Abstract
Bitter gourd (Momordica charantia) is widely cultivated as a vegetable and medicinal herb in many Asian and African countries. After the sequencing of the cucumber (Cucumis sativus), watermelon (Citrullus lanatus), and melon (Cucumis melo) genomes, bitter gourd became the fourth cucurbit species whose whole genome was sequenced. However, a comprehensive analysis of simple sequence repeats (SSRs) in bitter gourd, including a comparison with the three aforementioned cucurbit species has not yet been published. Here, we identified a total of 188,091 and 167,160 SSR motifs in the genomes of the bitter gourd lines ‘Dali-11’ and ‘OHB3-1,’ respectively. Subsequently, the SSR content, motif lengths, and classified motif types were characterized for the bitter gourd genomes and compared among all the cucurbit genomes. Lastly, a large set of 138,727 unique in silico SSR primer pairs were designed for bitter gourd. Among these, 71 primers were selected, all of which successfully amplified SSRs from the two bitter gourd lines ‘Dali-11’ and ‘K44’. To further examine the utilization of unique SSR primers, 21 SSR markers were used to genotype a collection of 211 bitter gourd lines from all over the world. A model-based clustering method and phylogenetic analysis indicated a clear separation among the geographic groups. The genomic SSR markers developed in this study have considerable potential value in advancing bitter gourd research.
Highlights
Over the past half century, the molecular markers utilized in research have shifted from enzymebased to various DNA-based types
According to the search criteria, we identified 129,947–331,062 simple sequence repeats (SSRs) motifs among seven cucurbit genomes
SSR motifs in the ‘Dali-11’ genome are summarized in Supplementary Table S4 and Figure 1, and they occurred at higher frequencies within gene regions
Summary
Over the past half century, the molecular markers utilized in research have shifted from enzymebased to various DNA-based types. More than twenty kinds of DNA marker systems have been established (Agarwal et al, 2008). Of these marker types, simple sequence repeats (SSRs), which consist of short (typically 1–6 bp in length) tandemly repeated nucleotide motifs, have been recognized as the best choice for many types of research owing to features including their high variability and ubiquitous occurrence (Powell et al, 1996; Schlötterer, 2004). The availability of a whole genome sequence of a particular species enables the genome-wide identification and development of SSR markers for that species (Cavagnaro et al, 2010; Song et al, 2015; Cheng et al, 2016).
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