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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Publications at this Location » Publication #349832

Research Project: Investigating Microbial, Digestive, and Animal Factors to Increase Dairy Cow Performance and Nutrient Use Efficiency

Location: Cell Wall Biology and Utilization Research

Title: Haplotype resolution of MHC in cattle through targeted enrichment and SMRT sequencing

Author
item Heimeier, Dorothea - The Pirbright Institute
item Schwartz, John - The Pirbright Institute
item Bickhart, Derek
item Smith, Timothy - Tim
item Hammond, John - The Pirbright Institute

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 5/9/2018
Publication Date: N/A
Citation: N/A

Interpretive Summary: Health and immunity to disease are desirable traits in the cattle breeding community. However, it is difficult to assess the genetics of these traits due to the complexity of the genes that are involved in keeping animals healthy. In this work, five different copies of a major gene related to animal health and immunity have been fully sequenced and characterized. With this information, it is now possible to assess structural differences between the genes and to identify genetic markers that can be used to track and validate them in a herd.

Technical Abstract: The MHC class I in cattle is highly diverse, including large copy number variations of polymorphic MHC class I genes, but our knowledge of this diversity is mostly limited to allelic diversity and not haplotype structure, with only three full haplotypes characterised. Haplotypes contain at least one to up to four classical class I genes between genes NC1 and TRIM26, with each classical gene belonging to one of six different allele groups. To date 114 cattle class I alleles have been deposited on the IPD-MHC database of which most are derived from the Holstein breed. The high structural diversity has made it difficult to assemble and fully characterise this region with short sequencing reads produced by second generation sequencing. Through targeted genome enrichment with Roche Nimblegen SeqCapEZ probes and subsequent long-read Single-Molecule-Real-Time (SMRT) sequencing we were able to de novo assemble five Holstein MHC haplotypes using individuals from an MHC homozygous herd. Approximately 80% of bases that mapped to the cattle chromosome 23 were located within the target region of ~3.4Mb, which included the class II region, producing an average coverage of 20x. The allele content was correct in each assembly and for the first time we have confirmed the location of each classical gene on the haplotype and generated the full gene sequence. Currently, we are adapting our analysis pipeline for heterozygous animals to identify new MHC haplotypes and alleles with confidence to develop our understanding of cattle MHC evolution.