Department of Animal and Dairy Science, The University of Georgia, Athens, GA.
USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT.
J Anim Sci. 2019 Jan 1;97(1):1-18. doi: 10.1093/jas/sky385.
This study aimed at assessing inbreeding and its effect on growth and fertility traits using the longtime closed line 1 Hereford cattle population. Inbreeding was estimated based on pedigree (FPED) and genomic information. For the latter, three estimates were derived based on the diagonal elements of the genomic relationship matrix using estimated (FGRM) or fixed (FGRM0.5) minor allele frequencies or runs of homozygosity (ROH) (FROH). A pedigree containing 10,186 animals was used to calculate FPED. Genomic inbreeding was evaluated using 785 animals genotyped for 30,810 SNP. Traits analyzed were birth weight (BWT), weaning weight (WWT), yearling weight (YWT), ADG, and age at first calving (AFC). The number of ROH per animal ranged between 6 and 119 segments with an average of 83. The shortest and longest segments were 1.36 and 64.86 Mb long, respectively, reflecting both ancient and recent inbreeding occurring in the last 30 to 40 generations. The average inbreeding was 29.2%, 16.1%, 30.2%, and 22.9% for FPED, FGRM, FGRM0.5, and FROH, respectively. FROH provided the highest correlations with FPED (r = 0.66). Across paternal half-sib families, with minimal variation in FPED, there were substantial variations in their genomic inbreeding. Inbreeding depression analyses showed that a 1% increase in an animal's FPED resulted in a decrease of 1.20 kg, 2.03 kg, and 0.004 kg/d in WWT, YWT, and ADG, respectively. Maternal inbreeding showed significantly negative effects on progeny growth performance. AFC increased by 1.4 and 0.8 d for each 1% increase in FPED of the cow and her dam, respectively. Using genomic inbreeding, similar impact on growth traits was observed although the magnitude of the effect varied between methods. Across all genomic measures, WWT, YWT, and ADG decreased by 0.21 to 0.53 kg, 0.46 to 1.13 kg, and 0.002 to 0.006 kg/d for each 1% increase in genomic inbreeding, respectively. Four chromosomes (9, 12, 17, and 27) were identified to have a significant association between their homozygosity (FROH-CHR) and growth traits. Variability in genomic inbreeding could be useful when deciding between full and half-sib selection candidates. Despite the high level of inbreeding in this study, its negative impact on growth performance was not as severe as expected, which may be attributed to the purging of the deleterious alleles due to natural or artificial selection over time.
本研究旨在评估长时间封闭的 1 号 Hereford 牛群体的近交及其对生长和繁殖性状的影响。基于系谱（FPED）和基因组信息来估计近交程度。对于后者，根据基因组关系矩阵的对角线元素，使用估计的（FGRM）或固定的（FGRM0.5）次要等位基因频率或纯合段（ROH）（FROH），衍生出三种估计值。使用包含 10,186 头动物的系谱来计算 FPED。使用 785 头动物的 30,810 个 SNP 进行基因组近交评估。分析的性状包括初生重（BWT）、断奶重（WWT）、1 岁重（YWT）、日增重（ADG）和首次配种年龄（AFC）。每个动物的 ROH 数量介于 6 到 119 个片段之间，平均为 83 个。最短和最长的片段分别为 1.36 和 64.86 Mb，反映了过去 30 到 40 代中发生的古老和近期近交。FPED、FGRM、FGRM0.5 和 FROH 的平均近交率分别为 29.2%、16.1%、30.2%和 22.9%。FROH 与 FPED 的相关性最高（r = 0.66）。在父系半同胞家庭中，FPED 变化最小，但基因组近交程度存在很大差异。近交衰退分析表明，动物的 FPED 增加 1%，WWT、YWT 和 ADG 分别减少 1.20 公斤、2.03 公斤和 0.004 公斤/天。母系近交对后代生长性能有显著的负面影响。AFC 每增加 1%，牛及其母系的 FPED 分别增加 1.4 和 0.8 天。使用基因组近交，虽然效应的大小在不同方法之间有所不同，但对生长性状的影响是相似的。在所有基因组测量中，WWT、YWT 和 ADG 分别减少了 0.21 到 0.53 公斤、0.46 到 1.13 公斤和 0.002 到 0.006 公斤/天，每增加 1%的基因组近交。鉴定出 9、12、17 和 27 号染色体上的同质性（FROH-CHR）与生长性状之间存在显著关联。基因组近交程度的变化在决定全同胞和半同胞选择候选者时可能有用。尽管本研究中的近交程度很高，但对生长性能的负面影响并不像预期的那么严重，这可能是由于随着时间的推移，自然或人工选择清除了有害等位基因。
