Selection signatures in the CIMMYT International Elite Spring and Semi‐arid Wheat Yield Trials

Abstract

The International Maize and Wheat Improvement Center (CIMMYT) annually distributes advanced wheat (Triticum aestivum L.) breeding lines to collaborators worldwide through the International Wheat Improvement Network. Lines are disseminated through international nurseries, including the Elite Spring Wheat Yield Trial (ESWYT) targeted to optimal (irrigated and high production) wheat production areas and the Semi‐arid Wheat Yield Trial (SAWYT) targeted to low rainfall environments. A total of 2,184 wheat lines that formed the ESWYT and SAWYT since 1979 and 1992, respectively, were genotyped using genotyping‐by‐sequencing to explore trends of genetic diversity and selection footprints associated with continuous crop improvement and adaptation. Due to a small population size of each trial, adjacent year trials were pooled into subpopulations. Population structure was evaluated using discriminant analysis of principal components and fixation index. High levels of admixture within and across the ESWYT and SAWYT subpopulations were revealed, indicating that the entire genetic diversity in the overall CIMMYT germplasm pool is harnessed to target core traits to individual mega‐environments. Genome wide scans of deviations of minor allele frequencies at each marker identified large linkage blocks in several chromosomes. The scans also revealed that 9.8 and 2.0% of the SNP markers could be associated to selection signatures over time and to environmental adaptation (significant deviations between ESWYT and SAWYT), respectively. Several known genes and previously identified haplotypes associated with grain yield in more recent CIMMYT elite germplasm did fall into genomic regions with directional selection.

Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm

“…Many previous studies in wheat have shown selection signatures for Vrn-1 loci 14,23,70,71 . In our study and an earlier study 72 , signatures of selection were not observed for Vrn-1.…”

Multiomics Based Association Mapping in Wheat Reveals Genetic Architecture of Quality and Allergenic Related Proteins

“…This introgression carries several important disease-resistance genes (e.g., Lr37 and Sr38-Yr17-Lr34 ) to various important rust diseases [ 39 , 40 ]. In addition, the introgression also appears to improve yield stability [ 41 ] and resistance to rice blast [ 42 ], all traits that are of great importance for many wheat breeding programs worldwide. For a large proportion of our wheat cultivars, molecular marker information for the disease resistance cluster Sr38-Yr17-Lr34 ( Table S3 ) is available, which matches almost perfectly with the different QTL alleles of prot288.…”

Wheat Omics: Advancements and Opportunities

“…Due to the high marker densities available in wheat, haplotypes-based GWAS studies and epistatic interaction analyses have become possible in wheat, providing high-resolution dissection of complex traits [ 75 , 76 , 77 , 78 , 79 , 80 , 81 , 82 , 83 , 84 ]. Additionally, a range of new genetics and genomics analyses are now possible, including genomic selection (GS) and selective sweep analyses, which require genome-wide high-density markers [ 85 , 86 , 87 , 88 ]. The integration of genomics in wheat improvement programs has restructured breeding programs globally, from conventional to genomics-assisted ones, promoting marker-assisted selection (MAS) and GS for achieving faster and more reliable breeding outcomes [ 89 ].…”