Genuíno Maria Victória Henrique, Bessa Ayrton Fernandes de Oliveira, da Silva Roney Teixeira, Câmara Giovanna Maria Dos Santos, Panetto João Cláudio do Carmo, Machado Marco Antônio, Caetano Sabrina Luzia, Ramos Salvador Boccaletti, Munari Danísio Prado, Sonstegard Tad, Barbosa da Silva Marcos Vinícius Gualberto, Buzanskas Marcos Eli
Universidade Federal da Paraíba (UFPB), Areia, PB, 58397-000, Brazil.
School of Agricultural and Veterinarian Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil.
Mamm Genome. 2025 Apr 2. doi: 10.1007/s00335-025-10125-z.
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.
基因组学和生物信息学的技术进步使得研究品种的遗传结构以及理解世代选择所导致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尔牛、吉尔牛和红信德牛的选择信号（SS），以识别由于种群形成和选择历史而产生的不同变异，重点关注来自巴西的动物的选择信号。使用种群间扩展单倍型纯合性（XP-EHH）、种群间位点特异性扩展单倍型纯合性比率（Rsb）和等位基因固定指数（Fst）来检测选择信号。考虑到50千碱基的窗口大小，采用非滑动窗口方法来定义选择信号区域。在内洛尔牛、吉尔牛和红信德牛的选择信号区域内分别共定位了62个、57个和72个基因，并用于对每个品种进行功能分析。大多数基因与生产和繁殖性状相关，而其他基因则与耐热性、免疫系统、性情和毛色有关。鉴于来自巴西和亚洲大陆的动物经历了不同的选择过程，所确定的选择信号表明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要求。与耐热性、性情和免疫系统相关基因的鉴定表明，特定等位基因使动物能够适应巴西的环境条件和选择标准。了解选择信号可以支持内洛尔牛、吉尔牛和红信德牛的育种策略，有助于增强抗性、适应性和生产力，以满足粮食生产需求。
