Isolation and characterization of 33 EST-SNP markers in Schizothorax prenanti
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TECHNICAL NOTE
Isolation and characterization of 33 EST-SNP markers in Schizothorax prenanti Jian Zhou1 · Bo Zhou1 · Qiang Li1 · Lu Zhang1 · Jun Du1 · Hua Ye2
Received: 15 June 2017 / Accepted: 22 June 2017 © Springer Science+Business Media B.V. 2017
Abstract Prenant’s schizothoracin, Schizothorax prenanti (Tchang), is one of the most important cold-water economic fish species in China. In this study, we reported the isolation and characterization of 33 SNP markers among 30 individuals from one cultured population. The observed and expected heterozygosities ranged from 0.0312 to 0.8438 and 0.0312 to 0.5079, respectively. Polymorphic information content ranged from 0.0302 to 0.3747. Significant deviation from HWE was observed for 5 loci and no significant linkage disequilibrium was found between pairs of loci. These EST-SNP markers are potentially useful for the study of population genetics, construction of genetic linkage and QTL maps in S. prenanti. Keywords Schizothorax prenanti · Single nucleotide polymorphism (SNPs) · Population diversity Prenant’s schizothoracin, Schizothorax prenanti (Tchang), is one of the most important cold-water economic fish species in China (Ding 1994). The wild population is facing serious challenges of germplasm degeneration due to water pollution, overfishing and construction of hydropower stations (Song et al. 2006; Liang et al. 2011; Zhang et al. 2015b). Therefore, it is very urgent to perform * Jun Du [email protected] * Hua Ye [email protected] 1
Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China
2
Fisheries Breeding and Healthy Cultivation Research Centre, Southwest University, Chongqing 402460, China
population genetic research on S. prenanti to protect the wild resources. However, only few studies have reported the population structure using mitochondrial DNA, AFLP and microsatellites of S. prenanti (Song et al. 2006, 2008; Wu et al. 2013a, b). Single-nucleotide polymorphisms (SNPs) are very powerful genetic markers because of their co-dominance, abundant genetic variations and wide genomic distribution (Vignal et al. 2002), so they have gradually become the primary choice for studies of population structure and applications to fishery management (Wang et al. 2015). In recent years, SNPs have been used in the development and protection of genetic resources in various aquacultural species, such as Crassostrea gigas (Kong et al. 2014), Larimichthys crocea (Jiang et al. 2015), Ctenopharyngodon idella (Zhang et al. 2015a), and Oncorhynchus keta (Small et al. 2015). So, there is an obvious need for more SNPs of S. prenanti for intensive study on the resource management and genetic mapping. One cultured S. prenanti population with 30 individuals collected from Emeishan in Sichuan province of China, was selected for analysis the characterization of SNP markers. Fin clip of each fish was collected to extract DNA according to the standard phenol–chloroform technique described by Sambrook (Sambrook et al. 1989). We mined candidate SNPs f
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