A High Throughput Genotyping Approach Reveals Distinctive Autosomal Genetic Signatures for European and Near Eastern Wild Boar

The lack of a Near Eastern genetic signature in modern European porcine breeds indicates that, although domestic pigs from the Fertile Crescent entered Europe during the Neolithic, they were completely replaced by their European counterparts in a short window of time. Whilst the absence of such genetic signature has been convincingly demonstrated at the mitochondrial level, variation at the autosomal genomes of European and Near Eastern Sus scrofa has not been compared yet. Herewith, we have explored the genetic relationships among 43 wild boar from Europe (N = 21), Near East (N = 19) and Korea (N = 3), and 40 Iberian (N = 16), Canarian (N = 4) and Mangalitza (N = 20) pigs by using a high throughput SNP genotyping platform. After data filtering, 37,167 autosomal SNPs were used to perform population genetics analyses. A multidimensional scaling plot based on genome-wide identity-by-state pairwise distances inferred with PLINK showed that Near Eastern and European wild boar populations are genetically differentiated. Maximum likelihood trees built with TreeMix supported this conclusion i.e. an early population split between Near Eastern and European Sus scrofa was observed. Moreover, analysis of the data with Structure evidenced that the sampled Iberian, Canarian and Mangalitza pigs did not carry any autosomal signature compatible with a Near Eastern ancestry, a finding that agrees well with previous mitochondrial studies.

现代欧洲猪品种中缺乏近东遗传特征，这表明尽管源自新月沃地的家猪在新石器时代传入欧洲，但它们在较短时间内便完全被欧洲本土家猪所替代。尽管该遗传特征的缺失在线粒体水平上已得到令人信服的验证，但欧洲与近东野猪（Sus scrofa）的常染色体基因组变异尚未被比较过。本研究利用高通量单核苷酸多态性（Single Nucleotide Polymorphism，SNP）基因分型平台，对43头野猪（欧洲(N=21)、近东(N=19)、韩国(N=3)）以及40头家猪（伊比利亚猪(N=16)、加那利猪(N=4)、曼加利察猪(N=20)）的遗传关系进行了探究。经数据过滤后，共保留37167个常染色体SNP位点用于群体遗传学分析。基于PLINK软件推断的全基因组逐态同一性成对距离绘制的多维标绘图显示，近东与欧洲野猪种群存在遗传分化。利用TreeMix软件构建的最大似然树也支持这一结论，即观察到近东与欧洲野猪（Sus scrofa）存在早期种群分化事件。此外，利用Structure软件对数据进行的群体结构分析表明，本次采样的伊比利亚猪、加那利猪与曼加利察猪均未携带任何与近东祖先起源相符的常染色体遗传特征，这一发现与此前的线粒体研究结果高度一致。