Genome‐wide association mapping of Hagberg falling number, protein content, test weight, and grain yield in U.K. wheat

Abstract

Association mapping using crop cultivars allows identification of genetic loci of direct relevance to breeding. Here, 150 U.K. wheat (Triticum aestivum L.) cultivars genotyped with 23,288 single nucleotide polymorphisms (SNPs) were used for genome‐wide association studies (GWAS) using historical phenotypic data for grain protein content, Hagberg falling number (HFN), test weight, and grain yield. Power calculations indicated experimental design would enable detection of quantitative trait loci (QTL) explaining ≥20% of the variation (PVE) at a relatively high power of >80%, falling to 40% for detection of a SNP with an R2≥ .5 with the same QTL. Genome‐wide association studies identified marker‐trait associations for all four traits. For HFN (h2 = .89), six QTL were identified, including a major locus on chromosome 7B explaining 49% PVE and reducing HFN by 44 s. For protein content (h2 = 0.86), 10 QTL were found on chromosomes 1A, 2A, 2B, 3A, 3B, and 6B, together explaining 48.9% PVE. For test weight, five QTL were identified (one on 1B and four on 3B; 26.3% PVE). Finally, 14 loci were identified for grain yield (h2 = 0.95) on eight chromosomes (1A, 2A, 2B, 2D, 3A, 5B, 6A, 6B; 68.1% PVE), of which five were located within 16 Mbp of genetic regions previously identified as under breeder selection in European wheat. Our study demonstrates the utility of exploiting historical crop datasets, identifying genomic targets for independent validation, and ultimately for wheat genetic improvement.

Nutritional Genomic Approach for Improving Grain Protein Content in Wheat

“…The consistent SNP on chromosome 3B ( BS00062734_51 ) is located at the position of 545,069,014 bp on the IWGSC RefSeq v1.1 map and is, therefore, distant from the two significant SNPs identified on the same chromosome in the study by Alemu et al [ 17 ] within the intervals 822,819,158–822,820,535 bp, and 795,567,173–795,572,772 bp, as well as far from the five significant SNPs on 3B reported by Leonova et al [ 18 ], altogether located between 29,356,100 and 493,122,600 bp. It is also far from the reported GPC-SNPs on chromosome 3B ( wsnp_Ex_c20652_29734133 at 292,024,034 bp, and RAC875_c58159_989 at 564,248,743 bp [ 48 ], and AX-94746929 at 800,933,346 bp [ 50 ]). The positions of the two stable SNPs, identified in the present study on chromosome 3A ( Excalibur_c13709_2568 at 518,897,423 bp and wsnp_Ku_c7811_13387117 at 714,304,435 bp), are far from the significant GPC-QTL peaked by wsnp_Ku_c30545_40369365 at 363,458,708 bp [ 48 ], as well as far from the two significant SNPs on 3A detected by Leonova et al [ 18 ] in single crop seasons (located at 20,019,900 and 739,397,100 bp).…”

“…It is also far from the reported GPC-SNPs on chromosome 3B ( wsnp_Ex_c20652_29734133 at 292,024,034 bp, and RAC875_c58159_989 at 564,248,743 bp [ 48 ], and AX-94746929 at 800,933,346 bp [ 50 ]). The positions of the two stable SNPs, identified in the present study on chromosome 3A ( Excalibur_c13709_2568 at 518,897,423 bp and wsnp_Ku_c7811_13387117 at 714,304,435 bp), are far from the significant GPC-QTL peaked by wsnp_Ku_c30545_40369365 at 363,458,708 bp [ 48 ], as well as far from the two significant SNPs on 3A detected by Leonova et al [ 18 ] in single crop seasons (located at 20,019,900 and 739,397,100 bp). In addition, both are distantly located from the multi-environmentally verified SNPs mapped to the 3A chromosome region between 191,530,793 and 484,643,825 bp [ 47 ].…”

“…Alemu et al [ 17 ] reported many chromosomal regions on 2A, 3B, 3D, 5B, 6A, 6B and 7B as the source of highly significant MTAs for GPC based on GWAS analysis in 802 elite spring breeding lines. The contribution of loci on chromosomes 1A, 2A, 2B, 3A, 3B, and 6B for protein content was confirmed in a GWAS study on UK wheat genotypes [ 48 ], whereas genomic regions on chromosome 6A were recently confirmed in a study on Russian spring cultivars [ 18 ]. QTNs for GPC under limited water supply were located on chromosomes 1B, 2A, 2B, and 6B [ 49 ], of which the QTL 6B.7 was co-mapped with the previously cloned gene Gpc-B1 associated with high grain protein [ 20 ].…”

Managing Data in Breeding, Selection and in Practice: A Hundred Year Problem That Requires a Rapid Solution

“…Subsequent Genome-Wide Association Studies GWAS using VCU yield data finds around a third of the signatures of selection identified in the pedigree paper to overlap with GWAS hits for yield (White et al, 2021). This demonstrates the principle that high-quality data that is publicly available can have scientific value far beyond that originally envisaged through linkage of newer datasets with historic data.…”

Multi-trait ensemble genomic prediction and simulations of recurrent selection highlight importance of complex trait genetic architecture in long-term genetic gains in wheat

“…Yield loss from weed competition has become even more problematic in intensified cropping systems (Storkey et al, 2021). Additionally, increased yield and starch grain filling has been subject to the long-standing trade-off between yield and grain protein content (Simmonds, 1995; White et al, 2021), and has led to dilution of wheat grain protein content (Austin et al, 1980; Fufa et al, 2005) and mineral nutrient density (Davis, 2009; Shrewry et al, 2016). This has also led to higher optimum nitrogen fertiliser application rates to meet milling wheat grain protein requirements with diminishing increases in yield, and thus poorer nitrogen use efficiency (Hawkesford, 2014).…”