influence. The length of time required by the plant to reach maturity, is also affected by the environmental factors; even though its effect is not too decisive. In this investigation the genotypic variance and the genotype-environment interaction variance which contribute to the total variance or phenotypic variance was analysed, with purpose to give an idea to the breeder how selection should be made. It was found that genotype-environment interaction variance is larger than the genotypic variance in contribution to total variance of protein-seed determination or yield. In the analysis of the time required to reach maturity it was found that genotypic variance is larger than the genotype-environment interaction variance. It is therefore clear, why selection for time required to reach maturity is much easier than selection for protein or yield. Selected protein in one location may be different from that to other locations. (author)

Protein extractability from defatted Moringa oleifera lam. seeds flour ...

African Journals Online (AJOL)

Protein extractability from defatted Moringa oleifera seed flour was studied under various conditions of pH (2-10), time (5-60 minutes), salts (NaCl and CaCl ), salt concentrations (0-2 M) and solvent to flour ratio (10:1-30:1). 2 Results showed that protein extractability was dependent on pH, type of salt, salt concentrations and ...

Redox-dependent interaction between thaumatin-like protein and β-glucan influences malting quality of barley.

Science.gov (United States)

Singh, Surinder; Tripathi, Rajiv K; Lemaux, Peggy G; Buchanan, Bob B; Singh, Jaswinder

2017-07-18

Barley is the cornerstone of the malting and brewing industry. It is known that 250 quantitative trait loci (QTLs) of the grain are associated with 19 malting-quality phenotypes. However, only a few of the contributing genetic components have been identified. One of these, on chromosome 4H, contains a major malting QTL, QTL2, located near the telomeric region that accounts, respectively, for 28.9% and 37.6% of the variation in the β-glucan and extract fractions of malt. In the current study, we dissected the QTL2 region using an expression- and microsynteny-based approach. From a set of 22 expressed sequence tags expressed in seeds at the malting stage, we identified a candidate gene, TLP8 ( thaumatin-like protein 8 ), which was differentially expressed and influenced malting quality. Transcript abundance and protein profiles of TLP8 were studied in different malt and feed varieties using quantitative PCR, immunoblotting, and enzyme-linked immunosorbent assay (ELISA). The experiments demonstrated that TLP8 binds to insoluble (1, 3, 1, 4)-β-D glucan in grain extracts, thereby facilitating the removal of this undesirable polysaccharide during malting. Further, the binding of TLP8 to β-glucan was dependent on redox. These findings represent a stride forward in our understanding of the malting process and provide a foundation for future improvements in the final beer-making process.

The proteins of the grape (Vitis vinifera L.) seed endosperm: fractionation and identification of the major components.

Science.gov (United States)

Gazzola, Diana; Vincenzi, Simone; Gastaldon, Luca; Tolin, Serena; Pasini, Gabriella; Curioni, Andrea

2014-07-15

In the present study, grape (Vitis vinifera L.) seed endosperm proteins were characterized after sequential fractionation, according to a modified Osborne procedure. The salt-soluble fraction (albumins and globulins) comprised the majority (58.4%) of the total extracted protein. The protein fractions analysed by SDS-PAGE showed similar bands, indicating different solubility of the same protein components. SDS-PAGE in non-reducing and reducing conditions revealed the polypeptide composition of the protein bands. The main polypeptides, which were similar in all the grape varieties analysed, were identified by LC-MS/MS as homologous to the 11S globulin-like seed storage proteins of other plant species, while a monomeric 43 kDa protein presented high homology with the 7S globulins of legume seeds. The results provide new insights about the identity, structure and polypeptide composition of the grape seed storage proteins. Copyright © 2014 Elsevier Ltd. All rights reserved.

The extraction of proteins from the neem seed ( Indica azadirachta A ...

African Journals Online (AJOL)

Techniques for maximizing the extraction of protein from the neem seed (Indica azadirachta A. Juss) were investigated. Extractants used were sodium chloride and sodium sulphate solutions of varying concentration and pH. Maximum extractions of 17.86 g of extractable protein was obtained from 1 kg of crude protein, using ...

Characterization of seed storage protein patterns of Heliotropium digynum

Directory of Open Access Journals (Sweden)

Mona Soliman Alwhibi

2017-09-01

Full Text Available Heliotropium digynum, is a shrub that has ecological importance. The height of the plant differs from one population to another and the difference in length of the inflorescence can be attributed to environmental factors, such as rainfall or type of soil and temperature. To date, no study has shed light on estimation in seed samples of H. digynum in Saudi Arabia. So, the aim is to evaluate and characterize the protein patterns of seed storage proteins of H. digynum to be used as fingerprint of this plant in Saudi Arabia. It is collected from different locations in the central region of Saudi Arabia and total protein extraction from plant was compared in SDS-PAGE. The genetic relationships among all cultivars were analyzed using UPGMA and NJ using Total Lab TL and in the same way using Jaccard Similarity Coefficient dendrogram using STATISTICA (ver.8 software. Results, our data show that amounts of protein are different, although they are of the same type or from the same geographical region. Amounts ranged between 22 and 1.5 mg/g of dry weight. Less amount of protein was obtained from the group of samples collected from Dir’iyah area, and the highest amount of protein was from the group of samples collected from Dyrab area in general.

Increasing the production yield of recombinant protein in transgenic seeds by expanding the deposition space within the intracellular compartment

OpenAIRE

Takaiwa, Fumio

2013-01-01

Seeds must maintain a constant level of nitrogen in order to germinate. When recombinant proteins are produced while endogenous seed protein expression is suppressed, the production levels of the foreign proteins increase to compensate for the decreased synthesis of endogenous proteins. Thus, exchanging the production of endogenous seed proteins for that of foreign proteins is a promising approach to increase the yield of foreign recombinant proteins. Providing a space for the deposition of r...

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.

Integrated and comparative proteomics of high-oil and high-protein soybean seeds.

Science.gov (United States)

Xu, Xiu Ping; Liu, Hui; Tian, Lihong; Dong, Xiang Bai; Shen, Shi Hua; Qu, Le Qing

2015-04-01

We analysed the global protein expression in seeds of a high-oil soybean cultivar (Jiyu 73, JY73) by proteomics. More than 700 protein spots were detected and 363 protein spots were successfully identified. Comparison of the protein profile of JY73 with that of a high-protein cultivar (Zhonghuang 13, ZH13) revealed 40 differentially expressed proteins, including oil synthesis, redox/stress, hydrolysis and storage-related proteins. All redox/stress proteins were less or not expressed in JY73, whereas the expression of the major storage proteins, nitrogen and carbon metabolism-related proteins was higher in ZH13. Biochemical analysis of JY73 revealed that it was in a low oxidation state, with a high content of polyunsaturated fatty acids and vitamin E. Vitamin E was more active than antioxidant enzymes and protected the soybean seed in a lower oxidation state. The characteristics of high oil and high protein in soybean, we revealed, might provide a reference for soybean nutrition and soybean breeding. Copyright © 2014 Elsevier Ltd. All rights reserved.

Albizia lebbeck Seed Coat Proteins Bind to Chitin and Act as a Defense against Cowpea Weevil Callosobruchus maculatus.

Science.gov (United States)

Silva, Nadia C M; De Sá, Leonardo F R; Oliveira, Eduardo A G; Costa, Monique N; Ferreira, Andre T S; Perales, Jonas; Fernandes, Kátia V S; Xavier-Filho, Jose; Oliveira, Antonia E A

2016-05-11

The seed coat is an external tissue that participates in defense against insects. In some nonhost seeds, including Albizia lebbeck, the insect Callosobruchus maculatus dies during seed coat penetration. We investigated the toxicity of A. lebbeck seed coat proteins to C. maculatus. A chitin-binding protein fraction was isolated from seed coat, and mass spectrometry showed similarity to a C1 cysteine protease. By ELM program an N-glycosylation interaction motif was identified in this protein, and by molecular docking the potential to interact with N-acetylglucosamine (NAG) was shown. The chitin-binding protein fraction was toxic to C. maculatus and was present in larval midgut and feces but not able to hydrolyze larval gut proteins. It did not interfere, though, with the intestinal cell permeability. These results indicate that the toxicity mechanism of this seed coat fraction may be related to its binding to chitin, present in the larvae gut, disturbing nutrient absorption.

Dynamic Proteomics Emphasizes the Importance of Selective mRNA Translation and Protein Turnover during Arabidopsis Seed Germination*

Science.gov (United States)

Galland, Marc; Huguet, Romain; Arc, Erwann; Cueff, Gwendal; Job, Dominique; Rajjou, Loïc

2014-01-01

During seed germination, the transition from a quiescent metabolic state in a dry mature seed to a proliferative metabolic state in a vigorous seedling is crucial for plant propagation as well as for optimizing crop yield. This work provides a detailed description of the dynamics of protein synthesis during the time course of germination, demonstrating that mRNA translation is both sequential and selective during this process. The complete inhibition of the germination process in the presence of the translation inhibitor cycloheximide established that mRNA translation is critical for Arabidopsis seed germination. However, the dynamics of protein turnover and the selectivity of protein synthesis (mRNA translation) during Arabidopsis seed germination have not been addressed yet. Based on our detailed knowledge of the Arabidopsis seed proteome, we have deepened our understanding of seed mRNA translation during germination by combining two-dimensional gel-based proteomics with dynamic radiolabeled proteomics using a radiolabeled amino acid precursor, namely [35S]-methionine, in order to highlight de novo protein synthesis, stability, and turnover. Our data confirm that during early imbibition, the Arabidopsis translatome keeps reflecting an embryonic maturation program until a certain developmental checkpoint. Furthermore, by dividing the seed germination time lapse into discrete time windows, we highlight precise and specific patterns of protein synthesis. These data refine and deepen our knowledge of the three classical phases of seed germination based on seed water uptake during imbibition and reveal that selective mRNA translation is a key feature of seed germination. Beyond the quantitative control of translational activity, both the selectivity of mRNA translation and protein turnover appear as specific regulatory systems, critical for timing the molecular events leading to successful germination and seedling establishment. PMID:24198433

Analysis of Recombinant Proteins in Transgenic Rice Seeds: Identity, Localization, Tolerance to Digestion, and Plant Stress Response.

Science.gov (United States)

Wakasa, Yuhya; Takaiwa, Fumio

2016-01-01

Rice seeds are an ideal production platform for high-value recombinant proteins in terms of economy, scalability, safety, and stability. Strategies for the expression of large amounts of recombinant proteins in rice seeds have been established in the past decade and transgenic rice seeds that accumulate recombinant products such as bioactive peptides and proteins, which promote the health and quality of life of humans, have been generated in many laboratories worldwide. One of the most important advantages is the potential for direct oral delivery of transgenic rice seeds without the need for recombinant protein purification (downstream processing), which has been attributed to the high expression levels of recombinant products. Transgenic rice will be beneficial as a delivery system for pharmaceuticals and nutraceuticals in the future. This chapter introduces the strategy for producing recombinant protein in the edible part (endosperm) of the rice grain and describes methods for the analysis of transgenic rice seeds in detail.

Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection.

Directory of Open Access Journals (Sweden)

Xianfa Xie

Full Text Available Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativa--indica and tropical japonica--as well as the ancestral wild rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups.

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.

Relative efficacy of casein or soya protein combined with palm or safflower-seed oil on hyperuricaemia in rats.

Science.gov (United States)

Lo, Hui-Chen; Wang, Yao-Horng; Chiou, Hue-Ying; Lai, Shan-Hu; Yang, Yu

2010-07-01

Diets that ameliorate the adverse effects of uric acid (UA) on renal damage deserve attention. The effects of casein or soya protein combined with palm or safflower-seed oil on various serum parameters and renal histology were investigated on hyperuricaemic rats. Male Wistar rats administered with oxonic acid and UA to induce hyperuricaemia were fed with casein or soya protein plus palm- or safflower-seed oil-supplemented diets. Normal rats and hyperuricaemic rats with or without allopurinol treatment (150 mg/l in drinking water) were fed with casein plus maize oil-supplemented diets. After 8 weeks, allopurinol treatment and soya protein plus safflower-seed oil-supplemented diet significantly decreased serum UA in hyperuricaemic rats (one-way ANOVA; P soya protein and casein attenuated hyperuricaemia-induced decreases in serum albumin and insulin, respectively (two-way ANOVA; P soya protein significantly decreased renal NO and nitrotyrosine and palm oil significantly decreased renal nitrotyrosine, TNF-alpha and interferon-gamma and increased renal transforming growth factor-beta. Casein with safflower-seed oil significantly attenuated renal tubulointerstitial nephritis, crystals and fibrosis. Comparing casein v. soya protein combined with palm or safflower-seed oil, the results support that casein with safflower-seed oil may be effective in attenuating hyperuricaemia-associated renal damage, while soya protein with safflower-seed oil may be beneficial in lowering serum UA and TAG.

Comparative Biochemical and Proteomic Analyses of Soybean Seed Cultivars Differing in Protein and Oil Content.

Science.gov (United States)

Min, Chul Woo; Gupta, Ravi; Kim, So Wun; Lee, So Eui; Kim, Yong Chul; Bae, Dong Won; Han, Won Young; Lee, Byong Won; Ko, Jong Min; Agrawal, Ganesh Kumar; Rakwal, Randeep; Kim, Sun Tae

2015-08-19

This study develops differential protein profiles of soybean (Glycine max) seeds (cv. Saedanbaek and Daewon) varying in protein (47.9 and 39.2%) and oil (16.3 and 19.7%) content using protamine sulfate (PS) precipitation method coupled with a 2D gel electrophoresis (2DGE) approach. Of 71 detected differential spots between Daewon and Saedanbaek, 48 were successfully identified by MALDI-TOF/TOF. Gene ontology analysis revealed that up-regulated proteins in Saedanbaek were largely associated with nutrient reservoir activity (42.6%), which included mainly seed-storage proteins (SSPs; subunits of glycinin and β-conglycinin). Similar results were also obtained in two cultivars of wild soybean (G. soja cv. WS22 and WS15) differing in protein content. Western blots confirmed higher accumulation of SSPs in protein-rich Saedanbaek. Findings presented and discussed in this study highlight a possible involvement of the urea cycle for increased accumulation of SSPs and hence the higher protein content in soybean seeds.

Correlation of protein content to flatulent galactooligosaccharides and exogenous amino acids in seeds of Phaseolus vulgaris L.

Directory of Open Access Journals (Sweden)

Ryszard Kosson

2014-01-01

Full Text Available In order to estimate the possible correlations among constituents of Phaseolus vulgaris seeds, the contents of protein, exogenous amino acids and flatulent galactooligosaccharides (raffinose and stachyose were analyzed in 16 Polish bean cultivars for dry seeds. A negative correlation coefficient (r =-0.9490 was found between protein and methionine contents. High positive correlations among exogenous amino acids, such as lysine and isoleucine, valine and isoleucine, lysine and tyrosine, were observed indicating a chance of selecting far more than one at a time. The small-seeded bean cultivars contained higher contents of protein and galactooligosaccharides than the large-seeded ones.

The ultrastructure of protein bodies isolated from Pisum sativum and Iris pseudoacorus L. seeds

Directory of Open Access Journals (Sweden)

Barbara Gabara

2015-01-01

Full Text Available Protein bodies of Pisum sativum and Iris pseudoacorus seeds have been isolated in sucrose gradient with addition of 50mM citrate buffer, pH 5. Their ultrastructure due to isolation procedure has been described. Two types of protein bodies are present in pea and iris seeds: simple and compex ones - with many inclusions. The method of isolation, used in this paper extracts partly proteins - probably albumins, and also substances present in globoids i.e. phytin and acid phosphatase.

Seed protein variations of Salicornia L. and allied taxa in Turkey.

Science.gov (United States)

Yaprak, A E; Yurdakulol, E

2007-06-01

Electrophoretic seed protein patterns of a number of accessions of Salicornia europaea L. sl., S. prostrata Palas, S. fragilis P.W. Ball and Tutin, Sarcocornia fruticosa (L.) A. J. Scott, Sarcocornia perennis (Miller.) A. J. Scott, Arthrocnemum glaucum (Del.) Ung.-Sternb., Microcnemum coralloides (Loscos and Pardo) subsp. anatolicum Wagenitz and Halocnemum strobilaceum (Pall.) Bieb. were electrophoretically analysed on SDS-PAGE. In total 48 different bands were identified. The obtained data have been treated numerically using the cluster analysis method of unweighted pair group (UPGMA). Finally it was determined that all species separated according to seed protein profiles. And the cladogram obtained studied taxa have been given.

Interspecific variation of total seed protein in wild rice germplasm using SDS-Page

International Nuclear Information System (INIS)

Shah, S.M.A.; Hidayat-ur-Rahman; Abbasi, F.M.; Ashiq, M.; Rabbani, A.M.; Khan, I.A.; Shinwari, Z.K.; Shah, Z.

2011-01-01

Variation in seed protein of 14 wild rice species (Oryza spp.) along with cultivated rice species (O. sativa) was studied using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) to assess genetic diversity in the rice germplasm. SDS bands were scored as present (1) or absent (0) for protein sample of each genotype. On the basis of cluster analysis, four clusters were identified at a similarity level of 0.85. O. nivara, O. rufipogon and O. sativa with AA genomes constituted the first cluster. The second cluster comprised O. punctata of BB genome and wild rice species of CC genome i.e., O. rhizomatis and O. officinalis. However, it also contained O. barthii and O. glumaepatula of AA genome. O. australiensis with EE genome, and O. latifolia, O. alta and O. grandiglumis having CCDD genomes comprised the third cluster. The fourth cluster consisted of wild rice species, O. brachyantha with EE genome along with two other wild rice species, O. longistaminata and O. meridionalis of AA genome. Overall, on the basis of total seed protein, the grouping pattern of rice genotypes was mostly compatible with their genome status. The results of the present work depicted considerable interspecific genetic variation in the investigated germplasm for total seed protein. Moreover, the results obtained in this study also suggest that analysis of seed protein can also provide a better understanding of genetic affinity of the germplasm. (author)

Protein damage and repair controlling seed vigor and longevity.

Science.gov (United States)

Ogé, Laurent; Broyart, Caroline; Collet, Boris; Godin, Béatrice; Jallet, Denis; Bourdais, Gildas; Job, Dominique; Grappin, Philippe

2011-01-01

The formation of abnormal isoaspartyl residues derived from aspartyl or asparaginyl residues is a major source of spontaneous protein misfolding in cells. The repair enzyme protein L: -isoaspartyl methyltransferase (PIMT) counteracts such damage by catalyzing the conversion of abnormal isoaspartyl residues to their normal aspartyl forms. Thus, this enzyme contributes to the survival of many organisms, including plants. Analysis of the accumulation of isoaspartyl-containing proteins and its modulation by the PIMT repair pathway, using germination tests, immunodetection, enzymatic assays, and HPLC analysis, gives new insights in understanding controlling mechanisms of seed longevity and vigor.

Identification of QTLs with main, epistatic and QTL by environment ...

Indian Academy of Sciences (India)

interaction effects for seed shape and hundred-seed weight in soybean ... worldwide. It provides about 69 and 30% of dietary protein ... as main component of plants is affected by seed shape. ... In this analysis, in 2010–2012, seed shape and.

A new method for protein estimation in large seeds using fast-neutron-activation analysis

International Nuclear Information System (INIS)

Gupta, U.C.; Misra, S.C.; Rao, U.S.

1974-01-01

A new method was developed for the determination of protein content of large seeds, using powders of different N content. The powders were obtained by mixing glucose with amino acids in different proportions and were irradiated with and without the seeds in the MeV neutron flux. The irradiated samples were counted under identical conditions and their activities were used to calculate the protein content of the seeds. The results were compared with those obtained by conventional activation technique and were found to be in good agreement. This new method has the advantage of being non-destructive. (author)

Purification and protein composition of oil bodies from Brassica napus seeds

Directory of Open Access Journals (Sweden)

Jolivet Pascale

2006-11-01

Full Text Available Seed oil bodies are intracellular particles to store lipids as food reserves in oleaginous plants. Description of oil body-associated proteins of Arabidopsis thaliana has been recently reported whereas only few data are available in the case of rapeseed. Oil bodies have been prepared from two double-low varieties of Brassica napus seeds, a standard variety (Explus and an oleic variety (Cabriolet. Oil bodies have been purified using floatation technique in the successive presence of high salt concentration, detergent or urea in order to remove non-specifically trapped proteins. The integrity of the oil bodies has been verified and their size estimated. Their protein and fatty acid contents have been determined. The proteins composing these organelles were extracted, separated by denaturing gel electrophoresis, digested by trypsin and their peptides were subsequently analyzed by liquid chromatography-tandem mass spectrometry. Protein identification was performed using Arabidopsis thaliana protein sequence database and a collection of Expressed Sequence Tag (EST of Brassica napus generated from the framework of the French plant genomics programme “Genoplante”. This led to the identification of a limited number of proteins: eight oleosins showing a high similarity each other and representing up to 75% of oil body proteins, a 11 β hydroxysteroid dehydrogenase-like protein highly homologous to the same protein from A. thaliana, and only few contaminating proteins associated with myrosinase activity.

