Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes
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.
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BioMed Central
2021
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Subjects: | AGRICULTURAL SCIENCES AND BIOTECHNOLOGY, Rare Alleles, HARD WHEAT, GENETIC LINKAGE, POPULATION STRUCTURE, SINGLE NUCLEOTIDE POLYMORPHISM, GENETIC DIVERSITY, ALLELES, LINKAGE DISEQUILIBRIUM, |
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dig-cimmyt-10883-214172022-03-17T16:08:34Z Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes Roncallo, P.F. Larsen, A.O. Achilli, A.L. Saint Pierre, C. Gallo, C.A. Dreisigacker, S. Echenique, V. AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Rare Alleles HARD WHEAT GENETIC LINKAGE POPULATION STRUCTURE SINGLE NUCLEOTIDE POLYMORPHISM GENETIC DIVERSITY ALLELES LINKAGE DISEQUILIBRIUM 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. 2021-04-20T00:20:12Z 2021-04-20T00:20:12Z 2021 Article Published Version https://hdl.handle.net/10883/21417 10.1186/s12864-021-07519-z English http://plants.ensembl.org/Triticum_turgidum/Info/Index http://purl.org/phylo/treebase/phylows/study/TB2:S27474 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07519-z#Sec20 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 Open Access London (United Kingdom) BioMed Central 1 22 1471-2164 BMC Genomics 233 |
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AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Rare Alleles HARD WHEAT GENETIC LINKAGE POPULATION STRUCTURE SINGLE NUCLEOTIDE POLYMORPHISM GENETIC DIVERSITY ALLELES LINKAGE DISEQUILIBRIUM AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Rare Alleles HARD WHEAT GENETIC LINKAGE POPULATION STRUCTURE SINGLE NUCLEOTIDE POLYMORPHISM GENETIC DIVERSITY ALLELES LINKAGE DISEQUILIBRIUM |
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AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Rare Alleles HARD WHEAT GENETIC LINKAGE POPULATION STRUCTURE SINGLE NUCLEOTIDE POLYMORPHISM GENETIC DIVERSITY ALLELES LINKAGE DISEQUILIBRIUM AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Rare Alleles HARD WHEAT GENETIC LINKAGE POPULATION STRUCTURE SINGLE NUCLEOTIDE POLYMORPHISM GENETIC DIVERSITY ALLELES LINKAGE DISEQUILIBRIUM Roncallo, P.F. Larsen, A.O. Achilli, A.L. Saint Pierre, C. Gallo, C.A. Dreisigacker, S. Echenique, V. Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes |
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. |
format |
Article |
topic_facet |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Rare Alleles HARD WHEAT GENETIC LINKAGE POPULATION STRUCTURE SINGLE NUCLEOTIDE POLYMORPHISM GENETIC DIVERSITY ALLELES LINKAGE DISEQUILIBRIUM |
author |
Roncallo, P.F. Larsen, A.O. Achilli, A.L. Saint Pierre, C. Gallo, C.A. Dreisigacker, S. Echenique, V. |
author_facet |
Roncallo, P.F. Larsen, A.O. Achilli, A.L. Saint Pierre, C. Gallo, C.A. Dreisigacker, S. Echenique, V. |
author_sort |
Roncallo, P.F. |
title |
Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes |
title_short |
Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes |
title_full |
Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes |
title_fullStr |
Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes |
title_full_unstemmed |
Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes |
title_sort |
linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including argentinian genotypes |
publisher |
BioMed Central |
publishDate |
2021 |
url |
https://hdl.handle.net/10883/21417 |
work_keys_str_mv |
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