Genetic Diversity and Population Structure of Cucumber (Cucumis sativus L.)

Abstract

Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR) markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.

Genetic Diversity Analysis of Capsicum Genus by SSR Markers

“…(Qin et al, 2014;Kim et al, 2014). On the one hand, our laboratory designed SSR makers in coding region (CDS) referring to the conception of the cucumber's primer (Ren et al, 2009;Lv et al, 2012). On the other hand, we used the primers that our laboratory had designed (Jia et al, 2017).…”

Population structure and genetic analysis of different utility types of mango (Mangifera indica L.) germplasm of Andhra Pradesh state of India using microsatellite markers

“…Bayesian clustering analyses have proven to be powerful tools to analyze population structure (Pritchard et al 2000) and it is widely used in conservation biology to quantify relationships and differences among populations (Breton et al 2008). Assessment of genetic diversity and population structure have been reported in horticulture crops such as apple (Urrestarazu et al 2012), plum (Horvath et al 2011), strawberry (Yoon et al 2012), olive (Belaj et al 2007), cucumber (Lv et al 2012).…”

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

“…We previously reported the genome sequence of cucumber (Huang et al, 2009;Li et al, 2011) as well as a variome map comprising ;3.3 M single nucleotide polymorphisms (SNPs) (Qi et al, 2013), based on the resequencing data from a core collection of 115 cucumber accessions with an average depth of 18.3X. The core collection was estimated to capture 77.2% of the total genetic diversity of 3342 accessions from a wide geographic distribution (Lv et al, 2012) and could be divided into four groups including one wild group (Indian) and three cultivated groups (East Asian, Eurasian, and Xishuangbanna) (Qi et al, 2013). In this study, we exploited this population-scale genome sequence resource to systematically investigate the occurrence, functional impact, and formation mechanisms of SVs in cucumber genomes.…”