Gao Junxin, Gonzalez-Prendes Rayner, Liu Ying, Kantanen Juha, Ginja Catarina, Ghanem Nasser, Kugonza Donald Rugira, Makgahlela Mahlako, Bovenhuis Henk, Groenen Martien A M, Crooijmans Richard P M A
Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands.
Natural Resources Institute Finland, Jokioinen, Finland.
BMC Genomics. 2025 Jul 1;26(1):615. doi: 10.1186/s12864-025-11828-y.
The Holstein Friesian (HF) cattle breed is the most dominant breed in commercial dairy farming worldwide and managed in more than 150 countries. These countries span diverse agro-climatic zones, ranging from tropical to cold regions. The introduction of HF animals in these regions occurred at different moments in the past which are poorly recorded and continued through importation of live animal and frozen semen. We hypothesize that the HF cattle populations in these regions underwent early forms of adaptation to these specific local environments. However, the detection of genetic variation associated with this adaptation remains poorly documented.
This study investigates genetic relationship and potential early selection signatures in HF populations from three African countries (Egypt, South Africa, Uganda) and three European countries (Finland, Portugal, The Netherlands), considering five animals per country. Approximately 16.0 million single nucleotide polymorphisms (SNPs) were detected in the 30 HF animals and used for further analyses. Across all countries, we identified dispersed regions totaling 3.3 megabase of ecosystem-specific genomic regions (43 genes), indicative of early selection signatures based on fixation indices (-statistic, st). Furthermore, comparing variants between tropical (Egypt and Uganda) and cold regions (Finland and The Netherlands) by st, nucleotide diversity ( ratio), and extended haplotype homozygosity (XP-EHH), we identified a total of 10 candidate regions, comprising 12 genes within a 0.57 megabase size. The regions were enriched with genes involved in signaling pathways associated directly or indirectly with adaptation, including the immune system (,, , , ,,and ), organ development and reproduction (, , , , , and ), thermogenic activation (), phospholipid metabolism ( and ), thermos-tolerance (), and stimulus response (, , and).
This study provides new insights into early forms of genetic plasticity of animals adapted to very diverse ecosystems. Our findings highlight candidate genes related to immune response, organ development, reproduction, metabolism, and thermo-tolerance, hypothesizing their role in facilitating adaptation to different environments.
The online version contains supplementary material available at 10.1186/s12864-025-11828-y.
荷斯坦奶牛品种是全球商业奶牛养殖中最主要的品种，在150多个国家均有养殖。这些国家跨越了从热带到寒冷地区的不同农业气候区。荷斯坦奶牛在这些地区的引入时间各不相同，且记录不详，目前仍通过活体动物和冷冻精液的进口持续进行。我们推测，这些地区的荷斯坦奶牛种群经历了早期适应这些特定当地环境的过程。然而，与这种适应相关的遗传变异的检测仍然记录较少。
本研究调查了来自三个非洲国家（埃及、南非、乌干达）和三个欧洲国家（芬兰、葡萄牙、荷兰）的荷斯坦奶牛种群的遗传关系和潜在的早期选择特征，每个国家选取了5头奶牛。在这30头荷斯坦奶牛中检测到了约1600万个单核苷酸多态性（SNP），并用于进一步分析。在所有国家中，我们确定了总计330万个碱基对的分散区域，这些区域是特定生态系统的基因组区域（43个基因），基于固定指数（F统计量，Fst）表明存在早期选择特征。此外，通过Fst、核苷酸多样性（π比值）和扩展单倍型纯合度（XP-EHH）比较热带地区（埃及和乌干达）和寒冷地区（芬兰和荷兰）之间的变异，我们总共确定了10个候选区域，在0.57兆碱基大小范围内包含12个基因。这些区域富含与适应直接或间接相关的信号通路中的基因，包括免疫系统（IL1A、IL1B、IL6、IL8、IL10、IL12B和ILX6）、器官发育和繁殖（HOXA10、HOXA11、HOXA13、HOXB13、WNT4和ESR1）、产热激活（UCP1）、磷脂代谢（PLCB1和PLCD3）、耐热性（HSP90AA1）以及刺激反应（FOS、JUN和EGR1）。
本研究为适应非常多样化生态系统的动物早期遗传可塑性形式提供了新的见解。我们的研究结果突出了与免疫反应、器官发育、繁殖、代谢和耐热性相关的候选基因，并推测了它们在促进适应不同环境中的作用。
在线版本包含可在10.1186/s12864-025-11828-y获取的补充材料。
