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

Abstract

BackgroundA 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.ResultsThe 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.ConclusionsThe 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.

De novo assembly and characterization of the spleen transcriptome of common carp (Cyprinus carpio) using Illumina paired-end sequencing

“…Due to the economical importance of common carp, research on different aspects of disease resistance in this species has been a focus for quite some time. Among them, genetic studies of common carp in the past decade have mainly focused on the development of genetic markers for breeding and genetic evaluation [22,23], based upon genome sequences [24], transcriptome profiles [16], and construction of genetic and physical maps [25,26]. However, immunogenetic studies are lacking in comparison to the genetic studies of common carp, accounting for only a few published reports [27e31].…”

Genome-Wide Association Study for Muscle Fat Content and Abdominal Fat Traits in Common Carp (Cyprinus carpio)

“…Significant progress has been made in developing common carp genomic tools in recent years. A greater amount of genomic resources is available for common carp research, such as a medium-density [1] and three high-density [2–4] genetic linkage maps, BAC libraries [5,6] and physical maps [7], and high-throughput genotyping chips [8]. Furthermore, the common carp genome has been sequenced and assembled [9], which provides important reference for genomic and comparative genomic researches of Cyprinidae fish and other species.…”

“…Many studies have been conducted to explore the genetic mechanism of various complex diseases and economic traits [27]. The recent development of high-throughput SNP genotyping array [8] facilitates GWAS analysis and identification of linked SNPs affecting phenotypic traits of interest in this species. In the present study, a GWAS was conducted for muscle fat content and abdominal traits in common carp derived from an F 2 family using the high-density SNP chips (250 K) to detect potential SNPs and candidate genes.…”

Genome Wide Identification, Phylogeny, and Expression of Aquaporin Genes in Common Carp (Cyprinus carpio)

“…It is an important economic and model species for various studies on ecology, environmental toxicology, developmental biology, nutrition, physiology, immunology, and evolutionary genomics. Therefore, significant genome resources have been developed in the past decade, including vast amount of genetic markers [7–10], genetic maps [11–13], BAC libraries and physical maps [14–16], expressed sequence tags (ESTs) [17], and transcriptome sequences [8, 18]. Recently, the common carp genome has been completely sequenced and assembled [19].…”