Dataset Information

Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data.

ABSTRACT: Since the time of their domestication, goats (Capra hircus) have evolved in a large variety of locally adapted populations in response to different human and environmental pressures. In the present era, many indigenous populations are threatened with extinction due to their substitution by cosmopolitan breeds, while they might represent highly valuable genomic resources. It is thus crucial to characterize the neutral and adaptive genetic diversity of indigenous populations. A fine characterization of whole genome variation in farm animals is now possible by using new sequencing technologies. We sequenced the complete genome at 12× coverage of 44 goats geographically representative of the three phenotypically distinct indigenous populations in Morocco. The study of mitochondrial genomes showed a high diversity exclusively restricted to the haplogroup A. The 44 nuclear genomes showed a very high diversity (24 million variants) associated with low linkage disequilibrium. The overall genetic diversity was weakly structured according to geography and phenotypes. When looking for signals of positive selection in each population we identified many candidate genes, several of which gave insights into the metabolic pathways or biological processes involved in the adaptation to local conditions (e.g., panting in warm/desert conditions). This study highlights the interest of WGS data to characterize livestock genomic diversity. It illustrates the valuable genetic richness present in indigenous populations that have to be sustainably managed and may represent valuable genetic resources for the long-term preservation of the species.

SUBMITTER: Benjelloun B

PROVIDER: S-EPMC4387958 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Publications

Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data.

Benjelloun Badr B Alberto Florian J FJ Streeter Ian I Boyer Frédéric F Coissac Eric E Stucki Sylvie S BenBati Mohammed M Ibnelbachyr Mustapha M Chentouf Mouad M Bechchari Abdelmajid A Leempoel Kevin K Alberti Adriana A Engelen Stefan S Chikhi Abdelkader A Clarke Laura L Flicek Paul P Joost Stéphane S Taberlet Pierre P Pompanon François F

Frontiers in genetics 20150407

Since the time of their domestication, goats (Capra hircus) have evolved in a large variety of locally adapted populations in response to different human and environmental pressures. In the present era, many indigenous populations are threatened with extinction due to their substitution by cosmopolitan breeds, while they might represent highly valuable genomic resources. It is thus crucial to characterize the neutral and adaptive genetic diversity of indigenous populations. A fine characterizati ...[more]

PMID: 25904931

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Project description:Animal emotional states can be investigated by evaluating their impact on cognitive processes. In this study, we used a judgement bias paradigm to determine if short-term positive human-animal interaction (grooming) induced a positive affective state in goats. We tested two groups of goats and trained them to discriminate between a rewarded and a non-rewarded location over nine training days. During training, the experimental group (n = 9) was gently groomed by brushing their heads and backs for five min over 11 days (nine training days, plus two testing days, total time 55 min). During training, the control group (n = 10) did not experience any direct interaction with the experimenter, but was kept unconstrained next to him for the same period of time. After successful completion of the training, the responses (latency time) of the two groups to reach ambiguous locations situated between the two reference locations (i.e., rewarded/non-rewarded) were compared over two days of testing. There was not a positive bias effect after the animals had been groomed. In a second experiment, 10 goats were tested to investigate whether grooming induced changes in physiological activation (i.e., heart rate and heart rate variability). Heart rate increased when goats were groomed compared to the baseline condition, when the same goats did not receive any contact with the experimenter. Also, subjects did not move away from the experimenter, suggesting that the grooming was positively accepted. The very good care and the regular positive contacts that goats received from humans at the study site could potentially account for the results obtained. Good husbandry outcomes are influenced by animals' perception of the events and this is based on current circumstances, past experiences and individual variables. Taking into account animals' individual characteristics and identifying effective strategies to induce positive emotions could increase the understanding and reliability of using cognitive biases paradigms to investigate and promote animal welfare.

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

Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data.

Publications

Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data.

Similar Datasets

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