Genome-Wide SNP Discovery from Transcriptome of Four Common Carp Strains

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Abstract

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.

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Most cited references 26

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A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers

Thomas Moen, Ben J. Hayes, Matthew Baranski … (2008)

Background The Atlantic salmon is a species of commercial and ecological significance. Like other salmonids, the species displays residual tetrasomy and a large difference in recombination rate between sexes. Linkage maps with full genome coverage, containing both type I and type II markers, are needed for progress in genomics. Furthermore, it is important to estimate levels of linkage disequilibrium (LD) in the species. In this study, we developed several hundred single nucleotide polymorphism (SNP) markers for the Atlantic salmon, and constructed male and female linkage maps containing SNP and microsatellite markers. We also investigated further the distribution of male and female recombination events across the genome, and estimated levels of LD between pairs of markers. Results The male map had 29 linkage groups and was 390 cM long. The female map had 30 linkage groups as was 1983 cM long. In total, the maps contained 138 microsatellite markers and 304 SNPs located within genes, most of which were successfully annotated. The ratio of male to female recombination events was either close to zero or very large, indicating that there is little overlap between regions in which male and female crossovers occur. The female map is likely to have close to full genome coverage, while the majority of male linkage groups probably lack markers in telomeric regions where male recombination events occur. Levels of r2 increased with decreasing inter-marker distance in a bimodal fashion; increasing slowly from ~60 cM, and more rapidly more from ~12 cM. Long-ranging LD may be consequence of recent admixture in the population, the population being a 'synthetic' breeding population with contributions from several distinct rivers. Levels of r2 dropped to half its maximum value (above baseline) within 15 cM, and were higher than 0.2 above baseline for unlinked markers ('useful LD') at inter-marker distances less than 5 cM. Conclusion The linkage map presented here is an important resource for genetic, comparative, and physical mapping of the Atlantic salmon. The female map is likely to have a map coverage that is not far from complete, whereas the male map length is likely to be significantly shorter than the true map, due to suboptimal marker coverage in the apparently small physical regions where male crossovers occur. 'Useful LD' was found at inter-marker distances less than 5 cM.

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Genome-wide association study of growth in crossbred beef cattle.

T Sonstegard, T McDaneld, R Thallman … (2010)

Chromosomal regions harboring variation affecting cattle birth weight and BW gain to 1 yr of age were identified by marker association using the highly parallel BovineSNP50 BeadChip (50K) assay composed of 54,001 individual SNP. Genotypes were obtained from progeny (F(1); 590 steers) and 2-, 3-, and 4-breed cross grandprogeny (F(1)(2) = F(1) x F(1); 1,306 steers and 707 females) of 150 AI sires representing 7 breeds (22 sires per breed; Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental). Genotypes and birth, weaning, and yearling BW records were used in whole-genome association analyses to estimate effects of individual SNP on growth. Traits analyzed included growth component traits: birth weight (BWT), 205-d adjusted birth to weaning BW gain (WG), 160-d adjusted postweaning BW gain (PWG); cumulative traits: 205-d adjusted weaning weight (WW = BWT + WG) and 365-d adjusted yearling weight (YW = BWT + WG + PWG); and indexes of relative differences between postnatal growth and birth weight. Modeled fixed effects included additive effects of calf and dam SNP genotype, year-sex-management contemporary groups, and covariates for calf and dam breed composition and heterosis. Direct and maternal additive polygenic effects and maternal permanent environment effects were random. Missing genotypes, including 50K genotypes of most dams, were approximated with a single-locus BLUP procedure from pedigree relationships and known 50K genotypes. Various association criteria were applied: stringent tests to account for multiple testing but with limited power to detect associations with small effects, and relaxed nominal P that may detect SNP associated with small effects but include excessive false positive associations. Genomic locations of the 231 SNP meeting stringent criteria generally coincided with described previously QTL affecting growth traits. The 12,425 SNP satisfying relaxed tests were located throughout the genome. Most SNP associated with BWT and postnatal growth affected components in the same direction, although detection of SNP associated with one component independent of others presents a possible opportunity for SNP-assisted selection to increase postnatal growth relative to BWT.

