Genome-Wide Association Study On Traits At Seedilng Stage In Processing Tomatoes

Tomato?Solanum lycopersicum?is one of the widely planted vegetable crops and it's also an important model plant for the study of genetic.Most of the traditional genetic studies are aimed at the analysis of certain sites on the tomato genome,and they cannot have a deep understanding of the whole genome.The rapid development of sequencing technology has provided the possibility for an in-depth study of tomatoes in the genomic level.This research was based on the whole-genomic low coverage re-sequencing technology to explore high-quality SNPs in a core collection of processing tomato.The obtained whole genomic data was used to illustrate the population structure and principal components.Genome-Wide Association Study was used to explore the possible loci controlling leaf area,flowering days and the node number of the first flower in this core collection of processing tomato.This study provided a scientific basis for understanding the genome variation of processing tomato subgroup and laied the foundation for genetic improvement of processing tomato.The main results obtained were listed as follows:?1?A core collection of 299 processing tomatoe germplasm were re-sequenced in 0.5 x depth.A total of 93 G clean data were obtained including 319,709 high quality SNPs.Further Analysis proved that theos SNPs were unevenly distributed on the chromosome,in which the chromosome 5 had the highest number of SNPs,and chromosome 8 had the least SNPs.The average density of SNP on the chromosomes was 0.40 SNPs/kb,249,050 SNPs were located intergenic regions,accounting for 77.90% of the total SNPs.Only 55,377 SNPs were in the non-synonymous mutation regions,accounting for 17.32% of the total SNPs.The analysis of the variants showed that the number of SNPs transition was 1.5 times more than transversion SNPs.?2?The phenotypical traits of fifth leaf area,sixth leaf area,flowering days and the node number of the first flower were analyzed.The results showed that the coefficient of variation of the four traits was varied greatly from 9.796% to 15.874%.The inter-regression correlation analysis of all traits showed significant.The frequency of the four traits are consistent with normal distributions.Hence all these traits might be controlled by the quantitative loci.?3?A total of 150 SNPs,covering more than 70% of whole genomic information,was used to analyze the population structure and principle component?PCA?.Both of which showed coincide results.This core collection was divided into two subgroups: one subgroup consists of 212 accessions and is 70.90% of the core collection,another one has 87 accessions and is about 21.10%.The results were consistent with the pedigree of the core collection.?4?By using two models of GLM+P and MLM+P+K,Genome-Wide Association Study was conducted with 320,000 SNPs and the four phynotypic traits.It was detected that 3 SNPs were significantly associated with the leaf area at SL 2.50ch04₅4764647?SL 2.50ch04₅4792363 and SL 2.50ch12₃070496,and 1 SNP with flowering days at SL 2.50chch09₃6916640.