Selection for a Zinc-Finger Protein Contributes to Seed Oil Increase during Soybean Domestication1[OPEN

Science.gov (United States)

Li, Qing-Tian; Lu, Xiang; Song, Qing-Xin; Chen, Hao-Wei; Wei, Wei; Tao, Jian-Jun; Ma, Biao; Bi, Ying-Dong; Li, Wei; Lai, Yong-Cai; Shui, Guang-Hou; Chen, Shou-Yi

2017-01-01

Seed oil is a momentous agronomical trait of soybean (Glycine max) targeted by domestication in breeding. Although multiple oil-related genes have been uncovered, knowledge of the regulatory mechanism of seed oil biosynthesis is currently limited. We demonstrate that the seed-preferred gene GmZF351, encoding a tandem CCCH zinc finger protein, is selected during domestication. Further analysis shows that GmZF351 facilitates oil accumulation by directly activating WRINKLED1, BIOTIN CARBOXYL CARRIER PROTEIN2, 3-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III, DIACYLGLYCEROL O-ACYLTRANSFERASE1, and OLEOSIN2 in transgenic Arabidopsis (Arabidopsis thaliana) seeds. Overexpression of GmZF351 in transgenic soybean also activates lipid biosynthesis genes, thereby accelerating seed oil accumulation. The ZF351 haplotype from the cultivated soybean group and the wild soybean (Glycine soja) subgroup III correlates well with high gene expression level, seed oil contents and promoter activity, suggesting that selection of GmZF351 expression leads to increased seed oil content in cultivated soybean. Our study provides novel insights into the regulatory mechanism for seed oil accumulation, and the manipulation of GmZF351 may have great potential in the improvement of oil production in soybean and other related crops. PMID:28184009

Physiological quality and gene expression related to heat-resistant proteins at different stages of development of maize seeds.

Science.gov (United States)

Andrade, T; Von Pinho, E V R; Von Pinho, R G; Oliveira, G E; Andrade, V; Fernandes, J S

2013-09-13

We quantified and characterized the expression of heat-resistant proteins during seed development of maize lines with distinct levels of tolerance to high drying temperature. A corn field was planted for multiplication of seeds of different lines, two tolerant and two non-tolerant to high drying temperatures. Harvest of the seeds was carried out at various stages of development and they were then subjected to tests of moisture content, germination, first count of germination, accelerated aging, and cold test. The seeds were stored in a freezer for later analysis of expression of heat-resistant proteins by means of real-time PCR, electrophoresis, and spectrophotometry. We observed that heat-resistant proteins are expressed in a differential manner in seeds from different lines and at different stages of development. The expression of heat-resistant proteins was earlier in lines tolerant to high drying temperatures. Greater germination and vigor values was found for seeds collected at the last stage of development.

Toxic Compound, Anti-Nutritional Factors and Functional Properties of Protein Isolated from Detoxified Jatropha curcas Seed Cake

Directory of Open Access Journals (Sweden)

Worapot Suntornsuk

2010-12-01

Full Text Available Jatropha curcas is a multipurpose tree, which has potential as an alternative source for biodiesel. All of its parts can also be used for human food, animal feed, fertilizer, fuel and traditional medicine. J. curcas seed cake is a low-value by-product obtained from biodiesel production. The seed cake, however, has a high amount of protein, with the presence of a main toxic compound: phorbol esters as well as anti-nutritional factors: trypsin inhibitors, phytic acid, lectin and saponin. The objective of this work was to detoxify J. curcas seed cake and study the toxin, anti-nutritional factors and also functional properties of the protein isolated from the detoxified seed cake. The yield of protein isolate was approximately 70.9%. The protein isolate was obtained without a detectable level of phorbol esters. The solubility of the protein isolate was maximal at pH 12.0 and minimal at pH 4.0. The water and oil binding capacities of the protein isolate were 1.76 g water/g protein and 1.07 mL oil/g protein, respectively. The foam capacity and stability, including emulsion activity and stability of protein isolate, had higher values in a range of basic pHs, while foam and emulsion stabilities decreased with increasing time. The results suggest that the detoxified J. curcas seed cake has potential to be exploited as a novel source of functional protein for food applications.

Toxic compound, anti-nutritional factors and functional properties of protein isolated from detoxified Jatropha curcas seed cake.

Science.gov (United States)

Saetae, Donlaporn; Suntornsuk, Worapot

2010-12-28

Jatropha curcas is a multipurpose tree, which has potential as an alternative source for biodiesel. All of its parts can also be used for human food, animal feed, fertilizer, fuel and traditional medicine. J. curcas seed cake is a low-value by-product obtained from biodiesel production. The seed cake, however, has a high amount of protein, with the presence of a main toxic compound: phorbol esters as well as anti-nutritional factors: trypsin inhibitors, phytic acid, lectin and saponin. The objective of this work was to detoxify J. curcas seed cake and study the toxin, anti-nutritional factors and also functional properties of the protein isolated from the detoxified seed cake. The yield of protein isolate was approximately 70.9%. The protein isolate was obtained without a detectable level of phorbol esters. The solubility of the protein isolate was maximal at pH 12.0 and minimal at pH 4.0. The water and oil binding capacities of the protein isolate were 1.76 g water/g protein and 1.07 mL oil/g protein, respectively. The foam capacity and stability, including emulsion activity and stability of protein isolate, had higher values in a range of basic pHs, while foam and emulsion stabilities decreased with increasing time. The results suggest that the detoxified J. curcas seed cake has potential to be exploited as a novel source of functional protein for food applications.

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.

Seed protein electrophoresis for identification of fine fibre cotton line in Gossypium hirsutum L

International Nuclear Information System (INIS)

Gao Guoqiang; Lv Tiexin; Su Xuehe; Liu Xiaoyong; Wu Defang; Zhu Doubei

2003-01-01

Gel electrophoresis was conducted to test seed ethanol resolvable protein in cotton. 13 lines were used, including a fine fibre cotton line (98301) in G. hirsutum L., 4 varieties in G. barbadense L. and 8 varieties in G. hirsutum L.. In results of the 98301 line, Zhongmiansuo 12 and Shiyuan 321, no different protein electro-phoresis band pattern was shown among different seeds belong to the same variety, respectively. In comparison among the 98301 seeds sampled from seven different growth sets in Shandong province, their protein band patterns were the same. On the gel plate, three special bands were distinctive to all the varieties in G. hirsutum L. and other three special bands were distinctive to all the varieties in G. barbadense L.. The three characteristic bands of G. hirsutum L. appeared in the protein band pattern of the 98301 line. It showed that the seed protein composition of the line was inclined to G. hirsutum L. mainly. And, a characteristic band of G. Barbadense L. in the band pattern of the 98301 line proved that the fine fibre cotton line derived from a hybrid between G. barbadense and G. hirsutum L.. The 98301 line was easily distinguished from other varieties in G. hirsutum L. by its distinctive band, i.e. band No.1, and another island cotton band, i.e. band No.10

ASP53, a thermostable protein from Acacia erioloba seeds that protects target proteins against thermal denaturation

CSIR Research Space (South Africa)

Mtwisha, L

2007-02-01

Full Text Available ) and the Typha pollen D7 protein was found to stabilise sugar glasses in an in vitro system (Wolkers et al. 2001). The cupin family of proteins comprises a wide variety of proteins from both prokaryotes and eukaryotes and includes the seed storage proteins...–268. Garay-Arroyo A, Colmenero-Flores JM, Garciarrubio A, Covarrubias AA (2000) Highly hydrophilic proteins in prokaryotes and eukaryotes are common during conditions of water deficit. Journal of Biological Chemistry 275, 5668–5674. doi: 10.1074/jbc.275...

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.

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.

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.

Proteomics for exploiting diversity of lupin seed storage proteins and their use as nutraceuticals for health and welfare.

Science.gov (United States)

Cabello-Hurtado, Francisco; Keller, Jean; Ley, José; Sanchez-Lucas, Rosa; Jorrín-Novo, Jesús V; Aïnouche, Abdelkader

2016-06-30

Lupins have a variety of both traditional and modern uses. In the last decade, reports assessing the benefits of lupin seed proteins have proliferated and, nowadays, the pharmaceutical industry is interested in lupin proteins for human health. Modern genomics and proteomics have hugely contributed to describing the diversity of lupin storage genes and, above all, proteins. Most of these studies have been centered on few edible lupin species. However, Lupinus genus comprises hundreds of species spread throughout the Old and New Worlds, and these resources have been scarcely explored and exploited. We present here a detailed review of the literature on the potential of lupin seed proteins as nutraceuticals, and the use of -omic tools to analyze seed storage polypeptides in main edible lupins and their diversity at the Lupinus inter- and intra-species level. In this sense, proteomics, more than any other, has been a key approach. Proteomics has shown that lupin seed protein diversity, where post-translational modifications yield a large number of peptide variants with a potential concern in bioactivity, goes far beyond gene diversity. The future extended use of second and third generation proteomics should definitely help to go deeper into coverage and characterization of lupin seed proteome. Some important topics concerning storage proteins from lupin seeds are presented and analyzed in an integrated way in this review. Proteomic approaches have been essential in characterizing lupin seed protein diversity, which goes far beyond gene diversity since the protein level adds to the latter differential proteolytic cleavage of conglutin pro-proteins and a diverse array of glycosylation forms and sites. Proteomics has also proved helpful for screening and studying Lupinus germplasm with the future aim of exploiting and improving food production, quality, and nutritional values. Copyright © 2016 Elsevier B.V. All rights reserved.

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)

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 ...

Gene/QTL discovery for Anthracnose in common bean (Phaseolus vulgaris L.) from North-western Himalayas.

Science.gov (United States)

Choudhary, Neeraj; Bawa, Vanya; Paliwal, Rajneesh; Singh, Bikram; Bhat, Mohd Ashraf; Mir, Javid Iqbal; Gupta, Moni; Sofi, Parvaze A; Thudi, Mahendar; Varshney, Rajeev K; Mir, Reyazul Rouf

2018-01-01

Common bean (Phaseolus vulgaris L.) is one of the most important grain legume crops in the world. The beans grown in north-western Himalayas possess huge diversity for seed color, shape and size but are mostly susceptible to Anthracnose disease caused by seed born fungus Colletotrichum lindemuthianum. Dozens of QTLs/genes have been already identified for this disease in common bean world-wide. However, this is the first report of gene/QTL discovery for Anthracnose using bean germplasm from north-western Himalayas of state Jammu & Kashmir, India. A core set of 96 bean lines comprising 54 indigenous local landraces from 11 hot-spots and 42 exotic lines from 10 different countries were phenotyped at two locations (SKUAST-Jammu and Bhaderwah, Jammu) for Anthracnose resistance. The core set was also genotyped with genome-wide (91) random and trait linked SSR markers. The study of marker-trait associations (MTAs) led to the identification of 10 QTLs/genes for Anthracnose resistance. Among the 10 QTLs/genes identified, two MTAs are stable (BM45 & BM211), two MTAs (PVctt1 & BM211) are major explaining more than 20% phenotypic variation for Anthracnose and one MTA (BM211) is both stable and major. Six (06) genomic regions are reported for the first time, while as four (04) genomic regions validated the already known QTL/gene regions/clusters for Anthracnose. The major, stable and validated markers reported during the present study associated with Anthracnose resistance will prove useful in common bean molecular breeding programs aimed at enhancing Anthracnose resistance of local bean landraces grown in north-western Himalayas of state Jammu and Kashmir.

Vernonia DGATs can complement the disrupted oil and protein metabolism in epoxygenase-expressing soybean seeds.

Science.gov (United States)

Li, Runzhi; Yu, Keshun; Wu, Yongmei; Tateno, Mizuki; Hatanaka, Tomoko; Hildebrand, David F

2012-01-01

Plant oils can be useful chemical feedstocks such as a source of epoxy fatty acids. High seed-specific expression of a Stokesia laevis epoxygenase (SlEPX) in soybeans only results in 3-7% epoxide levels. SlEPX-transgenic soybean seeds also exhibited other phenotypic alterations, such as altered seed fatty acid profiles, reduced oil accumulation, and variable protein levels. SlEPX-transgenic seeds showed a 2-5% reduction in total oil content and protein levels of 30.9-51.4%. To address these pleiotrophic effects of SlEPX expression on other traits, transgenic soybeans were developed to co-express SlEPX and DGAT (diacylglycerol acyltransferase) genes (VgDGAT1 & 2) isolated from Vernonia galamensis, a high accumulator of epoxy fatty acids. These side effects of SlEPX expression were largely overcome in the DGAT co-expressing soybeans. Total oil and protein contents were restored to the levels in non-transgenic soybeans, indicating that both VgDGAT1 and VgDGAT2 could complement the disrupted phenotypes caused by over-expression of an epoxygenase in soybean seeds. Copyright © 2011 Elsevier Inc. All rights reserved.

Association studies and legume synteny reveal haplotypes determining seed size in Vigna unguiculata

Directory of Open Access Journals (Sweden)

Mitchell R Lucas

2013-04-01

Full Text Available Highly specific seed market classes for cowpea and other grain legumes exists because grain is most commonly cooked and consumed whole. Size, shape, color, and texture are critical features of these market classes and breeders target development of cultivars for market acceptance. Resistance to biotic and abiotic stresses that are absent from elite breeding material are often introgressed through crosses to landraces or wild relatives. When crosses are made between parents with different grain quality characteristics, recovery of progeny with acceptable or enhanced grain quality is problematic. Thus genetic markers for grain quality traits can help in pyramiding genes needed for specific market classes. Allelic variation dictating the inheritance of seed size can be tagged and used to assist the selection of large-seeded lines. In this work we applied SNP genotyping and knowledge of legume synteny to characterize regions of the cowpea genome associated with seed size. These marker-trait associations will enable breeders to use marker based selection approaches to increase the frequency of progeny with large seed. For ~800 samples derived from eight bi-parental populations, QTL analysis was used to identify markers linked to ten trait determinants. In addition, the population structure of 171 samples from the USDA core collection was identified and incorporated into a genome-wide association study which supported more than half of the trait-associated regions important in the bi-parental populations. Seven of the total ten QTL were supported based on synteny to seed size associated regions identified in the related legume soybean. In addition to delivering markers linked to major trait determinants in the context of modern breeding, we provide an analysis of the diversity of the USDA core collection of cowpea to identify genepools, migrants, admixture, and duplicates.

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.

Protein quantity and quality of safflower seed improved by NP fertilizer and rhizobacteria (Azospirillum and Azotobacter spp.

Directory of Open Access Journals (Sweden)

Asia eNosheen

2016-02-01

Full Text Available Protein is an essential part of human diet. The aim of present study was to improve the protein quality of safflower seed by the application of plant growth promoting rhizobacteria (PGPR in combination with conventional nitrogen and phosphate (NP fertilizers. The seeds of two safflower cultivar Thori and Saif-32, were inoculated with Azospirillum and Azotobacter and grown under field conditions. Protein content and quality was assessed by crude protein, amino acid analysis and SDS-PAGE. Seed crude protein and amino acids (metheonine, phenylanine and glutamic acid showed significant improvement (55%–1250% by Azotobacter supplemented with quarter dose of fertilizers (BTQ at P≤0.05. Additional protein bands were induced in Thori and Saif-32 by BTQ and BTH (Azotobacter supplemented with half dose of fertilizers respectively. The Azospirillum in combination with half dose of fertilizers (SPH and BTQ enhanced the indole acetic acid (90% and gibberellic acid (23%–27% contents in safflower leaf. Taken together, these data suggest that Azospirillum and Azotobacter along with significantly reduced (up to 75% use of NP fertilizers improved the quality and quantity of safflower seed protein.

Variation in the protein profiles in the gamma-irradiated chick pea (Cicer arietinum L.) seeds

International Nuclear Information System (INIS)

Farook, S.A.F.; Nizam, Jafar

1978-01-01

Water soluble seed proteins from the control as well as gamma ray treated material from the M 2 generation of Chick pea (Cicer arietinum L.) were separated by disc electrophoresis using 7.5 percent poly acrylamide gels. Average Rf values and percentage of similarity values were calculated. The comparisons of number and Rf values of protein bands were made to elucidate the differences in the treated material. Differences obtained in the seed protein profiles of the treated material suggest the presence of the qualitative variation in the proteins. Attempts were made to correlate the variation in the protein bands with the morphological changes in the mutants. (author)

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.

Changes in seed oil and protein contents of maize cultivars at different positions on the ear in response to water limitation

Directory of Open Access Journals (Sweden)

Kazem Ghassemi-Golezani

2016-10-01

Full Text Available A field experiment was carried out as split-split plot in 2014 to assess the effects of four irrigation treatments (irrigations after 60, 80, 100 and 120 mm evaporation, respectively on oil and protein changes of maize cultivars (SC704, NS640 and DC303: Late, mid and early maturing cultivars, respectively at different seed positions on the ear (upper, middle and lower positions on the ear. Overall, the highest seed yield was obtained from SC704, followed by NS640 and DC303 cultivars. Seed yield of all cultivars was higher at lower seed position on ear than at middle and upper parts of the ear under different irrigation treatments. The highest oil and protein yields were also recorded for seeds at lower position on the ear. Seed yield of all maize cultivars at various seed positions decreased with increasing irrigation intervals. Oil percentage decreased, but protein percentage increased with decreasing water availability. Water limitation decreased oil and protein yields of maize cultivars. Changes in protein and oil yields of maize cultivars at different seed positions and irrigation treatments were attributed to changes in seed yield.

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)

Proteomic analysis of seed storage proteins in wild rice species of the Oryza genus.

Science.gov (United States)

Jiang, Chunmiao; Cheng, Zaiquan; Zhang, Cheng; Yu, Tengqiong; Zhong, Qiaofang; Shen, J Qingxi; Huang, Xingqi

2014-01-01

The total protein contents of rice seeds are significantly higher in the three wild rice species (Oryza rufipogon Grill., Oryza officinalis Wall. and Oryza meyeriana Baill.) than in the cultivated rice (Oryza sativa L.). However, there is still no report regarding a systematic proteomic analysis of seed proteins in the wild rice species. Also, the relationship between the contents of seed total proteins and rice nutritional quality has not been thoroughly investigated. The total seed protein contents, especially the glutelin contents, of the three wild rice species were higher than those of the two cultivated rice materials. Based on the protein banding patterns of SDS-PAGE, O. rufipogon was similar to the two cultivated rice materials, followed by O. officinalis, while O. meyeriana exhibited notable differences. Interestingly, O. meyeriana had high contents of glutelin and low contents of prolamine, and lacked 26 kDa globulin band and appeared a new 28 kDa protein band. However, for O. officinali a 16 kDa protein band was absent and a row of unique 32 kDa proteins appeared. In addition, we found that 13 kDa prolamine band disappeared while special 14 kDa and 12 kDa protein bands were present in O. officinalis. Two-dimensional gel electrophoresis (2-DE) analysis revealed remarkable differences in protein profiles of the wild rice species and the two cultivated rice materials. Also, the numbers of detected protein spots of the three wild rice species were significantly higher than those of two cultivated rice. A total of 35 differential protein spots were found for glutelin acidic subunits, glutelin precursors and glutelin basic subunits in wild rice species. Among those, 18 protein spots were specific and 17 major spots were elevated. Six differential protein spots for glutelin acidic subunits were identified, including a glutelin type-A 2 precursor and five hypothetical proteins. This was the first report on proteomic analysis of the three wild rice species

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

QTL mapping of soybean oil content for marker-assisted selection in plant breeding program.

