Genome‐wide association analysis of spike and kernel traits in the U.S. hard winter wheat

Abstract

A better understanding of the genetic control of spike and kernel traits that have higher heritability can help in the development of high‐yielding wheat varieties. Here, we identified the marker‐trait associations (MTAs) for various spike‐ and kernel‐related traits in winter wheat (Triticum aestivum L.) through genome‐wide association studies (GWAS). An association mapping panel comprising 297 hard winter wheat accessions from the U.S. Great Plains was evaluated for eight spike‐ and kernel‐related traits in three different environments. A GWAS using 15,590 single‐nucleotide polymorphisms (SNPs) identified a total of 53 MTAs for seven spike‐ and kernel‐related traits, where the highest number of MTAs were identified for spike length (16) followed by the number of spikelets per spike (15) and spikelet density (11). Out of 53 MTAs, 14 were considered to represent stable quantitative trait loci (QTL) as they were identified in multiple environments. Five multi‐trait MTAs were identified for various traits including the number of spikelets per spike (NSPS), spikelet density (SD), kernel width (KW), and kernel area (KA) that could facilitate the pyramiding of yield‐contributing traits. Further, a significant additive effect of accumulated favorable alleles on the phenotype of four spike‐related traits suggested that breeding lines and cultivars with a higher number of favorable alleles could be a valuable resource for breeders to improve yield‐related traits. This study improves the understanding of the genetic basis of yield‐related traits in hard winter wheat and provides reliable molecular markers that will facilitate marker‐assisted selection (MAS) in wheat breeding programs.

Genome-Wide Association Study for Grain Protein, Thousand Kernel Weight, and Normalized Difference Vegetation Index in Bread Wheat (Triticum aestivum L.)

“…Similarly, four MTAs were identified on 3D, 2D, 3A, and 2B for TKW. MTAs for TKW on the same chromosomes in different mapping populations were also identified in earlier reports on 1B [ 27 ], 2B [ 28 , 91 ], 2D [ 25 , 80 , 91 , 92 , 93 ], 3A [ 88 , 93 , 94 , 95 ] at different chromosomal locations. Cabral et al [ 27 ] identified a QTL, i.e., QGwt.crc-2B-2 , on the 2B chromosome, located at a confidence interval of 92.9–96.0 cM, which was similar to the MTA ( AX-95194336 ) detected in the current study on the same chromosome at 96.2 Mb.…”

Deciphering the genetic landscape of seedling drought stress tolerance in wheat (Triticum aestivum L.) through genome-wide association studies

“…GWAS has been successfully utilized in identifying the significant MTAs associated with drought tolerance at various developmental stages ( Gill et al., 2022 ; Tanin et al., 2022 ; Halder et al., 2023 ). Most of these studies were conducted at reproductive stages.…”

Association Mapping of Quantitative Trait Loci for Agronomic Traits in a Winter Wheat Collection Grown in Kazakhstan

“…A collection of winter wheat from Central Asia was compiled, including accessions from Kazakhstan (52), Kyrgyzstan (27), Tajikistan (9), and Uzbekistan (27). The samples from Central Asia, along with accessions from other parts of the world, were united to form the CAWBIN winter wheat collection, consisting of 277 genotypes.…”

“…For instance, grain productivity in the U.K. was 7.8 t/ha per year during 2021-2022 [4]. It is well known that grain yield is a complex trait and is associated with main components such as the number of productive spikes, spike length, number of spikelets per spike, number of kernels per spike, kernel size, and thousand-kernel weight [9]. The performance of these quantitative components is affected not only by environmental factors but also by genotype and is controlled by multiple quantitative trait loci (QTLs) located in different parts of the genome [10,11].…”