Population Genomics of Tomato

Tomato (Solanum lycopersicum L.) is an acknowledged model species for research in genetics and genomics, on fruit development and disease resistance, but it also deserves to be a model species for population genomics studies due to the availability of large genetic and genomic resources. In breeding, tomato breeding and genetic improvement largely depends on introgression of beneficial alleles from wild relative species. Since the first release of its high-quality genome sequence in 2012, the genomes of several hundreds of cultivated accessions and chosen wild relatives have been re-sequenced, allowing the discovery of millions single nucleotide polymorphisms (SNP). The study of these genomes confirmed the new phylogenetic organization of the tomato clade, Solanum section Lycopersicon, composed of 13 species. Recent population and ecological genomics approaches, notably using RNAseq approach, provided new results on speciation and interspecific reproductive barriers. The molecular mechanisms of adaptation to abiotic stress in cultivated and wild tomato species were also analysed and their roles underlined as factors of speciation and diversification. The diversity of ecological conditions of the wild relative species allowed the study of evolutionary and molecular mechanisms of adaptation to abiotic stress in crop and wild tomatoes. Population genomics studies provided key insights into the two steps of tomato domestication, the intensity of bottlenecks resulting from domestication and further modern breeding, and selection footprints and large genomic regions introgressed from the wild relative species. At the transcriptome level, it was also shown that domestication and modern breeding rewired global patterns of genome expression, notably for stress-related genes. Finally, the availability of genome sequences and SNP markers allowed studying large collections of varieties, developing genome-wide association studies (GWAS) and advancing our knowledge about the genome structure and dynamic (linkage disequilibrium decay, distribution of recombination), but also allowing genes and QTL involved in many traits to be mapped and using the information for breeding new varieties. In this chapter we describe the tomato history, its domestication and the diversity and phylogeny of its wild relative species. We then present the genomic resources and new insights into the evolution and diversity of tomato accessions due to the impact of domestication and breeding. Finally, some major prospects are discussed.