Design and characterization of a 52K SNP chip for goats - PubMed (original) (raw)

. 2014 Jan 22;9(1):e86227.

doi: 10.1371/journal.pone.0086227. eCollection 2014.

Philippe Bardou 2, Olivier Bouchez 3, Cédric Cabau 2, Richard Crooijmans 4, Yang Dong 5, Cécile Donnadieu-Tonon 3, André Eggen 6, Henri C M Heuven 7, Saadiah Jamli 8, Abdullah Johari Jiken 8, Christophe Klopp 9, Cynthia T Lawley 6, John McEwan 10, Patrice Martin 11, Carole R Moreno 12, Philippe Mulsant 1, Ibouniyamine Nabihoudine 2, Eric Pailhoux 13, Isabelle Palhière 12, Rachel Rupp 12, Julien Sarry 1, Brian L Sayre 14, Aurélie Tircazes 12, Jun Wang 15, Wen Wang 16, Wenguang Zhang 17; International Goat Genome Consortium

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Design and characterization of a 52K SNP chip for goats

Gwenola Tosser-Klopp et al. PLoS One. 2014.

Erratum in

Abstract

The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50-60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.

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Conflict of interest statement

Competing Interests: André Eggen and Cynthia T. Lawley are employees of Illumina, Inc. This work led to the development of a goat 50K SNP chip, sold by Illumina to any customer. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials.

Figures

Figure 1

Figure 1. Goat Genome scaffolds assembly.

The goat genome scaffolds were sorted by decreasing size (x-axis) and the cumulative proportion of the assembled genome was plotted on the y-axis for all the scaffolds. The vertical line shows that >10kb scaffolds represent 97.2% of the assembled goat genome.

Figure 2

Figure 2. SNP spacing on the goat scaffolds.

Spacing between the selected SNPs was calculated and the percentage of gaps (total number of gaps is 59,030 on goat scaffolds and 62,693 on UMD3.1 cattle assembly) is shown (y-axis) in each 5kb class ranging from 5 to 150kb (x-axis).

Figure 3

Figure 3. SNPs by category in final design.

The number of selected SNPs is indicated for each of the following categories. 1: SNP detected in an EST. 2: two alleles detected in the five considered breeds. 3: two alleles detected in Alpine and Saanen and Creole and (Boer or Savanna). 4: two alleles detected in two of the three milk and mixed breeds (Alpine, Saanen, Creole) and in Boer and Savanna. 5: two alleles detected in Alpine and Saanen and Creole. 6: two alleles detected in three out of the five breeds. 10: two alleles detected in each of the two milk breeds (Saanen and Alpine). 11: two alleles detected in one milk breed (Saanen or Alpine) and one meat breed (Creole or Boer or Katjang/Savanna). 12: two alleles detected in at least two meat breeds (Creole and Boer or Katjang/Savanna). 13: two alleles detected in one milk breed (Saanen or Alpine).

Figure 4

Figure 4. Distribution of estimated MAFs of the selected SNPs.

The MAF for all the 60,000 selected SNPs was estimated based on the read counts for the two alleles.

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Grants were funded by ANR (http://www.agence-nationale-recherche.fr/), ANR-09-GENM-009-03 GENIDOV, CHEST-454, funded by APIS-GENE; CAPRISNIP programme: UNCEIA, CAPGENES and APIS-GENE French Breeding organizations; and EC’s Seventh Framework Programme, 3SR Integrated Project(Sustainable Solutions for Small Ruminants) http://www.3srbreeding.eu). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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