Association Mapping Of Loci For Four Fruit Traits And Analysis Of Interactions Among Three QTLs For Fruit Weight In Tomato

Tomato (Solanum lycopersicum) fruit weight (FW), fruit shape, soluble solid content (SSC) and fruit color are crucial for yield, quality and consumer acceptability. They play important roles in human healthy and economic development. Thus, identifing new QTLs for fruit quality using association analysis and demonstrating the interactions of QTLs are useful for tomato genetic improvement and moleculer breeding.Domestication and selection has produced extremely large amount of diversity in tomato fruit size, fruit shape, SSC and fruit color. In this study, a 192 accessions tomato association panel comprising a mixture of 10 accessions wild species, 18 accessions cherry tomato and 164 accessions cultivited varieties collected from over 20 countries was genotyped with 547 InDel markers evenly distributed on 12 chromosomes and scored for FW, SSC, fruit shape index (FSI), and color parameters to identify the new QTLs and linked InDel markers. Meanwile, single, double and triple near isogenic lines carrying the cloned genes fw2.2,fw3.2 and fw11.3 in the wild tomato background (S. pimpinellifolium accession LA 1589) were developed to analyze potential interactions among three QTLs.The results showed that the 547 markers generated 1295 alleles in 192 tomato accession with a range of two to nine alleles for individual markers. Among the polymorphic markers, approximately 93% had two or three alleles with the dominance of bi-allele. As expected, all markers were polymorphic in the 192 accessions. However,polymorphisms within species was decreased from wild species S.pimpinellifolium to S. lycopersicum var. cerasiforme and then to S. lycopersicum, the cultivated tomato.The association panel was sorted into two subpopulations. The larger subpopulation was composed of 134 accessions, while the smaller subpopulation consisted of 58 accessions. Each subpopulation included S. pimpinellifolium, S. lycopersicum var. cerasiforme or cherry tomato, and S. lycopersicum.Although there was no certain trend of clustering in the larger subpopulation, the fresh-market accessions from Florida, USA formed one independent cluster. And 38 processing accessions were clustered together, while the seven accessions of S. pimpinellifolium formed one cluster. Linkage disequilibrium ranged from 3.0 Mb to 47.2 Mb across 12 chromosomes. A mean r3 of 0.393 was observed between all pairs of linked loci throughout the genome, with a mean maximum r2 value of 0.571 on chromosome 5 and a mean minimum r2 value of 0.086 on chromosome 10. A set of 102 markers significantly (p<1.19-1.30×10-4) associated with FW, fruit shape, SSC, and fruit color was identified on 11 of the 12 chromosomes using a mixed linear model. The 17 markers associated with FW could be assigned to 15 chromosomal regions on seven chromosomes and explained 2.06-22.94%of the phenotypic variation. Of the 15 associations between FSI and markers detected at 12 chromosomal regions on six chromosomes, the phenotypic variation explained by each marker ranged from 2.01% to 8.07%. Of the 24 genotype/phenotype associations identified for SSC and markers detected at 19 chromosomal regions on eight chromosomes, the phenotypic variation explained by each marker varied from 2.57% to 25.50%. A total of 46 genotype/phenotype associations were detected for three parameters of fruit color, of which 16,3, and 27 were for L*, Hue, and Chroma, respectively. The phenotypic variation explained by these markers ranged from 2.00- 23.39% for L*, 2.15-4.24% for Hue,and 3.52-26.30% for Chroma. One marker Sli685 on chromosome 6 was common for all three parameters.The functions of three major QTLs (fw2.2, Jw3.2 and fw11.3) conferring tomato fruit weight have been investigated in different genetic backgrounds. The effect of each locus on fruit weight has been described but comparative studies as well as interactive effects among these three loci in a same background have never been assessed. Thus, we conducted the morphological analyses of vegetative and productive organs among the fw2.2, fw3.2 and fw11.3 NILs in S. pimpinellifolium accession LA1589. This study revealed that fw11.3 showed the strongest effect on increasing tomato fruit weight by causing the cell endureduplication to produce larger cell size, which increased the fruit pericarp area,fruit columella and placenta area. In three biological replicates, no consistent interaction between any two of the three loci was found and no interaction was detected among the three loci either. fw2.2,fw3.2 and fw11.3 can increase the seed size, and fw11.3 showed the epistatic interaction with fw2.2 and fw3.2,respectively, in seed size.fw2.2 and fw3.2 increased the fruit weight by adding the cell layers (cell number) of fruit pericarp. Meantime, fw3.2 also decreased the flower number of each inflorescense,changed the leaf and terminal leaflet shape. fw2.2 had the weakest impact on increasing tomato fruit weight, leaf shape and flower number of each inflorescence. This study suggested that the three loci might regulate different pathways to control the fruit expansion.The results in this study demonstrated that association mapping could not only complement and enhance previous QTL information, but also identify novel loci for new variety breeding and genetic improvement of fruit traits in tomato. While, the work on interaction of three fruit weight QTLs (fw2.2,fw3.2 and fw11.3) in wild tomato LA1589 NILs could help pyramiding loci for fruit weight using molecaular approach.