Abstract
BackgroundThe management of farm animal genetic resources and the adaptation of animals to climate change will probably have major effects on the long-term sustainability of the livestock sector. Genomic data harbour useful relevant information that needs to be harnessed for effectively managing genetic resources. In this paper, we report the genome characterization of the highly productive Mediterranean Chios dairy sheep and focus on genetic diversity measures related with local adaptation and selection and the genetic architecture of animal resilience to weather fluctuations as a novel adaptative trait linked to climate change.ResultsWe detected runs of homozygosity (ROH) and heterozygosity (ROHet) that revealed multiple highly homozygous and heterozygous hotspots across the Chios sheep genome. A particularly highly homozygous region was identified on chromosome 13 as a candidate of directional genetic selection associated with milk traits, which includes annotated genes that were previously shown to be linked to local adaptation to harsh environmental conditions. Favourable heterozygosity related with a potentially protective role against livestock diseases and enhanced overall fitness was revealed in heterozygous-rich regions on sheep chromosomes 3, 10, 13 and 19. Furthermore, genomic analyses were conducted on sheep resilience phenotypes that display changes in milk production in response to weather variation. Sheep resilience to heat stress was a significantly heritable trait (h2 = 0.26) and genetically antagonistic to milk production. Genome-wide association and regional heritability mapping analyses revealed novel genomic markers and regions on chromosome 5 that were significantly associated with sheep resilience to climate change. Subsequently, an annotation analysis detected a set of genes on chromosome 5 that were associated with olfactory receptor complexes that could participate in heat stress mitigation through changes in respiration rate and respiratory evaporation. Other genes were grouped in previously reported biological processes relevant to livestock heat dissipation, including stress and immune response.ConclusionsOur results may contribute to the optimal management of sheep genetic resources and inform modern selective breeding programmes that aim at mitigating future environmental challenges towards sustainable farming, while better balancing animal adaptation and productivity. Our results are directly relevant to the studied breed and the respective environmental conditions; however, the methodology may be extended to other livestock species of interest.
Highlights
The management of farm animal genetic resources and the adaptation of animals to climate change will probably have major effects on the long-term sustainability of the livestock sector
Our results may contribute to the optimal management of sheep genetic resources and inform modern selective breeding programmes that aim at mitigating future environmental challenges towards sustainable farming, while better balancing animal adaptation and productivity
High Pearson correlations were estimated between F and FROH (0.97), and between coefficients of recent inbreeding (0.98), whereas lower estimates were obtained between recent and ancient inbreeding (0.78–0.80)
Summary
The management of farm animal genetic resources and the adaptation of animals to climate change will probably have major effects on the long-term sustainability of the livestock sector. The integration of methods to mitigate genetic erosion and comprehensively evaluate animal performance through the characterization of adaptive traits that are relevant to climate change adaptation [2] would facilitate the sustainable management of livestock biodiversity [3]. Assessment of genome diversity, by estimating homozygosity and heterozygosity levels and genomic inbreeding, is of paramount importance for the management and conservation of genetic resources [4]. The detection of ROH hotspots ( referred to as ROH islands) can identify suggestive genomic selected regions that harbour genes associated with animal domestication [14], breed formation [15], traits of economic importance [16], and local adaptation to new environments [12]. It has been proposed that highly heterozygous regions throughout the genome, known as heterozygosity-rich regions (ROHet) or ROHet islands [17], are strongly associated with animal fitness and survival, and heterotic balancing selection processes [17,18,19]
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