Genome wide assessment of genetic variation and population distinctiveness of the pig family in South Africa

Genetic diversity is of great importance and a prerequisite for genetic improvement and conservation programs in pigs and other livestock populations. The present study provides a genome wide analysis of the genetic variability and population structure of pig populations from different production systems in South Africa relative to global populations. A total of 234 pigs sampled in South Africa and consisting of village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5) and wild (n = 38) populations were genotyped using Porcine SNP60K BeadChip. In addition, 389 genotypes representing village and commercial pigs from America, Europe and Asia were accessed from a previous study and used to compare population clustering and relationships of South African pigs with global populations. Moderate heterozygosity levels, ranging from 0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn municipality in Eastern Cape province of South Africa were observed. Principal Component Analysis of the South African pigs resulted in four distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and Warthog and (iv) a cluster with the rest of the commercial (SA Large White and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and Windsnyer. The clustering demonstrated alignment with genetic similarities, geographic location and production systems.  The PCA with the global populations also resulted in four clusters that where populated with (i) all the village populations, wild boars, SA indigenous and the large white and landraces; (ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush pig. K= 10 (The number of population units) was the most probable ADMIXTURE based clustering, which grouped animals according to their populations with the exception of the village pigs that showed presence of admixture. AMOVA reported 19.92% – 98.62% of the genetic variation to be within populations. Sub structuring was observed between South African commercial populations as well as between Indigenous and commercial breeds. Population pairwise FSTanalysis showed genetic differentiation (P < 0.05)between the village, commercial and wild populations. A per marker per population pairwise FSTanalysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose metabolism processes and growth factors between both domestic populations as well as between wild and domestic breeds. Overall, the study provided a baseline understanding of porcine diversity and an important foundation for porcine genomics of South African populations.

Methods
Hair and Tissue samples were collected and genotyped using the PorcineSNP60K beadChip with GenomeStudio version 2.0 was used to process the genotype data

遗传多样性对于猪及其他畜禽种群的遗传改良与保护计划而言至关重要，亦是其核心前提。本研究针对南非不同生产体系下的猪种群开展全基因组遗传变异与种群结构分析，并与全球猪种群进行对比。本研究共采集南非地区234头猪的样本，涵盖村落养殖猪（n=91）、商品猪（n=60）、地方品种猪（n=40）、亚洲猪（n=5）以及野生猪（n=38），采用猪60K SNP芯片（Porcine SNP60K BeadChip）进行基因分型。此外，本研究调取了既往研究中的389份基因型数据，对应美洲、欧洲及亚洲的村落养殖猪与商品猪，用于对比南非猪种群与全球种群的群体聚类及亲缘关系。研究观测到中等水平的杂合度，范围从疣猪（Warthogs）的0.204到南非东开普省卡普里康自治市采集的村落养殖猪的0.371不等。针对南非猪种群的主成分分析（Principal Component Analysis, PCA）得到4个清晰的聚类群：(i) 杜洛克猪；(ii) 越南猪；(iii) 丛林猪（Bush pig）与疣猪；(iv) 由其余商品猪（南非大约克夏猪与兰德瑞斯猪）、村落养殖猪、野猪以及Koelbroek和Windsnyer地方品种猪构成的聚类群。该聚类结果与遗传相似性、地理分布及生产体系均呈现良好的一致性。纳入全球种群的主成分分析同样得到4个聚类群：(i) 所有村落养殖种群、野猪、南非地方品种猪以及大约克夏猪与地方品种类群；(ii) 杜洛克猪种群；(iii) 中国猪与越南猪种群；(iv) 疣猪与丛林猪种群。基于ADMIXTURE的聚类分析显示，当种群单位数K=10时为最适聚类模型，该模型可按照种群来源对个体进行分组，仅村落养殖猪呈现出明显的遗传混合特征。分子方差分析（Analysis of Molecular Variance, AMOVA）结果表明，19.92%~98.62%的遗传变异存在于种群内部。研究同时观测到南非商品猪种群之间、地方品种与商品品种之间存在显著的种群亚结构。种群两两FST分析显示，村落养殖猪、商品猪与野生猪种群之间存在显著的遗传分化（P < 0.05）。单标记-种群两两FST分析揭示，在家养种群之间以及野生与家养品种之间，存在与若干性状的数量性状基因座（Quantitative Trait Locus, QTL）相关的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点，这些性状涵盖肉质、细胞骨架与肌肉发育、葡萄糖代谢过程以及生长因子相关通路。总体而言，本研究为猪遗传多样性提供了基础认知，同时为南非猪种群的基因组学研究奠定了重要基础。

方法
本研究采集毛发与组织样本，采用猪SNP60K分型芯片（PorcineSNP60K beadChip）进行基因分型，并使用GenomeStudio 2.0版本软件处理基因型数据