Abstract
Schizothorax prenanti (S. prenanti), one of the important endemic commercial fish in China, is mainly distributing in the upstream of the River Yangtze and the tributaries. The wild population is facing serious challenges of germplasm degeneration due to the overfishing, water pollution and construction of hydropower stations; therefore, it is very urgent to develop genetic resource of S. prenanti to protect the wild population. In this study, we used Illumina Hiseq2500 sequencing to develop single nucleotide polymorphism (SNP) markers in S. prenanti. From 37,785 unigenes with functional annotation, 857,535 putative SNPs were identified. Among them, 33 SNPs from immune-related genes were randomly selected and 20 loci exhibited significant polymorphisms in genotyping by Sequenom MassARRAY. As far as our best knowledge, this is the first report about the SNP markers development in S. prenanti based on Illumina RNA sequencing. These SNP markers should not only be useful for population conversation, but also for construction of genetic linkage map and economic performance improvement of S. prenanti.
This is a preview of subscription content, log in via an institution to check access.
References
Ding R (1994) The Fishes of Sichuan. Sichuan Publishing House of Science and Technology, Chengdu
Du Z, Huang X, Wang K et al (2011) Isolation and Identification of Etiology of Skin Ulcer in Schizothorax prenanti. J Sichuan Agric Univ 29:274–279
Gao L, Chen M, Chang Y-Q et al (2013) Development of SNP markers associated with defense mechanism of sea cucumber, Apostichopus japonicas. Conserv Genet Resour 5:587–591. doi:10.1007/s12686-013-9858-z
Geng Y, Wang KY, Huang XL et al (2012) Streptococcus agalactiae, an emerging pathogen for cultured Ya-Fish, Schizothorax prenanti, in China. Transbound Emerg Dis 59:369–375. doi:10.1111/j.1865-1682.2011.01280.x
Jing Y, Dong Y, Yao H et al (2015) Characterization of 87 EST-SNP markers in hard clam Meretrix meretrix using high-resolution melting analysis. Conserv Genet Resour. doi:10.1007/s12686-015-0490-y
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760. doi:10.1093/bioinformatics/btp324
Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. doi:10.1093/bioinformatics/btp352
Liang J, Liu Y, Zhang X et al (2011) An observation of the loss of genetic variability in prenant’s schizothoracin, Schizothorax prenanti, inhabiting a plateau lake. Biochem Syst Ecol 39:361–370. doi:10.1016/j.bse.2011.05.005
McKenna A, Hanna M, Banks E et al (2010) The genome analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303. doi:10.1101/gr.107524.110
Song J, Song Z, Yue B, Zheng W (2006) Assessing genetic diversity of wild populations of Prenant’s schizothoracin, Schizothorax prenanti, using AFLP markers. Environ Biol Fishes 77:79–86. doi:10.1007/s10641-006-9056-x
Thomas PD, Kejariwal A (2004) Coding single-nucleotide polymorphisms associated with complex vs. Mendelian disease: evolutionary evidence for differences in molecular effects. Proc Natl Acad Sci 101:15398–15403. doi:10.1073/pnas.0404380101
Vignal A, Milan D, SanCristobal M, Eggen A (2002) A review on SNP and other types of molecular markers and their use in animal genetics. Genet Sel Evol 34:275–305. doi:10.1051/gse:2002009
Wang L, Huang SQ, Xia JH et al (2015a) Genome-wide discovery of gene-related SNPs in Barramundi Lates calcarifer. Conserv Genet Resour 7:605–608. doi:10.1007/s12686-015-0444-4
Wang P, Xiao S, Han Z, Wang Z (2015b) SNP discovery in large yellow croaker (Larimichthys crocea) using Roche 454 pyrosequencing sequencing platform. Conserv Genet Resour. doi:10.1007/s12686-015-0481-z
Wu Y, Wu C (1992) The Fishes of the Qinghai-Xizang Plateau. Sichuan Publishing House of Science and Technology, Chengdu
Wu J, Hou F, Liang J et al (2013a) Development of ten microsatellite DNA markers in a hexaploid fish, Schizothorax prenanti (Tchang). Conserv Genet Resour 5:545–547. doi:10.1007/s12686-012-9848-6
Wu J, Hou F, Wang Y et al (2013b) Isolation and characterization of twenty tetranucleotide microsatellite DNA makers in a schizothoracin fish, Schizothorax prenanti (Tchang). Conserv Genet Resour 5:891–894. doi:10.1007/s12686-013-9926-4
Yeh F, Yang R, Boyle T et al (2000) POPGENE 32, microsoft windows-based freeware for popllation genetic analysis, molecllar biology and biotechnology centre. University of Alberta, Edmonton
Zhang M, Nie J, Shen Y et al (2015a) Isolation and characterization of 25 novel EST-SNP markers in grass carp (Ctenopharyngodon idella). Conserv Genet Resour. doi:10.1007/s12686-015-0491-x
Zhang X, Gao X, Wang J, Cao W (2015b) Extinction risk and conservation priority analyses for 64 endemic fishes in the Upper Yangtze River, China. Environ Biol Fishes 98:261–272. doi:10.1007/s10641-014-0257-4
Acknowledgments
This research was supported by the National Natural Science Foundation of China (31402302, U1205122, 31300457), Scientific Research Fund of Hunan Provincial Education Department (15A087), Fundamental Research Funds for the Central Universities (XDJK2015C034, XDJK2014C152), and the project Supported by Scientific research initiation project aided by special Fund, Southwest university Rongchang campus (20700208).
Author information
Authors and Affiliations
Corresponding authors
Additional information
Hui Luo, Hua Ye, and Shi-jun Xiao have contributed equally to this work.
Rights and permissions
About this article
Cite this article
Luo, H., Ye, H., Xiao, Sj. et al. Development of SNP markers associated with immune-related genes of Schizothorax prenanti . Conservation Genet Resour 8, 223–226 (2016). https://doi.org/10.1007/s12686-016-0539-6
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12686-016-0539-6