Genetic Diversity, Population Structure and Phylogeny of Indigenous Goats of Mongolia Revealed by SNP Genotyping

Abstract

Mongolian goats are of great interest for studying ancient migration routes and domestication, and also represent a good model of adaptability to harsh environments. Recent climatic disasters and uncontrolled massive breeding endangered the valuable genetic resources of Mongolian goats and raised the question of their conservation status. Meanwhile, Mongolian goats have never been studied on genomic scale. We used Illumina Goat SNP50 to estimate genetic risks in five Mongolian goat breeds (Buural, Ulgii Red, Gobi GS, Erchim, Dorgon) and explored phylogenic relationships among these populations and in the context of other breeds. Various clustering methods showed that Mongolian goats grouped with other Asian breeds and were especially close to some neighboring Russian and Chinese breeds. The Buural breed showed the lowest estimates of inbreeding and exhibited the shortest genetic distances within the other Mongolian breeds, especially, to Ulgii Red and Gobi GS. These three breeds formed a single core group, being weakly differentiated from each other. Among them, Gobi GS displayed obvious signs of inbreeding probably resulted from artificial selection pressure. Dorgon and especially Erchim goats stand apart from the other Mongolian breeds according to various types of analyses, and bear unique features pointing to different breeding histories or distinct origins of these breeds. All populations showed strong decline in effective population size. However, none of them met formal criteria to be considered as endangered breeds. The SNP data obtained in this study improved the knowledge of Mongolian goat breeds and could be used in future management decisions in order to preserve their genetic diversity.

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

“…The observed and expected heterozygosity of more than 0.37 and the average genetic distance of 0.390 indicate that Uganda’s indigenous goats are genetically diverse. Similar values of heterozygosity were observed among indigenous goats in Ethiopia ( Tarekegn et al, 2021 ), Cameroon ( Tarekegn et al, 2019 ), China ( Berihulay et al, 2019 ), and Mongolia ( Mukhina et al, 2022 ). In addition, low and positive values of F IS and F ST obtained in this study indicate high heterozygosity and no deliberate inbreeding in the goat population, which limits the impact of deleterious alleles, inbreeding depression, and loss of variance ( Berihulay et al, 2019 ).…”

A Mitochondrial DNA-based Molecular Phylogenetics Study of the Mahalli Goat as a New Animal Genetic Resource in Southern Anatolia in Turkey

“…On the other hand, studies on genetic diversity in goats have also been carried out using microsatellite and single nucleotide polymorhisms (SNP) markers instead of mitochondrial DNA. Some examples of genetic diversity studies conducted with microsatellite markers are Rajkumar and Santpal (2020) and Verma et al (2022) in Indian goats and Pan et al (2023) in Chinese goats, while Mukhina et al (2022) used SNP markers in Mogolian goats.…”

Genome-wide association analysis of fleece traits in Northwest Xizang white cashmere goat

“…Sun et al reveal the potential genetic basis for litter size, coat color, and skin color by using genome-wide association analysis (GWAS), selection signature analysis, and ROH detection within the Youzhou dark goat population through GWAS; four SNPs were identified ( 10 ). Mukhina et al evaluated the genetic risk of five Mongolian goat breeds (Buural, Ulgii Red, Gobi GS, Erchim, and Dorgon) using Illumina Goat SNP50 genotyping data and explored the phylogenetic relationship between these populations and other breeds ( 11 ).…”