Department of Animal Science, North Carolina State University, Raleigh 27607.
Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, 50144 Florence, Italy.
J Dairy Sci. 2022 Nov;105(11):8956-8971. doi: 10.3168/jds.2022-22116. Epub 2022 Sep 22.
Maintaining a genetically diverse dairy cattle population is critical to preserving adaptability to future breeding goals and avoiding declines in fitness. This study characterized the genomic landscape of autozygosity and assessed trends in genetic diversity in 5 breeds of US dairy cattle. We analyzed a sizable genomic data set containing 4,173,679 pedigreed and genotyped animals of the Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey breeds. Runs of homozygosity (ROH) of 2 Mb or longer in length were identified in each animal. The within-breed means for number and the combined length of ROH were highest in Jerseys (62.66 ± 8.29 ROH and 426.24 ± 83.40 Mb, respectively; mean ± SD) and lowest in Ayrshires (37.24 ± 8.27 ROH and 265.05 ± 85.00 Mb, respectively). Short ROH were the most abundant, but moderate to large ROH made up the largest proportion of genome autozygosity in all breeds. In addition, we identified ROH islands in each breed. This revealed selection patterns for milk production, productive life, health, and reproduction in most breeds and evidence for parallel selective pressure for loci on chromosome 6 between Ayrshire and Brown Swiss and for loci on chromosome 20 between Holstein and Jersey. We calculated inbreeding coefficients using 3 different approaches, pedigree-based (F), marker-based using a genomic relationship matrix (F), and segment-based using ROH (F). The average inbreeding coefficient ranged from 0.06 in Ayrshires and Brown Swiss to 0.08 in Jerseys and Holsteins using F, from 0.22 in Holsteins to 0.29 in Guernsey and Jerseys using F, and from 0.11 in Ayrshires to 0.17 in Jerseys using F. In addition, the effective population size at past generations (5-100 generations ago), the yearly rate of inbreeding, and the effective population size in 3 recent periods (2000-2009, 2010-2014, and 2015-2018) were determined in each breed to ascertain current and historical trends of genetic diversity. We found a historical trend of decreasing effective population size in the last 100 generations in all breeds and breed differences in the effect of the recent implementation of genomic selection on inbreeding accumulation.
维持具有遗传多样性的奶牛群体对于保持对未来育种目标的适应能力以及避免适应能力下降至关重要。本研究对美国 5 个奶牛品种的自交系基因组景观进行了特征描述，并评估了遗传多样性的趋势。我们分析了一个包含 4173679 头具有谱系和基因型的阿伯丁安格斯牛、瑞士褐牛、娟姗牛、荷斯坦牛和泽西牛的大型基因组数据集。在每个动物中鉴定了 2 Mb 或更长的纯合区域（ROH）。ROH 的品种内平均值和总长度在泽西牛中最高（分别为 62.66 ± 8.29 ROH 和 426.24 ± 83.40 Mb；平均值 ± SD），而在阿伯丁安格斯牛中最低（分别为 37.24 ± 8.27 ROH 和 265.05 ± 85.00 Mb）。短 ROH 最为丰富，但中到大 ROH 构成了所有品种基因组自交的最大比例。此外，我们在每个品种中都鉴定到了 ROH 岛。这揭示了大多数品种在产奶量、生产寿命、健康和繁殖方面的选择模式，以及阿伯丁安格斯牛和瑞士褐牛之间第 6 号染色体上的位点以及荷斯坦牛和泽西牛之间第 20 号染色体上的位点之间平行的选择压力的证据。我们使用 3 种不同的方法计算了近交系数，基于系谱的（F）、基于标记的使用基因组关系矩阵的（F）和基于 ROH 的（F）。使用 F 计算的平均近交系数范围从阿伯丁安格斯牛和瑞士褐牛的 0.06 到泽西牛和荷斯坦牛的 0.08，使用 F 计算的从荷斯坦牛的 0.22 到瑞士褐牛和泽西牛的 0.29，以及从阿伯丁安格斯牛的 0.11 到泽西牛的 0.17。此外，在每个品种中确定了过去几代（5-100 代前）的有效种群大小、每年的近交率以及 3 个近期时期（2000-2009 年、2010-2014 年和 2015-2018 年）的有效种群大小，以确定当前和历史遗传多样性趋势。我们发现所有品种在过去 100 代中有效种群大小呈下降趋势，并且在最近实施基因组选择对近交积累的影响方面存在品种差异。
