van der Nest Magriet A, Hlongwane Nompilo, Hadebe Khanyisile, Chan Wai-Yin, van der Merwe Nicolaas A, De Vos Lieschen, Greyling Ben, Kooverjee Bhaveni B, Soma Pranisha, Dzomba Edgar F, Bradfield Michael, Muchadeyi Farai C
Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa.
Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
Front Genet. 2021 Jan 28;11:608650. doi: 10.3389/fgene.2020.608650. eCollection 2020.
In this study, we evaluated an admixed South African Simbra crossbred population, as well as the Brahman (Indicine) and Simmental (Taurine) ancestor populations to understand their genetic architecture and detect genomic regions showing signatures of selection. Animals were genotyped using the Illumina BovineLD v2 BeadChip (7K). Genomic structure analysis confirmed that the South African Simbra cattle have an admixed genome, composed of 5/8 Taurine and 3/8 Indicine, ensuring that the Simbra genome maintains favorable traits from both breeds. Genomic regions that have been targeted by selection were detected using the linkage disequilibrium-based methods iHS and Rsb. These analyses identified 10 candidate regions that are potentially under strong positive selection, containing genes implicated in cattle health and production (e.g., TRIM63, KCNA10, NCAM1, SMIM5, MIER3, and SLC24A4). These adaptive alleles likely contribute to the biological and cellular functions determining phenotype in the Simbra hybrid cattle breed. Our data suggested that these alleles were introgressed from the breed's original indicine and taurine ancestors. The Simbra breed thus possesses derived parental alleles that combine the superior traits of the founder Brahman and Simmental breeds. These regions and genes might represent good targets for physiological studies, selection of breeding material and eventually even gene editing, for improved traits in modern cattle breeds. This study represents an important step toward developing and improving strategies for selection and population breeding to ultimately contribute meaningfully to the beef production industry.
在本研究中，我们评估了一个南非辛布拉杂交群体，以及婆罗门牛（瘤牛）和西门塔尔牛（普通牛）这两个祖先群体，以了解它们的遗传结构，并检测显示选择特征的基因组区域。使用Illumina BovineLD v2 BeadChip（7K）对动物进行基因分型。基因组结构分析证实，南非辛布拉牛具有混合基因组，由5/8的普通牛和3/8的瘤牛组成，确保了辛布拉基因组保留了两个品种的优良性状。使用基于连锁不平衡的iHS和Rsb方法检测受选择靶向的基因组区域。这些分析确定了10个可能受到强烈正选择的候选区域，其中包含与牛的健康和生产相关的基因（例如，TRIM63、KCNA10、NCAM1、SMIM5、MIER3和SLC24A4）。这些适应性等位基因可能有助于决定辛布拉杂交牛品种表型的生物学和细胞功能。我们的数据表明，这些等位基因是从该品种的原始瘤牛和普通牛祖先那里渗入的。因此，辛布拉品种拥有源自亲本的等位基因，这些等位基因结合了创始品种婆罗门牛和西门塔尔牛的优良性状。这些区域和基因可能是生理学研究、育种材料选择乃至最终基因编辑的良好靶点，以改善现代牛品种的性状。这项研究是朝着制定和改进选择及群体育种策略迈出的重要一步，最终对牛肉生产行业做出有意义的贡献。
