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Analysis on SSR Loci in Transcriptome and Development of Molecular Markers in Luffa cylindrica
Zhu Haisheng, Zhang Qianrong, Liu Jianting, Chen Mindong, Wang Bin,Xue Zhuzheng, Li Dazhong, 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: A total of 58 073 unigenes (52 087 451 bp) were obtained and then 8 693 simple sequence repeats (SSR) loci were identified by transcriptome sequenceing analysis in Luffa cylindrica. The mean distribution distance of loci was 5.99 Kb in the unigenes. Among all SSR loci， dinucleotide repeat was the main type (45.89%)，followed by trinucleotide repeat motif (38.89%). AG/CT and AAG/CTT were the most frequent motifs in dinucleotide and trinucleotide repeats， respectively. A total of 7 563 SSR primers were designed and 30 primers were randomly selected for PCR amplification using 32 loofah materials， of which 22 primers could amplify clearly and reproducibly and showed polymorphism among the materials. According to the UPGMA analysis， 32 plants were divided into 2 groups: Luffa cylindrica Roem and Luffa acutangula Roxb， the 2 groups were divided into 2 sub-groupsis according to fruit shape， respectively. Classification was closely related to the presence or absence of ridges and had a highly correlated with fruit shape and color. These results indicated that high frequency and various types of SSR markers could be acquired in loofah by transcriptome sequencing analysis. And the large quantities of SSR markers would provide more reliable markers for genetic diversity analysis and genetic mapping construction in Luffa cylindrica.
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