Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio)

Chuankun Zhu,Lei Cheng,Jingou Tong,Xiaomu Yu

doi:10.3390/ijms13067343

Abstract

The common carp (Cyprinus carpio) is an important aquaculture fish worldwide but only limited single nucleotide polymorphism (SNP) markers are characterized from expressed sequence tags (ESTs) in this species. In this study, 1487 putative SNPs were bioinformatically mined from 14,066 online ESTs mainly from the European common carp, with the occurrence rate of about one SNP every 173 bp. One hundred and twenty-one of these SNPs were selected for validation using PCR fragment sequencing, and 48 out of 81 primers could amplify the expected fragments in the Chinese common carp genome. Only 26 (21.5%) putative SNPs were validated, however, 508 new SNPs and 68 indels were identified. The ratios of transitions to transversions were 1.77 for exon SNPs and 1.05 for intron SNPs. All the 23 SNPs selected for population tests were polymorphic, with the observed heterozygosity (Ho) ranging from 0.053 to 0.526 (mean 0.262), polymorphism information content (PIC) from 0.095 to 0.357 (mean 0.246), and 21 SNPs were in Hardy–Weinberg equilibrium. These results suggest that different common carp populations with geographic isolation have significant genetic variation at the SNP level, and these new EST-SNP markers are readily available for genetics and breeding studies in common carp.

Highlights

The common carp (Cyprinus carpio) is an important freshwater species for aquaculture and has been domesticated for ca. 4000 years [1]
After the additional filtering criterion was applied, a total of 1487 putative single nucleotide polymorphism (SNP) were obtained from 303 contigs, with an average frequency of one SNP per 173 bp of contig sequence, which was greater than frequencies reported in Atlantic salmon [10], brown trout [14] and Pacific salmon
A total 1487 putative SNPs were identified by mining from online common carp expressed sequence tags (ESTs) sequences

Summary

Introduction

The common carp (Cyprinus carpio) is an important freshwater species for aquaculture and has been domesticated for ca. 4000 years [1]. Single nucleotide polymorphisms (SNPs) are more promising molecular markers in genetics, genomics and aquaculture. Because of their high abundance in the genome, hereditable stability and allele portability, and the possibility for high-throughput analysis, they may replace traditional molecular markers in genetic studies [6,7]. EST-database mining is an efficient way to obtain SNP markers and was first applied for SNP discovery in human sequences [8], EST-SNPs were obtained in many fish species [9,10,11,12], while to date only limited EST-SNPs have been characterized [13] in common carp. Discovery of a set of EST-SNPs from online common carp EST databases and validation of selected EST-SNPs in the Chinese common carp were carried out, with the aims of (1) developing novel SNP resources for future studies of genetics and breeding in common carp; (2) validating and characterizing SNPs in common carp with different genetic backgrounds for the comparison of genetic variations

Results and Discussion

Detection and Annotation of Putative SNPs

Validation and Characterization of SNPs

Data Analysis

Conclusions