Analysis of SSR Information in EST Resources and Development of EST-SSR Marker in Paspalum vaginatum

Li Huayong,Wang Xiansheng,Wang Yanping,Wu Yan,Shen Qi and Jia Xinping

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Chinese Agricultural Science Bulletin ›› 2016, Vol. 32 ›› Issue (30) : 96-102. DOI: 10.11924/j.issn.1000-6850.casb16040046

Analysis of SSR Information in EST Resources and Development of EST-SSR Marker in Paspalum vaginatum

  • Li Huayong1, Wang Xiansheng1, Wang Yanping1, Wu Yan1, Shen Qi1, Jia Xinping2
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Abstract

The objective of this study was to characterize SSR derived from the Paspalum vaginatum EST sequences and to develop EST-SSR markers for genetic diversities analysis. In total, 81220 EST sequences from Paspalum vaginatum were investigated using the software SSRIT, and the distribution and characteristics of EST-SSR were analyzed. Fifty primers were designed using the software Primer 3.0, and the validity and polymorphism of the primers were tested by PCR amplification of 10 turfgrass cultivars. The results showed that 22721 SSRs were identified from the Paspalum vaginatum 13705 EST sequences with a frequency of 16.87%. Analysis of EST-SSRs motifs revealed that tri-nucleotide and mono-nucleotide were the dominant motifs, accounted for 31.71% and 29.28%, respectively. A total of 163 EST-SSR motif types were mined, A/T was the dominant repeat motif, followed by CCG/CGG and AGC/CTG. Fifty primers of EST-SSRs primers were synthesized and 37 primer pairs could amplify clear bands using the DNA template of ‘Adalady’. The polymorphisms of the primers were tested by PCR amplification of 10 turfgrass cultivars, and 12 primer pairs showed polymorphism. The cluster analysis based on EST-SSR markers indicated that 10 turfgrass cultivars were grouped into four classes. These results showed that it is an effective and feasible way to develop EST-SSR markers from the Paspalum vaginatum EST sequences, and EST-SSR markers developed in the study could be used for genetic diversity analysis in turfgrass.

Key words

Paspalum vaginatum; molecular marker; EST-SSR; genetic diversity

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Li Huayong,Wang Xiansheng,Wang Yanping,Wu Yan,Shen Qi and Jia Xinping. Analysis of SSR Information in EST Resources and Development of EST-SSR Marker in Paspalum vaginatum. Chinese Agricultural Science Bulletin. 2016, 32(30): 96-102 https://doi.org/10.11924/j.issn.1000-6850.casb16040046

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