Science.gov (United States)

Leite, D C; Pinheiro, J B; Campos, J B; Di Mauro, A O; Unêda-Trevisoli, S H

2016-03-18

The present study was undertaken to detect and map the quantitative trait loci (QTL) related to soybean oil content. We used 244 progenies derived from a bi-parental cross of the Lineage 69 (from Universidade Estadual Paulista "Júlio de Mesquita Filho"/Faculdade de Ciências Agrárias e Veterinárias - Breeding Program) and Tucunaré cultivar. A total of 358 simple sequence repeat (SSR; microsatellite) markers were used to investigate the polymorphism between the parental lines, and for the polymorphic lines all the F2 individuals were tested. Evaluation of the oil content and phenotype was performed with the aid of a Tango equipment by near infra-red reflectance spectroscopy, using single F2 seeds and F2:3 progenies, in triplicate. The data were analyzed by QTL Cartographer program for 56 SSR polymorphic markers. Two oil-content related QTLs were detected on K and H linkage groups. The total phenotypic variation explained by QTLs ranged from 7.8 to 46.75% for oil content. New QTLs were identified for the oil content in addition to those previously identified in other studies. The results reported in this study show that regions different from those already known could be involved in the genetic control of soybean oil content.

Genome-wide association mapping for seed protein and oil contents using a large panel of soybean accessions.

Science.gov (United States)

Li, Dongmei; Zhao, Xue; Han, Yingpeng; Li, Wenbin; Xie, Futi

2018-01-08

Soybean is globally cultivated primarily for its protein and oil. The protein and oil contents of the seeds are quantitatively inherited traits determined by the interaction of numerous genes. In order to gain a better understanding of the molecular foundation of soybean protein and oil content for the marker-assisted selection (MAS) of high quality traits, a population of 185 soybean germplasms was evaluated to identify the quantitative trait loci (QTLs) associated with the seed protein and oil contents. Using specific length amplified fragment sequencing (SLAF-seq) technology, a total of 12,072 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) ≥ 0.05 were detected across the 20 chromosomes (Chr), with a marker density of 78.7 kbp. A total of 31 SNPs located on 12 of the 20 soybean chromosomes were correlated with seed protein and oil content. Of the 31 SNPs that were associated with the two target traits, 31 beneficial alleles were identified. Two SNP markers, namely rs15774585 and rs15783346 on Chr 07, were determined to be related to seed oil content both in 2015 and 2016. Three SNP markers, rs53140888 on Chr 01, rs19485676 on Chr 13, and rs24787338 on Chr 20 were correlated with seed protein content both in 2015 and 2016. These beneficial alleles may potentially contribute towards the MAS of favorable soybean protein and oil characteristics. Copyright © 2018. Published by Elsevier Inc.

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

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.

The effect of thermal processing on protein quality and free amino acid profile of Terminalia catappa (Indian Almond) seed.

Science.gov (United States)

Adu, O B; Ogundeko, T O; Ogunrinola, O O; Saibu, G M; Elemo, B O

2015-07-01

The study examined the effect of various processing methods- boiling, drying and roasting- on the in vitro and in vivo protein digestibility and free amino acid profiles of Terminalia catappa seed. Moisture and crude protein of the various samples were determined. In vitro protein digestibility was determined after pepsin digestion. For the in vivo experiment, defatted T. catappa based diet was fed to 3 weeks old Wistar rats for 4 weeks and compared with animals maintained on casein based and nitrogen- free diets. The biological value (BV), net protein utilisation (NPU) and protein efficiency ratio (PER) of the diets were determined. Free amino acid composition was carried out using thin layer chromatography. Moisture was highest in the boiled T. catappa seed (8.30 ± 0.00 %). The raw, roasted and dried seeds had 5.55 ± 0.07, 3.88 ± 0.22 and 3.75 ± 0.07 % respectively. Crude protein was 19.19, 18.89, 17.62 and 16.36 % in the dried, roasted, boiled and raw seeds respectively. Roasted T. catappa seed had the highest in vitro protein digestibility with 37.52 %, while the dried, boiled and raw samples had digestibility values of 27.57, 27.07 and 24.45 % respectively. All nine essential amino acids were present in T. catappa in high concentrations except methionine and tryptophan. Glutamate was present in the highest concentration. Also, free amino acids were higher in the processed seeds compared to the raw seed. Animals fed T. catappa diet compared favourably with the casein group, thus indicating that the protein is of good quality.

Genetic analysis of seed proteins contents in cowpea ( Vigna ...

African Journals Online (AJOL)

In order to select cowpea genotypes with high food value, 10 varieties were genetically screened in Ngaoundéré (Cameroon) for seed crude protein and its soluble fractions contents. Five divergent lines were studied through a 5 x 5 half diallel cross mating. The genotypes presented a significant genetic variability for these ...

QTL analysis of seed dormancy in Arabidopsis using recombinant inbred lines and MQM mapping

NARCIS (Netherlands)

Schaar, Wybe van der; Alonso-Blanco, Carlos; Léon-Kloosterziel, Karen M.; Jansen, Ritsert C.; Ooijen, Johan W. van; Koornneef, Maarten

1997-01-01

The genetic differences for seed germination between two commonly used Arabidopsis thaliana ecotypes Ler and Col, both showing a low level of seed dormancy, were investigated. The analysis was performed with 98 recombinant inbred lines (RILs) derived from the cross between the two ecotypes, and

Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry

Directory of Open Access Journals (Sweden)

Pramod Kumar Singh

2016-01-01

Full Text Available Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE across a broad range 3.0–10.0 immobilized pH gradient (IPG strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected in these accessions. In-gel protein expression patterns revealed three protein spots as upregulated and three other as downregulated. Using trypsin in-gel digestion, these differentially expressed proteins were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS which showed 45% amino acid homology of chickpea seed storage proteins with Arabidopsis thaliana.

Characterization of a methionine-rich protein from the seeds of Cereus jamacaru Mill. (Cactaceae

Directory of Open Access Journals (Sweden)

T.C.F.R. Aragão

2000-08-01

Full Text Available We describe here the isolation and characterization of a major albumin from the seeds of Cereus jamacaru (Cactaceae, to which we gave the trivial name of cactin. This protein has a molecular mass of 11.3 kDa and is formed by a light chain (3.67 kDa and a heavy chain (7.63 kDa. This protein was isolated using a combination of gel filtration chromatography and reverse-phase HPLC. The amino acid composition of cactin was determined and found to resemble that of the 2S seed reserve protein from the Brazil nut, a protein remarkable for its high methionine content. The usefulness of cactin as a molecular marker in the taxonomy of the Cactaceae is discussed.

Profiling and relationship of water-soluble sugar and protein compositions in soybean seeds.

Science.gov (United States)

Yu, Xiaomin; Yuan, Fengjie; Fu, Xujun; Zhu, Danhua

2016-04-01

Sugar and protein are important quality traits in soybean seeds for making soy-based food products. However, the investigations on both compositions and their relationship have rarely been reported. In this study, a total of 35 soybean germplasms collected from Zhejiang province of China, were evaluated for both water-soluble sugar and protein. The total water-soluble sugar (TWSS) content of the germplasms studied ranged from 84.70 to 140.91 mg/g and the water-soluble protein (WSP) content varied from 26.5% to 36.0%. The WSP content showed positive correlations with the TWSS and sucrose contents but negative correlations with the fructose and glucose contents. The clustering showed the 35 germplasms could be divided into four groups with specific contents of sugar and protein. The combination of water-soluble sugar and protein profiles provides useful information for future breeding and genetic research. This investigation will facilitate future work for seed quality improvement. Copyright © 2015. Published by Elsevier Ltd.

QTLs for resistance to Phomopsis seed decay are associated with days to maturity in soybean (Glycine max).

Science.gov (United States)

Sun, Suli; Kim, Moon Young; Van, Kyujung; Lee, Yin-Won; Li, Baodu; Lee, Suk-Ha

2013-08-01

Phomopsis seed decay (PSD), primarily caused by Phomopsis longicolla, is a major contributor to poor soybean seed quality and significant yield loss, particularly in early maturing soybean genotypes. However, it is not yet known whether PSD resistance is associated with early maturity. This study was conducted to identify quantitative trait loci (QTLs) for resistance to PSD and days to maturity using a recombinant inbred line (RIL) population derived from a cross between the PSD-resistant Taekwangkong and the PSD-susceptible SS2-2. Based on a genetic linkage map incorporating 117 simple sequence repeat markers, QTL analysis revealed two and three QTLs conferring PSD resistance and days to maturity, respectively, in the RIL population. Two QTLs (PSD-6-1 and PSD-10-2) for PSD resistance were identified in the intervals of Satt100-Satt460 and Sat_038-Satt243 on chromosomes 6 and 10, respectively. Two QTLs explained phenotypic variances in PSD resistance of 46.3 and 14.1 %, respectively. At the PSD-6-1 QTL, the PSD-resistant cultivar Taekwangkong contributed the allele with negative effect decreasing the infection rate of PSD and this QTL does not overlap with any previously reported loci for PSD resistance in other soybean genotypes. Among the three QTLs for days to maturity, two (Mat-6-2 and Mat-10-3) were located at positions similar to the PSD-resistance QTLs. The identification of the QTLs linked to both PSD resistance and days to maturity indicates a biological correlation between these two traits. The newly identified QTL for resistance to PSD associated with days to maturity in Taekwangkong will help improve soybean resistance to P. longicolla.

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...

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.

Seed protein improvement in cereals and grain legumes

Energy Technology Data Exchange (ETDEWEB)

NONE

1978-12-15

Full text: This Symposium organized in co-operation with the Gesellschaft fur Strahlen- und Umweltforschung mbH (GSF), Neuherberg near Munich, Federal Republic of Germany, was the culmination of the eight year FAO/IAEA/GSF Co-ordinated Research Programme to Improve Protein Content and Quality of Crops by Nuclear Techniques The co-ordinated research programme has stimulated plant breeding in developing countries, assisted in the development of techniques for the identification and evaluation of nutritionally improved mutants and encouraged basic research on seed storage proteins. The Symposium comprised 90 scientific presentations plus equipment displays. Sixty-one scientific papers were orally presented and discussed in eight sessions. An additional 29 scientific contributions were presented as posters and were on display throughout the Symposium. One afternoon of the Symposium was devoted to examination and individual discussion of the poster displays. It was especially notable that this method of presentation and discussion of scientific results was very favourably received. Five items of scientific equipment demonstrated analytical systems in use for protein or amino acid assay in plant breeding programmes. The Symposium clearly demonstrated the reality of nutritional deficiencies in poor countries and outlined plant breeding strategies for overcoming these. Progress was reported in improving the nutritional quality of cereals (wheat, maize, rice, barley, sorghum, millet, triticale, oats), legumes (beans, peas, soybeans, field beans, chick peas, lentils, pigeon peas, cowpeas, grams, peanuts) and some other crops (cotton, buckwheat). Notable results have been achieved, but much of the work has been in progress less than 10 years, which is too short a time for the development, testing and release of commercial varieties. Chemical and nutritional assay methods, including some promising new methods were reviewed and assessed. Rapid developments in knowledge of the

Seed protein improvement in cereals and grain legumes

International Nuclear Information System (INIS)

1978-01-01

Full text: This Symposium organized in co-operation with the Gesellschaft fur Strahlen- und Umweltforschung mbH (GSF), Neuherberg near Munich, Federal Republic of Germany, was the culmination of the eight year FAO/IAEA/GSF Co-ordinated Research Programme to Improve Protein Content and Quality of Crops by Nuclear Techniques The co-ordinated research programme has stimulated plant breeding in developing countries, assisted in the development of techniques for the identification and evaluation of nutritionally improved mutants and encouraged basic research on seed storage proteins. The Symposium comprised 90 scientific presentations plus equipment displays. Sixty-one scientific papers were orally presented and discussed in eight sessions. An additional 29 scientific contributions were presented as posters and were on display throughout the Symposium. One afternoon of the Symposium was devoted to examination and individual discussion of the poster displays. It was especially notable that this method of presentation and discussion of scientific results was very favourably received. Five items of scientific equipment demonstrated analytical systems in use for protein or amino acid assay in plant breeding programmes. The Symposium clearly demonstrated the reality of nutritional deficiencies in poor countries and outlined plant breeding strategies for overcoming these. Progress was reported in improving the nutritional quality of cereals (wheat, maize, rice, barley, sorghum, millet, triticale, oats), legumes (beans, peas, soybeans, field beans, chick peas, lentils, pigeon peas, cowpeas, grams, peanuts) and some other crops (cotton, buckwheat). Notable results have been achieved, but much of the work has been in progress less than 10 years, which is too short a time for the development, testing and release of commercial varieties. Chemical and nutritional assay methods, including some promising new methods were reviewed and assessed. Rapid developments in knowledge of the

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.

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.

New ACE-Inhibitory Peptides from Hemp Seed (Cannabis sativa L.) Proteins.

Science.gov (United States)

Orio, Lara P; Boschin, Giovanna; Recca, Teresa; Morelli, Carlo F; Ragona, Laura; Francescato, Pierangelo; Arnoldi, Anna; Speranza, Giovanna

2017-12-06

A hemp seed protein isolate, prepared from defatted hemp seed meals by alkaline solubilization/acid precipitation, was subjected to extensive chemical hydrolysis under acid conditions (6 M HCl). The resulting hydrolysate was fractionated by semipreparative RP-HPLC, and the purified fractions were tested as inhibitors of angiotensin converting enzyme (ACE). Mono- and bidimensional NMR experiments and LC-MS analyses led to the identification of four potentially bioactive peptides, i.e. GVLY, IEE, LGV, and RVR. They were prepared by solid-phase synthesis, and tested for ACE-inhibitory activity. The IC 50 values were GVLY 16 ± 1.5 μM, LGV 145 ± 13 μM, and RVR 526 ± 33 μM, confirming that hemp seed may be a valuable source of hypotensive peptides.

Purification and characterization of a novel cholesterol-lowering protein from the seeds of Senna obtusifolia

Institute of Scientific and Technical Information of China (English)

LI ChuHuai; LI Mei; CHANG WenRui; GUO BaoJiang

2008-01-01

"Juemingzi", a source of traditional Chinese herbal medicine, has been demonstrated to play a role in decreasing serum cholesterol concentration. In this study, a novel protein, which has shown an in-hibitory effect on cholesterol biosynthesis, was isolated from Senna obtusifolia L. seed by gel filtration and ion exchange chromatography. The novel protein's molecular mass was 19.7 kD and its pl was 4.80. Both SDS-PAGE and isoelectric-focusing (IEF) revealed a single Coomassie brilliant blue stained band, indicating that the novel protein was a single peptide. The N-terminal amino acid sequence of the pro-tein was IPYISASFPLNIEFLPSE, which had no similarity with any other protein sequences in the NCBI protein database. Circular dichroism (CD) signals indicated that S. obtusifolia seed protein contained 12.5% α-helix, 55.6% β-sheet, and 31.9% random coil.

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

Seed storage protein polymorphism in ten elite rice (Oryza sativa L ...

African Journals Online (AJOL)

user

2011-02-14

Feb 14, 2011 ... for several economical traits by conserving landrace genotypes and ... plasm, seed storage protein analysis represents a valid alternative ... of each variety was taken and ground into fine powder using pestle and mortal and ...

Role of seed germination in adaptation and reproductive isolation in Arabidopsis lyrata.

Science.gov (United States)

Hämälä, Tuomas; Mattila, Tiina M; Leinonen, Päivi H; Kuittinen, Helmi; Savolainen, Outi

2017-07-01

Seed germination is an important developmental and life history stage. Yet, the evolutionary impact of germination has mainly been studied in the context of dormancy, or for its role in reproductive isolation between species. Here, we aim to examine multiple consequences of genetic divergence on germination traits between two Arabidopsis lyrata subspecies: ssp. petraea (Eurasia) and ssp. lyrata (North America). Postdormancy germination time, a potentially adaptive trait, showed differentiation between the populations, and quantitative trait loci (QTL) mapping revealed that the trait variation is mainly controlled by two antagonistic loci. These QTL areas contain several candidate genes with known function in postdormancy germination in A. thaliana. The sequence variation of three genes was consistent with differential selection, and they also included fixed nonsynonymous substitutions with potential to account for the phenotypic differentiation. We further show that the divergence between the subspecies has led to a slight but significant reduction in hybrid germination proportions, indicating incipient reproductive isolation. Comparison of reciprocal F 1 and F 2 progenies suggests that Bateson-Dobzhansky-Muller incompatibilities likely act through uniparentally inherited factors. Examination of genomewide transmission ratio distortion further revealed that cytonuclear interactions cause substantial pregermination inviability in the hybrids. These results confirm that seed germination has adaptive potential beyond the dormancy stage and that hybrid seed inviability can be one of the first reproductive barriers to arise during divergence. © 2017 John Wiley & Sons Ltd.

Seed protein and nitrogen fixation in chickpea mutant variety Hyprosola

Energy Technology Data Exchange (ETDEWEB)

Schroeder, H E; Gibson, A H; Oram, R N [CSIRO, Division of Plant Industry, Canberra ACT (Australia); Shaikh, M A.Q. [Bangladesh Institute of Nuclear Agriculture, Mymensingh (Bangladesh)

1989-01-01

Full text: 'Hyprosola' is a high yielding, high protein mutant cultivar obtained after gamma irradiation from the variety 'Faridpur-1'. The mutant yields 45 % more protein per unit area. The essential amino acid index is unchanged. It is likely that the high nutritional value in 'Hyprosola' seed protein arises from an increase in the albumin:globulin ratio. Nitrogen fixation rates of the mutant during the first 7 weeks of growth were found to be similar to 'Faridpur-1'. Under field conditions, the mutant may be able to nodulate more rapidly and more extensively than the parent variety. (author)

TOTAL AND FRACTIONAL CONTENTS OF PROTEINS IN BEAN SEEDS UNDER THE CONDITIONS OF VARIED FERTILISATION WITH MICROELEMENTS

Directory of Open Access Journals (Sweden)

Wojciech KOZERA

2013-03-01

Full Text Available Over 2003-2005 at the Experiment Station at Wierzchucinek at the University of Technology and Life Sciences in Bydgoszcz, there was performed a strict one-factor micro-plot experiment in split-splot design. The factor tested was a type of microelements [n=5: Cu, Zn, Mn, Mo, B]. The microelements were foliar sprayed in a chelated form, as the series of Symfonia fertilizers. The study aimed at comparing the effect of five agricultural-engineering basic microelements on the contents and protein composition of the seeds of Aura cultivar. The fertilization applied, boron and manganese in particular, showed an effect on the increase in the contents of total protein in bean seeds. It also modified the fractional composition of the bean seed protein. There was observed a clear increase in the fraction of albumins and globulins in seeds as a result of the microelements applied, except for boron. The fertilization with molybdenum, boron, copper and zinc reduced the content of glutelins, and the sum of glulelins and prolamines in the bean seeds.

Proteome-Level Analysis of Metabolism- and Stress-Related Proteins during Seed Dormancy and Germination in Gnetum parvifolium.

Science.gov (United States)

Chang, Ermei; Deng, Nan; Zhang, Jin; Liu, Jianfeng; Chen, Lanzhen; Zhao, Xiulian; Abbas, M; Jiang, Zeping; Shi, Shengqing

2018-03-21

Gnetum parvifolium is a rich source of materials for traditional medicines, food, and oil, but little is known about the mechanism underlying its seed dormancy and germination. In this study, we analyzed the proteome-level changes in its seeds during germination using isobaric tags for relative and absolute quantitation. In total, 1,040 differentially expressed proteins were identified, and cluster analysis revealed the distinct time points during which signal transduction and oxidation-reduction activity changed. Gene Ontology analysis showed that "carbohydrate metabolic process" and "response to oxidative stress" were the main enriched terms. Proteins associated with starch degradation and antioxidant enzymes were important for dormancy-release, while proteins associated with energy metabolism and protein synthesis were up-regulated during germination. Moreover, protein-interaction networks were mainly associated with heat-shock proteins. Furthermore, in accord with changes in the energy metabolism- and antioxidant-related proteins, indole-3-acetic acid, Peroxidase, and soluble sugar content increased, and the starch content decreased in almost all six stages of dormancy and germination analyzed (S1-S6). The activity of superoxide dismutase, abscisic acid, and malondialdehyde content increased in the dormancy stages (S1-S3) and then decreased in the germination stages (S4-S6). Our results provide new insights into G. parvifolium seed dormancy and germination at the proteome and physiological levels, with implications for improving seed propagation.

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.

Ribosomal protein NtRPL17 interacts with kinesin-12 family protein NtKRP and functions in the regulation of embryo/seed size and radicle growth.

