Selection signatures detection in Nelore, Gir, and Red Sindhi cattle breeds.

IF 2.7 4区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY
Maria Victória Henrique Genuíno, Ayrton Fernandes de Oliveira Bessa, Roney Teixeira da Silva, Giovanna Maria Dos Santos Câmara, João Cláudio do Carmo Panetto, Marco Antônio Machado, Sabrina Luzia Caetano, Salvador Boccaletti Ramos, Danísio Prado Munari, Tad Sonstegard, Marcos Vinícius Gualberto Barbosa da Silva, Marcos Eli Buzanskas
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引用次数: 0

Abstract

Technological advances in genomics and bioinformatics made it possible to study the genetic structure of breeds and understand genome changes caused by selection over generations. Our objective was to evaluate selection signatures (SS) in Nelore, Gir, and Red Sindhi cattle from Brazil and the Asian continent to identify divergent variants due to the history of formation and selection of populations, with a focus on the SS of animals from Brazil. Extended haplotype homozygosities between populations (XP-EHH), the ratio of site-specific extended haplotype homozygosity between populations (Rsb), and the allelic fixation index (Fst) were used to detect SS. Considering a window size of 50-kb, a non-sliding window approach was used to define SS regions. A total of 62, 57, and 72 genes were co-located within SS regions for Nelore, Gir, and Red Sindhi, respectively, and used to perform functional analyses per breed. Most genes were associated with productive and reproductive traits, while others were related to thermotolerance, the immune system, temperament, and coat color. The identified SS demonstrate how animal breeding programs shape the genetic makeup of these breeds to meet production system requirements, given that animals from Brazil and the Asian continent have undergone different selection processes. The identification of genes related to thermotolerance, temperament, and the immune system suggests specific alleles have enabled animals to adapt to environmental conditions and selection criteria in Brazil. Understanding SS can support breeding strategies for Nelore, Gir, and Red Sindhi cattle, contributing to enhanced resistance, adaptation, and productivity to meet food production demands.

Nelore, Gir和Red Sindhi牛品种的选择特征检测。
基因组学和生物信息学的技术进步使研究品种的遗传结构和了解世代选择引起的基因组变化成为可能。我们的目标是评估来自巴西和亚洲大陆的内洛雷牛、吉尔牛和红信德牛的选择特征(SS),以确定由于种群形成和选择的历史而产生的不同变异,重点关注巴西动物的选择特征。采用群体间扩展单倍型纯合子(XP-EHH)、群体间位点特异性扩展单倍型纯合子比率(Rsb)和等位基因固定指数(Fst)检测SS区域。考虑到窗口大小为50 kb,采用非滑动窗口法定义SS区域。在nore、Gir和Red Sindhi的SS区域内共定位了62个、57个和72个基因,并对每个品种进行了功能分析。大多数基因与生产和生殖性状有关,而其他基因则与耐热性、免疫系统、气质和毛色有关。确定的SS展示了动物育种计划如何塑造这些品种的基因组成,以满足生产系统的要求,因为来自巴西和亚洲大陆的动物经历了不同的选择过程。与耐热性、性情和免疫系统相关的基因鉴定表明,特定的等位基因使动物能够适应巴西的环境条件和选择标准。了解SS可以支持Nelore、Gir和Red Sindhi牛的育种策略,有助于增强抵抗力、适应性和生产力,以满足粮食生产需求。
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来源期刊
Mammalian Genome
Mammalian Genome 生物-生化与分子生物学
CiteScore
4.00
自引率
0.00%
发文量
33
审稿时长
6-12 weeks
期刊介绍: Mammalian Genome focuses on the experimental, theoretical and technical aspects of genetics, genomics, epigenetics and systems biology in mouse, human and other mammalian species, with an emphasis on the relationship between genotype and phenotype, elucidation of biological and disease pathways as well as experimental aspects of interventions, therapeutics, and precision medicine. The journal aims to publish high quality original papers that present novel findings in all areas of mammalian genetic research as well as review articles on areas of topical interest. The journal will also feature commentaries and editorials to inform readers of breakthrough discoveries as well as issues of research standards, policies and ethics.
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