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Dernière mise à jour : Mai 2018

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Axis 1: Genomic diversity and domestication

Domestication in Solanaceae

DADI 4

The consequences of domestication on the nucleotide and expression patterns have been examined using RNAseq data in a set of crop and wild accessions (http://www.arcad-project.org/, Sarah et al., 2016). We extended this approach to the Solanaceae family to conduct a comparative genomic approach in pepper, eggplant and wild green-fruited tomatoes to test for convergent domestication. RNAseq data have been produced for 24 accessions (12 crops/12 wild) in the three species. Thus, from site frequency spectrum, we aim at modelling the most probable demographic scenario that occurred during the domestication phase in these three species and compare these scenarios together.

Relevant Publications

Sauvage C, Rau A, Aichholtz C, Chadoeuf J, Sarah G, Ruiz M, Santoni S, Causse M, David J, Glémin S (2017) Domestication rewired gene expression and nucleotide diversity patterns in tomato. The Plant J 91, 631-645 ; doi: 10.1111/tpj.13592

Bauchet  G, S Grenier, N Samson, V Segura, A Kende, J Beekwilder, K Cankar, JL Gallois, J Gricourt, J Bonnet, C Baxter, L Grivet, M Causse (2017) Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit and implications for flavor improvement. New Phytologist (doi: 10.1111/nph.14615)

Bauchet G, Grenier S, Samson N, Bonnet J, Grivet L, Causse M (2017) Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study. Theor Appl Genet 130(5), 875-889 ; DOI 10.1007/s00122-017-2857-9

Pascual L, E Albert, C Sauvage, J Duangjit, JP Bouchet, F Bitton, N Desplat, D Brunel, MC Le Paslier, N Ranc, L Bruguier, B Chauchard, P Verschave, M Causse (2016) Dissecting quantitative trait variation in the resequencing era: complementarity of bi-parental, multi-parental and association panels. Plant Science 242: 120-130

Blanca J, J Montero-Pau, C Sauvage, G Bauchet, E Illa, MJ Diez, D Francis, M Causse, E van der Knaap and J Cañizares (2015) Genomic variation in the tomato, from wild ancestors to contemporary breeding accessions. BMC Genomics 16 : 257, doi:10.1186/s12864-015-1444-1

Lin T, G Zhu, J Zhang, X Xu, Q Yu, Z Zheng, Z Zhang, Y Lun, S Li, X Wang, Z Huang, J Li, Ci Zhang, T Wang, Y Zhang, A Wang, Y Zhang, K Lin, C Li, G Xiong, Y Xue, A Mazzucato, M Causse, Z Fei, JJ Giovannoni, R T Chetelat, D Zamir, T Städler, J Li, Z Ye, Y Du & S Huang 2014. Genomic analyses provide insights into the history of tomato breeding. Nature Genetics 46: 1220-1226; doi:10.1038/ng.3117

Sauvage C, V Segura, G Bauchet, R Stevens, P T Do, Z Nikoloski, A R Fernie and M Causse 2014. Genome Wide Association in tomato reveals 44 candidate loci for fruit metabolic traits. Plant Physiology 165: 1120–1132

Prunus diversity

DADI 5

The collections conserved in the GRC and in the team is a valuable resource which can be exploited in order to:

  • screen our genetic resources for different traits in order to broaden the genetic basis used in crosses, including wild-relative species;
  • search for resilient genotypes to be used as genetic backgrounds in which to introgress targeted traits;
  • study the structure and diversity of our collections, analyze the polymorphism of loci of interest;
  • develop GWAS analyses.

Relevant Publications

Bourguiba, H., Batnini, M.-A., Krichen, L., Trifi-Farah, N., Audergon, J. M. (2017). Population structure and core collection construction of apricot (Prunus armeniaca L.) in north Africa based on microsatellite markers. Plant Genetic Resources Characterization and Utilization, 15 (1), 21-28.

https://www.cambridge.org/core/journals/plant-genetic-resources/article/population-structure-and-core-collection-construction-of-apricot-prunus-armeniaca-l-in-north-africa-based-on-microsatellite-markers/D8C1CD82712C4A9F485D1AB2B4C95211#

Micheletti, D., Dettori, M. T., Micali, S., Aramini, V., Pacheco, I., da Silva Linge, C., Foschi, S., Banchi, E., Barreneche, T., Quilot-Turion, B., Lambert, P., Pascal, T., Ignasi, I., Carbo, J., Wang, L.-R., Ma, R.-J., Li, X., Gao, Z.-S., Nazzicari, N., Troggio, M., Bassi, D., Rossini, L., Verde, I., Laurens, F., Arús, P., Aranzana, M. J. (2015). Whole-genome analysis of diversity and SNP-major gene association in peach germplasm. Plos One, 10 (9), 19 p.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0136803