Construction of a RAPD and SSR-Based Linkage Map in Winter Squash (Cucurbita moschata)

We constructed a randomly amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) based linkage map in Cucurbita moschata  (2n=2x=40) from an F₂ population of 90 individuals derived from an intra-specific cross between the U.S. cultivar ‘Butterbush’ and a French heirloom variety ‘Sucrine DuBerry.’  Three hundred nineteen polymorphic loci were identified from 1200 RAPD markers.  Of the 240 SSR markers derived from C. moschata genomic DNA, 36 (15%) did not amplify but only 27 (11%) were polymorphic.  Of the 193 SSR markers derived from Cucurbita pepo genomic DNA, 60 (31%) did not amplify but only 8 (4%) were polymorphic.  The low level of polymorphism illustrates the high level of inbreeding present among C. moschata germplasm.  Of these, 270 loci (239 RAPD and 31 SSR), were used for linkage map construction.  Linkage groups were constructed using Kosambi’s mapping function in JoinMap 3.0 with a LOD score threshold of 3.0 and REC threshold of 0.45.  A total of 24 linkage groups were obtained with a total map length of 1109.1 cM, and averages of 46.2 cM per linkage group and 4.1 cM between markers. The creation of this linkage map in C. moschata will be used in future quantitative trait loci (QTL) studies to map regions of the genome associated with mesocarp coloration.