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

Abstract

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.

Fig. 1

Populations used to detect signatures of selection. Populations are color-coded according to their identified geographical groups. Populations in black were not considered in the analyses signatures of selection (see details in the text)

Fig. 2

Signatures of selection on chromosome 25 in the Angora group. Left panel: FLK (points) and hapFLK (line) signals. Middle panel: ROH signals. Right panel: iHS signals

Fig. 3

Genome scans for early adaptation based on differentiation between geographical groups. Left: Population tree built from the estimates of ancestral allele frequency in each continental group. Right: Manhattan plot of FLK p-values computed from the estimates of ancestral allele frequency and accounting for the ancestral tree structure

Fig. 4

ROH, F_ST and XP-EHH for fiber (a), and detail of the ROH analyses on chromosome 25 for the breeds that compose the group of “fiber-producing” goat breeds: Angora, Ankara and Cashmere (b). (a) The three analyses are shown with different plot colors, within the most external squared-based circle, where each color represent a chromosome (chromosome number outside the squares): green (external) = ROH; blue (middle) = F_ST; violet (internal): XP-EHH. For the three analyses, the regions above the threshold are marked in red. The region of high homozygosity (chromosome 25: 35,240,726-36,394,939 bp) is highlighted in red. (b) The three different breeds are labelled with different colors: green (external) = Angora; blue (middle) = Ankara; violet (internal): Cashmere. For the three breeds, the part corresponding to the 35-36 Mb region is marked in red when above the threshold

Fig. 5

Map of the worldwide distribution of genotypes for the snp24965-scaffold2564-131990 (3:1091508)

Fig. 6

F_ST plot of the comparison of the Tropical group vs. the other groups. The threshold line in red represents the 0.995 of the percentile distribution (F_ST = 0.391)