Braga Larissa G, Schenkel Flávio S, Chud Tatiane C S, Rodrigues Julia L, Saada Bacem, Machado Marco A, Panetto João C C, da Silva Marcos V G B, Munari Danísio P
Departamento de Ciências Exatas, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil 14884-900; Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1.
Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1.
J Dairy Sci. 2025 Sep;108(9):9876-9900. doi: 10.3168/jds.2024-26147. Epub 2025 Jun 11.
Natural and artificial selection leave footprints on the genome, known as selection signatures, that can indicate regions related to adaptive and economically important traits. The recurrent use of a limited number of sires and increased selection pressure may affect genetic diversity, potentially affecting long-term breeding programs. Among dairy cattle, the Holstein breed has been intensively selected to maximize productivity, particularly in Canada and the United States. In the dairy industry, the Gir breed plays an important role in milk production in tropical regions such as India and Latin America. Gir cattle were introduced into Brazil in the 19th and 20th centuries, and since 1985, this breed has been intensively selected for milk production. This study aimed to assess the genetic diversity and characterize the selection signatures in Holstein cattle from the United States and Canada (HOL), Gir cattle from India (GIR_IN), and Dairy Gir cattle from Brazil (GIR_BR). Genetic diversity was assessed by nucleotide diversity, single nucleotide variant density analysis, minor allele frequency, observed and expected heterozygosity, and the inbreeding coefficient. Selection signatures were identified via Tajima's D, the integrated haplotype score (iHS), the fixation index, and the cross-population extended haplotype homozygosity test for autosomes. Additionally, the analysis of selection signatures using Tajima's D and iHS was conducted for the X chromosome. Lower genetic diversity was observed in the HOL population, whereas the GIR_IN and GIR_BR populations presented greater diversity. Several genes previously related to economically important traits were identified as being under selection, including DNAJC18, FSHR, HELB, HMGA2, PLAG1, GAB3, and PTEN. In conclusion, the genes identified within the selection signatures were linked to several traits, including growth, reproduction, mastitis, milk production, heat tolerance, health, and adaptation.
自然选择和人工选择会在基因组上留下印记，即所谓的选择印记，这些印记可以指示与适应性和经济重要性状相关的区域。有限数量种公牛的反复使用以及选择压力的增加可能会影响遗传多样性，进而可能影响长期育种计划。在奶牛中，荷斯坦品种已被密集选育以实现生产力最大化，尤其是在加拿大和美国。在乳制品行业，吉尔品种在印度和拉丁美洲等热带地区的牛奶生产中发挥着重要作用。吉尔牛于19世纪和20世纪被引入巴西，自1985年以来，该品种一直在为产奶进行密集选育。本研究旨在评估美国和加拿大的荷斯坦牛（HOL）、印度的吉尔牛（GIR_IN）以及巴西的奶牛吉尔牛（GIR_BR）的遗传多样性，并对其选择印记进行特征分析。通过核苷酸多样性、单核苷酸变异密度分析、次要等位基因频率、观察到的和预期的杂合度以及近亲繁殖系数来评估遗传多样性。通过Tajima's D、综合单倍型评分（iHS）、固定指数以及常染色体的跨群体扩展单倍型纯合性检验来识别选择印记。此外，还对X染色体进行了使用Tajima's D和iHS的选择印记分析。在HOL群体中观察到较低的遗传多样性，而GIR_IN和GIR_BR群体表现出更高的多样性。先前与经济重要性状相关的几个基因被确定为处于选择状态，包括DNAJC18、FSHR、HELB、HMGA2、PLAG1、GAB3和PTEN。总之，在选择印记中鉴定出的基因与多个性状相关，包括生长、繁殖、乳腺炎、产奶、耐热性、健康和适应性。
