Genome-wide SNP discovery from transcriptome of four common carp strains

PLoS One. 2012;7(10):e48140. doi: 10.1371/journal.pone.0048140. Epub 2012 Oct 26.


Background: Single 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.

Results: Transcriptome 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.

Conclusions: Transcriptome 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Carps / genetics*
  • Genome / genetics*
  • Genome-Wide Association Study
  • Polymorphism, Single Nucleotide / genetics*
  • Transcriptome / genetics*

Grant support

This study was supported by the grants from National Department Public Benefit Research Foundation (200903045), National High-tech R&D Program of China (2009AA10Z105 and 2011AA100401), China Ministry of Agriculture “948” Program (2010-Z11) and National Natural Science Foundation (31101893). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.