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全基因组分析揭示了巴西印度瘤牛、欧洲牛、合成杂交牛和本地适应性牛的遗传结构及候选基因。

Genome-Wide Analyses Reveal the Genetic Architecture and Candidate Genes of Indicine, Taurine, Synthetic Crossbreds, and Locally Adapted Cattle in Brazil.

作者信息

Verardo Lucas Lima, E Silva Fabyano Fonseca, Machado Marco Antonio, do Carmo Panetto João Cláudio, de Lima Reis Faza Daniele Ribeiro, Otto Pamela Itajara, de Almeida Regitano Luciana Correia, da Silva Luiz Otávio Campos, do Egito Andréa Alves, do Socorro Maués Albuquerque Maria, Zanella Ricardo, da Silva Marcos Vinicius Gualberto Barbosa

机构信息

Animal Breeding Lab, Department of Animal Science, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Brazil.

Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil.

出版信息

Front Genet. 2021 Jul 27;12:702822. doi: 10.3389/fgene.2021.702822. eCollection 2021.

Abstract

Cattle population history, breeding systems, and geographic subdivision may be reflected in runs of homozygosity (ROH), effective population size ( ), and linkage disequilibrium (LD) patterns. Thus, the assessment of this information has become essential to the implementation of genomic selection on purebred and crossbred cattle breeding programs. In this way, we assessed the genotype of 19 cattle breeds raised in Brazil belonging to taurine, indicine, synthetic crossbreds, and Iberian-derived locally adapted ancestries to evaluate the overall LD decay patterns, , ROH, and breed composition. We were able to obtain a general overview of the genomic architecture of cattle breeds currently raised in Brazil and other tropical countries. We found that, among the evaluated breeds, different marker densities should be used to improve the genomic prediction accuracy and power of genome-wide association studies. Breeds showing low values indicate a recent inbreeding, also reflected by the occurrence of longer ROH, which demand special attention in the matting schemes to avoid extensive inbreeding. Candidate genes (e.g., , , , , , , , , and ) located in the identified ROH islands were evaluated, highlighting biological processes involved with milk production, behavior, rusticity, and fertility. Furthermore, we were successful in obtaining the breed composition regarding the taurine and indicine composition using single-nucleotide polymorphism (SNP) data. Our results were able to observe in detail the genomic backgrounds that are present in each breed and allowed to better understand the various contributions of ancestor breeds to the modern breed composition to the Brazilian cattle.

摘要

牛群的种群历史、繁育系统和地理细分可能会反映在纯合子片段(ROH)、有效种群大小( )和连锁不平衡(LD)模式中。因此,评估这些信息对于在纯种和杂交牛繁育计划中实施基因组选择至关重要。通过这种方式,我们评估了巴西饲养的19个牛品种的基因型,这些品种属于普通牛、瘤牛、合成杂交品种以及源自伊比利亚的本地适应品种,以评估总体LD衰减模式、 、ROH和品种组成。我们能够对巴西和其他热带国家目前饲养的牛品种的基因组结构有一个总体了解。我们发现,在所评估的品种中,应使用不同的标记密度来提高基因组预测准确性和全基因组关联研究的效能。显示低值的品种表明近期存在近亲繁殖,较长ROH的出现也反映了这一点,在配种方案中需要特别关注以避免广泛的近亲繁殖。对位于已识别的ROH岛中的候选基因(例如, 、 、 、 、 、 、 、 和 )进行了评估,突出了与产奶、行为、野性和繁殖力相关的生物学过程。此外,我们利用单核苷酸多态性(SNP)数据成功获得了关于普通牛和瘤牛组成的品种组成。我们的结果能够详细观察每个品种中存在的基因组背景,并有助于更好地理解祖先品种对巴西牛现代品种组成的各种贡献。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ebb/8353373/972d656acea8/fgene-12-702822-g001.jpg

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