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Open Access Research article

Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio)

Jian Xu1, Zixia Zhao1, Xiaofeng Zhang2, Xianhu Zheng2, Jiongtang Li1, Yanliang Jiang1, Youyi Kuang2, Yan Zhang1, Jianxin Feng3, Chuangju Li4, Juhua Yu5, Qiang Li1, Yuanyuan Zhu1, Yuanyuan Liu1, Peng Xu16* and Xiaowen Sun12*

Author Affiliations

1 Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China

2 Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China

3 Henan Academy of Fishery Sciences, Zhengzhou, Henan 450044, China

4 Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China

5 Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 430223, China

6 Visiting Professor Department of Zoology, College of Science, King Saud University, P. O. Box 24555, Riyadh 11451, Saudi Arabia

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BMC Genomics 2014, 15:307  doi:10.1186/1471-2164-15-307

Published: 24 April 2014

Abstract

Background

A large number of single nucleotide polymorphisms (SNPs) have been identified in common carp (Cyprinus carpio) but, as yet, no high-throughput genotyping platform is available for this species. C. carpio is an important aquaculture species that accounts for nearly 14% of freshwater aquaculture production worldwide. We have developed an array for C. carpio with 250,000 SNPs and evaluated its performance using samples from various strains of C. carpio.

Results

The SNPs used on the array were selected from two resources: the transcribed sequences from RNA-seq data of four strains of C. carpio, and the genome re-sequencing data of five strains of C. carpio. The 250,000 SNPs on the resulting array are distributed evenly across the reference C.carpio genome with an average spacing of 6.6 kb. To evaluate the SNP array, 1,072 C. carpio samples were collected and tested. Of the 250,000 SNPs on the array, 185,150 (74.06%) were found to be polymorphic sites. Genotyping accuracy was checked using genotyping data from a group of full-siblings and their parents, and over 99.8% of the qualified SNPs were found to be reliable. Analysis of the linkage disequilibrium on all samples and on three domestic C.carpio strains revealed that the latter had the longer haplotype blocks. We also evaluated our SNP array on 80 samples from eight species related to C. carpio, with from 53,526 to 71,984 polymorphic SNPs. An identity by state analysis divided all the samples into three clusters; most of the C. carpio strains formed the largest cluster.

Conclusions

The Carp SNP array described here is the first high-throughput genotyping platform for C. carpio. Our evaluation of this array indicates that it will be valuable for farmed carp and for genetic and population biology studies in C. carpio and related species.

Keywords:
SNP array; Affymetrix; Re-sequencing; Linkage disequilibrium; Identity by state; Cyprinus carpio; Common carp; Cyprinidae