Exploiting Illumina sequencing for the development of InDel markers in watermelon (Citrullus lanatus)

Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is a cross-pollinating diploid species and is one of the most important dicotyledonous plants belonging to the family Cucurbitaceae due to its high nutritional value, rapid growth, sweet and juicy taste, and refreshing nature as a summer fruit. However, the insertion–deletion (InDel) markers available for watermelon cannot satisfy the demand to identify and map resistance genes in this major crop. In this study, we have characterised and developed numerous polymorphic InDel markers using Illumina re-sequencing of a male parental line that is resistant to Fusarium wilt. In total, 25,701 potential InDel markers were identified, with a mean size of 18 bp. From these, 7,387 potential InDel markers > 10 bp were selected and tested as candidate InDel markers to locate resistance genes for map-based cloning and polymorphism analysis. We designed and synthesised 69 primer pairs using Primer 3 software. Overall, 54 primer pairs detected p...