Exploring inbreeding depression in Brazilian Angus cattle population using pedigree and genomic data.

IF 2.8 3区生物学 Q2 GENETICS & HEREDITY

Frontiers in Genetics Pub Date : 2025-06-09 eCollection Date: 2025-01-01 DOI:10.3389/fgene.2025.1613820

Henrique A Mulim, Gabriel S Campos, Fernando Flores Cardoso, Hinayah Rojas de Oliveira

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引用次数: 0

Abstract

Introduction: 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.

Material and methods: 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_PED), genomic relationship matrix-based inbreeding (F_GRM), observed vs. expected homozygosity (F_HOM1), genotyped homozygosity (F_HOM2), correlation between uniting gametes (F_UNI), and runs of homozygosity (F_ROH). Traits related to growth, conformation, meat quality, reproduction, resistance to ectoparasites, and heat stress were analyzed.

Results: 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).

Discussion: 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.

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近交衰退是指由于与共同祖先交配的个体近交水平升高而导致的性能下降。本研究旨在利用6种不同的指标，基于家系和基因组信息估算近交系数，并评估巴西安格斯协会正式评估的不同性状近交抑制。材料和方法：共有13777只基因型动物，计算密度为78,837个snp，家谱文件中有530,327只动物，延伸至17代，用于分析。评估的近交指标包括：基于家系的近交（FPED）、基于基因组关系矩阵的近交（FGRM）、观察到的与预期的纯合性（FHOM1）、基因型纯合性（FHOM2）、统一配子之间的相关性（FUNI）和纯合度（FROH）。分析了猪的生长、构象、肉质、繁殖、抗外寄生虫和热胁迫等性状。结果：结果显示了一系列近交系数，用ROHs估算近交系数最高（0.13）。近交对各性状的影响以负向为主，其中毛被等性状的近交抑制显著。一些性状，如肌内脂肪和出生体重，与近亲繁殖呈正相关，表明一种复杂的性状特异性关系。较短的ROH片段（16 Mb）。讨论：这些发现强调了近交抑制的复杂性，并强调了在评估近交对各种性状的影响时考虑近交的范围和历史深度的重要性。总的来说，这项研究为巴西安格斯种群近亲繁殖抑制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牲畜种群近亲繁殖影响方面的有用性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Frontiers in Genetics Biochemistry, Genetics and Molecular Biology-Molecular Medicine

CiteScore

5.50

自引率

8.10%

发文量

3491

审稿时长

14 weeks

期刊介绍： Frontiers in Genetics publishes rigorously peer-reviewed research on genes and genomes relating to all the domains of life, from humans to plants to livestock and other model organisms. Led by an outstanding Editorial Board of the world’s leading experts, this multidisciplinary, open-access journal is at the forefront of communicating cutting-edge research to researchers, academics, clinicians, policy makers and the public. The study of inheritance and the impact of the genome on various biological processes is well documented. However, the majority of discoveries are still to come. A new era is seeing major developments in the function and variability of the genome, the use of genetic and genomic tools and the analysis of the genetic basis of various biological phenomena.