Tailoring Genomic Selection for : A Comprehensive Review of SNP Arrays and Reference Genomes.

BACKGROUND

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.

METHODS

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.

RESULTS

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.

CONCLUSIONS

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.