Science.gov (United States)

Tian, Shujuan; Wu, Jingjing; Liu, Yuan; Huang, Xiaorong; Li, Fen; Wang, Zhaodan; Sun, Meng-Xiang

2017-11-28

We previously reported that a novel motor protein belonging to the kinesin-12 family, NtKRP, displays critical roles in regulating embryo and seed size establishment. However, it remains unknown exactly how NtKRP contributes to this developmental process. Here, we report that a 60S ribosomal protein NtRPL17 directly interacts with NtKRP. The phenotypes of NtRPL17 RNAi lines show notable embryo and seed size reduction. Structural observations of the NtRPL17-silenced embryos/seeds reveal that the embryo size reduction is due to a decrease in cell number. In these embryos, cell division cycle progression is delayed at the G2/M transition. These phenotypes are similar to that in NtKRP-silenced embryos/seeds, indicating that NtKRP and NtRPL17 function as partners in the same regulatory pathway during seed development and specifically regulate cell cycle progression to control embryo/seed size. This work reveals that NtRPL17, as a widely distributed ribosomal protein, plays a critical role in seed development and provides a new clue in the regulation of seed size. Confirmation of the interaction between NtKRP and NtRPL17 and their co-function in the control of the cell cycle also suggests that the mechanism might be conserved in both plants and animals. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

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.

Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

Science.gov (United States)

Fauteux, François; Strömvik, Martina V

2009-01-01

Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP) gene promoters from three plant families, namely Brassicaceae (mustards), Fabaceae (legumes) and Poaceae (grasses) using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L.) Heynh.), soybean (Glycine max (L.) Merr.) and rice (Oryza sativa L.) respectively. We have identified three conserved motifs (two RY-like and one ACGT-like) in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination of conserved motifs

Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

Directory of Open Access Journals (Sweden)

Fauteux François

2009-10-01

Full Text Available Abstract Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP gene promoters from three plant families, namely Brassicaceae (mustards, Fabaceae (legumes and Poaceae (grasses using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L. Heynh., soybean (Glycine max (L. Merr. and rice (Oryza sativa L. respectively. We have identified three conserved motifs (two RY-like and one ACGT-like in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination

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.

Purification and partial characterization of storage proteins in Lupinus angustifolius seeds

Directory of Open Access Journals (Sweden)

Millán, Francisco

2004-12-01

Full Text Available Lupinus angustifolius seed proteins have been purified by sequential dialysis and ion exchange chromatography, and their amino acid composition has been studied in order to determine their nutritional value as sources of essential amino acids. Albumins include a great variety of proteins. Globulins were resolved in α, β and δ conglutins. Conglutin α is the main protein in the seeds of L. angustifolius, representing 76.6% of the total. While lysine was found to be the limiting amino acid in L. Angustifolius seed proteins as a whole, tyrosine was the limiting amino acid in albumins, and methione and lysine were limiting in globulins. Lysine, methionine and histidine were limiting amino acids in  α conglutin.Se ha realizado una purificación por diálisis secuencial y cromatografía de intercambio iónico de las proteínas de la semilla de L. angustifolius, y su composición en aminoácidos ha sido estudiada para determinar su valor nutricional como fuentes de aminoácidos esenciales. Las albúminas están compuestas por una compleja mezcla de proteínas. Las globulinas se resolvieron en conglutinas α, β y δ. La conglutina  α es la proteína más abundante en las semillas de L. angustifolius representando el 76.6% del total. Las proteínas de la semilla de L. angustifolius son limitantes en lisina. Las albúminas son limitantes en tirosina y las globulinas en metionina y lisina. La α conglutina es limitante en lisina, metionina e histidina.

The purification and characterization of a third storage protein (convicilin) from the seeds of pea (Pisum sativum L.).

OpenAIRE

Croy, R R; Gatehouse, J A; Tyler, M; Boulter, D

1980-01-01

A third storage protein, distinct from legumin and vicilin, has been purified from the seeds of pea (Pisum sativum L.). This protein has been named 'convicilin' and is present in protein bodies isolated from pea seeds. Convicilin has a subunit mol.wt. of 71 000 and a mol.wt. in its native form of 290 000. Convicilin is antigenically dissimilar to legumin, but gives a reaction of identity with vicilin when tested against antibodies raised against both proteins. However, convicilin contains no ...

Molecular regulation and genetic improvement of seed oil content in Brassica napus L.

Directory of Open Access Journals (Sweden)

Wei HUA,Jing LIU,Hanzhong WANG

2016-09-01

Full Text Available As an important oil crop and a potential bioenergy crop, Brassica napus L. is becoming a model plant for basic research on seed lipid biosynthesis as well as seed oil content, which has always been the key breeding objective. In this review, we present current progress in understanding of the regulation of oil content in B. napus, including genetics, biosynthesis pathway, transcriptional regulation, maternal effects and QTL analysis. Furthermore, the history of breeding for high oil content in B. napus is summarized and the progress in breeding ultra-high oil content lines is described. Finally, prospects for breeding high oil content B. napus cultivars are outlined.

Effects of storage structures and moisture contents on seed quality attributes of quality protein maize

Directory of Open Access Journals (Sweden)

Gopal Bhandari

2017-12-01

Full Text Available The study was aimed to examine the effects of various storage structures and moisture contents on seed quality attributes of quality protein maize seed. The quality protein maize (QPM-1 seed was tested in conventional seed storage containers (Fertilizer sack and earthen pot and the improved hermetic ones (Metal bin, Super grain bag, and Purdue Improved Crop Storage (PICS bag at Seed Science and Technology Division, Khumaltar, Nepal during February, 2015 to January 2016. Ten treatments comprising 5 storage devices in two moisture regimes (11% and 9% replicated thrice and laid out in Completely Randomized Design (CRD. Data on temperature, relative humidity (RH, germination, electrical conductivity (EC, seed moisture content (MC were collected bimonthly. The conventional containers were found liable to the external environmental condition whereas the hermetic structures observed with controlled RH level below 40% in all combinations. Electrical conductivity (EC for seed vigor showed that hermetic containers provide higher seed vigor than the conventional ones. Up to 4 months all treatments were found statistically at par for germination. A significant difference was observed in each treatment after 4 months where PICS bag & Super grain bag showed best germination followed by metal bin while fertilizer bag & earthen-pot showed poorer and poorest germination respectively till one year. Almost all treatments with lower MC showed better results than the treatments with higher MC. A negative correlation (R2=69.7% was found between EC and Germination. All six figures from 2 to 12 months on MC showed statistically different where hermetic plastic bags were found maintaining MC as initial whereas MC of fertilizer bags and earthen pot was spiked than the basal figure. The finding evidenced that the hermetic containers and low MC are the seed storage approaches for retaining the quality of seed even in an ambient environmental condition for more than a year.

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

Proteomic Comparison between Maturation Drying and Prematurely Imposed Drying of Zea mays Seeds Reveals a Potential Role of Maturation Drying in Preparing Proteins for Seed Germination, Seedling Vigor, and Pathogen Resistance

DEFF Research Database (Denmark)

Wang, Wei-Qing; Ye, Jian-Qing; Rogowska-Wrzesinska, Adelina

2014-01-01

We have studied the role(s) of maturation drying in the acquisition of germinability, seedling vigor and pathogen resistance by comparing the proteome changes in maize embryo and endosperm during mature and prematurely imposed drying. Prematurely imposed dried seeds at 40 days after pollination...... (DAP) germinated almost as well as mature seeds (at 65 DAP), but their seedling growth was slower and they were seriously infected by fungi. A total of 80 and 114 proteins were identified to change at least two-fold (p ... abundant in this group and may contribute to the acquisition of seed germinability. However, a relatively large number of proteins changed in the embryo (47 spots) and endosperm (76 spots) specifically during maturation drying. Among these proteins, storage proteins in the embryo and defense proteins...

Proteomic Analysis of Sauvignon Blanc Grape Skin, Pulp and Seed and Relative Quantification of Pathogenesis-Related Proteins.

Directory of Open Access Journals (Sweden)

Bin Tian

Full Text Available Thaumatin-like proteins (TLPs and chitinases are the main constituents of so-called protein hazes which can form in finished white wine and which is a great concern of winemakers. These soluble pathogenesis-related (PR proteins are extracted from grape berries. However, their distribution in different grape tissues is not well documented. In this study, proteins were first separately extracted from the skin, pulp and seed of Sauvignon Blanc grapes, followed by trypsin digestion and analysis by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS. Proteins identified included 75 proteins from Sauvignon Blanc grape skin, 63 from grape pulp and 35 from grape seed, mostly functionally classified as associated with metabolism and energy. Some were present exclusively in specific grape tissues; for example, proteins involved in photosynthesis were only detected in grape skin and proteins found in alcoholic fermentation were only detected in grape pulp. Moreover, proteins identified in grape seed were less diverse than those identified in grape skin and pulp. TLPs and chitinases were identified in both Sauvignon Blanc grape skin and pulp, but not in the seed. To relatively quantify the PR proteins, the protein extracts of grape tissues were seperated by HPLC first and then analysed by SDS-PAGE. The results showed that the protein fractions eluted at 9.3 min and 19.2 min under the chromatographic conditions of this study confirmed that these corresponded to TLPs and chitinases seperately. Thus, the relative quantification of TLPs and chitinases in protein extracts was carried out by comparing the area of corresponding peaks against the area of a thamautin standard. The results presented in this study clearly demonstrated the distribution of haze-forming PR proteins in grape berries, and the relative quantification of TLPs and chitinases could be applied in fast tracking of changes in PR proteins during grape growth and

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

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.

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.

Biochemical Aspects of a Serine Protease from Caesalpinia echinata Lam. (Brazilwood Seeds: A Potential Tool to Access the Mobilization of Seed Storage Proteins

Directory of Open Access Journals (Sweden)

Priscila Praxedes-Garcia

2012-01-01

Full Text Available Several proteins have been isolated from seeds of leguminous, but this is the first report that a protease was obtained from seeds of Caesalpinia echinata Lam., a tree belonging to the Fabaceae family. This enzyme was purified to homogeneity by hydrophobic interaction and anion exchange chromatographies and gel filtration. This 61-kDa serine protease (CeSP hydrolyses H-D-prolyl-L-phenylalanyl-L-arginine-p-nitroanilide (Km 55.7 μM in an optimum pH of 7.1, and this activity is effectively retained until 50∘C. CeSP remained stable in the presence of kosmotropic anions (PO4 3−, SO4 2−, and CH3COO− or chaotropic cations (K+ and Na+. It is strongly inhibited by TLCK, a serine protease inhibitor, but not by E-64, EDTA or pepstatin A. The characteristics of the purified enzyme allowed us to classify it as a serine protease. The role of CeSP in the seeds cannot be assigned yet but is possible to infer that it is involved in the mobilization of seed storage proteins.

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 ...

Proteomic analysis of oil body membrane proteins accompanying the onset of desiccation phase during sunflower seed development

Science.gov (United States)

Thakur, Anita; Bhatla, Satish C

2015-01-01

A noteworthy metabolic signature accompanying oil body (OB) biogenesis during oilseed development is associated with the modulation of the oil body membranes proteins. Present work focuses on 2-dimensional polyacrylamide gel electrophoresis (2-D PAGE)-based analysis of the temporal changes in the OB membrane proteins analyzed by LC-MS/MS accompanying the onset of desiccation (20–30 d after anthesis; DAA) in the developing seeds of sunflower (Helianthus annuus L.). Protein spots unique to 20–30 DAA stages were picked up from 2-D gels for identification and the identified proteins were categorized into 7 functional classes. These include proteins involved in energy metabolism, reactive oxygen scavenging, proteolysis and protein turnover, signaling, oleosin and oil body biogenesis-associated proteins, desiccation and cytoskeleton. At 30 DAA stage, exclusive expressions of enzymes belonging to energy metabolism, desiccation and cytoskeleton were evident which indicated an increase in the metabolic and enzymatic activity in the cells at this stage of seed development (seed filling). Increased expression of cruciferina-like protein and dehydrin at 30 DAA stage marks the onset of desiccation. The data has been analyzed and discussed to highlight desiccation stage-associated metabolic events during oilseed development. PMID:26786011

The role of thioredoxin h in protein metabolism during wheat (Triticum aestivum L.) seed germination.

Science.gov (United States)

Guo, Hongxiang; Wang, Shaoxin; Xu, Fangfang; Li, Yongchun; Ren, Jiangping; Wang, Xiang; Niu, Hongbin; Yin, Jun

2013-06-01

Thioredoxin h can regulate the redox environment in the cell and play an important role in the germination of cereals. In the present study, the thioredoxin s antisense transgenic wheat with down-regulation of thioredoxin h was used to study the role of thioredoxin h in protein metabolism during germination of wheat seeds, and to explore the mechanism of the thioredoxin s antisense transgenic wheat seeds having high resistance to pre-harvest sprouting. The qRT-PCR results showed that the expression of protein disulfide isomerase in the thioredoxin s antisense transgenic wheat was up-regulated, which induced easily forming glutenin macropolymers and the resistance of storage proteins to degradation. The expression of serine protease inhibitor was also up-regulated in transgenic wheat, which might be responsible for the decreased activity of thiocalsin during the germination. The expression of WRKY6 in transgenic wheat was down-regulated, which was consistent with the decreased activity of glutamine oxoglutarate aminotransferase. In transgenic wheat, the activities of glutamate dehydrogenase, glutamic pyruvic transaminase and glutamic oxaloacetic transaminase were down-regulated, indicating that the metabolism of amino acid was lower than that in wild-type wheat during seed germination. A putative model for the role of thioredoxin h in protein metabolism during wheat seed germination was proposed and discussed. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

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.

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

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

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.

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

Fine mapping of a dominantly inherited powdery mildew resistance major-effect QTL, Pm1.1, in cucumber identifies a 41.1 kb region containing two tandemly arrayed cysteine-rich receptor-like protein kinase genes.

Science.gov (United States)

Xu, Xuewen; Yu, Ting; Xu, Ruixue; Shi, Yang; Lin, Xiaojian; Xu, Qiang; Qi, Xiaohua; Weng, Yiqun; Chen, Xuehao

2016-03-01

A dominantly inherited major-effect QTL for powdery mildew resistance in cucumber was fine mapped. Two tandemly arrayed cysteine-rich receptor-like protein kinase genes were identified as the most possible candidates. Powdery mildew (PM) is one of the most severe fungal diseases of cucumber (Cucumis sativus L.) and other cucurbit crops, but the molecular genetic mechanisms of powdery mildew resistance in cucurbits are still poorly understood. In this study, through marker-assisted backcrossing with an elite cucumber inbred line, D8 (PM susceptible), we developed a single-segment substitution line, SSSL0.7, carrying 95 kb fragment from PM resistance donor, Jin5-508, that was defined by two microsatellite markers, SSR16472 and SSR16881. A segregating population with 3600 F2 plants was developed from the SSSL0.7 × D8 mating; segregation analysis confirmed a dominantly inherited major-effect QTL, Pm1.1 in cucumber chromosome 1 underlying PM resistance in SSSL0.7. New molecular markers were developed through exploring the next generation resequenced genomes of Jin5-508 and D8. Linkage analysis and QTL mapping in a subset of the F2 plants delimited the Pm1.1 locus into a 41.1 kb region, in which eight genes were predicted. Comparative gene expression analysis revealed that two concatenated genes, Csa1M064780 and Csa1M064790 encoding the same function of a cysteine-rich receptor-like protein kinase, were the most likely candidate genes. GFP fusion protein-aided subcellular localization indicated that both candidate genes were located in the plasma membrane, but Csa1M064780 was also found in the nucleus. This is the first report of dominantly inherited PM resistance in cucumber. Results of this study will provide new insights into understanding the phenotypic and genetic mechanisms of PM resistance in cucumber. This work should also facilitate marker-assisted selection in cucumber breeding for PM resistance.

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.

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.

Utilization of Rubber Seed Meal as a Protein Supplement in Broiler ...

African Journals Online (AJOL)

A feeding triai was conducted to evaluate the performance of finisher broiler cbicks fed diets containing different levels of partially defatted rubber seed meal as a replacement for groundnut cake. Four isocaloric and isonitrogenous diets (A, B, C and D) were formulated using groundnut cake (GNC) as the reference protein ...

Purification, identification and preliminary crystallographic studies of a 2S albumin seed protein from Lens culinaris

International Nuclear Information System (INIS)

Gupta, Pankaj; Gaur, Vineet; Salunke, Dinakar M.

2008-01-01

A 2S albumin from L. culinaris was purified and crystallized and preliminary crystallographic studies were carried out. Lens culinaris (lentil) is a widely consumed high-protein-content leguminous crop. A 2S albumin protein (26.5 kDa) has been identified using NH 2 -terminal sequencing from a 90% ammonium sulfate saturation fraction of total L. culinaris seed protein extract. The NH 2 -terminal sequence shows very high homology to PA2, an allergy-related protein from Pisum sativum. The 2S albumin protein was purified using a combination of size-exclusion and ion-exchange chromatography. Crystals of the 2S seed albumin obtained using the hanging-drop vapour-diffusion method diffracted to 2.5 Å resolution and were indexed in space group P4 1 (or P4 3 ), with unit-cell parameters a = b = 78.6, c = 135.2 Å

DPPH radical scavenging activity of a mixture of fatty acids and peptide-containing compounds in a protein hydrolysate of Jatropha curcas seed cake.

Science.gov (United States)

Phengnuam, Thanyarat; Goroncy, Alexander K; Rutherfurd, Shane M; Moughan, Paul J; Suntornsuk, Worapot

2013-12-04

Jatropha curcas, a tropical plant, has great potential commercial relevance as its seeds have high oil content. The seeds can be processed into high-quality biofuel producing seed cake as a byproduct. The seed cake, however, has not gotten much attention toward its potential usefulness. This work was aimed to determine the antioxidant activity of different fractions of a protein hydrolysate from J. curcas seed cake and to elucidate the molecular structures of the antioxidants. Seed cake was first processed into crude protein isolate and the protein was hydrolyzed by Neutrase. The hydrolysate obtained from 1 h of Neutrase hydrolysis showed the strongest antioxidant activity against DPPH radical (2,2-diphenyl-1-picrylhydrazyl). After a purification series of protein hydrolysate by liquid chromatography, chemicals acting as DPPH radical inhibitors were found to be a mixture of fatty acids, fatty acid derivatives, and a small amount of peptides characterized by mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy.

The Seed Proteome Web Portal

Directory of Open Access Journals (Sweden)

Marc eGalland

2012-06-01

Full Text Available The Seed Proteome Web Portal (SPWP; http://www.seedproteome.com/ gives access to information both on quantitative seed proteomic data and on seed-related protocols. Firstly, the SPWP provides access to the 475 different Arabidopsis seed proteins annotated from 2 dimensional electrophoresis (2DE maps. Quantitative data are available for each protein according to their accumulation profile during the germination process. These proteins can be retrieved either in list format or directly on scanned 2DE maps. These proteomic data reveal that 40% of seed proteins maintain a stable abundance over germination, up to radicle protrusion. During sensu stricto germination (24 h upon imbibition about 50% of the proteins display quantitative variations, exhibiting an increased abundance (35% or a decreasing abundance (15%. Moreover, during radicle protrusion (24 h to 48 h upon imbibition, 41% proteins display quantitative variations with an increased (23% or a decreasing abundance (18%. In addition, an analysis of the seed proteome revealed the importance of protein post-translational modifications as demonstrated by the poor correlation (r2 = 0.29 between the theoretical (predicted from Arabidopsis genome and the observed protein isoelectric points. Secondly, the SPWP is a relevant technical resource for protocols specifically dedicated to Arabidopsis seed proteome studies. Concerning 2D electrophoresis, the user can find efficient procedures for sample preparation, electrophoresis coupled with gel analysis and protein identification by mass spectrometry, which we have routinely used during the last 12 years. Particular applications such as the detection of oxidized proteins or de novo synthetized proteins radiolabeled by [35S]-methionine are also given in great details. Future developments of this portal will include proteomic data from studies such as dormancy release and protein turnover through de novo protein synthesis analyses during germination.

Interrelationships among seed yield, total protein and amino acid composition of ten quinoa (Chenopodium quinoa) cultivars from two different agroecological regions.

