The Goat_IGGC_HTS_v3 chip is now available in 2 formats: HTS and XT.

384 samples have been genotyped to generate a cluster file. The .egt file together with the updated Manifest file will be available soon.

The design can be found here in csv and bpm formats and includes 83,511 markers (SNPs + Structural Variants).

The design is currently reviewed by Illumina.

The Axiom Caprine Genotyping v2 Array was designed in collaboration with the International Goat Genome Consortium and the VarGoats Consortium. It contains all the SNPs from the Illumina Goat_IGGC_65K_v2 minus 760 monomorphic SNPs, which itself overlaps the Illumina GoatSNP50 chip (53372 SNPs) design. In addition, it contains the ancestral markers selected for the IMAGE multi-species goat chip (1042 SNPs). This array also includes 261 structural variants. 135 of these were tiled as copy number regions and 126 were tiled with junction probes (966 SNPs).

The final set then contains 59,795 SNPs and 265 structural variants.

384 animals are currently genotyped on this chip to validate it and give MAF of the markers in an international panel.

Two formats are available:

• 384HT format,
• mini-96 format.

Design (with location of the SNPs on ARS1 assembly):

• copy_number_proposal.txt,
• proposal_tiled_final-annotated.txt.

Main features:

• overlap with the GoatSNP50 Illumina beadchip is around ~40,000,
• remaining 30,000 SNPs of content that does not overlap were selected to segregate in both fiber and dairy goat breeds with whole genome sequence data on nearly 300 animals,
• includes Parentage SNPs and Scrapie.

Annotated file (with location of the SNPs on ARS1 assembly): GGP_Goat_70K_POS_ARS1_Saanen.adjust.txt.

Description of the chip: Helene-Hofeneder-Barclay-Neogen-Presentation-Estonia.pdf.

Contact: Ran Li and Prof. Yu Jiang, PI of Laboratory for Genomic Big Data,
College of Animal Science and Technology, Northwest A&F University,
No.3 Taicheng Rd, Yangling, Shaanxi, 712100, China.

It contains:

• 8000 SNPs from Illumina GoatSNP50, included 195 parentage SNPs,
• 1000 SNPs in candidate genes (DGAT1, PIS, PRP, sexual and mitochondrial chromosomes…),
• 1000 ancestral SNPs.

See IMAGE project deliverable.

Goat_IGGC_65K_v2 is the version 2 of the GoatSNP50 Illumina chip and is available since january 2021.

This version 2 contains a final number of 59,727 SNPs described here.

The manifest file in bpm format (version 2 since January 22, 2021) and the cluster file are also downloadable.

The csv file gives the information contained in the bpm file with a more accurate SNP location.

Reference allele was recovered from ARS1 assembly as described here. The annot file contains 57049 SNPs.

Finally, as we had to reduce the information for the SNP location in the bpm file (see below), an auxiliary file is also downloadable. The auxiliary file is a table that you can import into GenomeStudio as additional columns and it will give you the information that the manifest file cannot contain.

The probes have been mapped on ARS1 assembly with the following naming of chromosomes/scaffolds:

• 1 to 29
• MT
• X.1 X.2 for scaffold assigned to X in the auxiliary and csv files, X in the bpm file
• Y.1 to Y.11 for scaffolds assigned to Y in the auxiliary and csv files, Y in the bpm file
• 0.scaffold_name…for unplaced scaffold (example: 0.NW_017191871.1) in the auxiliary and csv files, 0.NW_scaffold in the bpm file.

For probes either unlocalized or with multiple localizations or not confirmed as belonging to X or Y scaffolds (after studying the genotypes), localization was set to null.

The final number of SNPs per chromosome/scaffold is available here.

