A detailed physical map of the horse Y chromosome

Terje Raudsepp, Avni Santani, Barbara Wallner, Srinivas R. Kata, Chengwei Ren, Hong Bin Zhang, James E. Womack, Loren C. Skow, Bhanu P. Chowdhary

Research output: Contribution to journalArticlepeer-review

62 Citations (Scopus)


We herein report a detailed physical map of the horse Y chromosome. The euchromatic region of the chromosome comprises ≈15 megabases (Mb) of the total 45- to 50-Mb size and lies in the distal one-third of the long arm, where the pseudoautosomal region (PAR) is located terminally. The rest of the chromosome is predominantly heterochromatic. Because of the unusual organization of the chromosome (common to all mammalian Y chromosomes), a number of approaches were used to crossvalidate the results. Analysis of the 5,000-rad horse × hamster radiation hybrid panel produced a map spanning 88 centirays with 8 genes and 15 sequence-tagged site (STS) markers. The map was verified by several fluorescence in situ hybridization approaches. Isolation of bacterial artificial chromosome (BAC) clones for the radiation hybrid-mapped markers, end sequencing of the BACs, STS development, and bidirectional chromosome walking yielded 109 markers (100 STS and 9 genes) contained in 73 BACs. STS content mapping grouped the BACs into seven physically ordered contigs (of which one is predominantly ampliconic) that were verified by metaphase-, interphase-, and fiber-fluorescence in situ hybridization and also BAC fingerprinting. The map spans almost the entire euchromatic region of the chromosome, of which 20-25% (≈4 Mb) is covered by isolated BACs. The map is presently the most informative among Y chromosome maps in domesticated species, third only to the human and mouse maps. The foundation laid through the map will be critical in obtaining complete sequence of the euchromatic region of the horse Y chromosome, with an aim to identify Y specific factors governing male infertility and phenotypic sex variation.

Original languageEnglish
Pages (from-to)9321-9326
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number25
Publication statusPublished - Jun 22 2004
Externally publishedYes


  • Gene map

ASJC Scopus subject areas

  • General


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