Identification of candidate genes for watermelon (Citrullus lanatus) seed weight trait by BSA-seq

Watermelon seed size is a key agricultural trait with important economic significance. Seed weight is one of the standards for measuring seed size, yet its genetic mechanisms and variation remain unclear. In this study, the F₂ genetic population was constructed using Zhengzhou wild (big seeds) and [(microparticles × 102B4) × 102B4] (small seeds) as parents. Bulk segregant analysis sequencing (BSA-seq) was used to preliminarily locate the quantitative trait loci (QTL) related to seed weight traits in Chr06, with a physical distance of 0.85 Mb (5400000-6250000 bp, 97103 v2.5). We conducted a visualization analysis of the parental genome using Integrative Genomics Viewer (IGV) software, we designed seven KASP markers and successfully identified a 60.5 kb region associated with seed weight traits (K5540184-K5600687). Four distinct high-quality single-base mutations were found in this region. Subsequent genotype-phenotype association analysis indicated that these mutations led to allele variation in the F₂ population and 11 watermelon accessions, effectively distinguishing between big-seed and small-seed varieties. In addition, qRT-PCR, homology modeling, homologous protein alignment and phylogenetic analysis confirmed that Cla97C06G114610 and Cla97C06G114690 in the region were the most likely candidate genes. The gene Cla97C06G114610 is believed to potentially regulate seed weight by influencing ABA levels, while Cla97C06G114690 aligns with previous reports. Therefore, understanding the gene mapping or quantitative trait loci (QTL) that control these traits, as well as the development of markers, is of great value for the breeding of watermelon varieties.

The online version contains supplementary material available at 10.1007/s11032-025-01607-8.