Genome-wide association study identifies loci and candidate genes for grain micronutrients and quality traits in wheat (Triticum aestivum L.)

Abstract

Malnutrition due to micronutrients and protein deficiency is recognized among the major global health issues. Genetic biofortification of wheat is a cost-effective and sustainable strategy to mitigate the global micronutrient and protein malnutrition. Genomic regions governing grain zinc concentration (GZnC), grain iron concentration (GFeC), grain protein content (GPC), test weight (TW), and thousand kernel weight (TKW) were investigated in a set of 184 diverse bread wheat genotypes through genome-wide association study (GWAS). The GWAS panel was genotyped using Breeders' 35 K Axiom Array and phenotyped in three different environments during 2019–2020. A total of 55 marker-trait associations (MTAs) were identified representing all three sub-genomes of wheat. The highest number of MTAs were identified for GPC (23), followed by TKW (15), TW (11), GFeC (4), and GZnC (2). Further, a stable SNP was identified for TKW, and also pleiotropic regions were identified for GPC and TKW. In silico analysis revealed important putative candidate genes underlying the identified genomic regions such as F-box-like domain superfamily, Zinc finger CCCH-type proteins, Serine-threonine/tyrosine-protein kinase, Histone deacetylase domain superfamily, and SANT/Myb domain superfamily proteins, etc. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection.

Genetic dissection of grain iron and zinc, and thousand kernel weight in wheat (Triticum aestivum L.) using genome-wide association study

“…The decay of LD was found comparable in the B and D subgenomes (~ 5 cM) compared to the A subgenome, which had a shorter decay distance of around ~ 3 cM. A similar pattern of LD decay was also observed in other GWAS studies in wheat 49,78,79,91 .…”

“…The identified MTAs (5) for GFeC on chromosomes 6A, 3B, 1A, 7B, and 5A in this study were novel, as the earlier reported MTAs on the same chromosomes namely 3B, 7B, and 5A 43 , 44 , 1A, 3B, and 5A 23 , 26 , 1A 40 and 6A, 3B 91 were identified at different positions. A total of five novel MTAs was identified for GZnC on chromosome 7B, 6A, 2B, 5B, and 7B.…”

“…All the identified MTAs were mapped on 5A, 6A, 7B, 5B, 2D, 7A, and 5D located at 444.8 Mb, 68.9 Mb, 131.7 Mb, 689.9 Mb, and 461.3 Mb, 499.8 Mb, and 290.3 Mb respectively. Previous reports were also identified MTAs on 6A and 7B 29,48,50 , 5B 26,49 , 5A 26 , 1D 29 , 1A 48 and 2D, 5D, 7A and 7B 91 .…”

“…A total of five novel MTAs was identified for GZnC on chromosome 7B, 6A, 2B, 5B, and 7B. MTAs in the same chromosomes were also identified in different GWAS panels in previous experiments on 6A 47 , 2B 26 , 41 , 43 , 47 , 5B 23 , 43 , 47 , and 7B 23 , 41 , 91 . Zhou et al 47 identified an MTA on 5B chromosome located in a interval of 407.0 Mb – 412.1 Mb, which was similar to that of AX-94524014 located on 5B chromosome and mapped at 440.1 Mb explained 8.8% phenotypic variation.…”

“…Therefore, TKW is one of the important breeding objectives due to its twin effects on yield and protein. The MTAs have been identified for TKW 48 – 51 , 91 using different compositions of GWAS panels. Therefore, more GWAS studies would be helpful to identify the genomic regions governing nutritional traits in wheat and also to identify the candidate genes to develop biofortified cultivars.…”