| Tomato(Solanum lycopersicum) is world widely planted vegetable crop and also an important model system for fleshy fruit biology, so it has important economic value and scientific value. During recent years, the interpretation of the tomato genome sequence and the development of population genetics deepen our understanding of tomato from genome perspectives. In this research, high-density genomic data was used to study the tomato evolutionary relationship and population structure as well as the natural variations within the cultivar group by genome-wide association study. We also analyzed the introgression of disease resistance genes derived from wild resources in cultivars This study deepens the comprehensions about effects of human selection and modern breeding on tomato genome, and deciphered the genome framework of some commercial hybrids. The methods and results in this study will provide theories and practice for the genome-guided tomato breeding. The main results are as follows:1. Genome-wide 20,111 SNPs of 341 individuals(166 S. lycopersium, 112 S. lycopersium var. cerasiforme, 53 S. pimpinelliforlium, 3 S. cheesmaniae, 3 S. peruvianum, 3 S. neorickii, 1 S. habrochaites, 1 S. galapagense and 1 S. chilense) were used to construct phylogenetic trees. The results showed that CER(S. lycopersium var. cerasiforme) situated the evolution stage from BIG(S. lycopersium) to PIM(S. pimpinelliforlium). Structure analysis showed that the whole group was divided into two subgroups. Subgroup I included PIM and South America originated CER, while Subgroup II included BIG and non-South America originated CER.2. Population structure analysis found that cultivars included a new subgroup, modern processing tomato subgroup(K=3 or 4). We found 69,603 highly divergent sites(top 1%), of which 63,009 sites(90.53%) resides on chromosome 5. This chromosomal regions is a genome feature of processing tomatoes, and three soluble solid content related QTLs SSC5.1, SSC5.2, SSC5.3, and a fruit firmness QTL, fir5.1, are located in this region.3. A Total of 843,316 SNPs was used to performed genome-wide association study for fruit color, fruit weight, fruit shape index and locule number in 253 accessions. We found 11 significant associated signals, among which one signal for fruit color, two signals for fruit shape index and two signals for locule number were consistent with previous research, and six signals were newly identified.4. We found y-1, y-2 and y-3, three variations of fruit peel color based on genome re-sequenced data and molecular biology methods. The allele y-1 showed one 603 bp deletion in the promoter of the transcription factor Sl MYB12. y-2 had one A insertion in the second exon of Sl MYB12 leading to truncated protein. y-3 has one C-T substitution in the second exon of Sl MYB12 which also resulted in truncated protein.5. Similarity comparison of cultivars and wild tomatoes showed that the application of resistant genes in cultivars lead to large exotic fragments. The length of introgression fragments for Ty-1, Mi-1, Tm-2a, Ve are 30.9-32.5 Mb, 26.6-26.7 Mb, 51.7-54.7Mb and 1.8 Mb, respectively. These introgressions in cultivars will likely produce severe linkage drags. 6. Analysis of the genomic framework of 17 commercial hybrids showed that swept regions, introgression regions and heterozygous regions are 111.0 Mb, 92.2 Mb and 200 Mb, respectively. Introgression regions and swept regions totally occupied 26% of the genome space, which hinders the further improvement of modern tomato. |
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