Abstract
Previous molecular characterization studies conducted in Canadian wheat cultivars shed some light on the impact of plant breeding on genetic diversity, but the number of varieties and markers used was small. Here, we used 28,798 markers of the wheat 90K single nucleotide polymorphisms to (a) assess the extent of genetic diversity, relationship, population structure, and divergence among 174 historical and modern Canadian spring wheat varieties registered from 1905 to 2018 and 22 unregistered lines (hereinafter referred to as cultivars), and (b) identify genomic regions that had undergone selection. About 91% of the pairs of cultivars differed by 20–40% of the scored alleles, but only 7% of the pairs had kinship coefficients of < 0.250, suggesting the presence of a high proportion of redundancy in allelic composition. Although the 196 cultivars represented eight wheat classes, our results from phylogenetic, principal component, and the model-based population structure analyses revealed three groups, with no clear structure among most wheat classes, breeding programs, and breeding periods. FST statistics computed among different categorical variables showed little genetic differentiation (< 0.05) among breeding periods and breeding programs, but a diverse level of genetic differentiation among wheat classes and predicted groups. Diversity indices were the highest and lowest among cultivars registered from 1970 to 1980 and from 2011 to 2018, respectively. Using two outlier detection methods, we identified from 524 to 2314 SNPs and 41 selective sweeps of which some are close to genes with known phenotype, including plant height, photoperiodism, vernalization, gluten strength, and disease resistance.
Highlights
Canada is one of the top ten wheat producers and exporters globally with nearly 92% of its wheat produced in the three prairies provinces of Alberta, Saskatchewan, and Manitoba
Of the 81,587 single nucleotide polymorphisms (SNP) used for genotyping the association mapping panel, only 35.3% were used in the final analysis, each with a minor allele frequency of ≥ 0.01; other SNPs were either monomorphic or had > 20% missing data
Using a total of 270 spring wheat cultivars released in western Canada (47), USA (133), and Mexico 90), the former authors reported lower genetic diversity and high coefficients of parentage among cultivars belonging to the Canada Western Red Spring (CWRS) class, which is comparable to a group of full sibs or sister cultivars
Summary
Canada is one of the top ten wheat producers and exporters globally with nearly 92% of its wheat produced in the three prairies provinces of Alberta, Saskatchewan, and Manitoba (https://www150.statcan.gc.ca/). The authors found a significant reduction in allelic diversity in every part of the wheat genome associated with long-term wheat improvement, but the extent of reduction in diversity differed based on the breeding periods and breeding programs They reported that selection for some traits, such as early maturity introduced more new alleles, but other traits resulted in the loss of alleles[1]. The objectives of this study were, to (i) assess the molecular diversity, population structure, and genetic relationship among historical and modern Canadian spring wheat cultivars; (ii) compare the extent of molecular diversity indices and genetic differentiation (divergence) among different categorical variables (predicted groups, wheat classes, breeding periods, and breeding programs), and (iii) detect SNPs and genomic regions that have undergone selection using two contrasting outlier detection methods and explore if some of those regions are physically close to known genes that regulate phenotypic traits
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