Lipids-related Domestication Accounts for the Extreme Cold-sensitivity of Semiwild and Tropic Xishuangbanna cucumber (Cucumis sativus L. var. xishuangbannanesis)

Abstract

Abstract Xishuangbanna (XIS) cucumber (Cucumis sativus L. var. xishuangbannanesis) is a semiwild variety originated from low latitude tropic area, and therefore show extreme cold sensitivity and heat tolerance. Here, we mapped the quantitative trait loci (QTLs) that control cold-sensitivity and heat-tolerance of XIS cucumber seedlings. By bulked-segregant analysis (BSA), we identified three QTLs (HTT1.1, HTT3.1 and HTT3.2, in a total length of 11.98 Mb) for heat tolerance and two QTLs (LTT6.1 and LTT6.2, in a total length of 8.74 Mb) for cold sensitivity. The QTL LTT6.1 was then narrowed down to a length of 641 kb. Based on structural variants (SVs) and single nucleotide polymorphism (SNP), we found the LTT6.1 is covered by a high divergent region including a 50-kb deletion in XIS49 genome, which affect the gene structure of lipase ABHD6 (Csa_6G032560). Accordingly, there is a very big difference in lipid composition but not other osmoprotectants like free amino acids and fatty acids between XIS49 and cultivated cucumber CL. Moreover, we calculated the composite likelihood ratio (CLR) and identified selective sweeps from 115 resequencing data, and found that lipid- and fatty acid-related processes is a major aspect of the domestication of XIS group cucumber. LTT6.1 is such a special region positioned nearby lipid-related selective sweeps. These studies above suggested that lipids-related domestication of XIS cucumbers should account for their extreme cold sensitivity.