Integrated analysis of biparental and natural populations reveals CRIB domain-containing protein underlying seed coat crack trait in watermelon

Key messageThe scc locus of the watermelon seed coat crack trait was fine mapped on chromosome 3. Cla97C03G056110 (annotated as CRIB domain-containing protein) was regarded as the most likely candidate geneSeed coat crack (scc) is a special characteristic of watermelon compared with other cucurbit crops. However, information regarding the genetic basis of this trait is limited. We conducted a genetic analysis of six generations derived from PI 192938 (scc) and Cream of Saskatchewan (COS) (non-scc) parental lines and found that the scc trait was regulated by a single recessive gene through two years. Bulk segregant analysis sequencing (BSA-seq) and initial mapping placed the scc locus into an 808.8 kb region on chromosome 3. Evaluation of another 1152 F-2 plants narrowed the scc locus to a 277.11 kb region containing 37 candidate genes. Due to the lack of molecular markers in the fine-mapping interval, we extracted the genome sequence variations in this 277.11 kb region with in silico BSA among seventeen re-sequenced lines (6 scc and 11 non-scc) and finally delimited the scc locus to an 8.34 kb region with only one candidate gene Cla97C03G056110 (CRIB domain-containing protein). Three single nucleotide polymorphism loci in the promoter region of Cla97C03G056110 altered cis-acting elements that were highly correlated with the nature watermelon panel. The expression of Cla97C03G056110 in seed coat tissue was higher in non-scc than in scc lines and was specifically expressed in seed coat compared with fruit flesh.