Ogunbawo Adebisi R, Mulim Henrique A, Campos Gabriel S, Schinckel Allan P, Oliveira Hinayah Rojas de
Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA.
Department of Animal Biosciences, Interbull Centre, S-75007 Uppsala, Sweden.
Genes (Basel). 2024 Nov 21;15(12):1495. doi: 10.3390/genes15121495.
Advances in SNP arrays and reference genome assemblies have significantly transformed cattle genomics, particularly for (Zebu cattle). Many commercial SNP arrays were originally designed for , leading to ascertainment bias and the exclusion of crucial SNPs specific to Zebu populations. This review assesses progress in SNP array and reference genome development, with a focus on efforts tailored to Zebu populations and their impact on genomic selection and breeding efficiency.
We reviewed the relevant literature on the development of SNP arrays, reference genome assemblies, and SNP genotyping techniques used for Zebu cattle. Emphasis was placed on SNP arrays specifically designed for Zebu breeds, evaluating their contributions to genomic evaluations and identifying limitations in prediction accuracy.
Recent advancements, such as GeneSeek's low- and high-density SNP panels, have aimed to reduce ascertainment bias and include key SNPs for Zebu populations by providing breed-specific panels. These panels have been instrumental in identifying genomic regions associated with economically important traits in Nellore cattle. Studies show that tailored SNP arrays and breed-specific reference genomes can enhance genetic diversity assessment and improve genomic predictions, supporting more effective breeding programs for Zebu cattle.
Improved SNP arrays and breed-specific reference genomes are crucial for accurate genomic selection in Zebu cattle. Future efforts should prioritize expanding de novo assemblies, reducing ascertainment bias, and developing cost-effective genotyping solutions tailored to Zebu populations. Targeted genomic tools will ultimately enable more efficient breeding practices and enhance genomic selection for economically important traits in cattle.
单核苷酸多态性（SNP）芯片和参考基因组组装技术的进步显著改变了牛基因组学，尤其是对于瘤牛（泽布牛）。许多商业SNP芯片最初是为[未提及品种]设计的，导致了确定偏差，并排除了瘤牛群体特有的关键SNP。本综述评估了SNP芯片和参考基因组开发的进展，重点关注针对瘤牛群体的努力及其对基因组选择和育种效率的影响。
我们回顾了有关用于瘤牛的SNP芯片、参考基因组组装和SNP基因分型技术发展的相关文献。重点放在专门为瘤牛品种设计的SNP芯片上，评估它们对基因组评估的贡献，并确定预测准确性方面的局限性。
最近的进展，如GeneSeek的低密度和高密度SNP面板，旨在通过提供特定品种的面板来减少确定偏差，并纳入瘤牛群体的关键SNP。这些面板有助于识别与内洛尔牛经济重要性状相关的基因组区域。研究表明，定制的SNP芯片和特定品种的参考基因组可以增强遗传多样性评估并改善基因组预测，支持更有效的瘤牛育种计划。
改进的SNP芯片和特定品种的参考基因组对于瘤牛的准确基因组选择至关重要。未来的努力应优先扩大从头组装，减少确定偏差，并开发针对瘤牛群体的经济有效的基因分型解决方案。有针对性的基因组工具最终将实现更高效的育种实践，并增强对瘤牛经济重要性状的基因组选择。
