Dataset Information

Genetic Variations and Differential DNA Methylation to Face Contrasted Climates in Small Ruminants: An Analysis on Traditionally-Managed Sheep and Goats.

ABSTRACT: The way in which living organisms mobilize a combination of long-term adaptive mechanisms and short-term phenotypic plasticity to face environmental variations is still largely unknown. In the context of climate change, understanding the genetic and epigenetic bases for adaptation and plasticity is a major stake for preserving genomic resources and the resilience capacity of livestock populations. We characterized both epigenetic and genetic variations by contrasting 22 sheep and 21 goats from both sides of a climate gradient, focusing on free-ranging populations from Morocco. We produced for each individual Whole-Genome Sequence at 12X coverage and MeDIP-Seq data, to identify regions under selection and those differentially methylated. For both species, the analysis of genetic differences (F_ST) along the genome between animals from localities with high vs. low temperature annual variations detected candidate genes under selection in relation to environmental perception (5 genes), immunity (4 genes), reproduction (8 genes) and production (11 genes). Moreover, we found for each species one differentially methylated gene, namely AGPTA4 in goat and SLIT3 in sheep, which were both related, among other functions, to milk production and muscle development. In both sheep and goats, the comparison between genomic regions impacted by genetic and epigenetic variations suggests that climatic variations impacted similar biological pathways but different genes.

SUBMITTER: Denoyelle L

PROVIDER: S-EPMC8508783 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The aim of this study was to identify the main on-farm welfare issues likely to be encountered in extensive sheep farming systems. Thirty-two commercial sheep farms in Victoria, Australia were involved in this study. Of the 32 farms involved, 30 were visited twice (at mid-pregnancy and weaning), and 2 farms only once (both at weaning). In total, 62 visits were conducted and 6,200 ewes (aged 2-5 years) were examined using six animal-based indicators: body condition score (BCS), fleece condition, skin lesions, tail length, dag score and lameness. In addition, the number of ewes that needed further care (such as sick or injured sheep) was recorded and reported to the farmers. Generalised linear mixed models were conducted to investigate associations between welfare outcomes and visit, ewe breed and location, with all three, and their interactions, as fixed factors. In all instances, farm was set as a random factor to account for specific variation between farms. Overall, the welfare of the ewe flocks, based on the six indicators measured, was considered good. A total of 86.9% of the ewes were in adequate BCS (2.5-3.5), 91% had good fleece condition, 69.2% had no skin lesions, 97.1% had low dag scores, and overall lameness was 4.7%. An important and prevalent risk to welfare identified across farms was short tail length; with 85.7% of ewes having tails docked shorter than the third palpable joint. While the welfare of the flock was good, ewes in need of further care were identified at all farms. There were 185 (3.0%) cases needing further care, and the extent of welfare compromise of these animals was considered significant. Main reasons for further care were moderate/severe lameness or foot-related issues, BCS ? 2 and active dermatophilosis or broken wool. To our knowledge, this study constitutes the largest assessment of ewes conducted in Australia, and the findings provide valuable insight into the main welfare issues likely to be encountered in extensive sheep farming enterprises. Future studies should develop practical technologies that can assist in the detection of the welfare issues identified in this study. In addition, the thresholds identified here could be used for future comparison and sheep welfare benchmarking programs to assess farm performance and measure continuous improvements.

Dataset Information

Genetic Variations and Differential DNA Methylation to Face Contrasted Climates in Small Ruminants: An Analysis on Traditionally-Managed Sheep and Goats.

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