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

Creator: Roncallo, P.F.
Creator: Larsen, A.O.
Creator: Achilli, A.L.
Creator: Saint Pierre, C.
Creator: Gallo, C.A.
Creator: Dreisigacker, S.
Creator: Echenique, V.
Year: 2021
URI: https://hdl.handle.net/10883/21417
Language: English
Publisher: BioMed Central
Copyright: CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose
Type: Article
Place of Publication: London (United Kingdom)
Issue: 1
Volume: 22
DOI: 10.1186/s12864-021-07519-z
Keywords: Linkage Disequilibrium
Keywords: Rare Alleles
Description: 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.
Agrovoc: HARD WHEAT
Agrovoc: GENETIC LINKAGE
Agrovoc: POPULATION STRUCTURE
Agrovoc: SINGLE NUCLEOTIDE POLYMORPHISM
Agrovoc: GENETIC DIVERSITY
Agrovoc: ALLELES
Related Datasets: http://plants.ensembl.org/Triticum_turgidum/Info/Index
Related Datasets: http://purl.org/phylo/treebase/phylows/study/TB2:S27474
Related Datasets: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07519-z#Sec20
ISSN: 1471-2164
Journal: BMC Genomics
Article number: 233


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  • Wheat
    Wheat - breeding, phytopathology, physiology, quality, biotech

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