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:A wide range of species exhibit time- and context-consistent interindividual variation in a number of specific behaviors related to an individual's personality. Several studies have shown that individual differences in personality-associated behavioral traits have an impact on cognitive abilities. The aim of this study was to investigate the relationship between personality traits and learning abilities in dwarf goats. The behavior of 95 goats during a repeated open field (OF) and novel object test (NO) was analyzed, and two main components were identified using principal component analysis: boldness and activity. In parallel, the goats learned a 4-choice visual initial discrimination task (ID) and three subsequent reversal learning (RL) tasks. The number of animals that reached the learning criterion and the number of trials needed (TTC) in each task were calculated. Our results show that goats with the lowest learning performance in ID needed more TTC in RL1 and reached the learning criterion less frequently in RL2 and RL3 compared to animals with better learning performance in ID. This suggests a close relationship between initial learning and flexibility in learning behavior. To study the link between personality and learning, we conducted two analyses, one using only data from the first OF- and NO-test (momentary personality traits), while the other included both tests integrating only animals that were stable for their specific trait (stable personality traits). No relationship between personality and learning was found using data from only the first OF- and NO-test. However, stability in the trait boldness was found to have an effect on learning. Unbold goats outperformed bold goats in RL1. This finding supports the general hypothesis that bold animals tend to develop routines and show less flexibility in the context of learning than unbold individuals. Understanding how individual personality traits can affect cognitive abilities will help us gain insight into mechanisms that can constrain cognitive processing and adaptive behavioral responses.

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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