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Analysis on SSR Information in Transcriptome and Development of Molecular Markers in Cucurbita moschata Duch
Zhu Haisheng, WangBin, Ye Xinru, Liu Jianting, Li Yongping, Chen Mindong, Lin Hui, 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: In this study， 61 882 unigenes were obtained by transcriptome sequencing analysis from Cucurbita moschata Duch. 12 526 unigenes above 1 Kb pairs were found by MISA software， and a total of 5 407 SSR locis were identified that were distributed in 4 348 unigenes. The frequency of these SSR locis was 43.17%， and the mean distribution distance of loci was 4.76 Kb. Mean while， the major repeat motifs were mononucleotide， dinucleotide and trinucleotide， which accounted for 47.92%， 24.45% and 19.66%， respectively. Furthermore， the GA/TC were the predominant dinucleotide repeat motifs， and the GAA/TTC were the predominant trinucleotide repeat motifs. 6 489 pairs of SSR primers were designed by Primer 3.0， then 30 pairs of primers were randomly selected from 92 pairs of effective amplification primers for the polymorphism analysis of 30 Cucurbita moschata germplasms， and 18 out of 30 SSR primers showed stable and reproducible polymorphism. According to the UPGMA mapping results， 30 Cucurbita moschata samples were divided into 2 categories. Using transcriptome data of Cucurbita moschata to develop SSR markers can 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 moschata.
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