Co-identification of candidate regions associated with ovule number per ovary through QTL analysis and GWAS in Raphanus sativus L.

Ovule number per ovary (ONPO) directly determines seed quantity in plants. In this study, two radish (Raphanus sativus L.) accessions exhibiting marked phenotypic variation in ONPO and seed number per pod (SNPP) were selected to generate bi-parental populations for quantitative trait locus (QTL) analysis. Additionally, genome-wide association studies (GWAS) on ONPO using 206 radish accessions were conducted. Through an integrated analysis of QTL mapping and GWAS results, a major common QTL was identified spanning a 0.6 Mb region on the terminal of chromosome 5. Based on genomic position, gene ontology, and expression analyses, RsFLK was highlighted as the primary candidate, along with two other selected genes RsSGT and RsEMB3004. Subsequent comparison of the RsFLK promoter sequences in the parental lines revealed unique InDels that may affect its expression, potentially contributing to the high-ONPO. These findings provide new insights into the genetic regulation of ovule number in radishes.