VarGoats

Laboratoire d'Ecologie Alpine, France: François Pompanon.

Partner 2 is interested in inferring the history of the domestication process for sheep and goats. This involves reconstructing the demographic history (localisation of the domestication centre, migration routes, founder effects, etc.) and the adaptive history (genes involved in the domestication process or in local adaptation). Partner 2 is also interested in the conservation genetics of domestic species (especially traditional breeds). He has been involved in NextGen European project, focusing at wild and local sheep and goat breeds, which provided hundreds of publically available goat sequences. That will be analysed together with data generated in VarGoats and help us understand the specificity of domestic breeds.

Parco Tecnologico Padano, Italy: Alessandra Stella, Ezequiel Nicolazzi, Barbara Lazzari and Gabriele Marras.

Partner 3 will centralize the contributions regarding samples, will provide MTA to organize data analysis between partners and will provide Bioinformatic solutions for efficient merging of genomic data from independent sources.

ARS, USDA, USA: Derek M. Bickhart, George R. Wiggans.

Partner 4 conducts research to develop and transfer solutions to agricultural problems of high national priority and provide information access and dissemination to: ensure high-quality, safe food, and other agricultural products; assess the nutritional needs of Americans; sustain a competitive agricultural economy; enhance the natural resource base and the environment and provide economic opportunities for rural citizens, communities, and society as a whole.

International Goat Genome consortium.

Partner 5 is the International Goat Genome Consortium. Some details are given below for 4 participants and the complete list of participant laboratories can be found here.

Curt Van Tassell is a key participant to the The African Goat Improvement Network group (Partner 6).
Marcel Amills (Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Universitat Autònoma de Barcelona) will contribute with complementary DNA samples for goat breeds: goat samples from two Tinerfeña goat ecotypes and/or from feralized/domestic goats from Fuerteventura.
James Kijas (Australia), Wenguang Zhang and Wen Wang (China) are the key contacts to sample Cashmere goats adapted to different local environments (Australia, China).
Clet Wandui Masiga (Uganda-Africa) is the key contact to sample unique breeds adapted to different agroecological regions in Africa.
Licia Colli and Paola Crepaldi (Italy) are Work package leaders in ADAPTMAP Consortium.

Curtis P. Van Tassell, is a famous scientist who has a long experience in analysing genomics data. He was involved in the 1000 bull genomes project, in the design of genomic tools (SNP chips…).

Marcel Amills is interested in the analysis of the impact of domestication and breed formation on the genetic diversity of domestic species (mainly of pigs and goats) as well as in the identification of causal mutations that shape phenotypes of economic relevance.

James Kijas's current work involves the application of SNP genotyping to perform GWAS on a range of production traits and diseases in sheep, cattle and goats. Currently he is leading projects that aim to better understand the consequences of domestication and selection on genomic variation. He is the coordinator of the International Sheep Genomics Consortium (ISGC). The common theme to his research is the quest to link genomic variation with phenotypic changes in animal populations.

Clet Wandui Masiga is interested in understanding genetic diversity of goats and sheep to influence their utilization and conservation by the African communities and governments. He is particularly keen in using research data to help influence African governments and communities to access and utilize next generation technologies for farm development.

Licia Colli (UNICATT) and Paola Crepaldi (UNIMI) are members of the Italian Goat Consortium. They are interested in genetic diversity, domestication and adaptation processes, and in exploring the extent of hybridization between different species of the genus Capra through the analysis of SNP and whole-genome sequence data.

African Goat Improvement Network: Curtis P. Van Tassell, Prof. Johann (Hans) Sölkner, Timothy Gondwe, Henry Mulindwa.

The African Goat Improvement Network group has already sampled more than 1000 indigenous goats in Africa. This sampling includes collecting enough DNA for SNP50 and next generation sequencing analysis. Corresponding meta-data was also taken on these samples and includes digital imagery, GPS and GIS information, and morphometric measurements of the goats. It is currently using the goat SNP50 chip to study genetic composition to identify candidate goats for whole genome resequencing. The African Goat Improvement Network of the USDA/USAID Feed the Future project will contribute DNA from African goat breeds adapted to desertification in throughout Africa. These samples represent dozens of breeds including indigenous small East African breeds. This group also has access to St. Croix native breed, which is resistant to tick infection. This group will contribute 10X coverage of 192 animals from other African and U.S. goat breeds

The main interest of African Goat Improvement Network is to identify signatures of natural and artificial selection. These signatures will allow development of marker tools that can be used in community based breeding programs in developing nations to allow sustainable genetic improvement of these unimproved animals/populations for protein production.

Roslin Institute and the Centre for Tropical Livestock Genetics and Health (joined the original Consortium in 2017).

Emily Clark is interested in functional genomics and comparative genomics in sheep and goats. She is a member of the Ovine FAANG group and the International Sheep Genomics Consortium (ISGC). She works within the Centre for Tropical Livestock Genetics and Health at the Roslin Institute which aims to facilitate the application of genomics and genetics in the tropics for increased livestock productivity and a more sustainable environment. The Roslin Institute via a Global Challenges Research Fund data and resources grant will contribute 269 goat genomes, from goats sampled for the AGIN project, at 15x coverage run on the Illumina HiSeqX platform.