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Article|01 Sep 2021|OPEN
Genome-wide association study identifies QTL for eight fruit traits in cultivated tomato (Solanum lycopersicum L.)
Minkyung Kim1, Thuy Tien Phan Nguyen1, Joon-Hyung Ahn2, Gi-Jun Kim2 & Sung-Chur Sim1,3,
1Department of Bioresources Engineering, Sejong University, Seoul, Republic of Korea
2Asia Seed R&D center, Icheon, Republic of Korea
3Plant Engineering Research Institute, Sejong University, Seoul, Republic of Korea

Horticulture Research 8,
Article number: 203 (2021)
doi: 10.1038/hortres.2021.203
Views: 51

Received: 21 Mar 2021
Revised: 19 Jun 2021
Accepted: 25 Jun 2021
Published online: 01 Sep 2021

Abstract

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.