Appraising the Genetic Architecture of Kernel Traits in Hexaploid Wheat Using GWAS

Abstract

Kernel morphology is one of the major yield traits of wheat, the genetic architecture of which is always important in crop breeding. In this study, we performed a genome-wide association study (GWAS) to appraise the genetic architecture of the kernel traits of 319 wheat accessions using 22,905 single nucleotide polymorphism (SNP) markers from a wheat 90K SNP array. As a result, 111 and 104 significant SNPs for Kernel traits were detected using four multi-locus GWAS models (mrMLM, FASTmrMLM, FASTmrEMMA, and pLARmEB) and three single-locus models (FarmCPU, MLM, and MLMM), respectively. Among the 111 SNPs detected by the multi-locus models, 24 SNPs were simultaneously detected across multiple models, including seven for kernel length, six for kernel width, six for kernels per spike, and five for thousand kernel weight. Interestingly, the five most stable SNPs (RAC875_29540_391, Kukri_07961_503, tplb0034e07_1581, BS00074341_51, and BobWhite_049_3064) were simultaneously detected by at least three multi-locus models. Integrating these newly developed multi-locus GWAS models to unravel the genetic architecture of kernel traits, the mrMLM approach detected the maximum number of SNPs. Furthermore, a total of 41 putative candidate genes were predicted to likely be involved in the genetic architecture underlining kernel traits. These findings can facilitate a better understanding of the complex genetic mechanisms of kernel traits and may lead to the genetic improvement of grain yield in wheat.

Genome-wide association mapping for wheat morphometric seed traits in Iranian landraces and cultivars under rain-fed and well-watered conditions

“…Previous research exhibited that this trait is linked with genomic regions on Ch. 2B, 4A 29 , 33 , 34 , 4B, 6A, and 7A 28 . The GWAS identified 4 MTAs underlying seven putative QTL associated with grain compactness and solidity on chromosomes 1A 27 , 2A 27 , 4A 29 , 33 , 34 , and 7A 28 .…”

“…2B, 4A 29 , 33 , 34 , 4B, 6A, and 7A 28 . The GWAS identified 4 MTAs underlying seven putative QTL associated with grain compactness and solidity on chromosomes 1A 27 , 2A 27 , 4A 29 , 33 , 34 , and 7A 28 . For instance, we detected QTLs on chromosomes 1A, 2A, 2B, 2D, 3A, 4A, 5A, 5B, and 7A for TKW under well-irrigated conditions.…”

Unlocking the genetic control of spring wheat kernel traits under normal and heavy metals stress conditions

“…Kernel traits are important characteristics that influence wheat yield and end-use quality. Therefore, studying the genetic control of such important traits is urgently needed to improve wheat production (Liu et al 2018;Sallam et al 2018;Mourad et al 2019;Muhammad et al 2020;Al-Ashkar et al 2020). Furthermore, heavy metals contamination became a serious threatened that affect human health and crop growth all over the world.…”

QTL mapping of yield components and kernel traits in wheat cultivars TAM 112 and Duster

“…Thousand kernel weight is another important yield component, which has intensively selected during domestication and modern breeding (Golan et al, 2015;Qin et al, 2015). Similar to KPS and SPM, TKW QTL have been detected on all wheat chromosomes (Assanga et al, 2017;Sun et al, 2017;Li et al, 2018;Ma et al, 2018;Duan et al, 2020;Muhammad et al, 2020;Pang et al, 2020;Isham et al, 2021;Ren et al, 2021). TaGL3 (Yang et al, 2019a), TaGS1 (Guo et al, 2013), TaGS3 (Yang et al, 2019b), TaGS5 (Wang et al, 2015), TaGW2 (Su et al, 2011), TaGW7 (Wang et al, 2019), TaGW8 (Yan et al, 2019), TaTGW6 (Hanif et al, 2016), and TaTGW7 (Hu et al, 2016), have been characterized for association with kernel size and TKW.…”

“…Analysis of wheat breeding during practices from the past several decades show that yield improvement was mainly due to the continuous gains in KPS and SPM ( Feng et al., 2018 ; Würschum et al., 2018 ). QTL for KPS have been reported on all wheat chromosomes from various sources ( Assanga et al., 2017 ; Li et al., 2018 ; Liu et al., 2018 ; Yu et al., 2018 ; Muhammad et al., 2020 ; Pang et al., 2020 ). Several genes have been well-characterized and known for controlling KPS.…”