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Structure of Genetic Diversity

Structure of
genetic diversity

Research

Context and Issues

Plant breeding programs success largely depend on the exploitation of a large range of genetic variability mainly collected into genetic resources collections. However the phenotyping difficulties increase directly with the number of collected accessions, and an exhaustive collection characterization became unrealistic. A valuable alternative to this problem consists in a study of the genetic diversity structure as well as in the definition of core collections. A core collection corresponds to a limited number of accessions chosen to represent the maximum of the collection genetic diversity. The BrACySol Biological Resources Centre maintains genetic resources collections of different cultivated species, including Solanum and Brassica. The Solanum collection gathers: the cultivated species Solanum tuberosum (cultivars and hybrids), dihaploids (), relative species belonging to 32 species and interspecific hybrids (). All accessions are maintained as clones by vegetative multiplication. The Brassica collection gathers the cultivated species Brassica napusBrassica oleracea, Brassica rapa, few accessions B. carinata, B. nigra and B. juncea. Accessions are spread into national collections, network collections and INRA collections.

A characterization of the genetic diversity is under progress using different descriptors: morphological, agronomical and technological traits, molecular data (SSR, SNP …). The best understanding of the genetic diversity organisation will help for instance to optimize the choice of mapping populations, association panels, or core collections.

 

Objectives

  • Broadening and characterizing the genetic diversity of oilseed rape and potato
  • Understanding the organization of the genetic diversity inside polyploid genomes considering an autopolyploid model (Solanum tuberosum) and an allopolyploid  model (Brassica napus)

Methodology

Solanum: The genetic diversity and population structure of a collection of Solanum tuberosum L. genotypes including 350 worldwide potato varieties or breeders’ lines and 30 Chiloé Island landraces were examined using simple sequence repeat markers. Several structure analysis methods were performed The molecular data were used to define a core collection of this set of varieties. This core collection and a collection of 288 breeding lines originating from different research programs are currently being analysed with a SNP chip (8303 SNP). The molecular data are used to investigate the linkage disequilibrium patterns in potato.

Brassica: Since the quick conversion of B. napus cultivars to low erucic acid and low glucosinolates content in the 70’s-90’s the genetic basis exploited by breeders is narrow. This can be explained by the use of the limited set of progenitors cultivars. We aim at characterizing the available genetic diversity for B. napus, including both intra and inter-specific diversity, using molecular data (SSR and SNP).  Intraspecific diversity is represented by a set of 280 accessions. Interspecific diversity is represented by the two progenitor species: B. oleracea and B.rapa. Core collections would be then defined for each of the three species. A comparative study of genetic diversity between B. napus/B. oleracea /B. rapa will be carried out to study the impact of polyploidy and of genome organization.

Main Result

Solanum

The population structure analysis showed that there was no clear genetic structure of the analysed collection. This study also confirmed the genetic proximity of modern potatoes and Chiloé Island landraces. 

The SNP chip is a valuable tool to analyse our genetic resources collection. As potato is an autotetraploïd species, LD was assessed using a method which includes allelic dosage information. The LD pattern is being investigated for each linkage group and for specific genomic regions involved in traits of interest.

Brassica

Genetic diversity of B. napus, B. oleracea and B. rapa was characterized using SSR markers. B. oleracea and B. rapa accessions were mainly regrouped by cultigroups and geographic origins. B. napus diversity structure indicated a clear difference between winter and spring types. Among winter oilseed rape, recent accessions (post ~1995) were regrouped together. Preliminary core collections were defined for B. oleracea and B. napus but need to be validated.

Partners

  • UMR INRA-UBP 1095 Génétique Diversité et Écophysiologie des Céréales, Clermont-Ferrand
  • US 1279 Etude du Polymorphisme des Génomes Végétaux, Evry

Funding and Support

IBISA (2014-2015) (PI: F. Esnault): Improvement of the securing process of Brassica and Solanum collections

Métaprogramme SELGEN (2013-2015): Linkage disequilibrium analysis in potato

Publications

Esnault F., Solano J., Perretant M., Hervé M., Label A., Pellé R., Dantec J.P., Boutet G., Brabant P., Chauvin J.E. (2014) Genetic diversity analysis of a potato (Solanum tuberosum L.) collection including Chiloé Island landraces and a large panel of worldwide cultivars. Plant Genetic Resources: Characterization and Utilization, 12 (1): 74-82.

Solano J., Mathias M., Esnault F., Brabant P. (2013) Genetic diversity among native varieties and commercial cultivars of Solanum tuberosum ssp. tuberosum L. present in Chile. Electronic Journal of Biotechnology, DOI

Esnault F., Chauveau A., Bérard A., Boland A., Le Paslier M.C., Brunel D., Chauvin J.E. (2012) Diversity analysis of a potato (Solanum tuberosum L. subsp. tuberosum) core collection using the SolCAP chip. 9th Solanaceae Conference, From bench to innovative applications, August 26-30, 2012, Neuchâtel, Suisse, Abstract book p126 (Poster)

Laperche A, Falentin C, Wagner G, Boutet G, Glory P, Label A, Manzanares-Dauleux M, Renard M (2008) Structure of genetic diversity and elaboration of core collections in Brassica oleracea. Proceedings of 5th ISHS international symposium on Brassicas and the 16th Crucifer Genetics Workshop. Lillehammer, Norway 8-12 sept.