Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds

Abstract

Indigenous breeds develop their own genomic characteristics by adapting to local environments or cultures over long periods of time. Most of them are not particularly productive in commercial terms, but they have abilities to survive in harsh environments or tolerate to specific diseases. Their adaptive characteristics play an important role as genetic materials for improving commercial breeds. As a step toward this goal, we analyzed the genome of Korean indigenous goats within 10 goat breeds. We collected 136 goat individuals by sequencing 46 new goats and employing 90 publicly available goats. Our whole-genome data was comprised of three indigenous breeds (Korean indigenous goat, Iranian indigenous goat, and Moroccan indigenous goat; n = 29, 18, 20), six commercial breeds (Saanen, Boer, Anglo-Nubian, British Alpine, Alpine, and Korean crossbred; n = 16, 11, 5, 5, 2, 13), and their ancestral species ( Capra aegagrus ; n = 17). We identified that the Iranian indigenous goat and the Moroccan indigenous goat have relatively similar genomic characteristics within a large category of genomic diversity but found that the Korean indigenous goat has unique genomic characteristics distinguished from the other nine breeds. Through population analysis, we confirmed that these characteristics have resulted from a near-isolated environment with strong genetic drift. The Korean indigenous goat experienced a severe genetic bottleneck upon entering the Korean Peninsula about 2,000 years ago, and has subsequently rarely experienced genetic interactions with other goat breeds. From selection analysis and gene-set enrichment analysis, we revealed selection signals for Salmonella infection and cardiomyopathy in the genome of the Korean indigenous goat. These adaptive characteristics were further identified with genomic-based evidence. We uncovered genomic regions of selective sweeps in the LBP and BPI genes ( Salmonella infection) and the TTN and ITGB6 genes (cardiomyopathy), among several candidate genes. Our research presents unique genomic characteristics and distinctive selection signals of the Korean indigenous goat based on the extensive comparison. Although the adaptive traits require further validation through biological experiments, our findings are expected to provide a direction for future biodiversity conservation strategies and to contribute another option to genomic-based breeding programmes for improving the viability of Capra hircus .

Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats

“…There were two out-of-range findings of Y1B, in the Uganda Karamonja and in the Korean native breeds. Because of the popularity of Swiss dairy goats in both Uganda (NAADS, 2005) and Korea (Kim et al, 2019), crossbreeding again is the most likely explanation.…”

Identification of Genomic Characteristics and Selective Signals in a Du’an Goat Flock

“… 1 Inbreeding coefficient was estimated using a method of moments. 2 The genomic characteristics in these breeds was identified by Badr Benjelloun et al in 2019 [ 2 ]. …”

“…Domestic goats play an important role in the transition of human civilization from foraging and hunting to farming and herding by supplying milk, meat, and fiber. Due to natural and anthropogenic factors (e.g., climate changes, human migration, and population expansion), there are now more than 1006 million individuals and 557 registered breeds worldwide [ 2 , 3 ].…”

“…For example, a whole-genome sequencing study showed a very high diversity associated with linkage disequilibrium in Moroccan goat [ 6 ]. The selection sweep analysis of Korean indigenous goats revealed selective signals for Salmonella infection and cardiomyopathy [ 2 ]. One of the recently-published studies including 164 modern domestic goat, 52 ancient goat, 24 modern bezoar, and 4 ancient bezoar genomes indicated that Asian goats are genetically distinct from European and African samples.…”

Genomic Characteristics and Selection Signatures in Indigenous Chongming White Goat (Capra hircus)

“…Goats are important husbandry animals with an ancient domestication history and economic value. It has been reported that their domestication occurred approximately 10,000 years ago and spread worldwide following human migrations and trade routes ( Benjelloun et al, 2015 ; Kim et al, 2019 ). China is the global leader in terms of goat production ( Skapetas and Bampidis, 2016 ), including many commercial, indigenous, and composite breeds.…”