Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes
| Title: | Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes |
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| Authors: | Adelina Olga Larsen, Pablo Federico Roncallo, Cristian Andrés Gallo, Carolina Saint Pierre, Susanne Dreisigacker, Viviana Echenique, Ana Laura Achilli |
| Source: | BMC Genomics, Vol 22, Iss 1, Pp 1-17 (2021) BMC Genomics CONICET Digital (CONICET) Consejo Nacional de Investigaciones Científicas y Técnicas instacron:CONICET BMC Genomics 22 : article number: 233 (April 2021) INTA Digital (INTA) Instituto Nacional de Tecnología Agropecuaria instacron:INTA |
| Publisher Information: | BMC, 2021. |
| Publication Year: | 2021 |
| Subject Terms: | Durum, Linkage disequilibrium, Population structure, SNP, Diversity, Rare alleles, lcsh:Biotechnology, lcsh:TP248.13-248.65, lcsh:Genetics, lcsh:QH426-470, food and beverages, Research Article, Genetics, Biotechnology, SNP array, Single-nucleotide polymorphism, Genetic diversity, Genotype, Allele, Genetic variability, Biology, Evolutionary biology, Germplasm, DIVERSITY, DURUM, LINKAGE DISEQUILIBRIUM, POPULATION STRUCTURE, RARE ALLELES, purl.org/becyt/ford/4.4 [https], purl.org/becyt/ford/4 [https], Trigo, Trigo Duro, Triticum durum, Genotipos, Población Vegetal, Wheat, Hard Wheat, Genotypes, Plant Population, Argentina, Trigo Candeal |
| 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. Fil: Roncallo, Pablo Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina Fil: Larsen, Adelina Olga. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Barrow; Argentina Fil: Achilli, Ana Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina Fil: Saint Pierre, Carolina. Centro Internacional de Mejoramiento de Maíz y Trigo; México Fil: Gallo, Cristian Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina Fil: Dreisigacker, Susanne. Centro Internacional de Mejoramiento de Maíz y Trigo; México Fil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina |
| File Description: | application/pdf |
| Language: | English |
| ISSN: | 1471-2164 |
| Access URL: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3aacc1979c97aaaa209ce1ddbcaea48f https://doaj.org/article/7c4790d7c928409492bfe215807074af |
| Rights: | OPEN |
| Accession Number: | edsair.doi.dedup.....3aacc1979c97aaaa209ce1ddbcaea48f |
| Database: | OpenAIRE |
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| ISSN: | 14712164 |
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