Science.gov (United States)

Gonzalez, Juan A; Konishi, Yotaro; Bruno, Marcela; Valoy, Mariana; Prado, Fernando E

2012-04-01

Quinoa is a good source of protein and can be used as a nutritional ingredient in food products. This study analyses how much growing region and/or seasonal climate might affect grain yield and nutritional quality of quinoa seeds. Seeds of ten quinoa cultivars from the Andean highlands (Bolivia/Argentina site) and Argentinean Northwest (Encalilla site) were analysed for seed yield, protein content and amino acid composition. Grain yields of five cultivars growing at Encalilla were higher, and four were lower, compared with data from the Bolivia/Argentina site. Protein contents ranged from 91.5 to 155.3 and from 96.2 to 154.6 g kg(-1) dry mass for Encalilla and Bolivia/Argentina seeds respectively, while essential amino acid concentrations ranged from 179.9 to 357.2 and from 233.7 to 374.5 g kg(-1) protein respectively. Significant positive correlations were found between the content of essential amino acids and protein percentage. It appears that there are clear variations in seed yield, total protein content and amino acid composition among cultivars from the two sites. Essential amino acid composition was more affected than grain yield and protein level. The study revealed that both environmental and climatic factors influence the nutritional composition of quinoa cultivars growing in different agroecological regions. Copyright © 2011 Society of Chemical Industry.

Analysis of the embryo proteome of sycamore (Acer pseudoplatanus L.) seeds reveals a distinct class of proteins regulating dormancy release.

Science.gov (United States)

Pawłowski, Tomasz Andrzej; Staszak, Aleksandra Maria

2016-05-20

Acer pseudoplatanus seeds are characterized by a deep physiological embryo dormancy that requires a few weeks of cold stratification in order to promote germination. Understanding the function of proteins and their related metabolic pathways, in conjunction with the plant hormones implicated in the breaking of seed dormancy, would expand our knowledge pertaining to this process. In this study, a proteomic approach was used to analyze the changes occurring in seeds in response to cold stratification, which leads to dormancy release. In addition, the involvement of abscisic (ABA) and gibberellic acids (GA) was also examined. Fifty-three proteins showing significant changes were identified by mass spectrometry. An effect of ABA on protein variation was observed at the beginning of stratification, while the influence of GA on protein abundance was observed during the middle phase of stratification. The majority of proteins associated with dormancy breaking in the presence of only water, and also ABA or GA, were classified as being involved in metabolism and genetic information processing. For metabolic-related proteins, the effect of ABA on protein abundance was stimulatory for half of the proteins and inhibitory for half of the proteins. On the other hand, the effect on genetic information processing related proteins was stimulatory. GA was found to upregulate both metabolic-related and genetic information processing-related proteins. While seed dormancy breaking depends on proteins involved in a variety of processes, proteins associated with methionine metabolism (adenosine kinase, methionine synthase) and glycine-rich RNA binding proteins appear to be of particular importance. Copyright © 2016 Elsevier GmbH. All rights reserved.

Improvement of seed protein in rice through mutation breeding

International Nuclear Information System (INIS)

Monyo, J.H.; Sugiyama, T.

1978-01-01

Mutants selected from an M 4 generation on the basis of high yield potential and high grain protein content were grown in a preliminary yield trial. The two parent varieties, Faya Theresa and Kihogo Red, were grown as controls. Thirteen mutants originating from Faya Theresa and three mutants derived from Kihogo Red were found to be equal or superior in yield to the controls. The best improvement in protein content through mutagen treatment was 44% increase in a Faya Theresa mutant and 35% increase in a Kihogo Red mutant. The protein values obtained for the same mutants in the M 3 , M 4 and M 5 generations were found to be consistently higher than in the check varieties. Correlations between grain yield and yield attributes including seed protein per cent and protein per grain showed that these were mutagen-dependent. Grain yield showed negative correlations with protein per cent and protein per grain. However, a few mutants were found which combined high grain yield and high protein per cent. The correlation between protein per cent and protein per grain was positive and very highly significant. It was concluded that despite the high negative correlations between grain protein per cent and grain yield screening for high protein per cent in high-yielding mutants provides a great scope for the identification of the correlation breakers which combine high grain yield potential and high protein content. (author)

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 .

Arabidopsis IQM4, a Novel Calmodulin-Binding Protein, Is Involved With Seed Dormancy and Germination in Arabidopsis

Directory of Open Access Journals (Sweden)

Yu Ping Zhou

2018-06-01

Full Text Available Seed dormancy and germination are regulated by complex mechanisms controlled by diverse hormones and environmental cues. Abscisic acid (ABA promotes seed dormancy and inhibits seed germination and post-germination growth. Calmodulin (CaM signals are involved with the inhibition of ABA during seed germination and seedling growth. In this study, we showed that Arabidopsis thaliana IQM4 could bind with calmodulin 5 (CaM5 both in vitro and in vivo, and that the interaction was the Ca2+-independent type. The IQM4 protein was localized in the chloroplast and the IQM4 gene was expressed in most tissues, especially the embryo and germinated seedlings. The T-DNA insertion mutants of IQM4 exhibited the reduced primary seed dormancy and lower ABA levels compared with wild type seeds. Moreover, IQM4 plays key roles in modulating the responses to ABA, salt, and osmotic stress during seed germination and post-germination growth. T-DNA insertion mutants exhibited ABA-insensitive and salt-hypersensitive phenotypes during seed germination and post-germination growth, whereas IQM4-overexpressing lines had ABA- and osmotic-hypersensitive, and salt-insensitive phenotypes. Gene expression analyses showed that mutation of IQM4 inhibited the expression of ABA biosynthetic genes NCED6 and NCED9, and seed maturation regulators LEC1, LEC2, ABI3, and ABI5 during the silique development, as well as promoted the expression of WRKY40 and inhibited that of ABI5 in ABA-regulated seed germination. These observations suggest that IQM4 is a novel Ca2+-independent CaM-binding protein, which is positively involved with seed dormancy and germination in Arabidopsis.

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.

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.

Transgenic soya bean seeds accumulating β-carotene exhibit the collateral enhancements of oleate and protein content traits.

Science.gov (United States)

Schmidt, Monica A; Parrott, Wayne A; Hildebrand, David F; Berg, R Howard; Cooksey, Amanda; Pendarvis, Ken; He, Yonghua; McCarthy, Fiona; Herman, Eliot M

2015-05-01

Transgenic soya bean (Glycine max) plants overexpressing a seed-specific bacterial phytoene synthase gene from Pantoea ananatis modified to target to plastids accumulated 845 μg β carotene g(-1) dry seed weight with a desirable 12:1 ratio of β to α. The β carotene accumulating seeds exhibited a shift in oil composition increasing oleic acid with a concomitant decrease in linoleic acid and an increase in seed protein content by at least 4% (w/w). Elevated β-carotene accumulating soya bean cotyledons contain 40% the amount of abscisic acid compared to nontransgenic cotyledons. Proteomic and nontargeted metabolomic analysis of the mid-maturation β-carotene cotyledons compared to the nontransgenic did not reveal any significant differences that would account for the altered phenotypes of both elevated oleate and protein content. Transcriptomic analysis, confirmed by RT-PCR, revealed a number of significant differences in ABA-responsive transcripton factor gene expression in the crtB transgenics compared to nontransgenic cotyledons of the same maturation stage. The altered seed composition traits seem to be attributed to altered ABA hormone levels varying transcription factor expression. The elevated β-carotene, oleic acid and protein traits in the β-carotene soya beans confer a substantial additive nutritional quality to soya beans. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

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. ...

Relationship between proportion and composition of albumins, and in vitro protein digestibility of raw and cooked pea seeds (Pisum sativum L.).

Science.gov (United States)

Park, Sei Joon; Kim, Tae Wan; Baik, Byung-Kee

2010-08-15

Peas provide an excellent plant protein resource for human diets, but their proteins are less readily digestible than animal proteins. To identify the relationship between composition and in vitro digestibility of pea protein, eight pea varieties with a wide range of protein content (157.3-272.7 g kg(-1)) were determined for the proportion of albumins and globulins, their compositions using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and in vitro protein digestibility (IVPD) before and after heat treatment using a multi-enzyme (trypsin, chymotrypsin and peptidase) method. The proportion of albumins based on total seed protein content decreased from 229 to 147 g kg(-1) as seed protein content increased from 157.3 to 272.7 g kg(-1), while the proportion of globulins increased from 483 to 590 g kg(-1). The IVPDs of eight raw pea seeds were 79.9-83.5%, with significant varietal variations, and those were improved to 85.9-86.8% by cooking. Albumins, including (pea albumins 2) PA2, trypsin inhibitor, lectin and lipoxygenase, were identified as proteolytic resistant proteins. Globulins were mostly digested by protease treatment after heating. The quantitative ratio of albumins and globulins, and the quantitative variations of albumin protein components, including lipoxygenase, PA2, lectins and trypsin inhibitors, appear to influence the protein digestibility of both raw and cooked pea seeds. Copyright (c) 2010 Society of Chemical Industry.

Functional properties of pumpkin (Cucurbita pepo seed protein isolate and hydrolysate

Directory of Open Access Journals (Sweden)

Bučko Sandra Đ.

2016-01-01

Full Text Available Pumpkin seed protein isolate (PSPI was enzymatically hydrolysed by pepsin to obtain pumpkin seed protein hydrolysate, PSPH. Investigation on solubility, interfacial and emulsifying properties of both PSPI and PSPH was conducted under different conditions of pH (3-8 and ionic strength (0-1 mol/dm3 NaCl. PSPI had the lowest solubility, i.e. isoelectric point (pI, at pH 5. PSPH had higher solubility than PSPI over whole range of pH and ionic strengths tested. Decrease in surface and interfacial tension evidenced that both PSPI and PSPH adsorb at air/protein solution and oil/protein solution interface. Emulsions (20 % oil in water stabilized by 1 g/100cm3 PSPI or PSPH solution were prepared at pH 3, 5 and 8 and ionic strength of 0 and 0.5 mol/dm3 NaCl. PSPH stabilized emulsions from coalescence at all pH and ionic strengths tested. PSPI was able to stabilize emulsions at pH 3 and 0 mol/dm3 NaCl, and at pH 8 regardless of ionic strength, while emulsions at pH 5 and both 0 and 0.5 mol/dm3 NaCl and at pH 3 when ionic strength was increased separated to oil and serum layer immediately after preparation. All emulsions were susceptible to creaming instability. [Projekat Ministarstva nauke Republike Srbije, br. III 46010

The Interactomic Analysis Reveals Pathogenic Protein Networks in Phomopsis longicolla Underlying Seed Decay of Soybean

Directory of Open Access Journals (Sweden)

Shuxian Li

2018-04-01

Full Text Available Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla is the primary cause of Phomopsis seed decay (PSD in soybean, Glycine max (L. Merrill. This disease results in poor seed quality and is one of the most economically important seed diseases in soybean. The objectives of this study were to infer protein–protein interactions (PPI and to identify conserved global networks and pathogenicity subnetworks in P. longicolla including orthologous pathways for cell signaling and pathogenesis. The interlog method used in the study identified 215,255 unique PPIs among 3,868 proteins. There were 1,414 pathogenicity related genes in P. longicolla identified using the pathogen host interaction (PHI database. Additionally, 149 plant cell wall degrading enzymes (PCWDE were detected. The network captured five different classes of carbohydrate degrading enzymes, including the auxiliary activities, carbohydrate esterases, glycoside hydrolases, glycosyl transferases, and carbohydrate binding molecules. From the PPI analysis, novel interacting partners were determined for each of the PCWDE classes. The most predominant class of PCWDE was a group of 60 glycoside hydrolases proteins. The glycoside hydrolase subnetwork was found to be interacting with 1,442 proteins within the network and was among the largest clusters. The orthologous proteins FUS3, HOG, CYP1, SGE1, and the g5566t.1 gene identified in this study could play an important role in pathogenicity. Therefore, the P. longicolla protein interactome (PiPhom generated in this study can lead to a better understanding of PPIs in soybean pathogens. Furthermore, the PPI may aid in targeting of genes and proteins for further studies of the pathogenicity mechanisms.

Cottonseed protein, oil, and mineral status in near-isogenic Gossypium hirsutum cotton lines expressing fuzzy/linted and fuzzless/linted seed phenotypes under field conditions

Directory of Open Access Journals (Sweden)

Nacer eBellaloui

2015-03-01

Full Text Available Cotton is an important crop in the world and is a major source of oil for human consumption and cotton meal for livestock. Cottonseed nutrition (seed composition: protein, oil, and minerals determine the quality of seeds. Therefore, maintaining optimum levels of cottonseed nutrition is critical. Physiological and genetic mechanisms controlling the levels of these constituents in cottonseed are still largely unknown. Our previous research conducted under greenhouse conditions showed that seed and leaf nutrition differed between fuzzless and fuzzy seed isolines. Therefore, the objective of this research was to investigate the seed fuzz phenotype (trait effects on seed protein, oil, N, C, S, and minerals in five sets of near-isogenic mutant cotton lines for seed fuzz in a two-year experiment under field condition to evaluate the stability of the effect of the trait on seed nutrition. The isolines (genotypes in each set differ for the seed fuzz trait (fuzzless/linted seed line, N lines, and fuzzy/linted seed line, F lines. Results showed that seed protein was higher in the fuzzy genotype in all sets, but seed oil was higher in fuzzless genotype in all sets. The concentrations of seed Ca and C were higher in all fuzzless genotypes, but N, S, B, Fe, and Zn were higher in most of the fuzzy genotypes. Generally, minerals were higher in leaves of F lines, suggesting the translocation of minerals from leaves to seeds was limited. The research demonstrated that fiber development could be involved in cottonseed composition. This may be due to the involvement of fiber development in carbon and nitrogen metabolism, and the mobility of nutrients from leaves (source to seed (sink. This information is beneficial to breeders to consider fuzzless cottonseed for potential protein and oil use and select for higher oil or higher protein content, and to physiologists to further understand the mobility of minerals to increase the quality of cottonseed nutrition for

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.

Influence of watermelon seed protein concentrates on dough handling, textural and sensory properties of cookies.

Science.gov (United States)

Wani, Ali Abas; Sogi, D S; Singh, Preeti; Khatkar, B S

2015-04-01

Fruit processing wastes contain numerous by products of potential use in food & allied industry. Watermelon seeds represent a major by-product of the processing waste and contain high amount of nutritional proteins. Protein rich cereal based products are in demand due to their health promoting benefits. With this aim, wheat flour was fortified with watermelon seed protein concentrates (2.5 %, 5 %, 7.5 % and 10 % levels) to prepare cookies with desirable physical, nutritional, and textural and sensory properties. Substitution levels of 5 % and 10 % significantly (p ≤ 0.05) increased the dough stability and mixing tolerance index, however pasting properties and dough extensibility decreased considerably above 5 % substitution levels. Cookie fracture force (kg) increased significantly (p ≤ 0.05) above 5 % fortification levels. Cookie spread factor (W/T) increased from 2.5 % to 7.5 % fortification levels, further increase showed negative impact. Sensory scores of the cookies showed that protein concentrate may be added up to 7.5 % fortification levels. This study revealed that watermelon protein concentrates can be fortified with protein concentrates upto 5-7.5 % levels in cookies to improve their protein quality.

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

Tannin, protein contents and fatty acid compositions of the seeds of several Vicia L. species from Turkey

OpenAIRE

Kökten, Kağan; Koçak, Alpaslan; Bağci, Eyüp; Akçura, Mevlüt; Çelik, Sait

2010-01-01

The seedoils of six Vicia species (Leguminosae) were investigated for their protein, tannin contents and fatty acid compositions. The protein contents of the seeds were found to be between 21.87%-31.33%. The tannin contents of the seeds were found to be between 0.13%-1.07%. The fatty acid compositions of these six different species were determined by the GC of the methyl esters of their fatty acids. The oilseeds of Vicia species contain palmitic and stear...

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.

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

Biochemical and functional characterization of an albumin protein belonging to the hemopexin superfamily from Lens culinaris seeds.

Science.gov (United States)

Scarafoni, Alessio; Gualtieri, Elisa; Barbiroli, Alberto; Carpen, Aristodemo; Negri, Armando; Duranti, Marcello

2011-09-14

The present paper reports the purification and biochemical characterization of an albumin identified in mature lentil seeds with high sequence similarity to pea PA2. These proteins are found in many edible seeds and are considered potentially detrimental for human health due to the potential allergenicity and lectin-like activity. Thus, the description of their possible presence in food and the assessment of the molecular properties are relevant. The M(r), pI, and N-terminal sequence of this protein have been determined. The work included the study of (i) the binding properties to hemine to assess the presence of hemopexin structural domains and (ii) the binding properties of the protein to thiamin. In addition, the structural changes induced by heating have been evaluated by means of spectroscopic techniques. Denaturation temperature has also been determined. The present work provides new insights about the structural molecular features and the ligand-binding properties and dynamics of this kind of seed albumin.

Improvement of protein and amino acid contents in seeds of food legumes. A case study in Phaseolus

Directory of Open Access Journals (Sweden)

Baudoin J.P.

1999-01-01

Full Text Available Food legumes are considered as the major source of dietary proteins among the plant species. Protein and amino acid contents were evaluated in a wide sample of both wild and cultivated genotypes of Phaseolus species, with a view to investigate possibilities of genetic improvement in seed nutritional quality. Results indicate a variation in relation with taxa, biological status within species (such as in P. lunatus, ecological conditions, seed parts (testa, cotyledons and embryonic axis, and major protein groups. However, the sulphur containing amino acids remain a limiting factor, which could be better overcome by mixing food legumes with other plant species such as cereals.

Functions of the CCCH type zinc finger protein OsGZF1 in regulation of the seed storage protein GluB-1 from rice

NARCIS (Netherlands)

Chen, Y.; Sun, A.; Wang, M.; Zhu, Z.; Ouwerkerk, P.B.F.

2014-01-01

Glutelins are the most abundant storage proteins in rice grain and can make up to 80 % of total protein content. The promoter region of GluB-1, one of the glutelin genes in rice, has been intensively used as a model to understand regulation of seed-storage protein accumulation. In this study, we

Study on furundu, a traditional Sudanese fermented roselle (Hibiscus sabdariffa L.) seed: effect on in vitro protein digestibility, chemical composition, and functional properties of the total proteins.

Science.gov (United States)

Yagoub, Abu El-Gasim A; Mohamed, Babiker E; Ahmed, Abdel Halim R; El Tinay, Abdullahi H

2004-10-06

Furundu, a meat substitute, is traditionally prepared by cooking the karkade (Hibiscus sabdariffa L.) seed and then fermenting it for 9 days. Physicochemical and functional properties of raw and cooked seed and of furundu ferments were analyzed. Furundu preparation resulted in significant changes in karkade seed major nutrients. Total polyphenols and phytic acid were also reduced. The increase in total acidity and fat acidity coupled with a decrease in pH indicates microbial hydrolysis of the major nutrients; proteins, carbohydrates, and fats. In vitro digestibility of the seed proteins reached the maximum value (82.7%) at the sixth day of fermentation, but thereafter it significantly decreased. The effect of furundu preparation on N solubility profiles and functional properties, such as emulsification and foaming properties and other related parameters, is investigated in water and in 1 M NaCl extracts from defatted flour samples. The results show that cooking followed by fermentation affects proteins solubility in water and 1 M NaCl. The foaming capacity (FC) from the flour of raw seed decreased as a result of cooking. Fermentation for 9 days significantly increased the FC of the cooked seed, restoring the inherent value. Foam from fermented samples collapsed more rapidly during a period of 120 min as compared to the foam from raw and cooked karkade seeds; stability in 1 M NaCl was lower as compared to those in water. In water, the emulsion stability (ES) from the fermented samples was significantly higher than that of the raw seed flour. Addition of 1 M NaCl significantly decreased the ES of the fermented samples.

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.

Protein Bread Fortification with Cumin and Caraway Seeds and By-Product Flour.

Science.gov (United States)

Sayed Ahmad, Bouchra; Talou, Thierry; Straumite, Evita; Sabovics, Martins; Kruma, Zanda; Saad, Zeinab; Hijazi, Akram; Merah, Othmane

2018-02-25

Malnutrition continues to be a key health problem in developing regions. The valorization of food waste appears as an ideal way to prevent malnutrition and improve people's access to food. Cumin ( Cuminum cyminum L.) and caraway ( Carum carvi L.) oilseeds are commonly used for cuisine and medicinal purposes. However, remaining cakes after oil extraction are usually underutilized. In order to assess the usefulness of these by-products in food applications, this study investigated the effect of their addition to protein bread formulations. Different levels (2, 4 and 6%) of whole seeds and cakes flour were used in the study. Fortified protein bread samples were compared to control protein bread and evaluated for their sensory, color, moisture, hardness properties, nutritional values as well as their biological activity. Results indicated that bread fortification shows a significant effect on bread properties depending on fortification level. A higher acceptability was observed specially for bread fortified with by-products flour. Increased tendencies of color darkness, moisture content, bread hardness, nutritional values as well as total phenolic content and radical scavenging activity compared to control bread were observed as the percentage of fortification increased in both cases. The overall results showed that the addition of cumin and caraway seeds and by-product flour can improve the antioxidant potential and overall quality of protein bread.

