Assessing Bos taurus introgression in the UOA Bos indicus assembly

Authors: NAJI, MAULANA - University Of Natural Resources & Applied Life Sciences - Austria; UTSUNOMIYA, YURI - Sao Paulo State University (UNESP); SOLKNER, JOHANN - University Of Natural Resources & Applied Life Sciences - Austria; Rosen, Benjamin - Ben; MESZAROS, GABOR - University Of Natural Resources & Applied Life Sciences - Austria

Submitted to: Genetics Selection Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/29/2021
Publication Date: 12/18/2021
Citation: Naji, M.M., Utsunomiya, Y.T., Solkner, J., Rosen, B.D., Meszaros, G. 2021. Assessing Bos taurus introgression in the UOA Bos indicus assembly. Genetics Selection Evolution. 53:96. https://doi.org/10.1186/s12711-021-00688-1.
DOI: https://doi.org/10.1186/s12711-021-00688-1

Interpretive Summary: Reference genome sequences are essential in the analysis of genomic data. As the costs of sequencing decreases, many species now have access to multiple references. The correct choice of reference is essential to proper analysis of the genome. In this study, we confirmed that cross-alignments of individuals from one bovine subspecies to reference sequences of another leads to the discovery of three times more single-nucleotide variants (SNVs) with nearly fixed alternative alleles. Additionally, we report that 13.7% of the UOA_Brahman1 assembly is derived from B. taurus and provide a list of taurine segments within UOA_Brahman_1 assembly. This list will be useful in order to avoid confusing variant calling bias with interesting genomic features (e.g., signatures of selection, runs of homozygosity, increased mutation rate, etc) in the future re-sequencing analysis of indicine cattle.

Technical Abstract: Background: Reference genome sequences are essential in the analysis of genomic data. As the costs of sequencing decreases, multiple reference genomes are produced for a single species in order to cover nuances that are not captured by previous reference sequences. The latest reference sequence adopted by the scientific community for the analysis of cattle data is ARS_UCD1.2, built from DNA of a Hereford cow (Bos taurus). Complementary, the UOA_Brahman1 was recently built to represent the other cattle subspecies (Bos indicus) from a Brahman cow haplotype to further support the analysis of B. indicus data. In this study, we aligned sequence data of fifteen cattle breeds from B. taurus and B. indicus to both references. Results: We confirmed that cross-alignments of individuals from one bovine subspecies to reference sequences of another leads to the discovery of three times more single-nucleotide variants (SNVs) with nearly fixed alternative alleles. Interestingly, the alignment of B. taurus cattle to UOA_Brahman_1 revealed regions with lower than expected SNV counts with nearly fixed alternative alleles. Since Brahman cattle carry 10% of B. taurus introgression on average, we suggest that these regions comprise taurine DNA as opposed to indicine DNA in this particular genome. These taurine loci have been previously reported as being under positive selection in Brahman cattle, and include functional candidate genes implicated in feed efficiency, development and immunity. Overall, the taurine segments amounted to 13.7% of the UOA_Brahman1 assembly. Conclusions: We report a list of taurine segments within UOA_Brahman_1 assembly. This list will be useful in order to avoid confusing variant calling bias with interesting genomic features (e.g., signatures of selection, runs of homozygosity, increased mutation rate, etc) in the future re-sequencing analysis of indicine cattle.