Molecular mapping reveals structural rearrangements and quantitative trait loci underlying traits with local adaptation in semi-wild Xishuangbanna cucumber (Cucumis sativus L. var. xishuangbannanesis Qi et Yuan)

Comparative genetic mapping revealed the origin of Xishuangbanna cucumber through diversification selection after domestication. QTL mapping provided insights into the genetic basis of traits under diversification selection during crop evolution. The Xishuangbanna cucumber, Cucumis sativus L. var. xishuangbannanesis Qi et Yuan (XIS), is a semi-wild landrace from the tropical southwest China with some unique traits that are very useful for cucumber breeding, such as tolerance to low light, large fruit size, heavy fruit weight, and orange flesh color in mature fruits. In this study, using 124 recombinant inbred lines (RILs) derived from the cross of the XIS cucumber with a cultivated cucumber inbred line, we developed a linkage map with 269 microsatellite (or simple sequence repeat) markers which covered 705.9 cM in seven linkage groups. Comparative analysis of orders of common marker loci or marker-anchored draft genome scaffolds among the wild (C. sativus var. hardwickii), semi-wild, and cultivated cucumber genetic maps revealed that the XIS cucumber shares major chromosomal rearrangements in chromosomes 4, 5, and 7 between the wild and cultivated cucumbers suggesting that the XIS cucumber originated through diversifying selection after cucumber domestication. Several XIS-specific minor structural changes were identified in chromosomes 1 and 6. QTL mapping with the 124 RILs in four environments identified 13 QTLs for domestication and diversifying selection-related traits including 2 for first female flowering time (fft1.1, fft6.1), 5 for mature fruit length (fl1.1, fl3.1, fl4.1, fl6.1, and fl7.1), 3 for fruit diameter (fd1.1, fd4.1, and fd6.1), and 3 for fruit weight (fw2.1, fw4.1, and fw6.1). Six of the 12 QTLs were consistently detected in all four environments. Among the 13 QTLs, fft1.1, fl1.1, fl3.1, fl7.1, fd4.1, and fw6.1 were major-effect QTLs for respective traits with each explaining at least 10 % of the observed phenotypic variations. Results from this study provide insights into the cytological and genetic basis of crop evolution leading to the XIS cucumber. The molecular markers associated with the QTLs should be useful in exploring the XIS cucumber genetic resources for cucumber breeding.