Abstract
BackgroundSingle nucleotide polymorphisms (SNPs) have been used as genetic marker for genome-wide association studies in many species. Gene-associated SNPs could offer sufficient coverage in trait related research and further more could themselves be causative SNPs for traits. Common carp (Cyprinus carpio) is one of the most important aquaculture species in the world accounting for nearly 14% of freshwater aquaculture production. There are various strains of common carp with different economic traits, however, the genetic mechanism underlying the different traits have not been elucidated yet. In this project, we identified a large number of gene-associated SNPs from four strains of common carp using next-generation sequencing.ResultsTranscriptome sequencing of four strains of common carp (mirror carp, purse red carp, Xingguo red carp, Yellow River carp) was performed with Solexa HiSeq2000 platform. De novo assembled transcriptome was used as reference for alignments, and SNP calling was done through BWA and SAMtools. A total of 712,042 Intra-strain SNPs were discovered in four strains, of which 483,276 SNPs for mirror carp, 486,629 SNPs for purse red carp, 478,028 SNPs for Xingguo red carp and 488,281 SNPs for Yellow River carp were discovered, respectively. Besides, 53,893 inter-SNPs were identified. Strain-specific SNPs of four strains were 53,938, 53,866, 48,701, 40,131 in mirror carp, purse red carp, Xingguo red carp and Yellow River carp, respectively. GO and KEGG pathway analysis were done to reveal strain-specific genes affected by strain-specific non-synonymous SNPs. Validation of selected SNPs revealed that 48% percent of SNPs (12 of 25) were tested to be true SNPs.ConclusionsTranscriptome analysis of common carp using RNA-Seq is a cost-effective way of generating numerous reads for SNP discovery. After validation of identified SNPs, these data will provide a solid base for SNP array designing and genome-wide association studies.
Highlights
Common carp (Cyprinus carpio) is a widespread freshwater fish of eutrophic waters in lakes and large rivers in Europe and Asia
Due to the economical and ecological importance of common carp, genetic and genomic studies had been performed in the past decade, which focused on development of genetic markers [2,3,4,5,6] for breeding and genetic evaluation, construction of genetic maps [7,8] and physical map [9], collection of a large set of Expression Sequence Tags (ESTs) [10,11,12] and microRNA [1,13], construction of bacterial artificial chromosome (BAC) library [14] and collection BAC-end sequences (BES) [15], EST collection and transcriptome study [16], characterization of functional genes [17] and quantitative trait loci (QTL) analysis [18,19], etc
The cDNAs were sequenced on Illumina HiSeq2000 platform that generated 114.9 million pairedend reads for mirror carp, 111.4 million for purse red carp, 112.2 million for Xingguo red carp, 105.4 million for Yellow River carp with read length of 50 bp (Table 1)
Summary
Common carp (Cyprinus carpio) is a widespread freshwater fish of eutrophic waters in lakes and large rivers in Europe and Asia. Common carp and its closely related Cyprinidae species provide over 30% aquaculture production in the world [1]. Common carp (Cyprinus carpio) is one of the most important aquaculture species in the world accounting for nearly 14% of freshwater aquaculture production. There are various strains of common carp with different economic traits, the genetic mechanism underlying the different traits have not been elucidated yet. In this project, we identified a large number of gene-associated SNPs from four strains of common carp using next-generation sequencing
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