Genetic diversity estimation of Yunnan indigenous goat breeds using microsatellite markers

Abstract

Background To assess the genetic diversity of seven Yunnan indigenous goat populations (Fengqing hornless goat, Mile red‐bone goat, Longling goat, Ninglang black goat, Black‐bone goat, Yunling black goat, and Zhaotong goat), their population structures were investigated using 20 microsatellite markers. Results The results indicated that the genetic diversity of these goats was rich. The observed heterozygosity ranged from 0.4667 ± 0.0243 to 0.5793 ± 0.0230, and the mean number of alleles ranged from 4.80 ± 1.61 and 4.80 ± 1.64 to 6.20 ± 2.93. The population structure analysis showed that these seven goat populations were separated into two clusters, consistent with the results from phylogenetic networks, pairwise differences, and STRUCTURE analyses. We speculate that this may have been caused by natural geographical isolation, human migration and economic and cultural exchanges. We suggest removing CSRD247 and ILSTS005, two loci identified to be under positive selection in the present study, from the microsatellite evaluation system of goats. Conclusions The present study may provide a scientific basis for the conservation and utilization of Yunnan indigenous goats.

Genetic diversity and phylogenetic relationship of nine sheep populations based on microsatellite markers

“…The genetic diversity parameters of nine sheep populations, including mean number of effective alleles (N A ), the expected heterozygosity (H E ), the observed heterozygosity (H O ), the polymorphic information content (PIC) and Nei's unbiased gene diversity (H S ), were calculated using Microsatellite Toolkit software 3.1.1 (Park, 2008). The genetic parameters for each microsatellite locus, including the effective number of alleles (N E ), the allelic richness over all samples per locus (Rt), the fixation index within populations (F IS ), the fixation indices of total population (F IT ) and the pairwise differences between the populations (F ST ), were obtained using FSTAT 2.9.3.2 (Goudet et al, 2002). Dispan was used to calculate the genetic distance of D A and D S between populations and build the phylogenetic tree (Nei et al, 1983).…”

“…Dispan was used to calculate the genetic distance of D A and D S between populations and build the phylogenetic tree (Nei et al, 1983). Population structure was analyzed by Structure 2.3.4 with Bayesian clustering model, and its results were visualized by Distruct 1.1 (Falush et al, 2003;Pritchard et al, 2000;Rosenberg, 2003). TreeMix 1.13 was used to construct a maximum likelihood tree and infer migration events between branches (Pickrell et al, 2012).…”

Runs of Homozygosity Detection and Selection Signature Analysis for Local Goat Breeds in Yunnan, China

“…Yunnan province is located in southwestern China, bordering the countries of Myanmar, Laos, and Vietnam. It is characterized by its complex topography, diverse climate, and abundant biodiversity and is the home to the highest concentration of ethnic minorities [ 6 , 7 ]. During long-term natural and artificial selection, various local goat breeds in Yunnan province emerge with divergent traits.…”

“…Longling yellow goat is a unique breed with high meat quality and disease resistance and is included in the Yunnan Province Livestock and Poultry Genetic Resources Protection List to better safeguard this exceptional breed. This situation highlights the need for comprehensive genetic studies, such as those employing microsatellite markers to assess genetic diversity in Yunnan indigenous goat populations [ 7 ], underscoring the importance of conservation and utilization for these unique goat breeds in Yunnan. However, a comprehensive analysis of the genome-wide patterns of homozygosity and selection signatures in these breeds is still lacking.…”

Genetic Diversity Estimation of Six Goat Populations from Chongqing, China using Microsatellite Markers

“…In particular, H E of the six goat populations was higher than their H O in this study, thereby indicating that decreased heterozygosis is common in these goat populations. Notably, the small population size and unbalanced mating ratio, particularly when a few satisfactory breeding males provided the group a high proportion of spouse rights, will cause the population to deviate from the balance and lead to increased risks in the population (Yang et al, 2021;Guang-Xin et al, 2019;Basang et al, 2021). Therefore, some of these populations, especially JZG and BJG, still showed potential risks of inbreeding.…”