Dataset Information

Association and Validation of Yield-Favored Alleles in Chinese Cultivars of Common Wheat (Triticumaestivum L.).

ABSTRACT: Common wheat is one of the most important crops in China, which is the largest producer in the world. A set of 230 cultivars was used to identify yield-related loci by association mapping. This set was tested for seven yield-related traits, viz. plant height (PH), spike length (SL), spikelet number per spike (SNPS), kernel number per spike (KNPS), thousand-kernel weight (TKW), kernel weight per spike (KWPS), and sterile spikelet number (SSN) per plant in four environments. A total of 106 simple sequence repeat (SSR) markers distributed on all 21 chromosomes were used to screen the set. Twenty-one and 19 of them were associated with KNPS and TKW, respectively. Association mapping detected 73 significant associations across 50 SSRs, and the phenotypic variation explained (R2) by the associations ranged from 1.54 to 23.93%. The associated loci were distributed on all chromosomes except 4A, 7A, and 7D. Significant and potentially new alleles were present on 8 chromosomes, namely 1A, 1D, 2A, 2D, 3D, 4B, 5B, and 6B. Further analysis showed that genetic effects of associated loci were greatly influenced by association panels, and the R2 of crucial loci were lower in modern cultivars than in the mini core collection, probably caused by strong selection in wheat breeding. In order to confirm the results of association analysis, yield-related favorable alleles Xgwm135-1A138, Xgwm337-1D186, Xgwm102-2D144, and Xgwm132-6B128 were evaluated in a double haploid (DH) population derived from Hanxuan10 xLumai14.These favorable alleles that were validated in various populations might be valuable in breeding for high-yield.

SUBMITTER: Guo J

PROVIDER: S-EPMC4466017 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Association and Validation of Yield-Favored Alleles in Chinese Cultivars of Common Wheat (Triticumaestivum L.).

Guo Jie J Hao Chenyang C Zhang Yong Y Zhang Boqiao B Cheng Xiaoming X Qin Lin L Li Tian T Shi Weiping W Chang Xiaoping X Jing Ruilian R Yang Wuyun W Hu Wenjing W Zhang Xueyong X Cheng Shunhe S

PloS one 20150611 6

Common wheat is one of the most important crops in China, which is the largest producer in the world. A set of 230 cultivars was used to identify yield-related loci by association mapping. This set was tested for seven yield-related traits, viz. plant height (PH), spike length (SL), spikelet number per spike (SNPS), kernel number per spike (KNPS), thousand-kernel weight (TKW), kernel weight per spike (KWPS), and sterile spikelet number (SSN) per plant in four environments. A total of 106 simple ...[more]

PMID: 26067129

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Project description:Uncovering the genetic basis of yield-related traits is important for molecular improvement of wheat cultivars. In this study, a genome-wide association study was conducted using the wheat 55K genotyping assay and a diverse panel of 384 wheat genotypes. The accessions used included 18 founder parents and 15 widely grown cultivars with annual maximum acreages of over 667,000 ha, and the remaining materials were elite cultivars and breeding lines from several major wheat ecological areas of China. Field trials were conducted in five major wheat ecological regions of China over three consecutive years. A total of 460 significant loci were detected for eight yield-related traits. Forty-five superior alleles distributed over 31 loci for which differences in phenotypic values grouped by single nucleotide polymorphism (SNP) reached significant levels (P < 0.05) in nine or more environments, were detected; some of these loci were previously reported. Eleven of the 31 superior allele loci on chromosomes 4A, 5A, 3B, 5B, 6B, 7B, 5D, and 7D had pleiotropic effects. For example, AX-95152512 on 5D was simultaneously related to increased grain weight per spike (GWS) and decreased plant height (PH); AX-109860828 on 5B simultaneously led to a high 1,000-kernel weight (TKW) and short PH; and AX-111600193 on 4A was simultaneously linked to a high TKW and GWS, and short PH. The favorable alleles in each accession ranged from 2 to 30 with an average of 16 at the thirty-one loci in the population, and six accessions (Zhengzhou683, Suzhou7829, Longchun7, Ningmai6, Yunmai35 and Zhen7630) contained more than 27 favorable alleles. A significant association between the number of favorable alleles and yield was observed (r = 0.799, p < 0.0001), suggesting that pyramiding multiple QTL with marker-assisted selection may effectively increase yield of wheat. Furthermore, distribution of superior alleles in founder parents and widely grown cultivars was also discussed here. This study is useful for marker-assisted selection for yield improvement and dissecting the genetic mechanism of important cultivars in wheat.

