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, 15 (8), 953-969

Genome-wide Association Study for 13 Agronomic Traits Reveals Distribution of Superior Alleles in Bread Wheat From the Yellow and Huai Valley of China

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Genome-wide Association Study for 13 Agronomic Traits Reveals Distribution of Superior Alleles in Bread Wheat From the Yellow and Huai Valley of China

Congwei Sun et al. Plant Biotechnol J.

Abstract

Bread wheat is a leading cereal crop worldwide. Limited amount of superior allele loci restricted the progress of molecular improvement in wheat breeding. Here, we revealed new allelic variation distribution for 13 yield-related traits in series of genome-wide association studies (GWAS) using the wheat 90K genotyping assay, characterized in 163 bread wheat cultivars. Agronomic traits were investigated in 14 environments at three locations over 3 years. After filtering SNP data sets, GWAS using 20 689 high-quality SNPs associated 1769 significant loci that explained, on average, ~20% of the phenotypic variation, both detected already reported loci and new promising genomic regions. Of these, repetitive and pleiotropic SNPs on chromosomes 6AS, 6AL, 6BS, 5BL and 7AS were significantly linked to thousand kernel weight, for example BS00021705_51 on 6BS and wsnp_Ex_c32624_41252144 on 6AS, with phenotypic variation explained (PVE) of ~24%, consistently identified in 12 and 13 of the 14 environments, respectively. Kernel length-related SNPs were mainly identified on chromosomes 7BS, 6AS, 5AL and 5BL. Plant height-related SNPs on chromosomes 4DS, 6DL, 2DS and 1BL were, respectively, identified in more than 11 environments, with averaged PVE of ~55%. Four SNPs were confirmed to be important genetic loci in two RIL populations. Based on repetivity and PVE, a total of 41 SNP loci possibly played the key role in modulating yield-related traits of the cultivars surveyed. Distribution of superior alleles at the 41 SNP loci indicated that superior alleles were getting popular with time and modern cultivars had integrated many superior alleles, especially for peduncle length- and plant height-related superior alleles. However, there were still 19 SNP loci showing less than percentages of 50% in modern cultivars, suggesting they should be paid more attention to improve yield-related traits of cultivars in the Yellow and Huai wheat region. This study could provide useful information for dissection of yield-related traits and valuable genetic loci for marker-assisted selection in Chinese wheat breeding programme.

Keywords: GWAS; Bread wheat (Triticum aestivum L.); QTL mapping; Superior allele; Wheat 90K SNP assay; Yield-related traits.

Figures

Figure 1
Figure 1
Population structure of the natural population based on unlinked SNP markers. (a) Plot of delta K against putative K ranging from 1 to 10; (b) stacked bar plot of ancestry relationship of 163 cultivars; (c) plot of first principle component against second principle component; (d) plot of first principle component against second and third principle components.
Figure 2
Figure 2
The numbers of associated significant SNPs for 13 agronomic traits.
Figure 3
Figure 3
Manhattan and Q‐Q plots for TKW, kernel length, spike length and PH. (a) Thousand kernel weight (TKW), the black and red dots represent SNP named wsnp_Ex_c32624_41252144 and BS00021705_51, consistently detected in 13 and 12 environments, respectively; (b) kernel length (KL), the black, red and blue dots represent SNP named BS00036788_51, BS00010573_51 and IACX9238, consistently detected in ten, eight and eight environments, respectively; (c) spike length (SL), the black, red, blue and pink dots represent SNP named BS00085688_51, BS00046263_51, CAP12_rep_c3980_87 and BS00022060_51, consistently detected in 13, 13, 13 and 12 environments, respectively; (d) plant height (PH), the black, red, blue and pink dots represent SNP named Kukri_rep_c68594_530, Tdurum_contig29489_176, RAC875_c48703_148 and Tdurum_contig27385_131, consistently detected in 13, 11, 11 and 11 environments, respectively.
Figure 4
Figure 4
The phenotype values (a–b) and percentage of cultivars (c–d) with superior allele in different significant loci for TKW and KNS.
Figure 5
Figure 5
The superior allele loci distributions in popular cultivars. Red colours represent superior allele. The corresponding averaged TKW for each cultivar is in parentheses.
Figure 6
Figure 6
Percentages of superior alleles in cultivars released before 1980s, 1980s–2000s and after 2000s in the Yellow and Huai wheat region.

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