Construction Of The Core Collection And Genome-wide Association Study On The Key Agronomic Traits For Processingtomatoes

Tomato(Solanum lycopersicum)has a narrow genetic background due to its self-pollination nature along with the process of domestication and directional selection by plant breeding activtives. The modern cultivated tomato can be divided into two distinct subgroups named by their useage, the processing tomatoes group and fresh market tomatoes group. For each subgroup, the in depth analysis on the genetics diversities had been limited by lack of polymorphisms using the RLFP, SSR and CAPS markers. With the development of the genomics studies on tomato crop, the reference genome and resequencing of the variation population information had been released recently, together with enormous Single Nucletide Polymorphisms(SNPs). The SNP maker is a high-efficient tool with low cost has been used in some correlational studies of narrow genetic background populations in crops. In this research, 65 SNP markers are developed by using the resequencing data of 7 processing tomatoes online and were applied in the analysis of the genetic diversity of 3026 cultivated processing tomatoes collected in the group of PT IVF CAAS. The core collection of processing tomato germplasm in China was built by using 20 phenotypic traits and 46 SNP loci. In addition, Genome-wide association study(GWAS) was performed on 189 processing tomato materials with the low coverage(0.1X) sequence information. In total, 8 QTLs for 2 key agricultural traits for processing tomato were discovered. The results obtained in this study provide a foundation for the development of the Chinese tomato industry. The detailed contents and results were listed as follows:(1) Based on the re-sequence information of 7 processing tomatoes, 65 SNP markers which equally distributed on 12 chromsomes of tomato were selected. In total, 3026 processing tomato accessions were genotyped; the results assured that there are 46 SNPs can be used in the genetic diversity analysis for processing tomato materilas in IVF CAAS.(2) The genetic diversity and genetic background analysis were performed by genotyping of the processing tomato accessions from IVF CAAS. The collected processing tomato germplasms could be divided into two clusters and their genetic backgrounds are based on E6203 and M82 as the representative, respectively. The materials obtained from seed multi-natinonal companies can covered all the genetic background and have a good spread in the two groups, indicated that they have taken advantage of the tomato genetics resourses efficiently.(3) The Chinese processing tomato core collections was built by combining both phenotypic and genotypic information. In total five popular methods that were widly used to make gemplasm core collections were tested. By representative accesses of both phenotype and genotype, our results indicated that the M strategy is a valid method for core collection selection in processing tomato. The establishment of core collection will provide a convenient way to study and utilize the resources, and pave a way for the research on genetic improvement and breeding for tomato.(4) Genotyping by sequencing(GBS) was applied by using low coverage resequencing(0.1 X) for 189 processing tomato accessions, 620718 SNPs were discovered and used for GWAS on the key traitsfor processing toimatos. Intotal 8 loci were discovered associated with 2 traits, some of the significantly associated SNPs were consistent with results previously reported. Our results indicated that the SNPs discovered by low coverage resequencing can be used in the studies of GWAS. In the meantime, there were no any significant association signals with Brix contain for the tomato accession sequenced, a higher resequencing depth(0.5 X) was seted to get a better resolution for future analysis.