This study addresses the need for climate-resilient wheat by performing a high-resolution genetic analysis to unravel the complex genetic basis of yield stability. Using 158 recombinant inbred lines (RILs) across 12 environments, we identified thousands of significant SNPs. Key discoveries include environmentally stable, multi-trait genetic hubs particularly on chromosome group 1 and specific candidate genes. Our work provides a direct framework for marker-assisted breeding to develop wheat varieties with reliable performance under unstable growing conditions.
Climate volatility demands wheat varieties with enhanced yield stability. Unraveling the genetic basis of these traits, particularly genotype-by-environment (G×E) interactions, is critical. We performed a high-resolution genetic analysis on 158 wheat recombinant inbred lines (RILs), phenotyping 19 traits across 12 contrasting environments. Using 14,676 SNP markers, we conducted a multi-environment GWAS with Mixed Linear (MLM) and Fixed and Random Model Circulating Probability Unification (FarmCPU) models, followed by Linkage Disequilibrium (LD) block, haplotype, and pleiotropy analyses. Phenotypic data showed yield components were environmentally sensitive, while traits like plant height were strongly genetically controlled. Genomic analyses revealed distinct sub-genome architectures. Key results include the identification of 8,092 significant SNP-trait associations and the discovery of 57 environmentally stable, pleiotropic SNPs. The chromosome 1 group (1A, 1B, 1D) was a major hotspot, harboring 32 multi-trait loci. A single SNP on chromosome 1A (Tdurum_contig52332_94) explained 86.53% of phenotypic variance for plant height. Megabase-scale LD blocks indicated strong selective footprints, and haplotype analysis revealed diverse patterns from fixation to high diversity. We prioritized 40 high-confidence candidate genes and confirmed stable Quantitative trait loci (QTLs), including a yield QTL on 1A (qGY-1A.1) and a multi-trait region on 2A. This study elucidates the complex genetic architecture of wheat productivity. Our integrated approach disentangled G×E interactions and identified genomic regions under selection. The pleiotropic hubs, stable QTLs, and candidate genes provide a robust framework for marker-assisted breeding, accelerating the development of climate-resilient wheat.
Climate volatility demands wheat varieties with enhanced yield stability. Unraveling the genetic basis of these traits, particularly genotype-by-environment (G×E) interactions, is critical. We performed a high-resolution genetic analysis on 158 wheat recombinant inbred lines (RILs), phenotyping 19 traits across 12 contrasting environments. Using 14,676 SNP markers, we conducted a multi-environment GWAS with Mixed Linear (MLM) and Fixed and Random Model Circulating Probability Unification (FarmCPU) models, followed by Linkage Disequilibrium (LD) block, haplotype, and pleiotropy analyses. Phenotypic data showed yield components were environmentally sensitive, while traits like plant height were strongly genetically controlled. Genomic analyses revealed distinct sub-genome architectures. Key results include the identification of 8,092 significant SNP-trait associations and the discovery of 57 environmentally stable, pleiotropic SNPs. The chromosome 1 group (1A, 1B, 1D) was a major hotspot, harboring 32 multi-trait loci. A single SNP on chromosome 1A (Tdurum_contig52332_94) explained 86.53% of phenotypic variance for plant height. Megabase-scale LD blocks indicated strong selective footprints, and haplotype analysis revealed diverse patterns from fixation to high diversity. We prioritized 40 high-confidence candidate genes and confirmed stable Quantitative trait loci (QTLs), including a yield QTL on 1A (qGY-1A.1) and a multi-trait region on 2A. This study elucidates the complex genetic architecture of wheat productivity. Our integrated approach disentangled G×E interactions and identified genomic regions under selection. The pleiotropic hubs, stable QTLs, and candidate genes provide a robust framework for marker-assisted breeding, accelerating the development of climate-resilient wheat.
Salami