Genome Wide Characterization, Comparative and Genetic Diversity Analysis of Simple Sequence Repeats in Cucurbita Species
Lei Zhu,
Huayu Zhu,
Yanman Li,
Yong Wang,
Xiangbin Wu,
Jintao Li,
Zhenli Zhang,
Yanjiao Wang,
Jianbin Hu,
Sen Yang,
Luming Yang,
Shouru Sun
Affiliations
Lei Zhu
Henan Key Laboratory of Fruit and Cucurbit Biology, Henan Agricultural University, Zhengzhou 450002, China
Huayu Zhu
Henan Key Laboratory of Fruit and Cucurbit Biology, Henan Agricultural University, Zhengzhou 450002, China
Yanman Li
Henan Key Laboratory of Fruit and Cucurbit Biology, Henan Agricultural University, Zhengzhou 450002, China
Yong Wang
Henan Key Laboratory of Fruit and Cucurbit Biology, Henan Agricultural University, Zhengzhou 450002, China
Xiangbin Wu
International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
Jintao Li
International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
Zhenli Zhang
International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
Yanjiao Wang
International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
Jianbin Hu
Henan Key Laboratory of Fruit and Cucurbit Biology, Henan Agricultural University, Zhengzhou 450002, China
Sen Yang
Henan Key Laboratory of Fruit and Cucurbit Biology, Henan Agricultural University, Zhengzhou 450002, China
Luming Yang
Henan Key Laboratory of Fruit and Cucurbit Biology, Henan Agricultural University, Zhengzhou 450002, China
Shouru Sun
Henan Key Laboratory of Fruit and Cucurbit Biology, Henan Agricultural University, Zhengzhou 450002, China
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.
