Genome-wide Association Analysis Of Tomato Fruit Traits And Identification Of Splicing Quantitative Trait Loci(sQTL)

Tomato(Solanum lycopersicum)originated in the Andes,its plant morphology,adaptation to biotic and abiotic stresses and fruit size,shape and color changed significantly undergone domestication and improvement.In order to study the genetic basis of tomato fruit traits,we investigated 10 fruit traits in 455 tomato accessions and conducted a Genome-Wide Association Study(GWAS).In the end,we got a total of 8939 SNPs that exceeded the suggestive threshold,and 4200 SNPs exceeded the significant threshold.By comparing the association results of different duplications and different phenotypic treatments,we finally got 380 lead SNPs and 53 multieffect SNPs.By analyzing the linkage relationship between lead SNP and surrounding genes,as well as gene annotation,and literature reports,we finally identified 26 candidate genes and conducted a further analysis of the gene Solyc03g112880.The results indicated that the gene was likely to regulate fruit shape through changing its expression,and it was selected in domestication.Alternative splicing(AS)is a common phenomenon which due to the mismatch of the splicing site,the original transcript was changed,so that a single gene could be transcribed into multiple transcripts.AS changed in different tissues,different developmental periods,and under different environments,so it was of great significance to study the regulation of AS.In order to find the sites where AS was regulated by the whole genome,we used wholegenome association analysis on 405 tomato accessions to find splicing QTL(sQTL).In the AS events study on tomato populations,we found that AS played a significant role in the domestication and improvement of tomato.After the GO and KEGG enrichment analysis of genes with significant splicing differences between different populations,it was found that the splicing changes of the splisome itself were of great significance to tomato.Through association analysis results,we obtained a total of 86716 sQTLs,including 1714cis-sQTL and 85133 trans-sQTL,corresponding to 715 and 4651 annotated genes,respectively.Combined with differential splicing genes and e QTL genes,we identified 225 genes that were potentially important for tomato genes splicing,expression,and domestication.In general,our research is of great significance for identifying the regulatory sites of important agronomic traits of tomato fruit and cloning of related genes,laying a good foundation for the improvement of tomato fruit traits.The discovery of a large number of sQTLs laid a solid foundation for future research on AS regulation.