The Molecular Basis Of Tomato Genome Diversity And Evolution

Tomao (Solanum lycopersicum) has a worldwide distribution and is considered the leading vegetable crop, and is also an important model system for plants and especially for fleshy fruit biology. Tomato is considered originated from the Andean region.S. pimpinellifolium is the ancestor of cultivated tomato, and fruit mass is an important character for tomato evolution. However, how human selection has changed the tomato genome remains largely unknown. In this study,360 tomato accessions were re-sequenced and analyzed. We perfomed analyses on tomato population structure, genetic diversity, domestication, and population differentiation. The data obtained provided a single-nucleotide resolution map of tomato genome variation, and re-build the history of tomato evolution. It provided insights into the biology and genetic improvement of tomato breeding.1. With 5.7x resequencing of the 360 tomato accessions, we constructed a single-nucleotide resolution map of tomato genome variation consisting of 11,620,517 high quality SNPs and 1,303,213 insertions or deletions. These variants are likely important in the functional evolution of tomato breeding.2. Model-based analyses of population structure and phylogenetic reconstruction using tomato variantion map, we assigned the 331 red-fruited accssions into 3 groups:PIM (S. pimpinellifolium), CER (S. lycopersicum var. cerasiforme), BIG (S. lycopersicum). S. pimpinellifolium is the ancestor of cultivated tomato. The PIM group has a higher nucleotide diversity (3.23×10-3). The decay of linkage disequilibrium (LD) with physical distance between SNPs occurred at 8.8 kb in PIM (r2=0.2),256.8 kb in CER (r2=0.35) and 865.7 kb in BIG (r2= 0.35) accessions. The PIM group had more private SNPs (582,954). Compared with the Solanum pennellii genome,-3.5 million could be identified and on average,30.4% of these SNPs were presumably ancestral alleles.3. On the basis of passport information and population structure, we defined the tomato evolutionary processes yielding the CER group from PIM as’domestication’ and yielding the BIG group from CER as’improvement’. In total, we identified 186 domestication sweeps (64.6 Mb) and 133 improvement sweeps (54.5 Mb), respectively. We detected five QTLs and 13 QTLs related to fruit mass located within domestication and improvement sweeps, respectively. In additional, we verified 10 QTLs detected previously in an F2 population from a cross between CER and BIG lines using QTL-seq.4. As showed by FST, the freshmarket and processing tomatoes diverge substantially on chromosome 5, containing the four QTLs for higher SSC and better fruit firmness (sscS.1, ssc5.2, ssc5.3 and fir5.1). It represents a genomic signature of modern processing tomatoes. We discovered a 603-bp deletion in the upstream region of SIMYB12 in most pink-fruited accessions, and identified two nonsense mutations (a nucleotide substitution (C>T) and a 1-bp insertion (TG>TAG)), both resulting in the introduction of premature stop codons. These recessive alleles represent useful markers for pink tomato breeding.5. Genomic analysis between cultivated tomato and wild tomato germplasm, we determine the precise position and size of wild introgressions, such as Tm-2a, Ty-1, Mi-1, Sw-5 and AgpLl. It will enable the deployment of molecular markers to minimize the limitation from linkage drag and maximize the potential of wild germplasm. In final, the domestication and improvement sweeps (111.0 Mb) and linkage drags associated with introgression (92.2 Mb) jointly occupy nearly 200 Mb (25.6% of the assembled genome), limiting further improvement via conventional breeding. These efforts should enale a redesign of the genomic foundation for future tomato breeding.