Population-specific, recent positive selection signatures in cultivated Cucumis sativus L. (cucumber)

Abstract

Population-specific, positive selection promotes the diversity of populations and drives local adaptations in the population. However, little is known about population-specific, recent positive selection in the populations of cultivated cucumber (Cucumis sativus L.). Based on a genomic variation map of individuals worldwide, we implemented a Fisher's combination method by combining 4 haplotype-based approaches: integrated haplotype score (iHS), number of segregating sites by length (nSL), cross-population extended haplotype homozygosity (XP-EHH), and Rsb. Overall, we detected 331, 2,147, and 3,772 population-specific, recent positive selective sites in the East Asian, Eurasian, and Xishuangbanna populations, respectively. Moreover, we found that these sites were related to processes for reproduction, response to abiotic and biotic stress, and regulation of developmental processes, indicating adaptations to their microenvironments. Meanwhile, the selective genes associated with traits of fruits were also observed, such as the gene related to the shorter fruit length in the Eurasian population and the gene controlling flesh thickness in the Xishuangbanna population. In addition, we noticed that soft sweeps were common in the East Asian and Xishuangbanna populations. Genes involved in hard or soft sweeps were related to developmental regulation and abiotic and biotic stress resistance. Our study offers a comprehensive candidate dataset of population-specific, selective signatures in cultivated cucumber populations. Our methods provide guidance for the analysis of population-specific, positive selection. These findings will help explore the biological mechanisms of adaptation and domestication of cucumber.

Keywords: Cucumis sativus L; Fisher’s combination; cultivated cucumber; population-specific; recent positive selection.

Fig. 1.

Manhattan plots of combined P values of local adaptation in the East Asian a), Eurasian b), and Xishuangbanna populations c). The blue horizontal line indicates the cutoff of the Benjamini–Hochberg-adjusted P value equal to 0.01, and the sites above are selective. The red dots represent selective variants located in domestication sweeps identified in a previous study (Qi et al. 2013). Manhattan plots were generated using the qqman package (Turner 2018).

Fig. 2.

Venn diagram for selective sites in cultivated populations. Variants with Benjamini–Hochberg-adjusted P values less than 0.01 were identified as selective sites. A Venn diagram was generated using the package VennDiagram v1.6.20 (Chen and Boutros 2011).

Fig. 3.

Proportion of selective sweeps in cultivated populations. In each bar, the count and proportion of specifically selective sites for each sweep corresponding to the population are indicated.

Fig. 4.

Genes harboring soft and hard selective sites in cultivated populations. Tracks indicate the following: genes containing only hard selective sites in the East Asian (green), Eurasian (orange), and Xishuangbanna (blue) populations (A); hard selective variants in the East Asian population (B); soft selective variants in the East Asian population (C); hard selective variants in the Eurasian population (D); soft selective variants in the Eurasian population (E); hard selective variants in the Xishuangbanna population (F); soft selective variants in the Xishuangbanna population (G); and genes containing only soft selective sites in East Asian (green), Eurasian (orange), and Xishuangbanna (blue) populations (H). In the B–F tracks, dark triangle dots indicate selective sites located in gene regions, and light circle dots indicate selective sites located in intergenic regions. The plot was generated using Circos v0.69-9 (Krzywinski et al. 2009).