Genome-Wide Linkage Disequilibrium and the Extent of Effective Population Sizes in Six Chinese Goat Populations Using a 50K Single Nucleotide Polymorphism Panel

SIMPLE SUMMARY: Information on linkage disequilibrium (LD) and the extent of effective population size (Ne) has important implications for exploring the degree of biological diversity, for predicting underlying selection pressure, and for designing animal breeding programs. In this study, we assessed LD, Ne, and the distribution of minor allele frequency in six goat populations. Accordingly, the results of LD and Ne using a single nucleotide polymorphism (SNP) panel (Caprine SNP 50K BeadChip, Lincoln, NE, USA) are helpful for the sustainable conservation, proper management, and utilization of Chinese goat populations. ABSTRACT: Genome-wide linkage disequilibrium is a useful parameter to study quantitative trait locus (QTL) mapping and genetic selection. In many genomic methodologies, effective population size is an important genetic parameter because of its relationship to the loss of genetic variation, increases in inbreeding, the accumulation of mutations, and the effectiveness of selection. In this study, a total of 193 individuals were genotyped to assess the extent of LD and Ne in six Chinese goat populations using the SNP 50K BeadChip. Across the determined autosomal chromosomes, we found an average of 0.02 and 0.23 for r(2) and D’ values, respectively. The average r(2) between all the populations varied little and ranged from 0.055 r(2) for the Jining Grey to 0.128 r(2) for the Guangfeng, with an overall mean of 0.083. Across the 29 autosomal chromosomes, minor allele frequency (MAF) was highest on chromosome 1 (0.321) and lowest on chromosome 25 (0.309), with an average MAF of 0.317, and showing the lowest (25.5% for Louping) and highest (28.8% for Qingeda) SNP proportions at MAF values > 0.3. The inbreeding coefficient ranged from 0.064 to 0.085, with a mean of 0.075 for all the autosomes. The Jining Grey and Qingeda populations showed higher Ne estimates, highlighting that these animals could have been influenced by artificial selection. Furthermore, a declining recent Ne was distinguished for the Arbas Cashmere and Guangfeng populations, and their estimated values were closer to 64 and 95, respectively, 13 generations ago, which indicates that these breeds were exposed to strong selection. This study provides an insight into valuable genetic information and will open up the opportunity for further genomic selection analysis of Chinese goat populations.