A 1.4-Mb interval RH map of horse chromosome 17 provides detailed comparison with human and mouse homologues

Exceptional conservation of horse–human gene order on X chromosome revealed by high-resolution radiation hybrid mapping

“…This was followed by multiple alignment of the sequences in CLUSTALW (http:͞͞bioweb.pasteur.fr͞seqanal͞interfaces͞ clustalw-simple.html). The alignments were used to design heterologous primers for PCR amplification of horse DNA in a hamster DNA background, as described (45,47,48). Briefly, all primers were derived either from a single exon or from two adjacent exons, leaving an Ϸ500-to 700-bp intron between, and chosen for 100% sequence identity among human, cattle, pig, etc., orthologues but with one to three mismatches with the rodent (mouse, rat) sequences.…”

“…Horse and hamster genomic DNAs were used to optimize the PCR conditions for individual primer pairs, such that only horse-specific DNA amplification was obtained, and all equine PCR amplification products were verified by sequencing. The identities of the sequences were confirmed through BLAST (www.ncbi.nlm.nih.gov͞BLAST) and BLAT (http:͞͞genome.ucsc.edu͞cgi-bin͞hgBlat?commandϭ start) searches, as described (45), and all comparisons were revalidated against the latest build of sequence data at University of California, Santa Cruz, and Ensembl. For RPS6KA3 (see Table 1), new primers were designed by using sequence data obtained from the first primer pair.…”

“…Building on our recent success in developing high-resolution gene maps for ECA17 (45), ECA22 (A. L. Gustafson, T.R., M. L. Wagner, J.R.M., L.C.S., and B.P.C., unpublished work), and a targeted region of ECA26 (46), we undertook development of a high-resolution gene map of ECAX by stepwise selection of gene-specific markers from the human and mouse X chromosome sequence templates. This effort has resulted in a dense and comprehensive map second only to the detailed maps in humans and mice and will lay the foundation for identifying and analyzing X linked genes involved in equine reproduction and genetic disorders.…”

Mapping the horse genome and its impact on equine genomics for identification of genes for monogenic and complex traits – a review

“…A great progress was the more extensive 5000-rad whole-genome-radiation hybrid panel that was constructed using 92 horse x hamster hybrid cell lines and 730 equine markers (type I and type II markers) . This panel was one of the most essential tools to construct high-resolution and comparative maps for ECA11 , ECAX (RAUDSEPP et al, 2004), ECA17 (LEE et al, 2004), ECA22 (GUSTAFSON-SEABURY et al, 2005), ECA4 (DIERKS et al, 2006), equine homologs of HSA19 on ECA17, ECA10 and ECA21 (BRINKMEYER-LANGFORD et al, 2005) and equine homologs of HSA2 on ECA6p, ECA15 and ECA18 (WAGNER et al, 2006).…”

“…A detailed physical map of the equine Ychromosome was generated ) and compared to the human and other mammalian species with the result that the equine Y-chromosome shows the most homology with the Y-chromosome of the pig. A comparative RH map for ECA17 was developed by LEE et al (2004), and there exists a detailed RH map of ECA22 comparing the equine loci to human, dog, cat, bovids, elephant and bat, rodents, dolphins and other mammalians (GUSTAFSON-SEABURY et al, 2005). This map covered estimated 64 Mb of physical length of chromosome 22 (831 cR) and the 83 markers had an average distance of 10 cR.…”