Analysing the genomic distribution of sequence diversity, the new challenge for germplasm characterisation [B-47]

Glaszmann Jean-Christophe, Deu Monique. 2003. Analysing the genomic distribution of sequence diversity, the new challenge for germplasm characterisation [B-47]. In : 7th International Congress of Plant Molecular Biology, ISPMB 2003, Barcelona (Spain), June 23-28. Book of abstracts. ISPMB. Barcelone : ISPMB Office, Résumé, 22. International Congress of Plant Molecular Biology. 7, Barcelone, Espagne, 23 Juin 2003/28 Juin 2003.

Résumé : The distribution of sequence diversity across the genome allows revealing of statistical associations among alleles at neighbouring loci - a property known as "linkage disequilibrium" (LD), as opposed to associations between unlinked loci, which depict global population structure and history. LD has become the matter of intensive studies in human genetics with the objective of identifying genes for genetic diseases. Important applications of LD lie in "association studies" between molecular polymorphisms and particular traits of interest, and in genome scans for polymorphism in natural/artificial populations to detect genomic zones implied in adaptive response to different types of selection. In plants, extensive studies have been conducted on natural variation in Arabidopsis thaliana. LD appears to decay within 1cM/250kb in global populations, whereas high and variable levels of LD are observed in local populations, in accordance with expected founder effects. Among crops, the domestication process has had various impacts, that we illustrate here. Maize, as an annual outbreeder, displays very low LD, compatible with association studies between a trait and various SNPs in a candidate gene. In sugarcane, modern cultivars display strong associations between loci separated by up to 10 cM, as a result of a founder effect due to artificial interspecific hybridisation a century ago. Sorghum provides an example of predominantly selfing species. We assessed LD within a 6cM/800kb segment of a distal chromosomal region. A genome-wide RFLP survey revealed a global structure among 205 representative accessions. On this basis, we sampled a 100-accession reference "star" collection (yielding star-like diversity representations) as little structured as possible. In the target segment, LD commonly extends beyond 2 cM and decays within 4 cM. This opens the door to genome-wide association studies and supports the identification of reference collections for integrating phenotypic and molecular characterisation efforts. (Texte intégral)

Mots-clés Agrovoc : distribution des populations, séquence nucléotidique, variation génétique, gène, phylogénie

Classification Agris : F30 - Génétique et amélioration des plantes

Auteurs et affiliations

• Glaszmann Jean-Christophe, CIRAD-AMIS-BIOTROP (FRA) ORCID: 0000-0001-9918-875X
• Deu Monique, CIRAD-CA-CALIM (FRA)

Source : Cirad - Agritrop (https://agritrop.cirad.fr/514020/)

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