Identification of regions under selection and loci controlling agronomic traits in a soft red winter wheat population

Abstract

Comprehensive information of a breeding population is a necessity to design promising crosses. This study was conducted to characterize a soft red winter wheat breeding population that was subject of intensive germplasm introductions and introgression from exotic germplasm. We used genome-wide markers and phenotypic assessment to identify signatures of selection and loci controlling agronomic traits in a soft red winter wheat population. The study of linkage disequilibrium (LD) revealed that the extent of LD and its decay varied among chromosomes with chromosomes 2B and 7D showing the most extended islands of high-LD with slow rates of decay. Four sub-populations, two with North American origin and two with Australian and Chinese origins, were identified. Genome-wide scans for selection signatures using F ST and hapFLK identified 13 genomic regions under selection, of which five loci (LT, Fr-A2, Vrn-A1, Vrn-B1, Vrn3) were associated with environmental adaptation and two loci were associated with disease resistance genes (Sr36 and Fhb1). Genome-wide association studies identified major loci controlling yield and yield related traits. For days to heading and plant height, major loci with effects sizes of 2.2 days and 5 cm were identified on chromosomes 7B and 6A respectively. For test weight, number of spikes per square meter, and number of kernels per square meter, large effect loci were identified on chromosomes 1A, 4B, and 5A, respectively. However, for yield alone, no major loci were detected. A combination of selection for large effect loci for yield components and genomic selection could be a promising approach for yield improvement.

Harnessing genome-wide genetic diversity, population structure and linkage disequilibrium in Ethiopian durum wheat gene pool

“…However, chromosomes 1A, 1B, 6A, and 6B showed widespread variation across genomic regions suggesting that the influence of intense selection and domestication pressures on these chromosomes is minimal. The distal regions of all chromosomes showed higher genomic variation than the proximal regions and indicated the occurrence of balancing selections in these regions, in agreement with previous research in wheat ( Zhou et al., 2018 ; Liu et al., 2019 ; Maccaferri et al., 2019 ; Gaire et al., 2020 ; Mazzucotelli et al., 2020 ). Zhou et al.…”

Insights into breeding history, hotspot regions of selection, and untapped allelic diversity for bread wheat breeding

“…Approximately 32 or 47% of the identified genomic regions under selection overlapped with frequently or rarely occurring large chromosomal modifications, respectively (Table S5), i.e., introgressions from wheat wild relatives identified by coverage analysis (Keilwagen et al., 2019; Keilwagen et al., 2022). The connection between genomic regions under selection and genomic regions carrying introgressions has so far only been described for the 2B/2G introgression from Triticum timopheevii (Cavanagh et al., 2013; Gaire et al., 2020). To the best of our knowledge, besides the 2B/2G introgression, only for the frequently occurring introgressions on chromosome 2A and 2D information about the origin and the underlying genes are available (Table S5).…”

“…In previous studies, genomic regions under selection were identified in diverse wheat collections using different statistical approaches (Afzal et al., 2019; Cavanagh et al., 2013; Cheng et al., 2019; Fradgley et al., 2019; Gao et al., 2017; Gaire et al., 2020; Jordan et al., 2015; Liu et al., 2019; N'Diaye et al., 2018; Pont et al., 2019). Generally, it is difficult to compare results among studies that have used different marker systems, genotype collections, and maps (genetic versus physical).…”

Genome-Wide Association Study of Soybean Germplasm Derived From Canadian × Chinese Crosses to Mine for Novel Alleles to Improve Seed Yield and Seed Quality Traits

“…The recurrent use of a small population of modern commercial cultivars in breeding programs has been suggested to have exacerbated this problem ( Mikel et al, 2010 ; Keilwagen et al, 2014 ). Exotic or under-utilized germplasm has emerged as a desirable source of novel genetic variation that could help breeders overcome these concerns ( Sneller et al, 2005 ; Fox et al, 2015 ; Wang et al, 2017 ; Kofsky et al, 2018 ; Gaire et al, 2020 ; Kilian et al, 2020 ). However, the use of exotic germplasm has yet to be widely adopted despite a growing body of literature in support of the use of under-utilized germplasm, as well as occurrences of positive contributions from exotic or under-utilized germplasm sources ( Palomeque et al, 2009a , 2009b , 2010 ; Kim et al, 2011 ; Rossi et al, 2013 ; Akpertey et al, 2014 ; Bellaloui et al, 2017 ).…”