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Chinese Journal of Tropical Crops ›› 2020, Vol. 41 ›› Issue (3): 529-537.DOI: 10.3969/j.issn.1000-2561.2020.03.015

• Biotechnology and Tissue Culture • Previous Articles     Next Articles

EST-SSR Marker Development and Utilization Based on Transcriptome of Lagenariasiceraria (Mol.) Stand.

XU Duanxiang,DU Wenli,CHEN Zhongshan,ZHAO Ruili,XU Tongwei,GAO Shan()   

  1. Fuzhou Institute of Vegetable Science, Fuzhou, Fujian 350111, China
  • Received:2019-07-18 Revised:2019-08-28 Online:2020-03-25 Published:2020-04-16
  • Contact: GAO Shan

Abstract:

In order to enrich the molecular marker library, the SSR markers of Lagenariasiceraria (Mol.) Stand. 87 518 unigene sequences from bottle gourd transcriptome database were developed by the MISA software. A total of 11 029 SSR loci with an occurrence frequency of 9.85% were obtained from the transcriptome of Lagenariasiceraria (Mol.), the distribution distance of the SSRs was about 1 SSR per 8.3 kb ESTs. Around 6759 unigene sequences contained a single SSR loci, and the occurrence frequency was 7.72%. Average of 1858 unigene contained 2 or more than 2 SSR loci, and the occurrence frequency was 2.123%. 920 unigene contained the mixed SSR loci, and the occurrence frequency was 1.051%. Among the SSR locis, mononucleotide, trinucleotide and dinucleotide were the major types, accounting for 55.51%, 25.41% and 17.07% of the total, respectively. A/T, AG/CT and AAG/CTT were the dominant elements among mononucleotide, dinucleotide and trinucleotide, accounting for 98.22%, 55.39% and 39.86% of the total SSRs. 8617 pairs of SSR primers were found by Primer 3.0, six primer pairs were selected and applied in PCR amplification of 36 varieties, based on the clear and repeatable polymorphism, the fingerprint of the cultivars was constructed, however, there were no differences in some loci probably due to narrow genes. The cluster analysis showed that 36 bottle gourd varieties were divided into six categories when the genetic similarity coefficient was 0.68. The results aslo showed that the genetic diversity basis of bottle gourd germplasm resources in China was very low, limiting the potential of variety development using the existing bottle gourd germplasm resources. The introduction and exploration of specific wild bottle gourd germplasm should be highly emphasized. The results indicated that SSR markers could be acquired in bottle gourd by transcriptome sequencing analysis and abundant SSR markers would provide more reliable markers for genetic diversity analysis and genetic mapping construction in bottle gourd.

Key words: bottle gourd, transcriptome, EST-SSR, fingerprint, genetic diversity

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