Protein Bread Fortification with Cumin and Caraway Seeds and By-Product Flour

Science.gov (United States)

Sayed Ahmad, Bouchra; Talou, Thierry; Straumite, Evita; Sabovics, Martins; Kruma, Zanda; Saad, Zeinab; Hijazi, Akram

2018-01-01

Malnutrition continues to be a key health problem in developing regions. The valorization of food waste appears as an ideal way to prevent malnutrition and improve people’s access to food. Cumin (Cuminum cyminum L.) and caraway (Carum carvi L.) oilseeds are commonly used for cuisine and medicinal purposes. However, remaining cakes after oil extraction are usually underutilized. In order to assess the usefulness of these by-products in food applications, this study investigated the effect of their addition to protein bread formulations. Different levels (2, 4 and 6%) of whole seeds and cakes flour were used in the study. Fortified protein bread samples were compared to control protein bread and evaluated for their sensory, color, moisture, hardness properties, nutritional values as well as their biological activity. Results indicated that bread fortification shows a significant effect on bread properties depending on fortification level. A higher acceptability was observed specially for bread fortified with by-products flour. Increased tendencies of color darkness, moisture content, bread hardness, nutritional values as well as total phenolic content and radical scavenging activity compared to control bread were observed as the percentage of fortification increased in both cases. The overall results showed that the addition of cumin and caraway seeds and by-product flour can improve the antioxidant potential and overall quality of protein bread. PMID:29495324

Protein Bread Fortification with Cumin and Caraway Seeds and By-Product Flour

Directory of Open Access Journals (Sweden)

Bouchra Sayed Ahmad

2018-02-01

Full Text Available Malnutrition continues to be a key health problem in developing regions. The valorization of food waste appears as an ideal way to prevent malnutrition and improve people’s access to food. Cumin (Cuminum cyminum L. and caraway (Carum carvi L. oilseeds are commonly used for cuisine and medicinal purposes. However, remaining cakes after oil extraction are usually underutilized. In order to assess the usefulness of these by-products in food applications, this study investigated the effect of their addition to protein bread formulations. Different levels (2, 4 and 6% of whole seeds and cakes flour were used in the study. Fortified protein bread samples were compared to control protein bread and evaluated for their sensory, color, moisture, hardness properties, nutritional values as well as their biological activity. Results indicated that bread fortification shows a significant effect on bread properties depending on fortification level. A higher acceptability was observed specially for bread fortified with by-products flour. Increased tendencies of color darkness, moisture content, bread hardness, nutritional values as well as total phenolic content and radical scavenging activity compared to control bread were observed as the percentage of fortification increased in both cases. The overall results showed that the addition of cumin and caraway seeds and by-product flour can improve the antioxidant potential and overall quality of protein bread.

A Gene Module-Based eQTL Analysis Prioritizing Disease Genes and Pathways in Kidney Cancer

Directory of Open Access Journals (Sweden)

Mary Qu Yang

Full Text Available Clear cell renal cell carcinoma (ccRCC is the most common and most aggressive form of renal cell cancer (RCC. The incidence of RCC has increased steadily in recent years. The pathogenesis of renal cell cancer remains poorly understood. Many of the tumor suppressor genes, oncogenes, and dysregulated pathways in ccRCC need to be revealed for improvement of the overall clinical outlook of the disease. Here, we developed a systems biology approach to prioritize the somatic mutated genes that lead to dysregulation of pathways in ccRCC. The method integrated multi-layer information to infer causative mutations and disease genes. First, we identified differential gene modules in ccRCC by coupling transcriptome and protein-protein interactions. Each of these modules consisted of interacting genes that were involved in similar biological processes and their combined expression alterations were significantly associated with disease type. Then, subsequent gene module-based eQTL analysis revealed somatic mutated genes that had driven the expression alterations of differential gene modules. Our study yielded a list of candidate disease genes, including several known ccRCC causative genes such as BAP1 and PBRM1, as well as novel genes such as NOD2, RRM1, CSRNP1, SLC4A2, TTLL1 and CNTN1. The differential gene modules and their driver genes revealed by our study provided a new perspective for understanding the molecular mechanisms underlying the disease. Moreover, we validated the results in independent ccRCC patient datasets. Our study provided a new method for prioritizing disease genes and pathways. Keywords: ccRCC, Causative mutation, Pathways, Protein-protein interaction, Gene module, eQTL

SDS-Page Seed Storage Protein Profiles in Chili Peppers (Capsicum L.

Directory of Open Access Journals (Sweden)

Owk ANIEL KUMAR

2010-09-01

Full Text Available Seed protein banding patterns (SDS-PAGE were studied from eighteen genotypes of chili pepper (Capsicum L. A total of 21 protein polypeptide bands with molecular weight ranging from 18.6 to 72.0 kD were recorded. Among the genotypes CA18, CA21 and CA27 represented maximum number of protein bands (12. Band no. (11 and (5,12 are exclusive to C. annuum L. and C. frutescens L. genotypes respectively. Average percent similarity was highest (100% between CA2 and CA8 genotypes and the UPGMA dendrogram represented low genetic diversity. The study revealed that considerable intra and inter-specific differences were found in the genotypes. The variability of protein profiles in the genotypes suggested that these selected genotypes can be a good source for crop improvement through hybridization programs.

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.

Selection of single grain seeds by 14N(n,γ)15N nuclear reaction for protein improvement

International Nuclear Information System (INIS)

Andras, L.; Csoke, A.; Nagy, A.Z.; Balint, A.

1979-01-01

A new non-destructive screening technique was developed for determining the protein (total nitrogen) content of single grain seeds. Here, our first experiment is described where in the case of maize samples, 300 s was used to perform one measurement on a seed with a semiautomatic device. (author)

Effect of seed treatments on the chemical composition and properties of two amaranth species: starch and protein

NARCIS (Netherlands)

Gamel, T.H.; Linssen, J.P.H.; Mesallem, A.S.; Damir, A.A.; Shekib, L.A.

2005-01-01

The seeds of two Amaranth species were studied. The starch contents were 543 and 623 g kg-1 while crude protein contents were 154 and 169 g kg-1 for Amaranthus caudatus and Amaranthus cruentus seeds, respectively. The effect of several treatments, including cooking, popping and germination and flour

Seed Priming Improves Agronomic Trait Performance under Flooding and Non-flooding Conditions in Rice with QTL SUB1

Directory of Open Access Journals (Sweden)

Ramni Kumar SARKAR

2012-12-01

Full Text Available Farmers in South East Asia are adopting rice crop establishment methods from transplanting to direct wet or dry seeding as it requires less labour and time and comparatively less energy than transplanting. In contrast to irrigated condition, in rainfed lowland, direct seeding is a common practice. Early flooding controls weeds but decreases seedling establishment in direct seeded rice. Anaerobic germination is an important trait to counteract damages caused by early flooding. Management options which can help in crop establishment and improve crop growth under flooding might remove the constraints related to direct seeding. The investigation was carried out with two near isogenic lines Swarna and Swarna-Sub1. Swarna-Sub1 is tolerant to submergence whereas Swarna is susceptible. Seed priming was done with water and 2% Jamun (Syzygium cumini leaf extract, and it improved seedling establishment under flooding. Acceleration of growth occurred due to seed pretreatment, which resulted longer seedling and greater accumulation of biomass. Seed priming greatly hastened the activities of total amylase and alcohol dehydrogenase in Swarna-Sub1 than in Swarna. Swarna-Sub1 outperformed Swarna when the plants were cultivated under flooding. Weed biomass decreased significantly under flooding compared to non-flooding conditions. Seed priming had positive effects on yield and yield attributing parameters both under non-flooding and early flooding conditions.

Sequentially Integrated Optimization of the Conditions to Obtain a High-Protein and Low-Antinutritional Factors Protein Isolate from Edible Jatropha curcas Seed Cake.

Science.gov (United States)

León-López, Liliana; Dávila-Ortiz, Gloria; Jiménez-Martínez, Cristian; Hernández-Sánchez, Humberto

2013-01-01

Jatropha curcas seed cake is a protein-rich byproduct of oil extraction which could be used to produce protein isolates. The purpose of this study was the optimization of the protein isolation process from the seed cake of an edible provenance of J. curcas by an alkaline extraction followed by isoelectric precipitation method via a sequentially integrated optimization approach. The influence of four different factors (solubilization pH, extraction temperature, NaCl addition, and precipitation pH) on the protein and antinutritional compounds content of the isolate was evaluated. The estimated optimal conditions were an extraction temperature of 20°C, a precipitation pH of 4, and an amount of NaCl in the extraction solution of 0.6 M for a predicted protein content of 93.3%. Under these conditions, it was possible to obtain experimentally a protein isolate with 93.21% of proteins, 316.5 mg 100 g(-1) of total phenolics, 2891.84 mg 100 g(-1) of phytates and 168 mg 100 g(-1) of saponins. The protein content of the this isolate was higher than the content reported by other authors.

Assessment of the Antioxidant Activity of Silybum marianum Seed Extract and Its Protective Effect against DNA Oxidation, Protein Damage and Lipid Peroxidation

Directory of Open Access Journals (Sweden)

Aynur Serçe

2016-01-01

Full Text Available Antioxidant properties of ethanol extract of Silybum marianum (milk thistle seeds was investigated. We have also investigated the protein damage activated by oxidative Fenton reaction and its prevention by Silybum marianum seed extract. Antioxidant potential of Silybum marianum seed ethanol extract was measured using diff erent in vitro methods, such as lipid peroxidation, 1,1–diphenyl–2–picrylhydrazyl (DPPH and ferric reducing power assays. The extract significantly decreased DNA damage caused by hydroxyl radicals. Protein damage induced by hydroxyl radicals was also effi ciently inhibited, which was confirmed by the presence of protein damage markers, such as protein carbonyl formation and by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS–PAGE. The present study shows that milk thistle seeds have good DPPH free radical scavenging activity and can prevent lipid peroxidation. Therefore, Silybum marianum can be used as potentially rich source of antioxidants and food preservatives. The results suggest that the seeds may have potential beneficial health effects providing opportunities to develop value-added products.

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.

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.

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)

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.

Seed Protein Content and Consistency of Tofu Prepared with Different Magnesium Chloride Concentrations in Six Japanese Soybean Varieties

OpenAIRE

Toda, Kyoko; Ono, Tomotada; Kitamura, Keisuke; Hajika, Makita; Takahashi, Koji; Nakamura, Yoshiyuki

2003-01-01

The relationship between the protein content of soybean seeds and the consistency of tofu was examined for six Japanese soybean varieties, Enrei, Fukuyutaka, Sachiyutaka, Ayakogane, Hatayutaka and Tachinagaha. The seed protein content was estimated by determining the nitrogen content using the Dumas method. Tofu was prepared from a raw homogenate of water-soaked soybeans by heating and by the addition of MgCl_2 as a coagulant. The tofu consistency was evaluated by measuring the breaking stres...

A statistical model for estimating maternal-zygotic interactions and parent-of-origin effects of QTLs for seed development.

Directory of Open Access Journals (Sweden)

Yanchun Li

Full Text Available Proper development of a seed requires coordinated exchanges of signals among the three components that develop side by side in the seed. One of these is the maternal integument that encloses the other two zygotic components, i.e., the diploid embryo and its nurturing annex, the triploid endosperm. Although the formation of the embryo and endosperm contains the contributions of both maternal and paternal parents, maternally and paternally derived alleles may be expressed differently, leading to a so-called parent-of-origin or imprinting effect. Currently, the nature of how genes from the maternal and zygotic genomes interact to affect seed development remains largely unknown. Here, we present a novel statistical model for estimating the main and interaction effects of quantitative trait loci (QTLs that are derived from different genomes and further testing the imprinting effects of these QTLs on seed development. The experimental design used is based on reciprocal backcrosses toward both parents, so that the inheritance of parent-specific alleles could be traced. The computing model and algorithm were implemented with the maximum likelihood approach. The new strategy presented was applied to study the mode of inheritance for QTLs that control endoreduplication traits in maize endosperm. Monte Carlo simulation studies were performed to investigate the statistical properties of the new model with the data simulated under different imprinting degrees. The false positive rate of imprinting QTL discovery by the model was examined by analyzing the simulated data that contain no imprinting QTL. The reciprocal design and a series of analytical and testing strategies proposed provide a standard procedure for genomic mapping of QTLs involved in the genetic control of complex seed development traits in flowering plants.

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...

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.

Identification and validation of quantitative trait loci for seed yield, oil and protein contents in two recombinant inbred line populations of soybean.

Science.gov (United States)

Wang, Xianzhi; Jiang, Guo-Liang; Green, Marci; Scott, Roy A; Song, Qijian; Hyten, David L; Cregan, Perry B

2014-10-01

Soybean seeds contain high levels of oil and protein, and are the important sources of vegetable oil and plant protein for human consumption and livestock feed. Increased seed yield, oil and protein contents are the main objectives of soybean breeding. The objectives of this study were to identify and validate quantitative trait loci (QTLs) associated with seed yield, oil and protein contents in two recombinant inbred line populations, and to evaluate the consistency of QTLs across different environments, studies and genetic backgrounds. Both the mapping population (SD02-4-59 × A02-381100) and validation population (SD02-911 × SD00-1501) were phenotyped for the three traits in multiple environments. Genetic analysis indicated that oil and protein contents showed high heritabilities while yield exhibited a lower heritability in both populations. Based on a linkage map constructed previously with the mapping population and using composite interval mapping and/or interval mapping analysis, 12 QTLs for seed yield, 16 QTLs for oil content and 11 QTLs for protein content were consistently detected in multiple environments and/or the average data over all environments. Of the QTLs detected in the mapping population, five QTLs for seed yield, eight QTLs for oil content and five QTLs for protein content were confirmed in the validation population by single marker analysis in at least one environment and the average data and by ANOVA over all environments. Eight of these validated QTLs were newly identified. Compared with the other studies, seven QTLs for seed yield, eight QTLs for oil content and nine QTLs for protein content further verified the previously reported QTLs. These QTLs will be useful for breeding higher yield and better quality cultivars, and help effectively and efficiently improve yield potential and nutritional quality in soybean.

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.

Chernobyl seed project. Advances in the identification of differentially abundant proteins in a radio-contaminated environment.

Science.gov (United States)

Rashydov, Namik M; Hajduch, Martin

2015-01-01

Plants have the ability to grow and successfully reproduce in radio-contaminated environments, which has been highlighted by nuclear accidents at Chernobyl (1986) and Fukushima (2011). The main aim of this article is to summarize the advances of the Chernobyl seed project which has the purpose to provide proteomic characterization of plants grown in the Chernobyl area. We present a summary of comparative proteomic studies on soybean and flax seeds harvested from radio-contaminated Chernobyl areas during two successive generations. Using experimental design developed for radio-contaminated areas, altered abundances of glycine betaine, seed storage proteins, and proteins associated with carbon assimilation into fatty acids were detected. Similar studies in Fukushima radio-contaminated areas might complement these data. The results from these Chernobyl experiments can be viewed in a user-friendly format at a dedicated web-based database freely available at http://www.chernobylproteomics.sav.sk.

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.

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.

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.

Genome-Wide Association Mapping of Seed Coat Color in Brassica napus.

Science.gov (United States)

Wang, Jia; Xian, Xiaohua; Xu, Xinfu; Qu, Cunmin; Lu, Kun; Li, Jiana; Liu, Liezhao

2017-07-05

Seed coat color is an extremely important breeding characteristic of Brassica napus. To elucidate the factors affecting the genetic architecture of seed coat color, a genome-wide association study (GWAS) of seed coat color was conducted with a diversity panel comprising 520 B. napus cultivars and inbred lines. In total, 22 single-nucleotide polymorphisms (SNPs) distributed on 7 chromosomes were found to be associated with seed coat color. The most significant SNPs were found in 2014 near Bn-scaff_15763_1-p233999, only 43.42 kb away from BnaC06g17050D, which is orthologous to Arabidopsis thaliana TRANSPARENT TESTA 12 (TT12), an important gene involved in the transportation of proanthocyanidin precursors into the vacuole. Two of eight repeatedly detected SNPs can be identified and digested by restriction enzymes. Candidate gene mining revealed that the relevant regions of significant SNP loci on the A09 and C08 chromosomes are highly homologous. Moreover, a comparison of the GWAS results to those of previous quantitative trait locus (QTL) studies showed that 11 SNPs were located in the confidence intervals of the QTLs identified in previous studies based on linkage analyses or association mapping. Our results provide insights into the genetic basis of seed coat color in B. napus, and the beneficial allele, SNP information, and candidate genes should be useful for selecting yellow seeds in B. napus breeding.

Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry

OpenAIRE

Singh, Pramod Kumar; Shrivastava, Nidhi; Chaturvedi, Krishna; Sharma, Bechan; Bhagyawant, Sameer S.

2016-01-01

Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE) across a broad range 3.0–10.0 immobilized pH gradient (IPG) strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected ...

Effects of Cooking and Screw-Pressing on Functional Properties of Protein in Milkweed (Asclepias spp.) Seed Meals and Press Cakes

Science.gov (United States)

This study determined the effects of oil processing conditions on functional properties of milkweed seed proteins to evaluate their potential for value-added uses. Flaked milkweed seeds were cooked at 82 degrees C (180 degrees F) for 30, 60 or 90 min in the seed conditioner, and then screw-pressed ...

Effect of nigella sativa seeds extract on serum c-reactive protein in albino rats

International Nuclear Information System (INIS)

Bashir, M.U.; Qureshi, H.

2014-01-01

C-reactive protein (CRP) is an acute phase protein. It predicts future risk of cardiovascular diseases. Different medicinal plants and their active ingredients possess the ability to reduce serum CRP levels and hence inflammatory disorders and cardiovascular diseases. In our study, ethanolic extract of Nigella sativa seeds was evaluated in albino rats for its possible effect on serum CRP levels. Objective: The objective of this study was to determine the effect of ethanolic extract of Nigella sativa seeds on an acute inflammatory biomarker/mediator, C-reactive protein (CRP) in albino rats. Study Design: Randomized controlled trial (RCT). Place and Duration of Study: Physiology Department, Services Institute of Medical Sciences (SIMS), Lahore; from September to November, 2009. Subjects and Methods: The study was carried out on 90 male albino rats. Five percent (5%) formalin in a dose of 50 meu1 was injected into sub-plantar surface of right hind paw of each rat to produce inflammation. The rats were randomly divided into three groups of thirty each. Group A was given normal saline (control); group B was given Nigella sativa seed extract; and group C received diclofenac sodium, as a reference drug. CRP levels in each group were measured from blood samples taken 25 hours after giving formalin. Results: The ethanolic extract of Nigella sativa seeds, given intraperitoneally, caused highly significant (p<0.001) reduction in serum CRP levels as compared to control group. The reduction in CRP levels by ethanolic extract of Nigella sativa was also significantly (p<0.05) more than that produced by diclofenac sodium. Conclusion: Our results suggest that Nigella sativa possesses ability to reduce serum CRP levels significantly, after production of artificial inflammation, in albino rats. (author)

Relationships among oil content, protein content and seed size in soybeans

Directory of Open Access Journals (Sweden)

Mario Marega Filho

2001-03-01

Full Text Available During 1995/96 and 1996/97, experiments were carried out at Londrina State University, aiming at quantifying the oil and protein contents in two groups of soybean genotypes; estimating the phenotypic, genotypic and environmental correlations existent among oil, protein content and seed size, and identifying genotypes for direct human consumption with high protein content. The evaluated characters were Weight of a Hundred Seeds (WHS, expressed in grams/100 seeds, Oil Content (OC and Protein Content (PC, expressed in %. In the experiment carried out in the field, OC ranged from 12 to 20.37 % and PC from 35.66 to 41.75% while in the experiment carried out in the greenhouse OC ranged from 12.26 to 21.79 % and PC from 32.95 to 41.56 % . The correlations between oil and protein were negative and significant. The relationship among WHS with OC and PC was low and higly affected by the time effect. Due to their high protein content and stability to oil and protein contents, there were distinction among the treatments carried out in the field (GA23 and GA20, and those carried out in the greenhouse (PI408251, Waseda, B6F4 (L-3 less, PI423909 and Tambagura.Durante 1995/96 e 1996/97, foram conduzidos experimentos na Universidade Estadual de Londrina, visando: quantificar os teores de óleo e proteína em dois grupos de genótipos de soja tipo alimento; estimar as correlações fenotípicas e genotípicas existentes entre os teores de óleo, proteína e tamanho das sementes; e, identificar genótipos para consumo humano de forma direta, com elevado teor de proteína. Foram avaliados os caracteres Peso de Cem Sementes (PCS, expresso em gramas / 100 sementes, Teor de Óleo (TO, e Teor de Proteína (TP, expressos em %. Na população conduzida a campo, a característica TO variou de 12 a 20,4 %, e TP de 35,7 a 41,8 %. A população conduzida em casa de vegetação apresentou uma variação de 12,3 a 21,8 % para TO, e de 33 a 41,6 % para TP. As correla

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.

