Goats are important livestock in smallholder production systems in Laos, contributing economically, nutritionally, and culturally. Most goats in Laos are native breeds, distributed throughout the country, with almost half of the population in central regions. This thesis aimed to evaluate 1) the genetic diversity and population structure 2) signatures of selection and identify the candidate genome regions and potential genes in Lao goats that are associated with production traits and adaptation 3) animal movement patterns and the degree of mixing between herds across villages and 4) village breeding strategies to improve genetic merit for Lao native goats while controlling inbreeding.
Maintaining genetic diversity in livestock is important for long-term genetic improvement in breeding programs. In Laos, concerns have arisen about the possible reduction of genetic diversity and increasing inbreeding for Lao goats in smallholder systems. In Chapter 3 the genetic diversity and population structure of Lao goats was explored using their genomic data and comparing them with 163 global goat breeds. The genomic analyses revealed a close genetic relationship between Lao goats and those from China, Mongolia and Pakistan. Results show Lao goats have moderate genetic diversity, low inbreeding and adequate effective population size, with some genetic differences reflective of geography and culture.
Domestication, selection, and breeding have produced indigenous goats well-adapted to local environments, making them valuable genetic resources. Understanding the genetic adaptations can guide the development of effective breeding strategies. In Chapter 4, the signature of selection for Lao goats was investigated, using the decorrelation composite multiple signals method. We identified 24 genomic regions harbouring 68 unique coding genes linked to adaptation to the tropical monsoon climate and economic traits such as growth and status, reproduction, milk production and carcass characteristics.
In pastoral agricultural systems, the movement and mixing of animal cohorts is important for the understanding of mating patterns in free-roaming herds or flocks, as it impacts the degree of genetic diversity and levels of inbreeding. In Chapter 5, spatial data was used to track animal movement and examine the home range and the overlap home range between different villages while genomic data was used to track animal relatedness and gene flow between herds. The results show village-specific differences in home ranges, with males covering larger areas than females, and larger ranges in the dry season. There was low to moderate gene flow between villages even with minimal home range overlap between them. Within each village, the degree of gene flow is consistent with the degree of home range overlap between herds.
Chapter 6 presents a simulation study to assess potential genetic improvement for Lao native goats and mating strategies that limit the rate of inbreeding. A mating strategy where bucks are rotated among herds or villages offered a significant body weight improvement and allowed an increasing but comparatively low level of inbreeding. The village rotational mating strategy could be implemented for isolated villages, while the district rotational strategy could benefit areas where there are accessible trade networks and minimal geographical boundaries. In contrast, traditional random mating at the herd level showed minimal body weight improvement and a significant increase in inbreeding over time.