Construction of a genetic linkage map using a frame set of simple sequence repeat and high-resolution melting markers for watermelon (Citrullus spp.)

Abstract

Backcross breeding programs are widely used for rapid cultivar development by introgression of valuable traits from wild-type germplasm into elite lines. For efficient introgression from a distant cross, a genetic map is useful to select markers for maintaining the genetic background of elite lines. Construction of a genetic map in watermelon has been limited on one hand, by the relatively narrow genetic background within watermelon cultigens that results in little genetic polymorphism, and on the other hand, by high segregation distortion rates (SDR) of highly polymorphic markers found in a distant cross. In this study, we tried to develop a genetic map using expressed sequence tag (EST)-based simple sequence repeat (SSR) markers; however, only 33 EST-SSRs were anchored to the map, mainly because of multi-copies of repetitive sequences and SDR in the F2 mapping population derived from a cross of PI 189225 (Citrullus amarus; previously C. lanatus ssp. citroides) and ‘TS’ (Citrullus lanatus ssp. lanatus). To obtain more candidate markers, the whole genome of both parental lines was resequenced, and 2.5 and 0.3 million singlenucleotide polymorphisms (SNPs) were identified in PI 189225 and ‘TS’, respectively. By comparing these SNPs to the reference genome, we developed 200 high-resolution melting (HRM) candidate markers for genotyping the F2 progeny. Ultimately, 103 HRM markers were located on the genetic map, and 42 EST-SSR markers were consolidated in the map. The total map length was 1178.3 cM, the average length of the linkage groups was 107.1 cM, and the average inter-marker distance was 8.24 cM. Although these markers are not evenly distributed along the genome, they are considered to be successfully anchored. The EST-SSR and HRM markers in this genetic map will be useful in breeding programs as frame markers for foreground and background selection.