Development of SSR markers based on transcriptome sequence and analysis of genetic diversity in Sorghum sudanense

doi:10.11686/cyxb2017420

Abstract

Abstract: Sudangrass (Sorghum sudanense) is a poaceous forage with comparatively high yield and quality, and a lack of molecular markers for quality has been a limiting factor for the sudangrass breeding. EST-SSR markers based on the transcriptome sequence of sudangrass were developed and used to study the genetic diversity of 34 accessions of sudangrass and 2 accessions of Sorghum and further to validate the applicability of SSR primers. A total of 17548 SSR sites were identified from 80686 unigenes. These SSR sites were distributed in 13574 sequences at a frequency of 16.82%. The mononucleotide, dinucleotide, and trinucleotide repeat categories were, respectively, 38.59%, 19.18% and 39.09% of the total SSRs. The number of repeat units of the SSRs ranged from 5 to 23. Randomly selected pairs of primers (n=300) were validated and the success rate of amplification was 73.67%, resulting in 54 pairs of effective primers generated, for a total of 275 alleles. Of these, 205 (73.05%) were polymorphic. The average genetic diversity, as measured by the polymorphic information content, was 0.41, and the genetic similarity coefficient ranged from 0.3922 to 0.9022. Tested materials were classified into three groups based on UPGMA cluster analysis, and the clustering results were found to be related to geographic origin. Results of our study suggest the development of SSR markers based on transcriptome data could be used to analyse the genetic diversity and identify variation of germplasm resources in sudangrass or similar species, contributing to marker-assisted breeding.

Key words: Sorghum sudanense, transcriptome, EST-SSR marker, genetic diversity

ZHU Yong-qun, PENG Dan-dan, LIN Chao-wen, NIE Gang, XU Wen-zhi, HUANG Lin-kai, LUO Fu-xiang, PENG Jian-hua, ZHANG Xin-quan. Development of SSR markers based on transcriptome sequence and analysis of genetic diversity in Sorghum sudanense[J]. Acta Prataculturae Sinica, 2018, 27(5): 178-189.

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