Influence of Chemical Extraction on Rheological Behavior, Viscoelastic Properties and Functional Characteristics of Natural Heteropolysaccharide/Protein Polymer from Durio zibethinus Seed

Directory of Open Access Journals (Sweden)

Hamed Mirhosseini

2012-11-01

Full Text Available In recent years, the demand for a natural plant-based polymer with potential functions from plant sources has increased considerably. The main objective of the current study was to study the effect of chemical extraction conditions on the rheological and functional properties of the heteropolysaccharide/protein biopolymer from durian (Durio zibethinus seed. The efficiency of different extraction conditions was determined by assessing the extraction yield, protein content, solubility, rheological properties and viscoelastic behavior of the natural polymer from durian seed. The present study revealed that the soaking process had a more significant (p < 0.05 effect than the decolorizing process on the rheological and functional properties of the natural polymer. The considerable changes in the rheological and functional properties of the natural polymer could be due to the significant (p < 0.05 effect of the chemical extraction variables on the protein fraction present in the molecular structure of the natural polymer from durian seed. The natural polymer from durian seed had a more elastic (or gel like behavior compared to the viscous (liquid like behavior at low frequency. The present study revealed that the natural heteropolysaccharide/protein polymer from durian seed had a relatively low solubility ranging from 9.1% to 36.0%. This might be due to the presence of impurities, insoluble matter and large particles present in the chemical structure of the natural polymer from durian seed.

Two-dimensional gel electrophoresis pattern (pH 6-11) and identification of water-soluble barley seed and malt proteins by mass spectrometry

DEFF Research Database (Denmark)

Bak-Jensen, K.S.; Laugesen, S.; Roepstorff, P.

2004-01-01

A protocol was established for two-dimensional gel electrophoresis (2-DE) of barley seed and malt proteins in the pH range of 6-11. Proteins extracted from flour in a low-salt buffer were focused after cup-loading onto IPG strips. Successful separation in the second dimension was achieved using...... gradient gels in a horizontal SDS-PAGE system. Silver staining of gels visualized around 380 (seed) and 500 (malt) spots. Thirty-seven different proteins from seeds were identified in 60 spots, among these 46 were visualized also in the malt 2-D pattern. Proteins were identified by peptide mass...... in defence against pathogens (21 spots), 4 in storage, folding, and synthesis of proteins, and in nitrogen metabolism (5 spots), 6 in carbohydrate metabolism (11 spots), and 4 in stress and detoxification (9 spots). Six proteins (7 spots) were not grouped in these categories, and 3 were not ascribed...

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.

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.

Barley seed proteomics from spots to structures

DEFF Research Database (Denmark)

Finnie, Christine; Svensson, Birte

2009-01-01

forms on 2D-gels. Specific protein families, including peroxidases and alpha-amylases have been subjected to in-depth analysis resulting in characterisation of different isozymes, post-translational. modifications and processing. A functional proteomics study focusing on the seed thioredoxin system has...... with information from rice and other cereals facilitate identification of barley proteins. Several hundred barley seed proteins are identified and lower abundance proteins including membrane proteins are now being analysed. In the present review we focus on variation in protein profiles of seed tissues during...

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.

Mapping QTLs for submergence tolerance during germination in rice

African Journals Online (AJOL)

STORAGESEVER

2008-08-04

Aug 4, 2008 ... Key words: Oryza sativa L, anaerobic germination, QTL analysis. INTRODUCTION. Two main ... The study was conducted at NG-01 greenhouse, Genome and. Mapping (GML), the .... ABC transporter family protein ..... differences of germination habits in rice seeds with special reference to plant breeding (in ...

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.

The calmodulin-like protein, CML39, is involved in regulating seed development, germination, and fruit development in Arabidopsis.

Science.gov (United States)

Midhat, Ubaid; Ting, Michael K Y; Teresinski, Howard J; Snedden, Wayne A

2018-03-01

We show that the calcium sensor, CML39, is important in various developmental processes from seeds to mature plants. This study bridges previous work on CML39 as a stress-induced gene and highlights the importance of calcium signalling in plant development. In addition to the evolutionarily-conserved Ca 2+ sensor, calmodulin (CaM), plants possess a large family of CaM-related proteins (CMLs). Using a cml39 loss-of-function mutant, we investigated the roles of CML39 in Arabidopsis and discovered a range of phenotypes across developmental stages and in different tissues. In mature plants, loss of CML39 results in shorter siliques, reduced seed number per silique, and reduced number of ovules per pistil. We also observed changes in seed development, germination, and seed coat properties in cml39 mutants in comparison to wild-type plants. Using radicle emergence as a measure of germination, cml39 mutants showed more rapid germination than wild-type plants. In marked contrast to wild-type seeds, the germination of developing, immature cml39 seeds was not sensitive to cold-stratification. In addition, germination of cml39 seeds was less sensitive than wild-type to inhibition by ABA or by treatments that impaired gibberellic acid biosynthesis. Tetrazolium red staining indicated that the seed-coat permeability of cml39 seeds is greater than that of wild-type seeds. RNA sequencing analysis of cml39 seedlings suggests that changes in chromatin modification may underlie some of the phenotypes associated with cml39 mutants, consistent with previous reports that orthologs of CML39 participate in gene silencing. Aberrant ectopic expression of transcripts for seed storage proteins in 7-day old cml39 seedlings was observed, suggesting mis-regulation of early developmental programs. Collectively, our data support a model where CML39 serves as an important Ca 2+ sensor during ovule and seed development, as well as during germination and seedling establishment.

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.

Evolution of plant cell wall: Arabinogalactan-proteins from three moss genera show structural differences compared to seed plants.

Science.gov (United States)

Bartels, Desirée; Baumann, Alexander; Maeder, Malte; Geske, Thomas; Heise, Esther Marie; von Schwartzenberg, Klaus; Classen, Birgit

2017-05-01

Arabinogalactan-proteins (AGPs) are important proteoglycans of plant cell walls. They seem to be present in most, if not all seed plants, but their occurrence and structure in bryophytes is widely unknown and actually the focus of AGP research. With regard to evolution of plant cell wall, we isolated AGPs from the three mosses Sphagnum sp., Physcomitrella patens and Polytrichastrum formosum. The moss AGPs show structural characteristics common for AGPs of seed plants, but also unique features, especially 3-O-methyl-rhamnose (trivial name acofriose) as terminal monosaccharide not found in arabinogalactan-proteins of angiosperms and 1,2,3-linked galactose as branching point never found in arabinogalactan-proteins before. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

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.

Proteome profiling of flax (Linum usitatissimum) seed: characterization of functional metabolic pathways operating during seed development.

Science.gov (United States)

Barvkar, Vitthal T; Pardeshi, Varsha C; Kale, Sandip M; Kadoo, Narendra Y; Giri, Ashok P; Gupta, Vidya S

2012-12-07

Flax (Linum usitatissimum L.) seeds are an important source of food and feed due to the presence of various health promoting compounds, making it a nutritionally and economically important plant. An in-depth analysis of the proteome of developing flax seed is expected to provide significant information with respect to the regulation and accumulation of such storage compounds. Therefore, a proteomic analysis of seven seed developmental stages (4, 8, 12, 16, 22, 30, and 48 days after anthesis) in a flax variety, NL-97 was carried out using a combination of 1D-SDS-PAGE and LC-MSE methods. A total 1716 proteins were identified and their functional annotation revealed that a majority of them were involved in primary metabolism, protein destination, storage and energy. Three carbon assimilatory pathways appeared to operate in flax seeds. Reverse transcription quantitative PCR of selected 19 genes was carried out to understand their roles during seed development. Besides storage proteins, methionine synthase, RuBisCO and S-adenosylmethionine synthetase were highly expressed transcripts, highlighting their importance in flax seed development. Further, the identified proteins were mapped onto developmental seed specific expressed sequence tag (EST) libraries of flax to obtain transcriptional evidence and 81% of them had detectable expression at the mRNA level. This study provides new insights into the complex seed developmental processes operating in flax.

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

KAUST Repository

Ren, Zhonghai

2010-03-08

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

Fractionation, amino acid profiles, antimicrobial and free radical scavenging activities of Citrullus lanatus seed protein.

Science.gov (United States)

Dash, Priyanka; Ghosh, Goutam

2017-12-01

In the present study, a modified Osborne fractionation method was followed to isolate albumin (C alb ), globulin (C glo ), prolamin (C pro ) and glutelin (C glu ) successively from seeds of Citrullus lanatus (watermelon). This research work was undertaken to investigate the antimicrobial and antioxidant activities of isolated protein fractions of C. lanatus seed. Amino acid composition and molecular weight distribution were determined to establish their relationship with antimicrobial and antioxidant activity. Among all the fractions, C pro was found to be most effective against A. baumannii followed by C alb and C glo . The results showed that growth of inhibition of these protein fractions differ significantly from each other (p ≤ 0.05). In view of antioxidant potential, C glo exhibited strongest antioxidant capacity while C glu showed weakest antioxidant potential.

Seed reserve utilization and hydrolytic enzyme activities in germinating seeds of sweet corn

International Nuclear Information System (INIS)

Cheng, X.; Xiong, F.; Wang, C.; He, S.; Zhou, Y.

2018-01-01

In this study, two sh2 sweet corn cultivars (i.e., the initial seed dry weight for FT018 and TB010 was 0.16+-0.02 g/grain and 0.09+-0.01 g/grain, respectively) were used to determine the physiological characteristics of seed reserve utilization in germination. The data implied that the weight of mobilized seed reserve (WMSR) and seed reserve utilization efficiency (SRUE) increased with seed germination. FT018 exhibited higher SRUE than TB010 due to its sufficient energy production for growth. Sugar (sucrose and fructose) contents were at different levels in the germinating seed of sh2 sweet corn. The protein content and number of protein species were highest in the early stage of germination. Enzyme activity in the germinating seed indicated that enzymes for starch and sugar hydrolysis were important and that enzyme activities significantly differed at each germination stage and between the cultivars under dark conditions. Succinate dehydrogenase, sucrose synthase, and glucose-6-phosphate dehydrogenase accumulated in the late germination stage. Thus, appropriate efforts should be focused on improving the seed reserve utilization in sweet corn by identifying the physiological mechanism of germinating seed. (author)

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.

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).

Quantitative Trait Locus Analysis of seed germination and seedling vigour in Brassica rapa reveals QTL hotspots and epistatic interactions

NARCIS (Netherlands)

Basnet, R.K.; Duwal, A.; Tiwari, D.N.; Xiao, D.; Monakhos, S.; Bucher, J.; Visser, R.G.F.; Groot, S.P.C.; Bonnema, A.B.; Maliepaard, C.A.

2015-01-01

The genetic basis of seed germination and seedling vigour is largely unknown in Brassica species. We performed a study to evaluate the genetic basis of these important traits in a B. rapa doubled haploid population from a cross of a yellow-seeded oil-type yellow sarson and a black-seeded

Isolation and characterization of a reserve protein from the seeds of Opuntia ficus-indica (Cactaceae

Directory of Open Access Journals (Sweden)

Uchoa A.F.

1998-01-01

Full Text Available We describe here the isolation and characterization of a major albumin from the seeds of Opuntia ficus-indica (Cactaceae. This protein has a molecular mass of 6.5 kDa and was isolated by a combination of gel filtration chromatography and reverse-phase HPLC. The amino acid composition of this protein was determined and it was shown to have similarities with the amino acid composition of several proteins from the 2S albumin storage protein family. The N-terminal amino acid sequence of this protein is Asp-Pro-Tyr-Trp-Glu-Gln-Arg.

Investigation of isolation conditions and ion-exchange purification of protein coagulation components from common bean seed

Directory of Open Access Journals (Sweden)

Antov Mirjana G.

2007-01-01

Full Text Available Investigation of an extraction procedure of protein coagulants from common bean seed regarding concentration of NaCl and pH was performed. High values of protein concentration and coagulation activity in crude extract (9.19 g/l and 23.9%, respectively were obtained when the extraction was performed using 0.5 mol/l NaCl and water as solvent, which represents an advantage for economic and environmental reasons. Crude extract of common bean seed was purified by precipitation at two different percentages of (NH42SO4 saturation, followed by batch ion-exchange chromatography. The highest obtained coagulation activity, 45%, was determined in fraction that was eluated at 1.75 mol/l NaCl from resin loaded with proteins precipitated upon 80-100% (NH42SO4 saturation. High values of coagulation activity showed by some eluates suggest their application as natural coagulant for water purification. .

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.

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

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...

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

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.

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.

Chemical Characteristics of Pumpkin Seed Tempeh From Soybean and Pumpkin Seeds

OpenAIRE

Pujilestari, Shanti; Sandrasari, Diny A; Marida, Rimmaria

2017-01-01

The aim of this research was to find the effect of the combination of soybean and pumpkin seeds on the chemical characteristics of pumpkin seed tempeh. The pumpkin seed tempeh samples were analyzed for its water, ash, protein, fat, carbohydrate and crude fiber. Meanwhile, support data were isoflavone and zinc. Sensory hedonic was conducted by 25 untrained panelists for selecting the best formulation of soybean and pumpkin seeds in tempeh. The result shows the formulation of soybean and pumpki...

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

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.

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

Antioxidant and Antihypertensive Potential of Protein Fractions from Flour and Milk Substitutes from Canary Seeds (Phalaris canariensis L.).

Science.gov (United States)

Valverde, María Elena; Orona-Tamayo, Domancar; Nieto-Rendón, Blanca; Paredes-López, Octavio

2017-03-01

Canary seed (Phalaris canariensis) is used to feed birds but it has been recently considered a promising cereal with nutraceutical potential for humans. The aim of this work was to analyze the protein fractions from canary seed flour and from milk substitutes (prepared by soaking the seeds in water 12 and 24 h), and to evaluate antioxidant and antihypertensive capacity of peptides obtained after in vitro digestion. Prolamins were the major protein fraction, followed by glutelins. After digestion, albumins and prolamins fractions from milks presented higher levels of peptides than flour, globulins showed more peptides in flour and glutelins were found in similar concentrations in all samples; 24 h milk prolamins had the highest concentration of peptides. Purification by high performance liquid chromatography (HPLC), sequencing of peptides, in vitro antioxidant ABTS (2,2'-azino-bis, 3-ethylbenzothiazoline-6-sulphonic acid) and DPPH (2,2-diphenyl-1-picrylhydrazyl) assays, and antihypertensive capacity (angiotensin converting enzyme (ACE) assay), indicated that peptides from canary seed prolamins were the most efficient compounds with antioxidant and antihypertensive activity. Canary seeds may be considered an accessible and cheap source to prepare milk substitutes with high contents of bioactive peptides with remarkable functional properties to promote better human health and healthy ageing.

Proteomic analysis of Magnolia sieboldii K. Koch seed germination.

Science.gov (United States)

Lu, Xiu-Jun; Zhang, Xiao-Lin; Mei, Mei; Liu, Guang-Lin; Ma, Bei-Bei

2016-02-05

Magnolia sieboldii is a deciduous tree native to China. This species has a deep dormancy characteristic. To better understand seed germination, we used protein analysis of changes in seed protein at 0, 65, 110 and 150 d of stratification. Comparative 2DE analysis of M. sieboldii seed protein profiles at 0, 65, 110 and 150 d of stratification revealed 80 differentially abundance protein species. Comparative analysis showed that ADP-glucose pyrophosphorylase small subunit was degraded during germination. In particular, it was degraded almost completely at 110 d of germination. Starch granules in the microstructure decreased after 65 d of stratification. Starch granules provided a sufficient amount of substrates and ATPs for subsequent germination. Four storage protein species were identified, of which all were down accumulated. Spots 44 and 46 had different MW and pI values, spots 36 and 46 had nearly the same MW with pI shift in the 2-DE gels, suggesting that they might be present as different isoforms of the same protein family and the post translational modification. Our results suggested that degradation of starch granules and storage protein species prepared the seed embryo for growth, as well as regulated seed germination. The present proteomics analysis provides novel insights into the mobilisation of nutrient reserves during the germination of M. sieboldii seeds. To better understand seed germination, a complex developmental process, we developed a proteome analysis of M. sieboldii seed. We performed the first comprehensive proteomic and microstructure analysis during different seed stratification stages of M. sieboldii. Among the 80 protein species, 26 were identified, 7 and 14 protein species were up or down accumulated significantly. Many of the identified key proteins were involved in embryo development, starch biosynthesis and energy metabolism, Microstructure of stratification seed analysis revealed degradation of starch was used for preparing the seed

Engineering of soybean seed storage proteins

International Nuclear Information System (INIS)

Dickinson, C.D.; Floener, L.A.; Evans, R.P.; Nielsen, N.C.

1987-01-01

Protein engineering is one approach to the improvement of seed quality. With this in mind, a rapid in vitro system has been developed to assay the effect structural modifications have on the assembly of glycinin and β-conglycinin subunit complexes. Transcription plasmids were constructed for production of synthetic glycinin and β-conglycinin mRNAs by SP6 RNA-polymerase. Radiolabeled translation products from these messages were tested for their ability to form complexes. Gy4 and Gy5 proglycinins (group-2 subunits) and the a-subunit of β-conglycinin self-assembled into trimers. Proglycinin Gy2 (group-1 subunit) did not self-assemble, but assembled into mixed trimers in combination with Gy4 proglycinin. No assembly was observed for preproglycinins Gyl and Gy4, or for a Gy4 proglycinin which lacked 27 amino acids in a highly conserved internal sequence. Insertion of alternating MET-ARG residues in predicted turn regions of a hypervariable sequence in Gy4 proglycinin were tolerated when the string was short but inhibited trimer assembly as it became longer. The response to several different long deletions in this hypervariable region have also been tested. Different levels of trimer assembly were obtained and may depend on the secondary structures of the regions being joined in the engineered subunits. This system will be useful to study the assembly of storage protein complexes and to screen against modifications that interfere with subunit assembly

Implications of Partial Conjugation of Whey Protein Isolate to Durian Seed Gum through Maillard Reactions: Foaming Properties, Water Holding Capacity and Interfacial Activity

Directory of Open Access Journals (Sweden)

Bahareh Tabatabaee Amid

2013-12-01

Full Text Available This paper deals with the conjugation of durian seed gum (DSG with whey protein isolate (WPI through Maillard reactions. Subsequently, the functional properties of durian seed gum in the non-conjugated (control sample and conjugated forms were compared with several commercial gums (i.e., Arabic gum, sodium alginate, kappa carrageenan, guar gum, and pectin. The current study revealed that the conjugation of durian seed gum with whey protein isolate significantly (p < 0.05 improved its foaming properties. In this study, the conjugated durian seed gum produced the most stable foam among all samples. On the other hand, the emulsion stabilized with the conjugated durian seed gum also showed more uniform particles with a larger specific surface area than the emulsion containing the non-conjugated durian seed gum. The conjugated durian seed gum showed significant different foaming properties, specific surface area, particle uniformity and water holding capacity (WHC as compared to the target polysaccharide gums. The conjugated durian seed gum showed more similar functional properties to Arabic gum rather than other studied gums.

