Genetic Structure of Chinese Indigenous Goats and the Special Geographical Structure in the Southwest China as a Geographic Barrier Driving the Fragmentation of a Large Population

<div><p>Background</p><p>China has numerous native domestic goat breeds, however, extensive studies are focused on the genetic diversity within the fewer breeds and limited regions, the population demograogic history and origin of Chinese goats are still unclear. The roles of geographical structure have not been analyzed in Chinese goat domestic process. In this study, the genetic relationships of Chinese indigenous goat populations were evaluated using 30 microsatellite markers.</p><p>Methodology/Principal Findings</p><p>Forty Chinese indigenous populations containing 2078 goats were sampled from different geographic regions of China. Moderate genetic diversity at the population level (H_S of 0.644) and high population diversity at the species level (H_T value of 0.737) were estimated. Significant moderate population differentiation was detected (F_ST value of 0.129). Significant excess homozygosity (F_IS of 0.105) and recent population bottlenecks were detected in thirty-six populations. Neighbour-joining tree, principal components analysis and Bayesian clusters all revealed that Chinese goat populations could be subdivided into at least four genetic clusters: Southwest China, South China, Northwest China and East China. It was observed that the genetic diversity of Northern China goats was highest among these clusters. The results here suggested that the goat populations in Southwest China might be the earliest domestic goats in China.</p><p>Conclusions/Significance</p><p>Our results suggested that the current genetic structure of Chinese goats were resulted from the special geographical structure, especially in the Western China, and the Western goat populations had been separated by the geographic structure (Hengduan Mountains and Qinling Mountains-Huaihe River Line) into two clusters: the Southwest and Northwest. It also indicated that the current genetic structure was caused by the geographical origin mainly, in close accordance with the human’s migration history throughout China. This study provides a fundamental genetic profile for the conservation of these populations and better to understand the domestication process and origin of Chinese goats.</p></div

PCA analysis.

<p>PCA analysis.</p

Genetic diversity measures estimated using 30 microsatellite loci in each of 40 goat populations.

<p><i>Note: n</i>, sample size; <i>TNA</i>, total number alleles; <i>MNA</i>, mean number of alleles; <i>AR</i>, allelic richness, <i>H_E</i>, heterozygosity estimates, <i>H_O</i>, heterozygosity observed; <i>F_IS</i>, fixation index.</p

The neighbor-joining tree of 40 goat populations in China was constructed based on Nei’s genetic distance (D_A).

<p>The population abbreviations are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094435#pone-0094435-t001" target="_blank">Table 1</a>. The numbers on the nodes indicate the bootstrap values (%) obtained from 1000 replications.</p

Results of analysis of molecular variance (AMOVA) for 40 populations of Chinese goats.

<p>d.f., degrees of freedom.</p><p>***<i>P</i><0.001, <i>P</i>-values were obtained by 20000 permutations.</p

Geographic distribution of the 40 goat populations in China.

<p>Geographic distribution of the 40 goat populations in China.</p

Genetic diversity measures estimated at each 30 loci across the 40 Chinese indigenous goat populations.

<p>Note: <i>Location</i>, the locus located on the chromosomes; <i>T_A</i>, total number of alleles; <i>H_O</i>, observed heterozygosity; <i>H_S</i>, gene diversity; <i>H_T</i>, overall gene diversity; <i>F_IS</i>, <i>F_ST</i> and <i>F_IT</i>, measures of the F-statistics.</p><p>*<i>P</i><0.05;</p><p>**<i>P</i><0.01;</p><p>***<i>P</i><0.001.</p

Population structure of 40 goat breeds based on 30 microsatellite loci using STRUCTURE.

<p><i>K</i> was estimated using (A) the posterior probability of the data given each <i>K</i> (10 replicates) and (B) the distribution of Δ<i>K</i>, and (C) the colored clusters represented <i>K</i> from 2 to 10 were detected from STRUCTURE analysis. The number given below was corresponding to the name of each breed (seen in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094435#pone-0094435-t002" target="_blank">Table 2</a>).</p