Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome

Zhihua Jiang, Jenna S. Melville, Honghe Cao, Sudhir Kumar, Alan Filipski, Ann M. Verrinder Gibbins

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Based on published information, we have identified 991 genes and gene-family clusters for cattle and 764 for pigs that have orthologues in the human genome. The relative linear locations of these genes on human sequence maps were used as "rulers" to annotate bovine and porcine genomes based on a CSAM (contiguous sets of autosomal markers) approach. A CSAM is an uninterrupted set of markers in one genome (primary genome; the human genome in this study) that is syntenic in the other genome (secondary genome; the bovine and porcine genomes in this study). The analysis revealed 81 conserved syntenies and 161 CSAMs between human and bovine autosomes and 50 conserved syntenies and 95 CSAMs between human and porcine autosomes. Using the human sequence map as a reference, these 991 and 764 markers could correlate 72 and 74% of the human genome with the bovine and porcine genomes, respectively. Based on the number of contiguous markers in each CSAM, we classified these CSAMs into five size groups as follows: singletons (one marker only), small (2-4 markers), medium (5-10 markers), large (11-20 markers), and very large (>20 markers). Several bovine and porcine chromosomes appear to be represented as di-CSAM repeats in a tandem or dispersed way on human chromosomes. The number of potential CSAMs for which no markers are currently available were estimated to be 63 between human and bovine genomes and 18 between human and porcine genomes. These results provide basic guidelines for further gene and QTL mapping of the bovine and porcine genomes, as well as insight into the evolution of mammalian genomes.

Original languageEnglish (US)
Pages (from-to)769-776
Number of pages8
JournalGenome
Volume45
Issue number4
DOIs
StatePublished - 2002
Externally publishedYes

Fingerprint

Human Genome
Swine
Genome
swine
genome
cattle
autosomes
Chromosome Mapping
Human Chromosomes
Multigene Family
genes
Genes
chromosomes
Chromosomes
tandem repeat sequences
Guidelines
group size
quantitative trait loci

Keywords

  • Cattle
  • Comparative mapping
  • CSAM
  • Human
  • Orthologous genes
  • Pig

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biotechnology
  • Genetics
  • Genetics(clinical)

Cite this

Jiang, Z., Melville, J. S., Cao, H., Kumar, S., Filipski, A., & Verrinder Gibbins, A. M. (2002). Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome. Genome, 45(4), 769-776. https://doi.org/10.1139/g02-038

Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome. / Jiang, Zhihua; Melville, Jenna S.; Cao, Honghe; Kumar, Sudhir; Filipski, Alan; Verrinder Gibbins, Ann M.

In: Genome, Vol. 45, No. 4, 2002, p. 769-776.

Research output: Contribution to journalArticle

Jiang, Z, Melville, JS, Cao, H, Kumar, S, Filipski, A & Verrinder Gibbins, AM 2002, 'Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome', Genome, vol. 45, no. 4, pp. 769-776. https://doi.org/10.1139/g02-038
Jiang, Zhihua ; Melville, Jenna S. ; Cao, Honghe ; Kumar, Sudhir ; Filipski, Alan ; Verrinder Gibbins, Ann M. / Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome. In: Genome. 2002 ; Vol. 45, No. 4. pp. 769-776.
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