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Analysis on SSR Information in Transcriptome and Development of Molecular Markers in Summer Squash
Zhu Haisheng, Huang Lifang, Wang Bin, Liu Jianting, Ye Xinru, Chen Mindong, Zhang Qianrong, Lin Hui, Li Yongping*, Wen Qingfang*
Crops Research Institute, Fujian Academy of Agricultural Sciences; Vegetable Research Center, Fujian Academy of Agricultural Sciences; Fujian Engineering Research Center for Vegetables, Fuzhou 350013, China
Abstract: 83 650 unigenes were obtained by transcriptome sequencing analysis from Cucurbita pepo L. in this study. 15 356 unigenes above 1 kilo base pairs were found by MISA software， and a total of 7 478 SSR locis were identified that were distributed in 5 786 unigenes. The frequency of these SSR locis was 48.7%， and the mean distribution distance of loci was 4.08 Kb. Mean while， the major repeat motifs were mononucleotide， dinucleotide and trinucleotide， which accounted for 47.90%， 20.57% and 22.36%， respectively. Furthermore， the AG/CT were the predominant dinucleotide repeat motifs， and the AAG/CTT were the predominant trinucleotide repeat motifs. 5 786 pairs of SSR primers were designed by Primer 3.0， then 50 pairs of primers were randomly selected from 114 pairs of effective amplification primers for the polymorphism analysis of 28 Cucurbita pepo L. germplasms， and 35 out of 50 SSR primers showed stable and reproducible polymorphism. According to the UPGMA mapping results， 28 Cucurbita pepo L. samples were divided into 2 categories. Using transcriptome data of Cucurbita pepo L. to develop SSR markers could obtain higher frequencies of SSR locis and the types of them were rich. It provides more abundant and reliable marker selection for genetic diversity analysis and genetic map construction of Cucurbita pepo L.
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