SNP discovery in spotted halibut ( Verasper variegatus ) using restriction site-associated DNA sequencing(RAD-seq)
- PDF / 778,961 Bytes
- 5 Pages / 595.276 x 790.866 pts Page_size
- 101 Downloads / 163 Views
TECHNICAL NOTE
SNP discovery in spotted halibut (Verasper variegatus) using restriction site-associated DNA sequencing(RAD-seq) Li Bian1 · Changlin Liu1 · Gang Liu2 · Siqing Chen1 · Lele Zhang1,3 · Jianlong Ge1 · Fenghui Li1 · Jie Tan1
Received: 17 July 2017 / Accepted: 9 August 2017 © Springer Science+Business Media B.V. 2017
Abstract The spotted halibut (Verasper variegatus) is an important economic marine flatfish species in China and Japan. However, the wild population of V. variegatus has suffered a drastic decline in recent years. We implemented restriction site-associated DNA sequencing(RAD-seq) to develop SNP markers from 36 individuals. In total, 100 high quality SNPs were obtained after a stringent SNP filter process. The minor allele frequency of these SNPs ranged from 0.0455 to 0.5000. The range of observed heterozygosity and expected heterozygosity were from 0.0909 to 1.0000 and from 0.0881 to 0.5077, respectively. The inbreeding coefficient varied from −1.000 to 0.220. Among these SNPs, 16 loci deviated significantly from Hardy–Weinberg equilibrium after Bonferroni correction. These novel SNP markers will serve as a valuable tool for future population and conservation genetics studies for this species. Keywords SNP · Verasper variegatus · RAD-seq · Conservation genetics
Electronic supplementary material The online version of this article (doi:10.1007/s12686-017-0837-7) contains supplementary material, which is available to authorized users. * Siqing Chen [email protected] 1
Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
2
Huangdao Ocean and Fisheries Administration, Qingdao 266400, China
3
College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
Spotted halibut (Verasper variegatus) belongs to the family Pleuronectidae and mainly inhabits coastal areas around northwestern Pacific (Chen et al. 1992; Minami and Tanaka 1992). It is an important economic marine flatfish species in China and Japan with high market price (Wada et al. 2012; Ge et al. 2017). However, due to overfishing and ocean environment deterioration, the wild population of V. variegatus has declined drastically over the past 40 years (Wada et al. 2012). On the other hand, V. variegatus has recently become a promising aquaculture marine species in China with the breakthrough of its large-scale artificial breeding technology. The intensive culture and limited natural broodstock supply would cause great loss in genetic diversity. Development of reliable molecular markers is crucial to evaluate the genetic diversity and to conduct better conservation protection for this valuable marine species. Several kinds of molecular markers including random amplified polymorphic DNA (RAPD), amplified fragment length polymorphisms (AFLP) and microsatellite markers (SSR) have been developed to investigate the genetic diversity and population structure
Data Loading...
