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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #326741

Research Project: Genomic and Metagenomic Approaches to Enhance Efficient and Sustainable Production of Beef Cattle

Location: Genetics and Animal Breeding

Title: Identification and expression analysis of bovine X degenerate YcChromosome genes

item PONCE DE LEON, F - University Of Minnesota
item GUO, Y - University Of Minnesota
item CROOKER, B - University Of Minnesota
item McDaneld, Tara
item Smith, Timothy - Tim

Submitted to: International Society for Animal Genetics (ISAG)
Publication Type: Abstract Only
Publication Acceptance Date: 4/23/2016
Publication Date: 7/23/2016
Citation: Ponce De Leon, F.A., Guo, Y., Crooker, B.A., McDaneld, T.G., Smith, T.P.L. 2016. Identification and expression analysis of bovine X degenerate YcChromosome genes [abstract]. International Society for Animal Genetics (35th ISAG). Abstract Book. p. 75 (Abstract #P3045). Available:

Interpretive Summary:

Technical Abstract: The Y chromosome male-specific region known as the MSY region comprises approximately 95% of the DNA content of the Y chromosome. Based on the few Y chromosomes that have been sequenced, it has been determined that its euchromatic region contains at least four different types of sequences: X-transposed (99% similarity with X), X-degenerate (60-96% to the X), ampliconic, and centromere repetitive sequences. X-degenerate Y-chromosome genes, are single copy, have an X chromosome counterpart (sequence homolog) and are largely housekeeping genes with broad expression profiles, or in some cases have acquired more specific functions, such as SRY, which regulates male sex determination. Understanding of sequence differences between X-degenerate Y-chromosome and their corresponding X-chromosome homolog genes will allow dissecting their specific spatial and temporal functional gender differences and provide us with a tool to identify whether the male copy or the female copy of the gene, or both, and of their isoforms are being expressed in any particular tissue. Our hypothesis is that for some of these genes there exist Y specific and X specific isoforms versions and that these X degenerate Y-chromosome gene isoforms as well as the X chromosome counterpart genes are expressed differentially across the fifteen different tissues that are being examined. To investigate our hypothesis we have used single molecule real time (SMRT) isoform sequencing (IsoSeq) of several tissues from a sire-daughter pair of Hereford animals (Domino/Dominette). Iso-seq transcriptome testes and liver libraries were obtained from Domino and Iso-seq transcriptome liver, lung, adipose, muscle and hypothalamus were obtained for Dominette. These seven Iso-seq libraries were used for bioinformatic analysis and isoform characterization of X-degenerate Y chromosome genes. Sequence comparisons allowed the identification of two isoforms for UTY and three for UTX; one isoform for ZFY and three for ZFX; six isoforms for RPS4Y1 and three for RPS4X; three isoforms for TBL1Y and two for TBL1X. Similarly, development of specific primers targeting gene sequence sites that differ between the Y and the X copy of the gene has allowed the specific amplification of the X-degenerate Y-chromosome copy of UTY, ZFY and USP9Y genes but not of RPS4Y1 in male tissues.