Genome-Wide Association Study and Post-genome-Wide Association Study Analysis for Spike Fertility and Yield Related Traits in Bread Wheat

Abstract

Spike fertility and associated traits are key factors in deciding the grain yield potential of wheat. Genome-wide association study (GWAS) interwoven with advanced post-GWAS analysis such as a genotype-phenotype network (geno-pheno network) for spike fertility, grain yield, and associated traits allow to identify of novel genomic regions and represents attractive targets for future marker-assisted wheat improvement programs. In this study, GWAS was performed on 200 diverse wheat genotypes using Breeders’ 35K Axiom array that led to the identification of 255 significant marker-trait associations (MTAs) (–log10P ≥ 3) for 15 metric traits phenotyped over three consecutive years. MTAs detected on chromosomes 3A, 3D, 5B, and 6A were most promising for spike fertility, grain yield, and associated traits. Furthermore, the geno-pheno network prioritised 11 significant MTAs that can be utilised as a minimal marker system for improving spike fertility and yield traits. In total, 119 MTAs were linked to 81 candidate genes encoding different types of functional proteins involved in various key pathways that affect the studied traits either way. Twenty-two novel loci were identified in present GWAS, twelve of which overlapped by candidate genes. These results were further validated by the gene expression analysis, Knetminer, and protein modelling. MTAs identified from this study hold promise for improving yield and related traits in wheat for continued genetic gain and in rapidly evolving artificial intelligence (AI) tools to apply in the breeding program.

Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat

“…Cultivars carrying SVs within VRN1 genes showed association with many traits such as lower grain yield, biomass and harvest index compared to those with intact genes. It also has been described before that VRN1 polymorphism is associated with vernalization response, grain yield, spikelet number per spike, spike development, thousand grain weight, stem elongation, heading date, NRI and other developmental traits (Kamran et al, 2013(Kamran et al, , 2014Zheng et al, 2013;Zhang et al, 2014;Voss-Fels et al, 2018;Li et al, 2019;Chumanova et al, 2020;Dreisigacker et al, 2021;Sheoran et al, 2022). Analysis of SV spring alleles together with novel SV alleles revealed correlations with seven traits which have not been evaluated before, e.g., powdery mildew infection, kernels per m 2 , falling number, RUE, NUE, RIE and GCD.…”

Genetic Diversity and Genome-Wide Association Study for the Phenology Response of Winter Wheats of North America, Western Asia, and Europe

“…To identify unique and novel MTAs for specific traits and under specific conditions, genome-wide association studies have been used extensively in wheat [23,25,[65][66][67][68]. Previous studies have revealed that genes involved in flowering are mostly found on chromosomes 1A, 2B, 3A, 3B, 5A, 6A, 6B, 7A, 7B, and 7D [69][70][71]. In the current study, a total of 30 significant markers associated with five phenological traits were identified.…”

Genome-Wide Association Study for Spike Traits and Distribution of Two QTLs for Grain Number in Chinese Wheat Cultivars

“…However, improving grain yield through the selection process encounters significant challenges primarily due to three factors: (1) the pronounced interaction between genotypes and environmental conditions, (2) relatively low heritability, and (3) the complex genetic architecture of this trait, which depends on several related traits [52]. Thus, selecting for grain yield indirectly via highly heritable and related traits would be a practicable way.…”