Signatures of selection and environmental adaptation across the goat genome post-domestication

Background: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds. Results: Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments. Conclusions: These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide

VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity

Background: Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra. Findings: A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin. Conclusions: We report on an unprecedented international effort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal effects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies

Genetic evaluation systems and breeding programs in sheep and goats: an international perspective.

Genetic selection has been a key tool for improving productive performance in small ruminant populations around the world, especially in Europe. This has been achieved through selective breeding for numerous traits, using diverse genetic evaluation systems and breeding schemes. Knowledge of the alternative approaches taken is paramount to the design of efficient and integrated genomic breeding programs. In this study, we summarised information on 48 sheep and goat breeding programs, genetic and genomic evaluation systems and resources available in 12 countries involved in the SMARTER project. This was done using published reports and surveys distributed to all partners. Responses to the surveys reveals information for more than 9, 16, and 20 dairy goat, dairy sheep, and meat sheep breeds involved in genetic schemes, respectively, with ~3,083,562 animals included in data collection schemes. The main groups of traits recorded across countries are: (1) milk yield and composition, mastitis indicators, udder andbody conformation, and reproduction in dairy sheep and dairy goats; and (2) growth, reproduction, health, ultrasound, wool, and carcass in meat sheep. Seven countries have progeny testing schemes, but only 5 use artificial insemination. There are numerous challenges to be addressed (e.g. disparity of trait recording, SNP panels, statistical models used, joining pedigrees across countries as well as grouping breeds based on genetic similarity, and an average of ~30% of animals with unknown sires). However, there are many opportunities to use the current resources and develop collaborative approaches to optimise selection for novel breeding goals such as resilience and efficiency in small ruminants across countries