Mulim Henrique A, Campos Gabriel S, Cardoso Fernando Flores, Rojas de Oliveira Hinayah
Department of Animal Science, Purdue University, West Lafayette, IN, United States.
Brazilian Agricultural Research Corporation, Embrapa South Livestock Center, Bage, Brazil.
Front Genet. 2025 Jun 9;16:1613820. doi: 10.3389/fgene.2025.1613820. eCollection 2025.
Inbreeding depression refers to the decline in performance caused by increased levels of inbreeding, which results from mating individuals with common ancestors. This study aimed to estimate inbreeding coefficients based on both pedigree and genomic information using six different metrics and evaluate, the inbreeding depression on different traits officially evaluated by the Brazilian Angus Association.
A total of 13,777 genotyped animals, imputed to a density of 78,837 SNPs, and 530,327 animals in the pedigree file, extending up to 17 generations, were used in the analysis. The inbreeding metrics evaluated included: pedigree-based inbreeding (F), genomic relationship matrix-based inbreeding (F), observed vs. expected homozygosity (F), genotyped homozygosity (F), correlation between uniting gametes (F), and runs of homozygosity (F). Traits related to growth, conformation, meat quality, reproduction, resistance to ectoparasites, and heat stress were analyzed.
The results revealed a range of inbreeding coefficients, with inbreeding estimated using ROHs showing the highest values (0.13). The impact of inbreeding on various traits was predominantly negative, with significant inbreeding depression observed for traits such as hair coat. Some traits, such as intramuscular fat and birth weight, had positive associations with inbreeding, indicating a complex trait-specific relationship. Shorter ROH segments (<2 Mb) generally had smaller or beneficial effects compared to longer ROH segments (>16 Mb).
These findings underscore the complexity of inbreeding depression and highlight the importance of considering both the extent and historical depth of inbreeding when evaluating its effects on various traits. Overall, this research provides valuable insights into the genetic basis of inbreeding depression in the Brazilian Angus population and demonstrates the usefulness of genomic data in understanding and mitigating the impacts of inbreeding in livestock populations.
近亲繁殖衰退是指由于近亲繁殖程度增加而导致的性能下降，近亲繁殖是由具有共同祖先的个体交配引起的。本研究旨在使用六种不同指标，基于系谱和基因组信息估计近亲繁殖系数，并评估巴西安格斯协会官方评估的不同性状的近亲繁殖衰退情况。
分析中使用了总共13777头基因分型动物，推算至78837个单核苷酸多态性（SNP）的密度，以及系谱文件中的530327头动物，系谱延伸至17代。评估的近亲繁殖指标包括：基于系谱的近亲繁殖（F）、基于基因组关系矩阵的近亲繁殖（F）、观察到的与预期的纯合度（F）、基因分型纯合度（F）、结合配子之间的相关性（F）以及纯合性连续片段（F）。分析了与生长、体型、肉质、繁殖、对外寄生虫的抗性和热应激相关的性状。
结果显示了一系列近亲繁殖系数，使用纯合性连续片段估计的近亲繁殖显示出最高值（0.13）。近亲繁殖对各种性状的影响主要是负面的，在被毛等性状上观察到显著的近亲繁殖衰退。一些性状，如肌内脂肪和出生体重，与近亲繁殖呈正相关，表明存在复杂的性状特异性关系。与较长的纯合性连续片段（>16 Mb）相比，较短的纯合性连续片段（<2 Mb）通常具有较小或有益的影响。
这些发现强调了近亲繁殖衰退的复杂性，并突出了在评估其对各种性状的影响时考虑近亲繁殖程度和历史深度的重要性。总体而言，本研究为巴西安格斯种群近亲繁殖衰退的遗传基础提供了有价值的见解，并证明了基因组数据在理解和减轻家畜种群近亲繁殖影响方面的有用性。
