Development of the catfish 250K SNP array for genome-wide association studies

Liu, Shikai; Sun, Luyang; Li, Yun; Sun, Fenyong; Jiang, Yanliang; Zhang, Yu; Zhang, Jiaren; Feng, Jianbin; Kaltenboeck, Ludmilla; Kucuktas, Huseyin; Liu, Zhanjiang

doi:10.1186/1756-0500-7-135

Cited by 91 publications

(58 citation statements)

References 40 publications

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“…Compared to the catfish 250 K SNP array30, the 690 K array has significantly more markers, more even genomic distribution, higher qualities of SNPs based on p-convert values, greater level of polymorphic contents, and greater level of coverage for the whole genome. The final set SNPs on the array consisted of channel catfish specific, blue catfish specific, and inter-species SNPs.…”

Section: Discussionmentioning

confidence: 99%

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Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence

Zeng

et al. 2017

Sci Rep

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Single nucleotide polymorphisms (SNPs) are capable of providing the highest level of genome coverage for genomic and genetic analysis because of their abundance and relatively even distribution in the genome. Such a capacity, however, cannot be achieved without an efficient genotyping platform such as SNP arrays. In this work, we developed a high-density SNP array with 690,662 unique SNPs (herein 690 K array) that were relatively evenly distributed across the entire genome, and covered 98.6% of the reference genome sequence. Here we also report linkage mapping using the 690 K array, which allowed mapping of over 250,000 SNPs on the linkage map, the highest marker density among all the constructed linkage maps. These markers were mapped to 29 linkage groups (LGs) with 30,591 unique marker positions. This linkage map anchored 1,602 scaffolds of the reference genome sequence to LGs, accounting for over 97% of the total genome assembly. A total of 1,007 previously unmapped scaffolds were placed to LGs, allowing validation and in few instances correction of the reference genome sequence assembly. This linkage map should serve as a valuable resource for various genetic and genomic analyses, especially for GWAS and QTL mapping for genes associated with economically important traits.

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Section: Discussionmentioning

confidence: 99%

“…Recently, we developed the catfish 250 K SNP array using Affymetrix axiom technology30. This array has been of great use for various genetic analysis including genetic linkage mapping2628 and analysis of performance traits using GWAS313233.…”

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confidence: 99%

Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence

Zeng

et al. 2017

Sci Rep

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“…Affymetrix probe sets are classified into six categories (Table 2) by the Affymetrix Axiom software based on quality control metrics; the SNP clustering properties for each of the six categories is graphically illustrated in Liu et al [8]. A SNP is (1) “PolyHighResolution” if three good resolution clusters (i.e., homozygous wild, heterozygous, homozygous individuals) are formed; (2) “NoMinorHom” if only two clusters are formed with no genotype for one homozygous individual; (3) “MonoHighResolution” if the called genotypes are all monomorphic; (4) “Off-target variants”, if three clusters are formed, but with one additional off-target cluster due to sequence dissimilarity between the probes and the target genome regions; (5) “CallRateBelowThreshold” if the call rate of the SNP is below the call rate threshold but the cluster properties are above the threshold, and (6) “Other” if more than one of the cluster properties are below the threshold.…”

Section: Discussionmentioning

confidence: 99%

Inter- and intra-reproducibility of genotypes from sheep technical replicates on Illumina and Affymetrix platforms

Berry

O’Brien

Wall³

et al. 2016

Genet Sel Evol

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BackgroundAccurate genomic analyses are predicated upon access to accurate genotype input data. The objective of this study was to quantify the reproducibility of genotype data that are generated from the same genotype platform and from different genotyping platforms.MethodsGenotypes based on 51,121 single nucleotide polymorphisms (SNPs) for 84 animals that were each genotyped on Illumina and Affymetrix platforms and for another 25 animals that were each genotyped twice on the same Illumina platform were compared. Genotypes based on 11,323 SNPs for an additional 21 animals that were genotyped on two different Illumina platforms by two different service providers were also compared. Reproducibility of the results was measured as the correlation between allele counts and as genotype and allele concordance rates.ResultsA mean within-animal correlation of 0.9996 was found between allele counts in the 25 duplicate samples that were genotyped on the same Illumina platform and varied from 0.9963 to 1.0000 per animal. The mean (minimum, maximum) genotype and allele concordance rates per animal between the 25 duplicate samples were equal to 0.9996 (0.9968, 1.0000) and 0.9993 (0.9937, 1.0000), respectively. The concordance rate between the two different Illumina platforms was also near 1. A mean within-animal correlation of 0.9738 was found between genotypes that were generated on the Illumina and Affymetrix platforms and varied from 0.9505 to 0.9812 per animal. The mean (minimum, maximum) within-animal genotype and allele concordance rates between the Illumina and Affymetrix platforms were equal to 0.9711 (0.9418, 0.9798) and 0.9845 (0.9695, 0.9889), respectively. The genotype concordance rate across all genotypes increased from 0.9711 to 0.9949 when the SNPs used were restricted to those with three high-resolution genotype clusters which represented 75.2% of the called genotypes.Conclusions and implicationsOur results suggest that, regardless of the genotype platform or service provider, high genotype concordance rates are achieved especially if they are restricted to high-quality extracted DNA and SNPs that result in high-quality genotypes.

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“…; channel catfish, Ictalurus punctatus , Liu et al . ; common carp, Cyprinus carpio , Xu et al . ; rainbow trout, Oncorhynchus mykiss , Palti et al .…”

Section: Introductionmentioning

confidence: 99%

Applications of genotyping by sequencing in aquaculture breeding and genetics

Robledo

Palaiokostas

Bargelloni

et al. 2017

Reviews in Aquaculture

217

172

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Selective breeding is increasingly recognized as a key component of sustainable production of aquaculture species. The uptake of genomic technology in aquaculture breeding has traditionally lagged behind terrestrial farmed animals. However, the rapid development and application of sequencing technologies has allowed aquaculture to narrow the gap, leading to substantial genomic resources for all major aquaculture species. While high‐density single‐nucleotide polymorphism (SNP) arrays for some species have been developed recently, direct genotyping by sequencing (GBS) techniques have underpinned many of the advances in aquaculture genetics and breeding to date. In particular, restriction‐site associated DNA sequencing (RAD‐Seq) and subsequent variations have been extensively applied to generate population‐level SNP genotype data. These GBS techniques are not dependent on prior genomic information such as a reference genome assembly for the species of interest. As such, they have been widely utilized by researchers and companies focussing on nonmodel aquaculture species with relatively small research communities. Applications of RAD‐Seq techniques have included generation of genetic linkage maps, performing genome‐wide association studies, improvements of reference genome assemblies and, more recently, genomic selection for traits of interest to aquaculture like growth, sex determination or disease resistance. In this review, we briefly discuss the history of GBS, the nuances of the various GBS techniques, bioinformatics approaches and application of these techniques to various aquaculture species.

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Development of the catfish 250K SNP array for genome-wide association studies

Cited by 91 publications

References 40 publications

Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence

Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence

Inter- and intra-reproducibility of genotypes from sheep technical replicates on Illumina and Affymetrix platforms

Applications of genotyping by sequencing in aquaculture breeding and genetics

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