Genome-Wide Association Study for Pre-harvest Sprouting Resistance in a Large Germplasm Collection of Chinese Wheat Landraces

Abstract

Pre-harvest sprouting (PHS) is mainly caused by the breaking of seed dormancy in high rainfall regions, which leads to huge economic losses in wheat. In this study, we evaluated 717 Chinese wheat landraces for PHS resistance and carried out genome-wide association studies (GWAS) using to 9,740 DArT-seq and 178,803 SNP markers. Landraces were grown across six environments in China and germination testing of harvest-ripe grain was used to calculate the germination rate (GR) for each accession at each site. GR was highly correlated across all environments. A large number of landraces (194) displayed high levels of PHS resistance (i.e., mean GR < 0.20), which included nine white-grained accessions. Overall, white-grained accessions displayed a significantly higher mean GR (42.7–79.6%) compared to red-grained accessions (19.1–56.0%) across the six environments. Landraces from mesic growing zones in southern China showed higher levels of PHS resistance than those sourced from xeric areas in northern and north-western China. Three main quantitative trait loci (QTL) were detected by GWAS: one on 5D that appeared to be novel and two co-located with the grain color transcription factor Tamyb10 on 3A and 3D. An additional 32 grain color related QTL (GCR-QTL) were detected when the set of red-grained landraces were analyzed separately. GCR-QTL occurred at high frequencies in the red-grained accessions and a strong correlation was observed between the number of GCR-QTL and GR (R2 = 0.62). These additional factors could be critical for maintaining high levels of PHS resistance and represent targets for introgression into white-grained wheat cultivars. Further, investigation of the origin of haplotypes associated with the three main QTL revealed that favorable haplotypes for PHS resistance were more common in accessions from higher rainfall zones in China. Thus, a combination of natural and artificial selection likely resulted in landraces incorporating PHS resistance in China.

Unraveling Molecular and Genetic Studies of Wheat (Triticum aestivum L.) Resistance against Factors Causing Pre-Harvest Sprouting

“…In addition, a novel QTL for GC was also identified on chromosome 1B. Zhou et al [37] identified three main QTLs for PHS resistance by GWAS, including a novel locus on chromosome 5D and two loci co-located with Tamyb10-1 genes on chromosomes 3A and 3D. Furthermore, 32 GC-related QTLs (GCR-QTL) were also detected, and a strong correlation was observed between the number of GCR-QTL and seed germination rate.…”

“…The interaction between QTL epistasis (Q × Q) and the environment (Q × E, Q × Q × E) for PHS resistance has been studied to understand the complex genetic structure of QTL [213][214][215]. In wheat, PHS resistance is controlled jointly by multiple QTLs located an almost 21 chromosomes (1A, 1B, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 5B, 5D, 6A, 6B, 6D, 7A, 7B and 7D) [1,14,18,[21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][216][217][218][219][220] (Table 1).…”

“…PHS resistance is a typical quantitative trait controlled by numerous QTL/genes. Many quantitative trait loci (QTL) have been identified for PHS resistance in wheat [1,14,18,[21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37]. Several candidate genes for PHS resistance have also identified, including TaSdr, TaPHS1, TaMFT, TaVp-1, Tamyb10, and TaMKK3-A [38][39][40][41][42][43][44][45][46].…”

Distribution and Nucleotide Diversity of Yr15 in Wild Emmer Populations and Chinese Wheat Germplasm

“…A total of 189 wheat landraces from ten major wheat-growing zones (Table S2) [40], as well as 583 wheat prebreeding lines/varieties covering most important wheat-producing regions in China (Table S3), were also included in the current study.…”

Exome sequencing of bulked segregants identified a novel TaMKK3-A allele linked to the wheat ERA8 ABA-hypersensitive germination phenotype

“…Quantitative trait loci (QTL) for PHS and dormancy have been identified throughout the allohexaploid wheat genome (Zanetti et al 2000;Ogbonnaya et al 2008;Munkvold et al 2009;Kulwal et al 2012;Jaiswal et al 2012;Zhou et al 2017;Martinez et al 2018). While homologues of ABA signaling genes have been found on wheat chromosomes 3A, 4A, and 5A, only Viviparous-1/ABA-insensitive3 (VP1/ABI3) has been linked to differences in wheat PHS tolerance (Nakamura and Toyama 2001;McKibbin et al 2002;Nakamura et al 2007).…”