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. 2018 Oct 2;19(10):3011.
doi: 10.3390/ijms19103011.

Genome-Wide Association Study Reveals Novel Genomic Regions for Grain Yield and Yield-Related Traits in Drought-Stressed Synthetic Hexaploid Wheat

Madhav Bhatta  1 , Alexey Morgounov  2 , Vikas Belamkar  3 , P Stephen Baenziger  4
Affiliations

Genome-Wide Association Study Reveals Novel Genomic Regions for Grain Yield and Yield-Related Traits in Drought-Stressed Synthetic Hexaploid Wheat

Madhav Bhatta et al. Int J Mol Sci. .

Abstract

Synthetic hexaploid wheat (SHW; 2n = 6x = 42, AABBDD, Triticum aestivum L.) is produced from an interspecific cross between durum wheat (2n = 4x = 28, AABB, T. turgidum L.) and goat grass (2n = 2x = 14, DD, Aegilops tauschii Coss.) and is reported to have significant novel alleles-controlling biotic and abiotic stresses resistance. A genome-wide association study (GWAS) was conducted to unravel these loci [marker⁻trait associations (MTAs)] using 35,648 genotyping-by-sequencing-derived single nucleotide polymorphisms in 123 SHWs. We identified 90 novel MTAs (45, 11, and 34 on the A, B, and D genomes, respectively) and haplotype blocks associated with grain yield and yield-related traits including root traits under drought stress. The phenotypic variance explained by the MTAs ranged from 1.1% to 32.3%. Most of the MTAs (120 out of 194) identified were found in genes, and of these 45 MTAs were in genes annotated as having a potential role in drought stress. This result provides further evidence for the reliability of MTAs identified. The large number of MTAs (53) identified especially on the D-genome demonstrate the potential of SHWs for elucidating the genetic architecture of complex traits and provide an opportunity for further improvement of wheat under rapidly changing climatic conditions.

Keywords: D-genome; bread wheat; complex traits; durum wheat; genes; genotyping-by-sequencing; haplotype block; marker–trait association; root traits; single nucleotide polymorphism.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Principal component bi-plot analysis of 123 drought-stressed synthetic hexaploid wheat grown in two seasons (2016 and 2017) in Konya, Turkey. AWLN, awn length; BMWT, biomass weight; FLA, flag leaf area; FLLN, flag leaf length; FLW, flag leaf width; GVWT, grain volume weight; GY, grain yield; HI, harvest index; RTLN, root length; STMDIA, stem diameter; and TKW, thousand kernel weight.
Figure 2
Figure 2
Significant markers trait associations identified on each chromosome for grain yield and yield-related traits obtained from the genome-wide association study of 123 synthetic hexaploid wheats grown in 2016 and 2017 in Konya, Turkey.
Figure 3
Figure 3
Linkage disequilibrium (LD) values (R2) and haplotype blocks with significant marker–trait associations (MTAs; ≥2) observed (A) on chromosome 7A for GY, (B) on chromosome 3A for GY, (C) on chromosome 3A for BMWT, (D) on chromosome 3B for STMDIA, (E) on chromosome 1A for FLA, (F), on chromosome 6B for FLA, (G) on chromosome 7D for FLA, and (H) on chromosome 6D for RTLN and phenotypic variance explained (PVE) by each haplotype block. Dark red color represents the strong LD whereas light red color represents the weak LD between pairs of MTAs.
Figure 4
Figure 4
Potential candidate gene functions harboring SNPs affecting yield and yield-related traits under drought stress. The count of marker–trait associations (for either single or multiple traits) located within genes that have the same gene annotation is shown. AWLN, awn length; BMWT, biomass weight; FLA, flag leaf area; FLLN, flag leaf length; FLW, flag leaf width; GVWT, grain volume weight; GY, grain yield; HI, harvest index; RTLN, root length; STMDIA, stem diameter; and TKW, thousand kernel weight.
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