Genetic relationships between Japanese native and commercial breeds using 70 chicken autosomal SNP genotypes by the DigiTag2 assay
Genetic relationships between Japanese native and commercial breeds using 70 chicken autosomal SNP genotypes by the DigiTag2 assay
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DOI：
10.1111/j.1365-2052.2011.02206.x
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发表时间：
2012-02-01
期刊：
影响因子：
2.4
通讯作者：
Yasue, H.
中科院分区：
文献类型：
--
作者：
Shimogiri, T.;Nishida, N.;Yasue, H.
最近，单核苷酸多态性（SNP）已被用来识别负责经济性状（包括家畜遗传疾病）的基因或基因组区域，并检查种群的遗传多样性。本研究利用DigiTag2技术对70只鸡的常染色体SNPs进行了基因分型，以了解日本地方鸡种Satsumadori和Ingie的遗传结构，以及这些鸡种与其他已建立的鸡种罗得岛红（RIR）、商品肉鸡和蛋鸡的关系。对5个品种（每种约20只鸡）的平均期望杂合度进行了测定，结果表明：肉鸡、萨摩通、RIR、蛋鸡和Ingie的平均期望杂合度分别为0.265、0.254、0.244、0.179和0.176。系统发育分析使用串联的70个常染色体SNP基因型区分所有鸡，并形成集群的鸡属于各自的品种。此外，前两个主成分的二维散点图与聚类树一致。与成对Fst距离一起，肉鸡和RIR彼此靠近，而Ingie远离其他品种。结构分析表明，可能的遗传聚类数（K）是6和4的最大似然和？K值，分别。最大似然聚类分析结果表明，除了其他5个品种的聚类，Satsumadori被细分为两个遗传聚类。集群与？K值分析表明，肉鸡和罗得岛红鸡属于同一遗传簇。
Recently, single nucleotide polymorphisms (SNPs) have been used to identify genes or genomic regions responsible for economic traits, including genetic diseases in domestic animals, and to examine genetic diversity of populations. In this study, we genotyped 70 chicken autosomal SNPs using DigiTag2 assay to understand the genetic structure of the Japanese native chicken breeds Satsumadori and Ingie, and the relationship of these breeds with other established breeds, Rhode Island Red (RIR), commercial broiler and layer. Five breeds, each consisting of approximately 20 chickens, were subjected to the assay, revealing the following: Average expected heterozygosities of broiler, Satsumadori, RIR, layer and Ingie were 0.265, 0.254, 0.244, 0.179 and 0.176, respectively. Phylogenetic analysis using the concatenated 70 autosomal SNP genotypes distinguished all chickens and formed clusters of chickens belonging to the respective breeds. In addition, the 2-D scatter plot of the first two principal components was consistent with the phylogenic tree. Taken together with the pairwise Fst distances, broiler and RIR were closely positioned near each other, while Ingie was positioned far from the other breeds. Structure analysis revealed that the probable number of genetic clusters (K) was six and four with maximum likelihood and ?K values, respectively. The clustering with maximum likelihood revealed that, in addition to the clustering of the other five breeds, the Satsumadori was subdivided into two genetic clusters. The clustering with ?K value indicated that the broiler and Rhode Island Red were assigned to the same genetic cluster.