Genome-wide association study for grain yield and component traits in bread wheat (Triticum aestivum L.)

Abstract

Genomic regions governing days to heading (DH), grain filling duration (GFD), grain number per spike (GNPS), grain weight per spike (GWPS), plant height (PH), and grain yield (GY) were investigated in a set of 280 diverse bread wheat genotypes. The genome-wide association studies (GWAS) panel was genotyped using a 35K Axiom Array and phenotyped in five environments. The GWAS analysis showed a total of 27 Bonferroni-corrected marker-trait associations (MTAs) on 15 chromosomes representing all three wheat subgenomes. The GFD showed the highest MTAs (8), followed by GWPS (7), GY (4), GNPS (3), PH (3), and DH (2). Furthermore, 20 MTAs were identified with more than 10% phenotypic variation. A total of five stable MTAs (AX-95024590, AX-94425015, AX-95210025 AX-94539354, and AX-94978133) were identified in more than one environment and associated with the expression of DH, GFD, GNPS, and GY. Similarly, two novel pleiotropic genomic regions with associated MTAs i.e. AX-94978133 (4D) and AX-94539354 (6A) harboring co-localized QTLs governing two or more traits were also identified. In silico analysis revealed that the SNPs were located on important putative candidate genes such as F-box-like domain superfamily, Lateral organ boundaries, LOB, Thioredoxin-like superfamily Glutathione S-transferase, RNA-binding domain superfamily, UDP-glycosyltransferase family, Serine/threonine-protein kinase, Expansin, Patatin, Exocyst complex component Exo70, DUF1618 domain, Protein kinase domain involved in the regulation of grain size, grain number, growth and development, grain filling duration, and abiotic stress tolerance. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection (MAS).

Mapping QTL for Phenological and Grain-Related Traits in a Mapping Population Derived from High-Zinc-Biofortified Wheat

“…The highest number of 12 QTLs were identified for PH on the 1B, 2B, 3A, 3B, 3D, 4A, 5A, 5D, 7B, and 7D chromosomes. Plant height is one of the important yield component traits in wheat, and therefore many QTLs were also identified in previous reports on chromosomes 1B [ 10 , 19 , 37 , 40 , 51 ], 2B [ 10 , 40 , 45 , 51 , 53 ], 3A [ 26 , 54 ], 3B [ 10 , 19 , 22 , 40 ], 4A [ 26 , 45 , 52 , 53 ], 5A [ 19 , 26 , 45 , 51 , 53 , 55 , 56 ], and 7B [ 10 ], at different positions. In addition, Alemu et al [ 52 ] identified a QTL on the 4A chromosome at 41cM, which was similar to that of QPH-4A and mapped at 41cM, explaining a 4.58% phenotypic variation.…”

“…Genome-wide association studies (GWAS) and quantitative-trait-loci (QTL) mapping are the two widely used methods to dissect the genetic basis of complex quantitative traits in crop plants. In previous studies, GWAS panels have been phenotyped in a range of production conditions including drought, irrigated, heat, salt stress, and different nitrogen regimes, to identify QTLs associated with grain yield and its contributing traits through GWAS [ 10 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 ]. Similarly, several QTLs associated with yield and contributing traits have been identified through bi-parental populations-based QTL mapping under diverse production conditions (irrigated, drought, heat, organic) and different genetic backgrounds (synthetic wheat, Rye selections or translocations, non-adapted background) [ 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 ].…”

Marker-assisted backcross breeding for heat tolerance in bread wheat (Triticum aestivum L.)

“…MABB is considered as one of the reliable methods to improve a crop variety by incorporating the desired gene(s)/QTLs that govern the trait expression in which the variety is essentially deficient. Numerous reports are available on molecular markers linked with the expression of QTLs for heat-stress tolerance (Devate et al, 2022;Khan et al, 2022;Pinto et al, 2010;Gupta et al, 2012;Gupta et al, 2017) but their use in wheat-breeding programs is still rare. The present study is an attempt of the transfer of QTLs associated with heat stress in to the background of high-yielding wheat varieties using MABB.…”

Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and drought stress conditions in wheat

“…High-density SNP markers, which are employed in GWASs, may screen large gene pools of breeding material. GWASa have been widely utilized in numerous crops to predict candidate genes using genome-wide-dense markers for various complex traits ( Sukumaran et al., 2015 ; Liu et al., 2018 ; Srivastava et al., 2020 ; Alseekh et al., 2021 ; Danakumara et al., 2021 ; Devate et al., 2022a ; Khan et al., 2022 ; Tiwari et al., 2022 ). The benefits of GWASs include the ability to identify Marker trait association (MTAs) with high resolution utilizing diverse germplasm, making the method more efficient and less expensive than biparental QTL mapping ( Jin et al., 2016 ).…”