ena-STUDY-INRA-19-04-2018-10:22:59:373-264
Investigation of domestication footprints in three major Solanaceae species
The proposed research project is related to evolutionary biology and aims to investigate the variation in evolutionary patterns of polymorphism induced by domestication, at the genome scale, using Next Generation Sequencing technologies (NGS), in 3 related horticultural crop species, belonging to the Solanaceae family (tomato, pepper and eggplant) both at (1) the intra specific level and (2) the interspecific level. Surprisingly, only few studies have investigated such patterns in nuclear genes in plants. Within Solanaceae these species are of both economical and scientific interest and have undergone different domestication history. We are specifically targeting the transcriptome of both domestic and wild accessions in each species while using (1) methodological approaches in evolutionary biology to reveal genes under positive or stabilizing selection and (2) use statistical developments to investigate domestication scenarios. Factors such as GC content or codon usage bias will be analyzed in relation to their contribution to evolution. We will perform association mapping with the most interesting genes in each species. This will provide direct applications for breeding purposes. The proposed project represents a unique opportunity to develop a transversal approach and will be one of the first projects investigating molecular signatures of evolutionary changes at the genome scale. It will allow the release of a large amount of data produced using NGS and the associated statistical methods (i.e. short reads assembly, comparative genomic).
The proposed research project is related to evolutionary biology and aims to investigate the variation in evolutionary patterns of polymorphism induced by domestication, at the genome scale, using Next Generation Sequencing technologies (NGS), in 3 related horticultural crop species, belonging to the Solanaceae family (tomato, pepper and eggplant) both at (1) the intra specific level and (2) the interspecific level. Surprisingly, only few studies have investigated such patterns in nuclear genes in plants. Within Solanaceae these species are of both economical and scientific interest and have undergone different domestication history. We are specifically targeting the transcriptome of both domestic and wild accessions in each species while using (1) methodological approaches in evolutionary biology to reveal genes under positive or stabilizing selection and (2) use statistical developments to investigate domestication scenarios. Factors such as GC content or codon usage bias will be analyzed in relation to their contribution to evolution. We will perform association mapping with the most interesting genes in each species. This will provide direct applications for breeding purposes. The proposed project represents a unique opportunity to develop a transversal approach and will be one of the first projects investigating molecular signatures of evolutionary changes at the genome scale. It will allow the release of a large amount of data produced using NGS and the associated statistical methods (i.e. short reads assembly, comparative genomic).