Dataset Information

Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication.

ABSTRACT: BACKGROUND:Domestic goats (Capra hircus) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar (Capra aegagrus). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics. RESULTS:We constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely have accompanied goat domestication and breed formation. Thirteen copy number variation genes associated with coat color were identified in domestic goats, among which ASIP gene duplication contributes to the generation of light coat-color phenotype in domestic goats. Analysis of rapidly evolving genes identified genic changes underlying behavior-related traits, immune response and production-related traits. CONCLUSION:Based on the comparison studies of copy number variation genes and rapidly evolving genes between wild and domestic goat, our findings and methodology shed light on the genetic mechanism of animal domestication and will facilitate future goat breeding.

SUBMITTER: Dong Y

PROVIDER: S-EPMC4455334 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature

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Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication.

Dong Yang Y Zhang Xiaolei X Xie Min M Arefnezhad Babak B Wang Zongji Z Wang Wenliang W Feng Shaohong S Huang Guodong G Guan Rui R Shen Wenjing W Bunch Rowan R McCulloch Russell R Li Qiye Q Li Bo B Zhang Guojie G Xu Xun X Kijas James W JW Salekdeh Ghasem Hosseini GH Wang Wen W Jiang Yu Y

BMC genomics 20150605

<h4>Background</h4>Domestic goats (Capra hircus) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar (Capra aegagrus). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics.<h4>Results</h4>We constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely ...[more]

PMID: 26044654

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Project description:BackgroundIran is an area of particular interest for investigating goat diversity. Archaeological remains indicate early goat domestication (about 10,000 years ago) in the Iranian Zagros Mountains as well as in the high Euphrates valley and southeastern Anatolia. In addition, mitochondrial DNA data of domestic goats and wild ancestors (C. aegagrusor bezoar) suggest a pre-domestication management of wild populations in southern Zagros and central Iranian Plateau. In this study genetic diversity was assessed in seven Iranian native goat breeds, namely Markhoz, Najdi, Taleshi, Khalkhali, Naini, native Abadeh and Turki-Ghashghaei. A total of 317 animals were characterized using 14 microsatellite loci. Two Pakistani goat populations, Pahari and Teddy, were genotyped for comparison.ResultsIranian goats possess a remarkable genetic diversity (average expected heterozygosity of 0.671 across loci, 10.7 alleles per locus) mainly accounted for by the within-breed component (GST?=?5.9%). Positive and highly significant FIS values in the Naini, Turki-Ghashghaei, Abadeh and Markhoz breeds indicate some level of inbreeding in these populations. Multivariate analyses cluster Iranian goats into northern, central and western groups, with the western breeds relatively distinct from the others. Pakistani breeds show some relationship with Iranian populations, even if their position is not consistent across analyses. Gene flow was higher within regions (west, north, central) compared to between regions but particularly low between the western and the other two regions, probably due to the isolating topography of the Zagros mountain range. The Turki-Ghashghaei, Najdi and Abadeh breeds are reared in geographic areas where mtDNA provided evidence of early domestication. These breeds are highly variable, located on basal short branches in the neighbor-joining tree, close to the origin of the principal component analysis plot and, although highly admixed, they are quite distinct from those reared on the western side of the Zagros mountain range.ConclusionsThese observations call for further investigation of the nuclear DNA diversity of these breeds within a much wider geographic context to confirm or re-discuss the current hypothesis (based on maternal lineage data) of an almost exclusive contribution of the eastern Anatolian bezoar to the domestic goat gene pool.

Project description:Motor self-regulation is the ability to inhibit a prepotent response to a salient cue in favour of a more appropriate response. Motor self-regulation is an important component of the processes that interact to generate effective inhibitory control of behaviour, and is theorized to be a prerequisite of complex cognitive abilities in humans and other animals. In a large comparative study using the cylinder task, motor self-regulation was studied in 36 different species, mostly birds and primates. To broaden the range of species to comprehensively evaluate this phenomenon, motor self-regulation was studied in the domestic goat, which is a social ungulate species and moderate food specialist. Using the cylinder task, goats were first trained to perform a detour-reaching response to retrieve a reward from an opaque cylinder. Subsequently, an otherwise identical transparent cylinder was substituted for the opaque cylinder over 10 test trials. The goats' ability to resist approaching the visible reward directly by touching the cylinder and to retain the trained detour-reaching response was measured. The results indicated that goats showed motor self-regulation at a level comparable to or better than that of many of the bird and mammal species tested to date. However, the individual reaction patterns revealed large intra- and inter-individual variability regarding motor self-regulation. An improvement across trials was observed only in latency to make contact with the reward; no improvement in the proportion of accurate trials was observed. A short, distinct pointing gesture by the experimenter during baiting did not have any impact on the side of the cylinder to which the goats detoured. In half of goats, individual side biases were observed when detouring to the side of the cylinder, but there was no bias at the population level for either the left or right side. The results underline the need for a detailed examination of individual performance and additional measures to achieve a complete understanding of animal performance in motor self-regulation tasks.

Dataset Information

Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication.

Publications

Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication.

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