Genome-wide association study identifies QTL for eight fruit traits in cultivated tomato (Solanum lycopersicum L.)

• Published in: Horticulture research Vol. 8; no. 1; p. 203
• Main Authors: Kim, Minkyung, Nguyen, Thuy Tien Phan, Ahn, Joon-Hyung, Kim, Gi-Jun, Sim, Sung-Chur
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.12.2021; Oxford University Press
• Subjects: 631/449/447/8; 631/449/711; Agriculture; Alleles; Association analysis; Biomedical and Life Sciences; Chromosomes; Cultivation; Datasets; Ecology; Frequency analysis; Fruit cultivation; Fruits; Gene frequency; Gene mapping; Genetic diversity; Genome-wide association studies; Genomes; Life Sciences; Marker-assisted selection; Markers; Missing data; Pericarp; Phenotypic variations; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Plant Sciences; Population structure; Quantitative trait loci; Single-nucleotide polymorphism; Solanum lycopersicum; Tomatoes; Weight
• ISSN: 2662-6810; 2052-7276; 2052-7276
• DOI: 10.1038/s41438-021-00638-4

Genome-wide association study (GWAS) is effective in identifying favorable alleles for traits of interest with high mapping resolution in crop species. In this study, we conducted GWAS to explore quantitative trait loci (QTL) for eight fruit traits using 162 tomato accessions with diverse genetic backgrounds. The eight traits included fruit weight, fruit width, fruit height, fruit shape index, pericarp thickness, locule number, fruit firmness, and brix. Phenotypic variations of these traits in the tomato collection were evaluated with three replicates in field trials over three years. We filtered 34,550 confident SNPs from the 51 K Axiom ® tomato array based on < 10% of missing data and > 5% of minor allele frequency for association analysis. The 162 tomato accessions were divided into seven clusters and their membership coefficients were used to account for population structure along with a kinship matrix. To identify marker-trait associations (MTAs), four phenotypic data sets representing each of three years and combined were independently analyzed in the multilocus mixed model (MLMM). A total of 30 significant MTAs was detected over data sets for eight fruit traits at P  < 0.0005. The number of MTA per trait ranged from one (brix) to seven (fruit weight and fruit width). Two SNP markers on chromosomes 1 and 2 were significantly associated with multiple traits, suggesting pleiotropic effects of QTL. Furthermore, 16 of 30 MTAs suggest potential novel QTL for eight fruit traits. These results facilitate genetic dissection of tomato fruit traits and provide a useful resource to develop molecular tools for improving fruit traits via marker-assisted selection and genomic selection in tomato breeding programs.