Population structure and genetic characterization of indigenous goat breeds from different climatic zones as a climate change and adaptation mechanism

Abstract

Indigenous goats are essential to many livelihoods, yet they face significant challenges, including indiscriminate crossbreeding, habitat destruction, and disease prevalence, harsh environments, traditional production systems, and sociocultural contexts which have shaped their genetic diversity. However, these factors, combined with the increasing effects of climate change, influence their genetic diversity, which remains critical for their adaptation and long-term survival under increasing environmental stresses. The present doctoral research employed pedigree and molecular data to understand their genetic make-up. For objective one, the study assessed population structure and genetic diversity of Kenyan Galla and Small East African (SEA) goats using pedigree information. A total of 7,384 animals, 5,222 of the Galla and 2,162 of the SEA breeds, born between the years 1983 and 2022, were utilized. To assess various parameters, ENDOG software was used. For objectives 2 to 4, the study aimed to understand the population structure, genetic diversity, and adaptive mechanisms of the indigenous goat population in selected countries of Asia, Africa, and Europe. A total of 372 goats were genotyped using the CaprineSNP70K Bead Chip array with 51,119 SNP markers. For pedigree analysis, both Galla and SEA goat breeds had similarly deep but partially incomplete pedigrees (14.6 and 14.5 generations traced, with only 6 and 5 complete, respectively), shorter generation intervals in Galla and long in SEA (3.84 and 4.4 years, respectively), and low rates of inbreeding (0.04 and 0.05 per generation, respectively). Despite these, both breeds showed critically small effective population sizes (Ne ≈ 5), a fa/fe ratio of 1.00, and a disproportionate contribution to genetic variability by very few ancestors (3 for Galla, 1 for SEA), underscoring the need for breed specific management to conserve diversity and mitigate inbreeding. For genomic analysis, the HO was moderate in all the study populations, ranging from 0.34 in Philippine goats to 0.441 in Shokpar (Kazakhstan), with the inbreeding coefficients varying such that Philippine Native Antipas Cotabato recorded the highest inbreeding across all the measures and relatively low levels of heterozygosity, whereas Shokpar, Kenes (Kazakhstan), and Old Hungarian Native populations showed higher heterozygosity and lower inbreeding coefficients. The distribution of ROH revealed that most populations had a high frequency of short run segments (0–24 Mb), suggesting ancient inbreeding and a history of population bottlenecks, while population structure analyses identified four major genetic clusters reflecting geographic origins and historical gene flow, with high levels of admixture observed in some African populations which may be due to cross boarder livestock movement, trade interactions, and crossbreeding among herds across regions. The observed decline in effective population sizes in all the study populations highlights the risk of genetic drift and loss in genetic diversity, which calls for attention for designing proper conservation and breeding programs geared towards sustaining the genetic health by balancing productivity and genetic diversity conservation to ensure the sustainability of indigenous goat breeds globally. The study identified important candidate genes related to immunity (PRPF6, DIP2C, and CD58), adaptation (DIP2C, ATP1A1), reproduction (OPRL1, DIP2C, and ATP12A), milk fat content (NFX1) and growth and development (NTRK2, ADAMTSL3, and SOX18), which provides a valuable insight into the genetic mechanisms underlying economically and biologically important traits in this indigenous populations, offering useful markers for future breeding, conservation, and improvement programs aimed at enhancing productivity, resilience, and long-term sustainability of indigenous goat populations.