Project description:BackgroundSoil salinization is a major threat to wheat production. It is essential to understand the genetic basis of salt tolerance for breeding and selecting new salt-tolerant cultivars that have the potential to increase wheat yield.ResultIn this study, a panel of 191 wheat accessions was subjected to genome wide association study (GWAS) to identify SNP markers linked with adult-stage characters. The population was genotyped by Wheat660K SNP array and eight phenotype traits were investigated under low and high salinity environments for three consecutive years. A total of 389 SNPs representing 11 QTLs were significantly associated with plant height, spike number, spike length, grain number, thousand kernels weight, yield and biological mass under different salt treatments, with the phenotypic explanation rate (R2) ranging from 9.14 to 50.45%. Of these, repetitive and pleiotropic loci on chromosomes 4A, 5A, 5B and 7A were significantly linked to yield and yield related traits such as thousand kernels weight, spike number, spike length, grain number and so on under low salinity conditions. Spike length-related loci were mainly located on chromosomes 1B, 3B, 5B and 7A under different salt treatments. Two loci on chromosome 4D and 5A were related with plant height in low and high salinity environment, respectively. Three salt-tolerant related loci were confirmed to be important in two bi-parental populations. Distribution of favorable haplotypes indicated that superior haplotypes of pleiotropic loci on group-5 chromosomes were strongly selected and had potential for increasing wheat salt tolerance. A total of 14 KASP markers were developed for nine loci associating with yield and related traits to improve the selection efficiency of wheat salt-tolerance breeding.ConclusionUtilizing a Wheat660K SNPs chip, QTLs for yield and its related traits were detected under salt treatment in a natural wheat population. Important salt-tolerant related loci were validated in RIL and DH populations. This study provided reliable molecular markers that could be crucial for marker-assisted selection in wheat salt tolerance breeding programs.

Project description:Genomic selection (GS) is a strategy to predict the genetic merits of individuals using genome-wide markers. However, GS prediction accuracy is affected by many factors, including missing rate and minor allele frequency (MAF) of genotypic data, GS models, trait features, etc. In this study, we used one wheat population to investigate prediction accuracies of various GS models on yield and yield-related traits from various quality control (QC) scenarios, missing genotype imputation, and genome-wide association studies (GWAS)-derived markers. Missing rate and MAF of single nucleotide polymorphism (SNP) markers were two major factors in QC. Five missing rate levels (0%, 20%, 40%, 60%, and 80%) and three MAF levels (0%, 5%, and 10%) were considered and the five-fold cross validation was used to estimate the prediction accuracy. The results indicated that a moderate missing rate level (20% to 40%) and MAF (5%) threshold provided better prediction accuracy. Under this QC scenario, prediction accuracies were further calculated for imputed and GWAS-derived markers. It was observed that the accuracies of the six traits were related to their heritability and genetic architecture, as well as the GS prediction model. Moore-Penrose generalized inverse (GenInv), ridge regression (RidgeReg), and random forest (RForest) resulted in higher prediction accuracies than other GS models across traits. Imputation of missing genotypic data had marginal effect on prediction accuracy, while GWAS-derived markers improved the prediction accuracy in most cases. These results demonstrate that QC on missing rate and MAF had positive impact on the predictability of GS models. We failed to identify one single combination of QC scenarios that could outperform the others for all traits and GS models. However, the balance between marker number and marker quality is important for the deployment of GS in wheat breeding. GWAS is able to select markers which are mostly related to traits, and therefore can be used to improve the prediction accuracy of GS.

Dataset Information

Association and Validation of Yield-Favored Alleles in Chinese Cultivars of Common Wheat (Triticumaestivum L.).

Publications

Association and Validation of Yield-Favored Alleles in Chinese Cultivars of Common Wheat (Triticumaestivum L.).

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