Acknowledgements:
We thank the SNP providers and the group of scientists & engineers who analyzed the genotyping data on a set of 456 relevant animals (kindly provided by AgResearch, LECA, UNIMI, VarGoats project and an INRAE inhouse project).
We thank Sigenae for bioinformatics analysis, data and information releases.
We thank Illumina for providing chips for genotyping 384 animals and INRAE and Valogene for funding extra animals genotyping costs and cluster file generation costs.
We thank Labogena & INRAE (http://www.labogena.fr/) for their collaborative work on cluster file generation.
We thank Roger Pelle & collaborators (ILRI) and Vlatka Cubric Curik & collaborators (Zagreb University) for sharing extra genotyping data used for the analysis of low allele frequency SNPs.

VarGoats is the first step of a 1000 goat genomes project and is lead by Gwenola Tosser-Klopp (INRA, France).

Ensembl will annotate the goat genome assembly (GCA_001704415.1, submitted by USDA ARS 2016/08/24). The annotation is planned for release in the 2017 summer. Transcriptomics data are a valuable tool to annotate genomes. I thus encourage you to make your transcriptomics data accessioned and publicly available by 31st January 2017.
If you need any help for the submission, please contact: Data submission at EBI.
Before submitting your data, look at the FAANG documentation and the FAANG standards. If you follow these, any data you create will also be integrated into the FAANG resource.

Available resources:

• Assembly page on NCBI
• FTP repository
• Updated location of the SNPs on genome assembly ARS1 (goat)

Published in Nature Genetics, doi: 10.1038/ng.3802
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
Bickhart DM, Rosen BD, Koren S, Sayre BL, Hastie AR, Chan S, Lee J, Lam ET, Liachko I, Sullivan ST, Burton JN, Huson HJ, Nystrom JC, Kelley CM, Hutchison JL, Zhou Y, Sun J, Crisà A, Ponce de León FA, Schwartz JC, Hammond JA, Waldbieser GC, Schroeder SG, Liu GE, Dunham MJ, Shendure J, Sonstegard TS, Phillippy AM, Van Tassell CP, Smith TP (2017)

I would like to acknowledge our collaborators from the following institutions, in no particular order: The Pirbright Institute, Phase Genomics, BioNano Genomics, the USDA ARS, Cornell University, University of Washington, Virginia State University, the NHGRI, South China Agricultural Research University, CRA Agricultural Research Council, the University of Minnesota, NIFA AFRI, and Recombinetics.
Contact: Benjamin D Rosen and Derek Bickhart.

See the Animal Genetics, Breeding and Reproduction web page and the presentation at PAG meeting. Contact: Wenguang Zhang.
Download the Goat Genome Reference Sequence data:

• 285,375 scaffolds representing 2,662,629,614 bp of Yunnan black goat genome (chinese assembly v1)
• the assembly into 30 chromosomes (chinese assembly v2)

Published in Small Ruminant Research:
A whole-genome radiation hybrid panel for goat
XY Du, JE Womack, KE Owens, JS Elliott, B Sayre, PJ Bottcher, D Milan, M Garcia Podesta, SH Zhao, M Malek (2012)
Upcoming website. Contact: Brian Sayre.

Available since 2012, see the 50K goat SNP chip page and the presentation at PAG meeting.
Publication in dbSNP.
Cluster file.

Published in PLoS One, doi:10.1371/journal.pone.0086227
Design and Characterization of a 52K SNP Chip for Goats
Tosser-Klopp G, Bardou P, Bouchez O, Cabau C, Crooijmans R, et al. (2013)
Contact: Gwenola Tosser-Klopp.

2014, September: updated location of the SNPs on genome assemblies CHI_1.0 (goat), OAR3.1 (sheep) and UMD3.1 (cow).
2017, March: updated location of the SNPs on genome assembly ARS1 (goat).
2017, November: updated location of the SNPs on genome assemblies CHI_1.0 (goat), ARS1 (goat), OAR3.1 (sheep) and UMD3.1 (cow).
2019, August: updated price $20 for Consortium members ($22 otherwise). To get an accurate quotation, including shipping costs, please contact Illumina.
Chip replaced by Goat_IGGC_65K_v2.

Please visit the Goat ADAPTmap website. Contacts: Alessandra Stella and Ezequiel Luis Nicolazzi.