Climate resilience of goat breeds in India: A review

Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda's indigenous goat populations

Knowledge about genetic diversity and population structure among goat populations is essential for understanding environmental adaptation and fostering efficient utilization, development, and conservation of goat breeds. Uganda's indigenous goats exist in three phenotypic groups: Mubende, Kigezi, and Small East African. However, a limited understanding of their genetic attributes and population structure hinders the development and sustainable utilization of the goats. Using the Goat Illumina 60k chip International Goat Genome Consortium V2, the whole-genome data for 1,021 indigenous goats sourced from 10 agroecological zones in Uganda were analyzed for genetic diversity and population structure. A total of 49,337 (82.6%) single-nucleotide polymorphism markers were aligned to the ARS-1 goat genome and used to assess the genetic diversity, population structure, and kinship relationships of Uganda's indigenous goats. Moderate genetic diversity was observed. The observed and expected heterozygosities were 0.378 and 0.383, the average genetic distance was 0.390, and the average minor allele frequency was 0.30. The average inbreeding coefficient (Fis) was 0.014, and the average fixation index (Fst) was 0.016. Principal component analysis, admixture analysis, and discriminant analysis of principal components grouped the 1,021 goat genotypes into three genetically distinct populations that did not conform to the known phenotypic populations but varied across environmental conditions. Population 1, comprising Mubende (90%) and Kigezi (8.1%) goats, is located in southwest and central Uganda, a warm and humid environment. Population 2, which is 59% Mubende and 49% Small East African goats, is located along the Nile Delta in northwestern Uganda and around the Albertine region, a hot and humid savannah grassland. Population 3, comprising 78.4% Small East African and 21.1% Mubende goats, is found in northeastern to eastern Uganda, a hot and dry Commiphora woodlands. Genetic diversity and population structure information from this study will be a basis for future development, conservation, and sustainable utilization of Uganda's goat genetic resources.

Selection signatures and landscape genomics analysis to reveal climate adaptation of goat breeds

Goats have achieved global prominence as essential livestock since their initial domestication, primarily owing to their remarkable adaptability to diverse environmental and production systems. Differential selection pressures influenced by climate have led to variations in their physical attributes, leaving genetic imprints within the genomes of goat breeds raised in diverse agroecological settings. In light of this, our study pursued a comprehensive analysis, merging environmental data with single nucleotide polymorphism (SNP) variations, to unearth indications of selection shaped by climate-mediated forces in goats. Through the examination of 43,300 SNPs from 51 indigenous goat breeds adapting to different climatic conditions using four analytical methods: latent factor mixed models (LFMM), F-statistics (Fst), Extended haplotype homozygosity across populations (XPEHH), and spatial analysis method (SAM), A total of 74 genes were revealed to display clear signs of selection, which are believed to be influenced by climatic conditions. Among these genes, 32 were consistently identified by at least two of the applied methods, and three genes (DENND1A, PLCB1, and ITPR2) were confirmed by all four approaches. Moreover, our investigation yielded 148 Gene Ontology (GO) terms based on these 74 genes, underlining pivotal biological pathways crucial for environmental adaptation. These pathways encompass functions like vascular smooth muscle contraction, cellular response to heat, GTPase regulator activity, rhythmic processes, and responses to temperature stimuli. Of significance, GO terms about endocrine regulation and energy metabolic responses, key for local adaptation were also uncovered, including biological processes, such as cell differentiation, regulation of peptide hormone secretion, and lipid metabolism. These findings contribute to our knowledge of the genetic structure of climate-triggered adaptation across the goat genome and have practical implications for marker-assisted breeding in goats.

Variability in body weight and morphology of Uganda's indigenous goat breeds across agroecological zones

Indigenous goat breeds in Uganda are classified based on average body size parameters and coat color. However, variations in the body size of animals may be influenced by several factors, including management and the environment. To understand the effect of the agroecological zone on the physical characteristics and live weight of Uganda's indigenous goats, this study evaluated the body size characteristics of the three indigenous goat breeds of Uganda across ten agroecological zones. The cross-sectional survey was conducted in 323 households from the ten zones, where 1020 goats composed of three breeds (Mubende, Kigezi, and Small East African) were sampled and measured for body weight, linear body size, and age. We confirmed that Mubende and Kigezi goats from the original homeland had a higher mean body weight than reported in FAO reports. In addition, Mubende appeared to perform better in pastoral rangelands, with a higher mean body weight (38.1 kg) and body size being significantly higher (P < 0.0001) compared to other zones. The mean body weight for the Kigezi breed in the original homeland (34 kg) was comparable to those from Western Savannah grasslands and pastoral rangelands and less than that initially reported by FAO (30 kg). Similarly, there was no significant difference in the linear body size characteristics of Kigezi goats in the home zone of highland ranges relative to those found in other agroecological zones (P > 0.05). Although the Small East African goats were originally found in Northwestern Savannah grassland and Northeastern dryland zones, they performed poorly regarding mean body weight and body size characteristics in the former zone. In the Northwestern Savannah grasslands, the mean body weight (23.8 kg) was even less than that reported by FAO, which ranged between 25 and 30 kg. Finally, we confirmed that Mubende and Kigezi goats are significantly heavier than small East African goats (p ≤ 0.0001). The results of this study can be useful in designing precise management strategies to improve indigenous goat productivity in different environments in Uganda.