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Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array

Shikai Liu, Zunchun Zhou, Jianguo Lu … (2011)

Background Single nucleotide polymorphisms (SNPs) have become the marker of choice for genome-wide association studies. In order to provide the best genome coverage for the analysis of performance and production traits, a large number of relatively evenly distributed SNPs are needed. Gene-associated SNPs may fulfill these requirements of large numbers and genome wide distribution. In addition, gene-associated SNPs could themselves be causative SNPs for traits. The objective of this project was to identify large numbers of gene-associated SNPs using high-throughput next generation sequencing. Results Transcriptome sequencing was conducted for channel catfish and blue catfish using Illumina next generation sequencing technology. Approximately 220 million reads (15.6 Gb) for channel catfish and 280 million reads (19.6 Gb) for blue catfish were obtained by sequencing gene transcripts derived from various tissues of multiple individuals from a diverse genetic background. A total of over 35 billion base pairs of expressed short read sequences were generated. Over two million putative SNPs were identified from channel catfish and almost 2.5 million putative SNPs were identified from blue catfish. Of these putative SNPs, a set of filtered SNPs were identified including 342,104 intra-specific SNPs for channel catfish, 366,269 intra-specific SNPs for blue catfish, and 420,727 inter-specific SNPs between channel catfish and blue catfish. These filtered SNPs are distributed within 16,562 unique genes in channel catfish and 17,423 unique genes in blue catfish. Conclusions For aquaculture species, transcriptome analysis of pooled RNA samples from multiple individuals using Illumina sequencing technology is both technically efficient and cost-effective for generating expressed sequences. Such an approach is most effective when coupled to existing EST resources generated using traditional sequencing approaches because the reference ESTs facilitate effective assembly of the expressed short reads. When multiple individuals with different genetic backgrounds are used, RNA-Seq is very effective for the identification of SNPs. The SNPs identified in this report will provide a much needed resource for genetic studies in catfish and will contribute to the development of a high-density SNP array. Validation and testing of these SNPs using SNP arrays will form the material basis for genome association studies and whole genome-based selection in catfish.

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Author and article information

Contributors

Zhanjiang Liu: Role: Editor

Journal

Journal ID (nlm-ta): PLoS One

Journal ID (iso-abbrev): PLoS ONE

Journal ID (publisher-id): plos

Journal ID (pmc): plosone

Title: PLoS ONE

Publisher: Public Library of Science (San Francisco, USA )

ISSN (Electronic): 1932-6203

Publication date Collection: 2012

Publication date (Electronic): 26 October 2012

Volume: 7

Issue: 10

Electronic Location Identifier: e48140

Affiliations

[1 ]Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, People’s Republic of China

[2 ]Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, People’s Republic of China

[3 ]Henan Academy of Fishery Sciences, Zhengzhou, Henan, People’s Republic of China

[4 ]National Fish Hatchery of Xingguo Red Carp, Xingguo, Jiangxi, People’s Republic of China

Auburn University, United States of America

Author notes

* E-mail: xupeng@ 123456cafs.ac.cn (PX); sunxw2002@ 123456163.com (XS)

Competing Interests: The authors have declared that no competing interests exist.

Conceived and designed the experiments: PX XS. Performed the experiments: JX PJ ZZ YZ JL XZ LZ JW. Analyzed the data: JX PJ. Contributed reagents/materials/analysis tools: JF GL. Wrote the paper: JX PX.

Article

Publisher ID: PONE-D-12-20023

DOI: 10.1371/journal.pone.0048140

PMC ID: 3482183

PubMed ID: 23110192

SO-VID: 1fd280a6-7f47-4858-926d-aa54e0bf1b15

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

History

Date received : 7 July 2012

Date accepted : 20 September 2012

Page count

Pages: 10

Funding

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.

Genome-Wide SNP Discovery from Transcriptome of Four Common Carp Strains

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Most cited references 26

A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers

Genome-wide association study of growth in crossbred beef cattle.

Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array

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