Abstract
Simple sequence repeats (SSRs) are widely used in mapping constructions and comparative and genetic diversity analyses. Here, 103,056 SSR loci were found in Cucurbita species by in silico PCR. In general, the frequency of these SSRs decreased with the increase in the motif length, and di-nucleotide motifs were the most common type. For the same repeat types, the SSR frequency decreased sharply with the increase in the repeat number. The majority of the SSR loci were suitable for marker development (84.75% in Cucurbita moschata, 94.53% in Cucurbita maxima, and 95.09% in Cucurbita pepo). Using these markers, the cross-species transferable SSR markers between C. pepo and other Cucurbitaceae species were developed, and the complicated mosaic relationships among them were analyzed. Especially, the main syntenic relationships between C. pepo and C. moschata or C. maxima indicated that the chromosomes in the Cucurbita genomes were highly conserved during evolution. Furthermore, 66 core SSR markers were selected to measure the genetic diversity in 61 C. pepo germplasms, and they were divided into two groups by structure and unweighted pair group method with arithmetic analysis. These results will promote the utilization of SSRs in basic and applied research of Cucurbita species.
Highlights
The Cucurbita genus (2n = 2x = 40), belonging to the Cucurbitaceae family, contains more than 13 species [1]
When the Polymorphic information content (PIC) of an SSR marker was below 0.25, it was considered as a low polymorphic marker, and a marker was considered highly polymorphic if its PIC was above 0.5
The AAT, AAAT, AAAAT, AAAAAT, AAAAAAT, and AAAAAAAT motifs (AATAATAT motif in C. maxima) were the most frequent types in each class. These results indicated that AnT-rich motifs were the most abundant in all SSR motifs in the C. moschata, C. maxima, and C. pepo genomes
Summary
Based on the conserved sequences among species or genera, some amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), and SSR markers were developed in previous studies [16,17,18,19,20] These restricted markers are insufficient for research on genetic diversity, genetic mapping, and comparative genomics. We conducted a genome-wide identification of SSR motifs in three Cucurbita species, analyzed the distribution and frequency of different repeat types, identified cross-species transferable SSR markers by in silico PCR analysis, and studied the chromosome synteny of C. pepo with other Cucurbitaceae crops. Our study will be useful for research on the population structure, genetic diversity, molecular-assisted selection, and map-based cloning in Cucurbita species
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