Genetic diversity and population structure assessment of Western Canadian barley cooperative trials

Abstract

Studying the population structure and genetic diversity of historical datasets is a proposed use for association analysis. This is particularly important when the dataset contains traits that are time-consuming or costly to measure. A set of 96 elite barley genotypes, developed from eight breeding programs of the Western Canadian Cooperative Trials were used in the current study. Genetic diversity, allelic variation, and linkage disequilibrium (LD) were investigated using 5063 high-quality SNP markers via the Illumina 9K Barley Infinium iSelect SNP assay. The distribution of SNPs markers across the barley genome ranged from 449 markers on chromosome 1H to 1111 markers on chromosome 5H. The average polymorphism information content (PIC) per locus was 0.275 and ranged from 0.094 to 0.375. Bayesian clustering in STRUCTURE and principal coordinate analysis revealed that the populations are differentiated primarily due to the different breeding program origins and ear-row type into five subpopulations. Analysis of molecular variance based on PhiPT values suggested that high values of genetic diversity were observed within populations and accounted for 90% of the total variance. Subpopulation 5 exhibited the most diversity with the highest values of the diversity indices, which represent the breeding program gene pool of AFC, AAFRD, AU, and BARI. With increasing genetic distance, the LD values, expressed as r2, declined to below the critical r2 = 0.18 after 3.91 cM, and the same pattern was observed on each chromosome. Our results identified an important pattern of genetic diversity among the Canadian barley panel that was proposed to be representative of target breeding programs and may have important implications for association mapping in the future. This highlight, that efforts to identify novel variability underlying this diversity may present practical breeding opportunities to develop new barley genotypes.

Genome-wide association analysis provides insights into the genetic basis of photosynthetic responses to low-temperature stress in spring barley

“…To investigate the genetic factors associated with low-temperature tolerance in barley, a GWAS analysis was conducted for the chlorophyll fluorescence related-traits from 96 spring barley genotypes with a set of 5063 high-quality SNP markers. The average r 2 value of the genome was 0.02, and the LD decay was found to start at an r 2 value of 0.38 and reached half-decay at 0.2, representing the genome’s threshold distance for linkage analysis ( Capo-Chichi et al., 2023 ). In total, 52 significant quantitative trait nucleotides (QTNs) were detected.…”

“…In our previous study, an important pattern of genetic diversity was detected in the population studied. Our previous study revealed that this panel is differentiated due to the ear-row type and breeding program origins into five subpopulations ( Capo-Chichi et al., 2023 ).…”

“…This model is based on the genotype data (G), population structure (Q) as fixed effects, and the Kinship-matrix (K) as random effects ( Pasam et al., 2012 ). In our previous study, Genome-wide LD decay was plotted as R 2 of an SNP marker against the corresponding genetic distance using the mixed-model method ( Capo-Chichi et al., 2023 ). A strong LD with an approximate average value of 0.021 when the distance was 0.391 cM was observed among the 5063 marker pairs in the studied population.…”