50K SNP chip update

Any marker addition will be considered. Please contact Gwenola Tosser-Klopp and Philippe Bardou. Here is the requested format (coordinates on ARS1 genome assembly). We will add up to 5,000 markers. The following classes of markers have been identified as interesting and a non exhaustive list of scientists able to select them is indicated:

  • chromosome Y markers (Hans Lenstra)
  • mitochondrial markers (Licia Colli)
  • SNPs with different MAF profiles (Curt Van Tassell)
  • SNPs identified in regions related to adaptation & selection signatures in VarGoats data (Licia Colli et al.)
  • causal mutations) and QTL markers (increase the 50K density using VarGoats data) for diseases, interesting traits = seasonality, wattles, PRP, dairy traits...(C.Droegmuller, S.White, Rachel Rupp, A.Stella, INRA, literature)
  • MHC markers (Paola Crepaldi)
  • include Breeds not represented in the discovery dataset
  • include markers to be able to join with GBS data (AgResearch as a partner)
  • fill remaining gaps (determined after mapping the SNPs on ARS1 assembly).

The deadlines are:

  • assemble a list of markers, end of February, 2019
  • transfer the list to Illumina after checking duplicates, end of March, 2019
  • availability of the updated chip, end of June, 2019.

VarGoats project

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

PacBio genome assembly annotation: submit your transcriptomics data

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.

PacBio genome assembly (ARS1)

Available resources:

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.

Goat Genome Reference Sequence and 25 breeds resequencing

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:

RH panel

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.

50K goat SNP chip

Now available, 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).

Hapmap project: ADAPTmap

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


Gwenola Tosser-Klopp

Wenguang Zhang