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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #356972

Research Project: Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Short communication: Identification of the pseudoautosomal region in the Hereford bovine reference genome assembly ARS-UCD1.2

Author
item JOHNSON, THOMAS - Collaborator
item KEEHAN, MICHAEL - Collaborator
item HARLAND, CHAD - Collaborator
item LOPDELL, THOMAS - Collaborator
item SPELMAN, RICHARD - Collaborator
item DAVIS, STEVE - Collaborator
item Rosen, Benjamin
item Smith, Timothy - Tim
item COULDREY, CHRISTINE - Collaborator

Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/4/2018
Publication Date: 4/1/2019
Citation: Johnson, T., Keehan, M., Harland, C., Lopdell, T., Spelman, R.J., Davis, S.R., Rosen, B.D., Smith, T.P., Couldrey, C. 2019. Short communication: Identification of the pseudoautosomal region in the Hereford bovine reference genome assembly ARS-UCD1.2. Journal of Dairy Science. 102(4):3254-3258. https://doi.org/10.3168/jds.2018-15638.
DOI: https://doi.org/10.3168/jds.2018-15638

Interpretive Summary: Genetic analysis of the X chromosome in cattle is complicated because most, but not all of the chromosome is single copy. For this reason, it is often ignored in genome wide association studies (GWAS) and genomic selection. Precise identification of the shared region between the X and Y chromosomes (pseudoautosomal region - PAR) will enable researchers to split the chromosome into defined segments to analyze with separate statistical models. Here we report the use of SNPchip genotypes, short read sequence, and long read sequences to fine map the PAR. These results greatly facilitate the inclusion of chromosome X in GWAS, genomic selection and other genetic analysis undertaken in cattle.

Technical Abstract: In cattle, the X chromosome accounts for approximately 3% and 6% of the genome in bulls and cows respectively. In spite of the large size of this chromosome, very few studies report analysis of the X chromosome in genome wide association studies (GWAS) and genomic selection. This lack of genetic interrogation is likely due to the complexities of undertaking these studies given the hemizygous state of some, but not all, of the X chromosome in males. The first step in facilitating analysis of this gene rich chromosome is to accurately identify coordinates for the pseudoautosomal boundary (PAB) in order to split the chromosome into a region that may be treated as autosomal sequence (pseudoautosomal region; PAR) and a region that requires more complex statistical models. With the recent release of ARS-UCD1.2, a more complete and accurate assembly of the cattle genome than was previously available, it is timely to fine map the PAB for the first time. Here we report the use of SNPchip genotypes, short read sequence, and long read sequences to fine map the PAB (ChrX:133,300,518) and simultaneously determine the neighbouring regions of reduced homology and true PAR. These results greatly facilitate the inclusion of chromosome X in GWAS, genomic selection and other genetic analysis undertaken on this reference genome.