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

Abstract

BackgroundSince 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.ResultsSeveral 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.ConclusionsThese 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.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0421-y) contains supplementary material, which is available to authorized users.

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“…In the current study, we confirmed three selection signatures detected by Bertolini et al . () and found two new selection signatures never detected before. The very well‐known genes involved in coat color determination, ADAMTS20 on chromosome 5 and ASIP on chromosome 13, had already been found in several groups of breeds: for the ADAMTS20 gene, the southwestern European group (which includes the Pyrénées population; the Argentata dell'Etna breed from the southeastern European group; and the Sahel, Peuhl and Targi breeds from northwestern Africa) and for the ASIP gene, the Kacchan population from the Pakistani breeds and the Alpine, Poitevine and Valdostana breeds from the Alpine group.…”

Keep Garfagnina alive. An integrated study on patterns of homozygosity, genomic inbreeding, admixture and breed traceability of the Italian Garfagnina goat breed

“…Blood samples of forty eight female GRF goats were collected and animals were genotyped with the Illumina GoatSNP50 BeadChip (Illumina Inc., San Diego, CA) containing 53,347 Single Nucleotide Polymorpishms (SNPs) [12]. Genomic data of nine Italian autochthonous goat breeds, namely Argentata dell’Etna (ARG), Bionda dell’Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS) were downloaded from the online repository (https://datadryad.org/stash/dataset/doi:10.5061/dryad.v8g21pt10.5061/dryad.v8g21pt) of the ADAPTmap project [3,13]. The breeds were selected based on the breed abbreviation on the plink fam file downloaded from the repository and the breed description (code and country) reported in Table 1 of [13].…”

“…Genomic data of nine Italian autochthonous goat breeds, namely Argentata dell’Etna (ARG), Bionda dell’Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS) were downloaded from the online repository (https://datadryad.org/stash/dataset/doi:10.5061/dryad.v8g21pt10.5061/dryad.v8g21pt) of the ADAPTmap project [3,13]. The breeds were selected based on the breed abbreviation on the plink fam file downloaded from the repository and the breed description (code and country) reported in Table 1 of [13]. The two datasets were merged and quality control was conducted in PLINK v1.9 [3, 4] on the final dataset based on the following criteria: 1) only autosomes were kept, ii) call rate per SNP >95% and ii) missing values per sample <10%.…”