Department of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
USDA, ARS, Dale Bumpers Small Farms Research Center, Booneville, Arkansas, USA.
J Anim Breed Genet. 2024 May;141(3):304-316. doi: 10.1111/jbg.12842. Epub 2023 Dec 18.
The Katahdin hair breed gained popularity in the United States as low input and prolific, with a propensity to exhibit parasite resistance. With the introduction of genomically enhanced estimated breeding values (GEBV) to the Katahdin genetic evaluation, defining the diversity present in the breed is pertinent. Utilizing pedigree records (n = 92,030) from 1984 to 2019 from the National Sheep Improvement Program, our objectives were to (i) estimate the completeness and quality of the pedigree, (ii) calculate diversity statistics for the whole pedigree and relevant reference subpopulations and (iii) assess the impact of current diversity on genomic selection. Reference 1 was Katahdins born from 2017 to 2019 (n = 23,494), while reference 2 was a subset with at least three generations of Katahdin ancestry (n = 9327). The completeness of the whole pedigree, and the pedigrees of reference 1 and reference 2, were above 50% through the fourth, fifth and seventh generation of ancestors, respectively. Effective population size (N) averaged 111 animals with a range from 42.2 to 451.0. The average generation interval was 2.9 years for the whole pedigree and reference 1, and 2.8 years for reference 2. The mean individual inbreeding and average relatedness coefficients were 1.62% and 0.91%, 1.74% and 0.90% and 2.94% and 1.46% for the whole pedigree, reference 1, and reference 2, respectively. There were over 300 effective founders in the whole pedigree and reference 1, with 169 in reference 2. Effective number of ancestors were over 150 for the whole pedigree and reference 1, while there were 67 for reference 2. Prediction accuracies increased as the reference population grew from 1k to 7.5k and plateaued at 15k animals. Given the large number of founders and ancestors contributing to the base genetic variation in the breed, the N is sufficient to maintain diversity while achieving progress with selection. Stable low rates of inbreeding and relatedness suggest that incorporating genetic conservation in breeding decisions is currently not of high priority. Current N suggests that with limited genotyping, high levels of accuracy for genomic prediction can be achieved. However, intense selection on GEBV may cause loss of genetic diversity long term.
卡他丁毛羊品种在美国因其低投入和多产而广受欢迎，且具有寄生虫抗性。随着基因组增强估计育种值 (GEBV) 引入卡他丁遗传评估，定义该品种的多样性具有重要意义。本研究利用 1984 年至 2019 年国家绵羊改良计划的 pedigree 记录（n=92030），目的是：(i) 估计 pedigree 的完整性和质量，(ii) 计算整个 pedigree 及相关参考亚群的多样性统计数据，以及 (iii) 评估当前多样性对基因组选择的影响。参考 1 为 2017 年至 2019 年出生的卡他丁羊（n=23494），参考 2 为至少有三代卡他丁血统的亚群（n=9327）。整个 pedigree 以及参考 1 和参考 2 的 pedigree 的完整性都超过了第四、五和七代祖先，分别为 50%以上。有效种群大小 (N) 平均为 111 只，范围为 42.2 至 451.0。整个 pedigree 和参考 1 的平均世代间隔为 2.9 年，参考 2 为 2.8 年。整个 pedigree、参考 1 和参考 2 的平均个体近交系数和平均亲缘关系系数分别为 1.62%和 0.91%、1.74%和 0.90%和 2.94%和 1.46%。整个 pedigree 和参考 1 中有超过 300 个有效祖先，参考 2 中有 169 个。整个 pedigree 和参考 1 的有效祖先数超过 150，而参考 2 只有 67 个。随着参考群体从 1000 只增加到 7500 只，预测准确性增加，并在 15000 只动物时达到稳定。鉴于为该品种的基础遗传变异做出贡献的大量创始者和祖先，N 足以维持多样性，同时实现选择的进展。稳定的低近交率和亲缘关系表明，目前在育种决策中纳入遗传保护并不是首要任务。目前的 N 表明，在有限的基因分型下，基因组预测的高精度可以实现。然而，对 GEBV 的强烈选择可能会导致长期遗传多样性的丧失。