Genome-wide scans for delineation of candidate genes regulating seed-protein content in chickpea

Directory of Open Access Journals (Sweden)

Hari Deo eUpadhyaya

2016-03-01

Full Text Available Identification of potential genes/alleles governing complex seed-protein content (SPC trait is essential in marker-assisted breeding for quality trait improvement of chickpea. Henceforth, the present study utilized an integrated genomics-assisted breeding strategy encompassing trait association analysis, selective genotyping in traditional bi-parental mapping population and differential expression profiling for the first-time to understand the complex genetic architecture of quantitative SPC trait in chickpea. For GWAS (genome-wide association study, high-throughput genotyping information of 16376 genome-based SNPs (single nucleotide polymorphism discovered from a structured population of 336 sequenced desi and kabuli accessions [with 150-200 kb LD (linkage disequilibrium decay] was utilized. This led to identification of seven most effective genomic loci (genes associated [10 to 20% with 41% combined PVE (phenotypic variation explained] with SPC trait in chickpea. Regardless of the diverse desi and kabuli genetic backgrounds, a comparable level of association potential of the identified seven genomic loci with SPC trait was observed. Five SPC-associated genes were validated successfully in parental accessions and homozygous individuals of an intra-specific desi RIL (recombinant inbred line mapping population (ICC 12299 x ICC 4958 by selective genotyping. The seed-specific expression, including differential up-regulation (> 4-fold of six SPC-associated genes particularly in accessions, parents and homozygous individuals of the aforementioned mapping population with high level of contrasting seed-protein content (21-22% was evident. Collectively, the integrated genomic approach delineated diverse naturally occurring novel functional SNP allelic variants in six potential candidate genes regulating SPC trait in chickpea. Of these, a non-synonymous SNP allele-carrying zinc finger transcription factor gene exhibiting strong association with SPC trait

Comparative studies on the carbohydrate, protein and acid phosphatase contents in seeds of some rye (Secale cereale varieties

Directory of Open Access Journals (Sweden)

B. Morawiecka

2015-01-01

Full Text Available The contents of sugars. proteins and acid phosphatase extracted with 0.1 M acetate buffer, pH 5.1, from some rye varieties were determined. The total sugar level amounted to 3.25-9.70 g per 100 g of seeds; the estimates for pentoses were 1.7-2.9 g and those for proteins 0.91-1.60 g per 100 g of seeds. Acid phosphatase showed and activity level between 0.18 and 1.26 units/mg protein. After disc electrophoresis proteins were separated into 10 to 11 bands: at pH 9.4 or into 4-7 bands at pH 3.8. Essential variety differences were expressed in protein patterns after electrophoresis at pH 3.8. Acid phosphatase was separated into 5 and 4 activity bands at pH 9.4 and 3.3,. respectively. No variations in zymogram patterns were observed in respect to variety differences or cultivation in various climate and soil conditions.

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.

Roles of endoplasmic reticulum stress and unfolded protein response associated genes in seed stratification and bud endodormancy during chilling accumulation in Prunus persica.

Directory of Open Access Journals (Sweden)

Xi Ling Fu

Full Text Available Dormancy mechanisms in seeds and buds arrest growth until environmental conditions are optimal for development. A genotype-specific period of chilling is usually required to release dormancy, but the underlying molecular mechanisms are still not fully understood. To discover transcriptional pathways associated with dormancy release common to seed stratification and bud endodormancy, we explored the chilling-dependent expression of 11 genes involved in endoplasmic reticulum stress and the unfolded protein response signal pathways. We propose that endoplasmic reticulum stress and the unfolded protein response impact on seed as well as bud germination and development by chilling-dependent mechanisms. The emerging discovery of similarities between seed stratification and bud endodormancy status indicate that these two processes are probably regulated by common endoplasmic reticulum stress and unfolded protein response signalling pathways. Clarification of regulatory pathways common to both seed and bud dormancy may enhance understanding of the mechanisms underlying dormancy and breeding programs may benefit from earlier prediction of chilling requirements for uniform blooming of novel genotypes of deciduous fruit tree species.

Nutrient composition of Dacryodes edulis seed and seed coat mixture

Directory of Open Access Journals (Sweden)

C.U. OGUNKA-NNOKA

2017-07-01

Full Text Available This study investigated the nutrient composition of D. edulis seed and seed coat mixture. Qualitative and quantitative phytochemicals, proximate, and vitamin compositions were evaluated using standard methods. Saponins were very high, alkaloids, flavonoids, and tannins were high, while terpenoids were low, and glycosides, aldehydes, and steroids were absent. The quantitative phytochemical determination followed the order; saponin > kaempferol > rutin > catechin > tannin > sapogenin > lunamarine > phenol > ribalinidine > anthocyanin > oxalate > phytate. For the proximate composition, carbohydrates had the highest concentration, followed by lipids and fibre, while, protein concentration was the lowest. Vitamin E (5.42 mg/100g, vitamin C (3.24 mg/100g, and vitamin A (2.84 mg/100g were the highest occurring constituent vitamins while vitamin B12 (0.035 mg/100g and vitamin B2 (0.075 mg/100g were the least occurring vitamins. This study has shown the rich phytochemical composition of D. edulis seed and seed coat mixture while showing deficiencies in proteins, distinct vitamins, and ash contents.

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...

Correlation between seed size, protein and oil contents, and fatty acid composition in soybean genotypes

Directory of Open Access Journals (Sweden)

Maestri, Damián M.

1998-12-01

Full Text Available Eighteen soybean genotypes (Glycine max (L. Merrill with maturity groups IV, V, VI or VII were grown in 1995/96 at the Estación Experimental Agropecuaria (EEA-INTA of Manfredi and Marcos Juárez, Argentina. The aim of this research was to determine possible associations between seed size, protein and oil contents, and fatty composition. Seed size varied between 13.9-21.0 g/100 seeds. Protein and oil contents ranged from 331 to 448 and from 198 to 267 g kg^-1, respectively, and showed no significant correlation with seed size. There were significant correlations between seed size and individual fatty adds: positive with stearic and oleic and negative with linoleic. The results obtained suggest that seed size and its relationship with individual fatty acids must be considered in soybean breeding programs.

Se analizaron 18 genotipos de soja (Glycine max (L. Merrill con grupos de madurez IV, V, VI o VIl, cultivados en 1995/96 en la Estación Experimental Agropecuaria (EEA-INTA de Manfredi y Marcos Juárez, Argentina. El propósito de la investigación fue determinar posibles asociaciones entre el tamaño del grano, los contenidos de proteínas y aceite y la composición de ácidos grasos del mismo. El tamaño del grano varió entre 13.9-21.0 g/100 granos. Los porcentajes de proteínas y aceite estuvieron comprendidos entre 331-448 y entre 198-267 g kg^-1 respectivamente, y no mostraron correlaciones significativas con el tamaño del grano. Se observaron correlaciones significativas entre el tamaño del grano y determinados ácidos grasos: positivas con esteárico y oleico y negativa con linoleico. Las asociaciones encontradas podrían ser de utilidad en programas de mejoramiento de soja.

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.

Natural variation and QTL analysis for cationic mineral content in seeds of Arabidopsis thaliana.

NARCIS (Netherlands)

Vreugdenhil, D.; Aarts, M.G.M.; Koornneef, M.; Nelissen, H.J.M.; Ernst, W.H.O.

2004-01-01

Naturally occurring genetic variation for contents of cationic minerals in seeds of Arabidopsis thaliana was studied by screening a series of accessions (ecotypes) for Ca, Fe, K, Mg, Mn, Na, Zn, and for total contents of P. Variation was observed for all minerals and correlations between contents of

Nutritional evaluation of dried tomato seeds.

Science.gov (United States)

Persia, M E; Parsons, C M; Schang, M; Azcona, J

2003-01-01

Two samples of tomato seeds, a by-product of the tomato canning industry were evaluated to determine proximate analysis, amino acid content, and digestibility, TMEn, and protein efficiency ratio. Tomato seeds were also used to replace corn and soybean meal (SBM) in a chick diet on an equal true amino acid digestibility and TMEn basis. Tomato seeds were found to contain 8.5% moisture, 25% CP, 20.0% fat, 3.1% ash, 35.1% total dietary fiber, 0.12% Ca, 0.58% P, and 3,204 kcal/kg of TMEn. The total amounts of methionine, cystine, and lysine in the tomato seeds were 0.39, 0.40, and 1.34%, respectively, and their true digestibility coefficients, determined in cecectomized roosters, were 75, 70, and 54%, respectively. The protein efficiency ratio (weight gain per unit of protein intake) value when fed to chicks at 9% CP was 2.5 compared to 3.6 for SBM (P seeds could replace corn and SBM without any adverse affects on chick weight gain, feed intake, or gain:feed ratio from 8 to 21 d posthatch. Tomato seeds at any level in the diet did not significantly affect skin pigmentation. Although the protein quality of tomato seeds may not be as high as SBM, tomato seeds do contain substantial amounts of digestible amino acids and TMEn. When formulating diets on a true digestible amino acid and TMEn basis, tomato seeds can be supplemented into chick rations at up to 15% without any adverse affects on growth performance.

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.

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.

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.

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).

Introgression of a Rare Haplotype from Southeastern Africa to Breed California Blackeyes with Larger Seeds

Directory of Open Access Journals (Sweden)

Mitchell R Lucas

2015-03-01

Full Text Available Seed size distinguishes most crops from their wild relatives and is an important quality trait for the grain legume cowpea. In order to breed cowpea varieties with larger seeds we introgressed a rare haplotype associated with large seeds at the Css-1 locus from an African buff seed type cultivar, IT82E-18 (18.5g/100 seeds, into a blackeye seed type cultivar, CB27 (22g/100 seed. Four RILs derived from these two parents were chosen for marker-assisted breeding based on SNP genotyping with a goal of stacking large seed haplotypes into a CB27 background. Foreground and background selection were performed during two cycles of backcrossing based on genome-wide SNP markers. The average seed size of introgression lines homozygous for haplotypes associated with large seeds was 28.7g/100 seed and 24.8g/100 seed for cycles 1 and 2, respectively. One cycle 1 introgression line with desirable seed quality was selfed for two generations to make families with very large seeds (28-35g/100 seeds. Field-based performance trials helped identify breeding lines that not only have large seeds but are also desirable in terms of yield, maturity, and plant architecture when compared to industry standards. A principal component analysis was used to explore the relationships between the parents relative to a core set of landraces and improved varieties based on high-density SNP data. The geographic distribution of haplotypes at the Css-1 locus suggest the haplotype associated with large seeds is unique to accessions collected from Southeastern Africa. Therefore this QTL has a strong potential to develop larger seeded varieties for other growing regions which is demonstrated in this work using a California pedigree.

The ribosome-inactivating, antiproliferative and teratogenic activities and immunoreactivities of a protein from seeds of Luffa aegyptiaca (Cucurbitaceae).

Science.gov (United States)

Ng, T B; Chan, W Y; Yeung, H W

1993-05-01

1. The protein isolated from Luffa aegyptiaca seeds was capable of inhibiting protein synthesis in a rabbit reticulocyte lysate system and [3H]thymidine uptake by mouse melanoma (B16) cells. 2. It also adversely affected the development of mouse embryos in culture. 3. In enzyme-linked immunosorbent assay it reacted with antisera raised against other ribosome-inactivating proteins.

An analysis of the development of cauliflower seed as a model to improve the molecular mechanism of abiotic stress tolerance in cauliflower artificial seeds.

Science.gov (United States)

Rihan, Hail Z; Al-Issawi, Mohammed; Fuller, Michael P

2017-07-01

The development stages of conventional cauliflower seeds were studied and the accumulation of dehydrin proteins through the maturation stages was investigated with the aim of identifying methods to improve the viability of artificial seeds of cauliflower. While carbohydrate, ash and lipids increased throughout the development of cauliflower traditional seeds, proteins increased with the development of seed and reached the maximum level after 75 days of pollination, however, the level of protein started to decrease after that. A significant increase in the accumulation of small size dehydrin proteins (12, 17, 26 KDa) was observed during the development of cauliflower seeds. Several experiments were conducted in order to increase the accumulation of important dehydrin proteins in cauliflower microshoots (artificial seeds). Mannitol and ABA (Absisic acid) increased the accumulation of dehydrins in cauliflower microshoots while cold acclimation did not have a significant impact on the accumulation of these proteins. Molybdenum treatments had a negative impact on dehydrin accumulation. Dehydrins have an important role in the drought tolerance of seeds and, therefore, the current research helps to improve the accumulation of these proteins in cauliflower artificial seeds. This in turns improves the quality of these artificial seeds. The current results suggest that dehydrins do not play an important role in cold tolerance of cauliflower artificial seeds. This study could have an important role in improving the understanding of the molecular mechanism of abiotic stress tolerance in plants. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

New insight into quinoa seed quality under salinity: changes in proteomic and amino acid profiles, phenolic content, and antioxidant activity of protein extracts

Directory of Open Access Journals (Sweden)

Iris eAloisi

2016-05-01

Full Text Available Quinoa (Chenopodium quinoa Willd is an ancient Andean seed-producing crop well known for its exceptional nutritional properties and resistance to adverse environmental conditions, such as salinity and drought. Storage proteins, amino acid composition, and bioactive compounds play a crucial role in determining the nutritional value of quinoa seeds. Seeds harvested from three Chilean landraces of quinoa, one belonging to the salares ecotype (R49 and two to the coastal-lowlands ecotype, VI-1 and Villarrica (VR, exposed to two levels of salinity (100 and 300 mM NaCl were used to conduct a sequential extraction of storage proteins in order to obtain fractions enriched in albumins/globulins, 11S globulin and in prolamin-like proteins. The composition of the resulting protein fractions was analyzed by one- and two-dimensional polyacrylamide gel electrophoresis. Results confirmed a high polymorphism in seed storage proteins; the two most representative genotype-specific bands of the albumin/globulin fraction were the 30- and 32-kDa bands, while the 11S globulin showed genotype-specific polymorphism for the 40- and 42-kDa bands. Spot analysis by mass spectrometry followed by in silico analyses were conducted to identify the proteins whose expression changed most significantly in response to salinity in VR. Proteins belonging to several functional categories (i.e., stress protein, metabolism, and storage were affected by salinity. Other nutritional and functional properties, namely amino acid profiles, total polyphenol (TPC and flavonoid (TFC contents, and antioxidant activity (AA of protein extracts were also analyzed. With the exception of Ala and Met in R49, all amino acids derived from protein hydrolysis were diminished in seeds from salt-treated plants, especially in landrace VI-1. By contrast, several free amino acids were unchanged or increased by salinity in R49 as compared with VR and VI-1, suggesting a greater tolerance in the salares landrace

New Insight into Quinoa Seed Quality under Salinity: Changes in Proteomic and Amino Acid Profiles, Phenolic Content, and Antioxidant Activity of Protein Extracts

Science.gov (United States)

Aloisi, Iris; Parrotta, Luigi; Ruiz, Karina B.; Landi, Claudia; Bini, Luca; Cai, Giampiero; Biondi, Stefania; Del Duca, Stefano

2016-01-01

Quinoa (Chenopodium quinoa Willd) is an ancient Andean seed-producing crop well known for its exceptional nutritional properties and resistance to adverse environmental conditions, such as salinity and drought. Seed storage proteins, amino acid composition, and bioactive compounds play a crucial role in determining the nutritional value of quinoa. Seeds harvested from three Chilean landraces of quinoa, one belonging to the salares ecotype (R49) and two to the coastal-lowlands ecotype, VI-1 and Villarrica (VR), exposed to two levels of salinity (100 and 300 mM NaCl) were used to conduct a sequential extraction of storage proteins in order to obtain fractions enriched in albumins/globulins, 11S globulin and in prolamin-like proteins. The composition of the resulting protein fractions was analyzed by one- and two-dimensional polyacrylamide gel electrophoresis. Results confirmed a high polymorphism in seed storage proteins; the two most representative genotype-specific bands of the albumin/globulin fraction were the 30- and 32-kDa bands, while the 11S globulin showed genotype-specific polymorphism for the 40- and 42-kDa bands. Spot analysis by mass spectrometry followed by in silico analyses were conducted to identify the proteins whose expression changed most significantly in response to salinity in VR. Proteins belonging to several functional categories (i.e., stress protein, metabolism, and storage) were affected by salinity. Other nutritional and functional properties, namely amino acid profiles, total polyphenol (TPC) and flavonoid (TFC) contents, and antioxidant activity (AA) of protein extracts were also analyzed. With the exception of Ala and Met in R49, all amino acids derived from protein hydrolysis were diminished in seeds from salt-treated plants, especially in landrace VI-1. By contrast, several free amino acids were unchanged or increased by salinity in R49 as compared with VR and VI-1, suggesting a greater tolerance in the salares landrace. VR had the

A legume biofortification quandary: variability and genetic control of seed coat micronutrient accumulation in common beans

Science.gov (United States)

Blair, Matthew W.; Izquierdo, Paulo; Astudillo, Carolina; Grusak, Michael A.

2013-01-01

Common beans (Phaseolus vulgaris L.), like many legumes, are rich in iron, zinc, and certain other microelements that are generally found to be in low concentrations in cereals, other seed crops, and root or tubers and therefore are good candidates for biofortification. But a quandary exists in common bean biofortification: namely that the distribution of iron has been found to be variable between the principal parts of seed; namely the cotyledonary tissue, embryo axis and seed coat. The seed coat represents ten or more percent of the seed weight and must be considered specifically as it accumulates much of the anti-nutrients such as tannins that effect mineral bioavailability. Meanwhile the cotyledons accumulate starch and phosphorus in the form of phytates. The goal of this study was to evaluate a population of progeny derived from an advanced backcross of a wild bean and a cultivated Andean bean for seed coat versus cotyledonary minerals to identify variability and predict inheritance of the minerals. We used wild common beans because of their higher seed mineral concentration compared to cultivars and greater proportion of seed coat to total seed weight. Results showed the most important gene for seed coat iron was on linkage group B04 but also identified other QTL for seed coat and cotyledonary iron and zinc on other linkage groups, including B11 which has been important in studies of whole seed. The importance of these results in terms of physiology, candidate genes and plant breeding are discussed. PMID:23908660

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

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.

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.

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.

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.

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 ...

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.

Cucurbitaceae Seed Protein Hydrolysates as a Potential Source of Bioactive Peptides with Functional Properties

Directory of Open Access Journals (Sweden)

César Ozuna

2017-01-01

Full Text Available Seeds from Cucurbitaceae plants (squashes, pumpkins, melons, etc. have been used both as protein-rich food ingredients and nutraceutical agents by many indigenous cultures for millennia. However, relatively little is known about the bioactive components (e.g., peptides of the Cucurbitaceae seed proteins (CSP and their specific effects on human health. Therefore, this paper aims to provide a comprehensive review of latest research on bioactive and functional properties of CSP isolates and hydrolysates. Enzymatic hydrolysis can introduce a series of changes to the CSP structure and improve its bioactive and functional properties, including the enhanced protein solubility over a wide range of pH values. Small-sized peptides in CSP hydrolysates seem to enhance their bioactive properties but adversely affect their functional properties. Therefore, medium degrees of hydrolysis seem to benefit the overall improvement of bioactive and functional properties of CSP hydrolysates. Among the reported bioactive properties of CSP isolates and hydrolysates, their antioxidant, antihypertensive, and antihyperglycaemic activities stand out. Therefore, they could potentially substitute synthetic antioxidants and drugs which might have adverse secondary effects on human health. CSP isolates and hydrolysates could also be implemented as functional food ingredients, thanks to their favorable amino acid composition and good emulsifying and foaming properties.

Functionality-driven fractionation of lupin seeds

NARCIS (Netherlands)

Berghout, J.A.M.

2015-01-01

Functionality-driven fractionation of lupin seeds

The growth in the world population requires an increase in the production of protein-rich foods from plant-based materials. Lupin seeds have potential to become a novel plant protein source for food products because they are rich

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

Isotope labeling-based quantitative proteomics of developing seeds of castor oil seed (Ricinus communis L.)

DEFF Research Database (Denmark)

Nogueira, Fábio C S; Palmisano, Giuseppe; Schwämmle, Veit

2013-01-01

In this study, we used a mass spectrometry-based quantification approach employing isotopic (ICPL) and isobaric (iTRAQ) labeling to investigate the pattern of protein deposition during castor oil seed (Ricinus communis L.) development, including that of proteins involved in fatty acid metabolism...... give important insights into certain aspects of the biology of castor oil seed development such as carbon flow, anabolism, and catabolism of fatty acid and the pattern of deposition of SSPs, toxins, and allergens such as ricin and 2S albumins. We also found, for the first time, some genes of SSP......, seed-storage proteins (SSPs), toxins, and allergens. Additionally, we have used off-line hydrophilic interaction chromatography (HILIC) as a step of peptide fractionation preceding the reverse-phase nanoLC coupled to a LTQ Orbitrap. We were able to identify a total of 1875 proteins, and from these 1748...