Genomic Surveillance of Reproductive and Adaptive Variation in Indigenous Sheep Populations for Sustainable Livestock Production at the Human Animal Environment Interface

The indigenous sheep have valuable genetic resources to be utilized for sustainable livestock production in arid and harsh environments where productivity and food security rely on good reproductive performance, adaptability and disease resistance. Currently, however, genomic knowledge of local sheep populations is still limited, limiting the assessment of genetic diversity, the identification of variants related to economically important reproductive traits, and the development of evidence-based breeding and conservation strategies. This study introduces a novel framework for integrated genomic surveillance of indigenous sheep that integrates population genomics, reproductive phenotyping, environmental characterization and the One Health principles to assess reproductive and adaptive variation in the human–animal–environment interface.

It combines the genome-wide molecular information with standard reproductive records such as the number of lambs, fertility, interval, reproductive seasonality and reproductive resilience. Population structure, genetic diversity and differentiation and signatures of selection, as well as genomic inbreeding and runs of homozygosity, will be evaluated using principal component analysis, ancestry inference, homozygosity analysis and genome-wide selection scans. Genomic regions and candidate genes associated with reproductive performance, endocrine function, environmental adaptation and immune function will be identified through genome-wide association analysis. The results of these genome studies will be analyzed alongside key environmental factors, such as exposure to high temperatures, nutrient deficiency, water shortage, and local environmental conditions.

Such integration of genomic, reproductive and environmental data into a single analysis can help achieve the identification of resilient animals, precision breeding and reduce the loss of locally adapted genetic diversity. The proposed framework connects reproductive sustainability to animal health, ecosystem resilience, food security and conservation priorities, unlike traditional livestock genomics approaches. It thus serves as a practical basis for the creation of breeding and conservation programmes for indigenous sheep at a One Health approach.