Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes

RONCALLO P; LARSEN A; ACHILLI A; SAINT PIERRE C; GALLO C; DREISIGACKER S; ECHENIQUE V

BMC GENOMICS

BIOMED CENTRAL LTD

Lugar: Londres; Año: 2021 vol. 22

1471-2164

Background:Durum wheat (Triticum turgidumL. ssp.durumDesf. Husn) is the main staple crop used to makepasta products worldwide. Under the current climate change scenarios, genetic variability within a crop plays acrucial role in the successful release of new varieties with high yields and wide crop adaptation. In this study weevaluated a durum wheat collection consisting of 197 genotypes that mainly comprised a historical set ofArgentinian germplasm but also included worldwide accessions.Results:We assessed the genetic diversity, population structure and linkage disequilibrium (LD) patterns in thiscollection using a 35 K SNP array. The level of polymorphism was considered, taking account of the frequent andrare allelic variants. A total of 1547 polymorphic SNPs was located within annotated genes. Genetic diversity in thegermplasm collection increased slightly from 1915 to 2010. However, a reduction in genetic diversity using SNPswith rare allelic variants was observed after 1979. However, larger numbers of rare private alleles were observed inthe 2000?2009 period, indicating that a high reservoir of rare alleles is still present among the recent germplasm ina very low frequency. The percentage of pairwise loci in LD in the durum genome was low (13.4%) in ourcollection. Overall LD and the high (r2> 0.7) or complete (r2= 1) LD presented different patterns in thechromosomes. The LD increased over three main breeding periods (1915?1979, 1980?1999 and 2000?2020).Conclusions:Our results suggest that breeding and selection have impacted differently on the A and B genomes,particularly on chromosome 6A and 2A. The collection was structured in five sub-populations and modernArgentinian accessions (cluster Q4) which were clearly differentiated. Our study contributes to the understanding ofthe complexity of Argentinian durum wheat germplasm and to derive future breeding strategies enhancing the useof genetic diversity in a more efficient and targeted way.