Huson Heather J, Sonstegard Tad S, Godfrey James, Hambrook David, Wolfe Cari, Wiggans George, Blackburn Harvey, VanTassell Curtis P
Department of Animal Science, Cornell University, Ithaca, NY, United States.
Acceligen, Eagan, MN, United States.
Front Genet. 2020 Apr 17;11:366. doi: 10.3389/fgene.2020.00366. eCollection 2020.
For two centuries, Jersey cattle were exported globally, adapting to varying climates and production systems, yet the founding population remained genetically isolated on the Island of Jersey. The Island of Jersey formally allowed the importation of pure Jersey cattle in 2008. This study characterized the genetic variation of 49 popular bulls from the Island of Jersey born from 1964 to 2004 and compared them to 47 non-Island Jersey bulls and cows, primarily from the United States In addition, 21 Guernsey cattle derived from the Island of Guernsey and 71 Holstein cattle served as reference populations for genetic comparison. Cattle were genotyped on the Illumina BovineHD Beadchip producing 777,962 SNPs spanning the genome. Principal component analysis revealed population stratification within breed reflective of individual animal's continental origin. When compared to Holstein and Guernsey, all Jersey clustered together by breed. The Jersey breed demonstrated increased inbreeding in comparison to Holstein or Guernsey with slightly higher estimates of inbreeding coefficients and identity-by-descent. The Island and United States Jersey have relatively similar, yet statistically different inbreeding estimates despite vastly different population sizes and gene flow. Signatures of selection within Island Jersey were identified using genome-wide homozygosity association and marker-based F that provided population informative single-nucleotide polymorphism (SNPs). Biological significance of the homozygosity association results identified multiple genes on chromosomes 5, 24, and 27, involved in immune function and cellular processes. Overall, genomic variation was identified between the Island and non-Island Jersey cattle producing population informative SNPs and differing runs of homozygosity (ROH) over immune regulation and metabolic genes. Results on inbreeding measures and ROH may reflect varying effective population size or differential selection with grazing systems promoting natural selection for traits such as parasite resistance, whereas confinement systems demonstrate a more intensive artificial selection. More broadly, differences in breed formation, particularly between the two Channel Island breeds, likely contributed to the variation in ROH and inbreeding. This research provides a reference for the Jersey breed based on the genetic foundation of the Island cattle as compared to the intensively selected United States cattle, and identifies regions of the genome for future investigation of immune regulation and metabolic processes.
两个世纪以来，泽西牛被出口到全球各地，适应了不同的气候和生产系统，但其创始种群在泽西岛上仍保持着基因隔离。泽西岛于2008年正式允许进口纯种泽西牛。本研究对1964年至2004年出生在泽西岛的49头受欢迎的公牛的基因变异进行了表征，并将它们与47头非泽西岛的公牛和母牛（主要来自美国）进行了比较。此外，21头源自根西岛的根西牛和71头荷斯坦牛作为基因比较的参考种群。牛在Illumina BovineHD Beadchip上进行基因分型，产生了跨越基因组的777,962个单核苷酸多态性（SNP）。主成分分析揭示了品种内的种群分层，反映了个体动物的大陆起源。与荷斯坦牛和根西牛相比，所有泽西牛按品种聚集在一起。与荷斯坦牛或根西牛相比，泽西品种的近亲繁殖有所增加，近亲繁殖系数和同源性估计值略高。尽管种群规模和基因流动差异巨大，但泽西岛和美国的泽西牛的近亲繁殖估计值相对相似，但在统计学上存在差异。利用全基因组纯合性关联和基于标记的F值确定了泽西岛牛群中的选择信号，该方法提供了群体信息丰富的单核苷酸多态性（SNP）。纯合性关联结果的生物学意义确定了5号、24号和27号染色体上的多个基因，这些基因参与免疫功能和细胞过程。总体而言，在泽西岛和非泽西岛的泽西牛种群之间发现了基因组变异，产生了群体信息丰富的SNP，并在免疫调节和代谢基因上有不同的纯合性片段（ROH）。近亲繁殖措施和ROH的结果可能反映了有效种群大小的差异或不同的选择方式，放牧系统促进了对寄生虫抗性等性状的自然选择，而圈养系统则表现出更强烈的人工选择。更广泛地说，品种形成的差异，特别是两个海峡群岛品种之间的差异，可能导致了ROH和近亲繁殖的变化。本研究为泽西品种提供了一个基于泽西岛牛基因基础的参考，与经过高强度选择的美国牛相比，并确定了基因组区域，以供未来对免疫调节和代谢过程进行研究。
