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

Abstract

Background Durum wheat (Triticum turgidum L. ssp. durum Desf. Husn) is the main staple crop used to make pasta products worldwide. Under the current climate change scenarios, genetic variability within a crop plays a crucial role in the successful release of new varieties with high yields and wide crop adaptation. In this study we evaluated a durum wheat collection consisting of 197 genotypes that mainly comprised a historical set of Argentinian germplasm but also included worldwide accessions. Results We assessed the genetic diversity, population structure and linkage disequilibrium (LD) patterns in this collection using a 35 K SNP array. The level of polymorphism was considered, taking account of the frequent and rare allelic variants. A total of 1547 polymorphic SNPs was located within annotated genes. Genetic diversity in the germplasm collection increased slightly from 1915 to 2010. However, a reduction in genetic diversity using SNPs with rare allelic variants was observed after 1979. However, larger numbers of rare private alleles were observed in the 2000–2009 period, indicating that a high reservoir of rare alleles is still present among the recent germplasm in a very low frequency. The percentage of pairwise loci in LD in the durum genome was low (13.4%) in our collection. Overall LD and the high (r2 > 0.7) or complete (r2 = 1) LD presented different patterns in the chromosomes. 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 modern Argentinian accessions (cluster Q4) which were clearly differentiated. Our study contributes to the understanding of the complexity of Argentinian durum wheat germplasm and to derive future breeding strategies enhancing the use of genetic diversity in a more efficient and targeted way.

Identification of genomic regions of wheat associated with grain Fe and Zn content under drought and heat stress using genome-wide association study

“…The rate of LD decay varies depending on the rate of recombination between the marker pairs (Borah et al, 2018). In general, in outcrossing crop species such as maize, LD decays rapidly, in contrast to self-pollinated crops, which show slow decay, as in wheat (Yu et al, 2014;Roncallo et al, 2021). Genome-wide 10,546 SNPs over 282 genotypes were used to identify the markers associated with grain Fe and Zn contents across control (IR), drought (RI), and heat stress (LS) treatments.…”

Genome-wide association mapping for component traits of drought and heat tolerance in wheat

“…In outcrossing crop species like maize, LD block was observed at a short distance and thus decays were faster, and in the case of self-pollinated crops longer distance is attributed to a lower decay rate as in wheat (Yu et al, 2014 ; Roncallo et al, 2021 ). For example, the genome-wide LD decay distance is ~100 kb in rice and ~2 kb in maize (Huang and Han, 2014 ); however, in wheat, up to 30.4 mb LD decay was observed in Argentinian germplasm collection (Roncallo et al, 2021 ). LD is important in population genetics and crop improvement using molecular techniques (Gupta et al, 2005 ).…”

Allelic Variation at Glutenin Loci (Glu-1, Glu-2 and Glu-3) in a Worldwide Durum Wheat Collection and Its Effect on Quality Attributes

“…However, a wider screening of modern and historical Argentinian genotypes, as well as worldwide accessions, could help to identify favourable alleles or allele combinations with greater effect on quality. For this purpose, we used a collection composed of South American and Mediterranean germplasms, also including CIMMYT/ICARDA genotypes or derivatives [32]. This collection was previously evaluated for genetic diversity, population structure and linkage disequilibrium patterns, exhibiting high genetic differences between subpopulations, making it possible to trace the origin of the South American germplasm.…”

“…The characterisation and availability of glutenin allelic composition could be beneficial to implement its use in marker-assisted selection (MAS) in breeding programs. In the present study, we assessed (i) the allelic variations in five glutenin genes using a worldwide durum wheat collection composed mainly of Argentinian genotypes [32], (ii) the effect of Glu haplotypes or individual allelic variants on gluten strength and protein content, (iii) the association of predictive traits and rheological parameters for different glutenin haplotypes using historical datasets, (iv) the changes in gluten composition due to breeding activities between periods or origins. In addition, a detailed description of LMW subunits, not previously available for Argentinian durum wheat, was undertaken.…”