SNP discovery and Characterization from transcriptomes of Asian yellow pond turtle, Mauremys mutica
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TECHNICAL NOTE
SNP discovery and Characterization from transcriptomes of Asian yellow pond turtle, Mauremys mutica Jian Zhao1 • Xincheng Zhang1,2 • Wei Li1 • Kunci Chen1 • Dandan Zhang1 • Xinping Zhu1
Received: 9 December 2015 / Accepted: 16 December 2015 Ó Springer Science+Business Media Dordrecht 2015
Abstract Asian yellow pond turtle (Mauremys mutica) is an endangered species, being listed in the IUCN red list of threatened species. In China, most living resources are kept in turtle farms. Insufficient molecular markers have hindered the effective management and artificial breeding programs of this important species. In this study, we discovered and validated 43 novel polymorphic bi-allelic SNP markers for M. mutica from the transcriptome of brain and gonad tissue. The observed and expected heterozygosity ranged from 0.0303 to 0.5758 and 0.0303–0.5072, respectively. These markers would be used in genetic studies helping conservation and management of M. mutica. Keywords Mauremys mutica Asian yellow pond turtle SNP Transcriptome The Asian yellow pond turtle (Mauremys mutica Cantor, 1842) is widely distributed in East and Southeast Asia, mainly in China, Vietnam and Japan (Hendrie 2000; Yasukawa et al. 1996). In China, the turtle was once abundant in history, but now has been listed in the IUCN red list of threatened species as endangered species. Rapid decline of the turtle resources was mainly caused by over exploitation for its high values for food, traditional Chinese & Xinping Zhu [email protected] 1
Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, People’s Republic of China
2
Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 214081, People’s Republic of China
medicine, and ornamentation. Besides over exploitation, low fecundity of the turtle would be another reason, because only four to five siblings could be produced per year for one mature female, rather lower for wild turtles. In China, wild resources of M. mutica are near extinction, and most are conserved in breeding farms. For effective conservation and management, genetic improvement for high fecundity lineage, stable and abundant molecular markers should be developed for pedigree identification and molecular assisted breeding. Zhu et al. (2008) and Zhao et al. (2015) developed RAPD and SSR markers in M. mutica, for population identification and genetic diversity analysis. But single nucleotide polymorphism (SNP) markers, especially gene related SNPs, have not been developed. SNP markers are common in the genome, and some loci directly influence the function, especially in genes. In recent years, SNP markers are more and more widely used in evolutionary studies, molecular assisted breeding, population genetics, and pedigree identification (Cabal et al. 2014; Maccaferri et al. 2015; Zhang et al. 2015). Transcriptome is a proper resource for developing SNPs m
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