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Assessing Bos taurus introgression in the UOA Bos indicus assembly.

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Comparing cattle genomes reveals taurine DNA segments within the indicine reference assembly. This finding aids in analyzing genetic variations and selection signatures in indicine cattle breeds.

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Area of Science:

  • Genomics
  • Comparative Genomics
  • Animal Genetics

Background:

  • Reference genomes are crucial for genomic data analysis.
  • Multiple reference genomes within species improve accuracy and reduce bias.
  • ARS_UCD1.2 (B. taurus) and UOA_Brahman_1 (B. indicus) are key cattle reference genomes.

Purpose of the Study:

  • To evaluate the impact of using two different cattle reference genomes (ARS_UCD1.2 and UOA_Brahman_1) on variant detection.
  • To identify potential misassemblies or regions of introgression in the UOA_Brahman_1 reference genome.
  • To provide a resource for analyzing genomic features in indicine cattle.

Main Methods:

  • Alignment of sequence data from 15 Bos taurus and Bos indicus breeds to both ARS_UCD1.2 and UOA_Brahman_1 reference genomes.
  • Single-nucleotide variant (SNV) calling and analysis of variant frequencies.
  • Principal component and admixture analyses to identify introgressed regions.

Main Results:

  • Alignment to UOA_Brahman_1 identified millions more SNVs in B. taurus and B. indicus samples compared to ARS_UCD1.2.
  • Regions with fewer than expected SNVs in B. taurus alignments to UOA_Brahman_1 suggest taurine DNA introgression.
  • These introgressed taurine segments constitute 13.7% of the UOA_Brahman_1 assembly and contain genes under positive selection.

Conclusions:

  • A list of taurine segments within the UOA_Brahman_1 assembly has been identified.
  • These findings are valuable for interpreting genomic features in indicine cattle.
  • The identified segments will aid future re-sequencing analyses for signatures of selection and other genomic patterns.