ArticleBMC genomics2014
Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio).
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- First development of a 100 K SNP array for small yellow croaker and its application in genomic selection for growth and disease resistance.BMC genomics · 2025Article
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- Decoding the fish genome opens a new era in important trait research and molecular breeding in China.Science China. Life sciences · 2024Review
- Transcriptomic and epigenomic landscapes of muscle growth during the postnatal period of broilers.Journal of animal science and biotechnology · 2024Article
- Genetic improvement and genomic resources of important cyprinid species: status and future perspectives for sustainable production.Frontiers in genetics · 2024Review
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- Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations.Animals : an open access journal from MDPI · 2023Review
- Development and Evaluation of High-Density SNP Arrays for the Eastern Oyster Crassostrea virginica.Marine biotechnology (New York, N.Y.) · 2023Article
- Animal board invited review: Widespread adoption of genetic technologies is key to sustainable expansion of global aquaculture.Animal : an international journal of animal bioscience · 2022Review
- Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus.Scientific reports · 2021Article
- Article
- A High-Density Genetic Linkage Map and Fine Mapping of QTL For Feed Conversion Efficiency in Common Carp (Frontiers in genetics · 2021Article
- Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs.BMC genomics · 2020Article
- Development and Validation of an Open Access SNP Array for Nile Tilapia (G3 (Bethesda, Md.) · 2020Article
- Genome Wide Analysis for Growth at Two Growth Stages in A New Fast-Growing Common Carp Strain (Cyprinus carpio L.).Scientific reports · 2020Article
- Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus).BMC genomics · 2020Article
- Fine Mapping of the High-pH Tolerance and Growth Trait-Related Quantitative Trait Loci (QTLs) and Identification of the Candidate Genes in Pacific White Shrimp (Litopenaeus vannamei).Marine biotechnology (New York, N.Y.) · 2020Article
- An Axiom SNP genotyping array for Douglas-fir.BMC genomics · 2020Article
- Article
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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