The Molecular Basis Of Cucumber Diversity And Domestication

Cucumber is one of the most important vegetables in the globe, with China contributes to morethan half of the world’s annual yield. However, limited knowledge of important agronomic genes ishampering the development of new varieties. The success of genome sequencing of cucumber line9930had greatly enhanced the functional genomics and molecular breeding of cucumber. After fingerprinting3342cucumber lines collected worldwide, we built a core collection consisting of115lines.With deep re-sequencing of the core set, a high density cucumber genomic variation map wasconstructed, based on which we performed analysis on cucumber domestication, populationdifferentiation and linkage disequilibrium, data obtained in this study can provide insights into thebiology and genetic improvement of this important fruit crop. Results as follows:1. Employing23highly polymorphic SSR markers, a cucumber core collection was extracted from3342accessions of universal distribution. The core collection, which captures77.2%of the totalgenetic diversity, can be divided into4geographic groups: Indian(30accessions),Xishuangbanna(19), Eurasian(29) and Eastasian(37).2. With18.3×deep resequcing of the core collection, a map of cucumber genome variation whichencompasses3,305,010SNPs,336,081small insertions and deletions and594PAVs wassuccessfully constructed. The accuracy of the predicted SNPs was estimated to be98.9%.3. Model-based analyses of population structure and phylogenetic reconstruction using25,228four-fold degenerate-site SNPs support the notion that the core collection can be divided into fourgroups. The basal nature of the Indian group compared to the other three groups is supported byits significantly higher nucleotide diversity π, fast decay of linkage disequilibrium (LD) measuredby r2and high percentage of private SNPs and Indels. dadi proposed that the three cultivatedgroups are monophyletic and domesticated separately from their respective ancestral types. TheEastasian cucumbers were brought to China by diplomat Zhang Qian2,700years ago.4. As shown by FST, the three cultivated groups diverge substantially. We further identified~500geneswhich were differently selected during cucumber differentiation, a phenomenon possibly caused bydifferential selection to adapt to their respective local environments. There were43highlydifferentiated nonsynonymous SNPs fixed between the Xishuangbanna group and the other3groups (FST=1), but only one resided within the physical interval(within gene Csa3G183920) thatspans the ore locus. Co-expression of wild-type and mutant the specific gene with pAC-BETAshowed that Csa3G183920defines the ore locus, and designated CsaBCH1in this study.5. Cucumbers must have undergone severe bottleneck during domestication, as shown by itsπW/πC(1.96). Genomic regions with the largest reduction in diversity within cultivated groups andextreme divergence in allele frequency between wild and cultivated groups can be regarded as selective sweeps. A total of112such regions were identified, with7of which overlapped withpreviously mapped QTLs(4concerning fruit length). There is no diversity in the cultivated groupsin the region to which Bt was mapped, a strong signature of a selective sweep during domestication,implying that Bt is responsible for the domestication trait of non-bitter fruit. Selected sweeps can becandidate regions harboring important agronomic traits.