Dataset Information

Genome-Wide Association of Stem Water Soluble Carbohydrates in Bread Wheat.

ABSTRACT: Water soluble carbohydrates (WSC) in stems play an important role in buffering grain yield in wheat against biotic and abiotic stresses; however, knowledge of genes controlling WSC is very limited. We conducted a genome-wide association study (GWAS) using a high-density 90K SNP array to better understand the genetic basis underlying WSC, and to explore marker-based breeding approaches. WSC was evaluated in an association panel comprising 166 Chinese bread wheat cultivars planted in four environments. Fifty two marker-trait associations (MTAs) distributed across 23 loci were identified for phenotypic best linear unbiased estimates (BLUEs), and 11 MTAs were identified in two or more environments. Liner regression showed a clear dependence of WSC BLUE scores on numbers of favorable (increasing WSC content) and unfavorable alleles (decreasing WSC), indicating that genotypes with higher numbers of favorable or lower numbers of unfavorable alleles had higher WSC content. In silico analysis of flanking sequences of trait-associated SNPs revealed eight candidate genes related to WSC content grouped into two categories based on the type of encoding proteins, namely, defense response proteins and proteins triggered by environmental stresses. The identified SNPs and candidate genes related to WSC provide opportunities for breeding higher WSC wheat cultivars.

SUBMITTER: Dong Y

PROVIDER: S-EPMC5089554 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Genome-Wide Association of Stem Water Soluble Carbohydrates in Bread Wheat.

Dong Yan Y Liu Jindong J Zhang Yan Y Geng Hongwei H Rasheed Awais A Xiao Yonggui Y Cao Shuanghe S Fu Luping L Yan Jun J Wen Weie W Zhang Yong Y Jing Ruilian R Xia Xianchun X He Zhonghu Z

PloS one 20161101 11

Water soluble carbohydrates (WSC) in stems play an important role in buffering grain yield in wheat against biotic and abiotic stresses; however, knowledge of genes controlling WSC is very limited. We conducted a genome-wide association study (GWAS) using a high-density 90K SNP array to better understand the genetic basis underlying WSC, and to explore marker-based breeding approaches. WSC was evaluated in an association panel comprising 166 Chinese bread wheat cultivars planted in four environm ...[more]

PMID: 27802269

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Project description:Most investigations to date aiming to identify the genetic basis of the stress response of wheat (Triticum aestivum L.) have focused on the response to single stress agents such as high temperature or drought, even though in the natural situation, these stresses tend often to occur together. Here, a panel of 108 spring type bread wheat cultivars was phenotyped for 15 yield and yield related traits for two years (2014/15 and 2015/16) under non-stressed conditions, under high temperature stress, under drought and under a combined high temperature and drought regime. The mean loss in grain yield caused by all stress regimes was 51.33%. Analysis of variance (ANOVA) of yield trait showed significant differences among genotypes environments and their interactions (G×E). All the studied traits had higher heritability values which ranged from 0.35-0.94 under [C], 0.58-0.95 under [D], 0.62-0.93 under [H] and 0.60-0.95 under [HD]. GWAS was performed by using 9,646 informative SNP markers and based on these polymorphic SNPs population structure analysis divided whole germplasm into five major sub-populations. Mixed model association analysis detected 503 marker-trait associations (MTAs) at P ?0.001 while 329 MTAs crossed FDR ? 0.05 for all traits with phenotypic variances (R2) ranged from 24.83% to 12.51%. Seven new pleiotropic SNPs on chromosome 7D and IAAV8258 (86.91cM) and wsnp_Ex_c7168_12311649 (57.93cM) on chromosome 5A were most stable association in present study. Furthermore, candidate genes Psy and Sr25 (TG0040) were also significant in present study, these genes were previously mapped on 7A and 7D. The region on 7D was assiociated with 7DL.7Ag translocation from Lophopyrum carring rust resistance Yr16 and many other genes. Similarly region on chromosome 7A which was associated with Psy gene was linked with grain yellow pigment content QTLs. Favourable alleles controlling grain yield were of vital importance and incorporation of these alleles after validation through marker assisted selection and fine mapping could be helpful in wheat yield improvement stress and non-stress conditions.

Project description:BackgroundIdentification of loci for grain yield (GY) and related traits, and dissection of the genetic architecture are important for yield improvement through marker-assisted selection (MAS). Two genome-wide association study (GWAS) methods were used on a diverse panel of 166 elite wheat varieties from the Yellow and Huai River Valleys Wheat Zone (YHRVWD) of China to detect stable loci and analyze relationships among GY and related traits.ResultsA total of 326,570 single nucleotide polymorphism (SNP) markers from the wheat 90 K and 660 K SNP arrays were chosen for GWAS of GY and related traits, generating a physical distance of 14,064.8 Mb. One hundred and twenty common loci were detected using SNP-GWAS and Haplotype-GWAS, among which two were potentially functional genes underpinning kernel weight and plant height (PH), eight were at similar locations to the quantitative trait loci (QTL) identified in recombinant inbred line (RIL) populations in a previous study, and 78 were potentially new. Twelve pleiotropic loci were detected on eight chromosomes; among these the interval 714.4-725.8 Mb on chromosome 3A was significantly associated with GY, kernel number per spike (KNS), kernel width (KW), spike dry weight (SDW), PH, uppermost internode length (UIL), and flag leaf length (FLL). GY shared five loci with thousand kernel weight (TKW) and PH, indicating significantly affected by two traits. Compared with the total number of loci for each trait in the diverse panel, the average number of alleles for increasing phenotypic values of GY, TKW, kernel length (KL), KW, and flag leaf width (FLW) were higher, whereas the numbers for PH, UIL and FLL were lower. There were significant additive effects for each trait when favorable alleles were combined. UIL and FLL can be directly used for selecting high-yielding varieties, whereas FLW can be used to select spike number per unit area (SN) and KNS.ConclusionsThe loci and significant SNP markers identified in the present study can be used for pyramiding favorable alleles in developing high-yielding varieties. Our study proved that both GWAS methods and high-density genetic markers are reliable means of identifying loci for GY and related traits, and provided new insight to the genetic architecture of GY.

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Dataset Information

Genome-Wide Association of Stem Water Soluble Carbohydrates in Bread Wheat.

Publications

Genome-Wide Association of Stem Water Soluble Carbohydrates in Bread Wheat.

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