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Open Access Research article

Integrating linkage and radiation hybrid mapping data for bovine chromosome 15

Warren M Snelling1*, Mathieu Gautier2, John W Keele1, Timothy PL Smith1, Roger T Stone1, Gregory P Harhay1, Gary L Bennett1, Naoya Ihara3, Akiko Takasuga3, Haruko Takeda3, Yoshikazu Sugimoto3 and André Eggen2

Author Affiliations

1 USDA, ARS, U.S. Meat Animal Research Center, Spur 18D, Clay Center, Nebraska 68933-0166, USA

2 Biochemical Genetics and Cytogenetics Unit, Department of Animal Genetics, Laboratory of Genetics and Biochemistry, INRA-CRJ 78350 Jouy-en-Josas, France

3 Shirakawa Institute of Animal Genetics, Livestock Technology Association of Japan, Fukushima, Japan

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BMC Genomics 2004, 5:77  doi:10.1186/1471-2164-5-77

Published: 8 October 2004

Abstract

Background

Bovine chromosome (BTA) 15 contains a quantitative trait loci (QTL) for meat tenderness, as well as several breaks in synteny with human chromosome (HSA) 11. Both linkage and radiation hybrid (RH) maps of BTA 15 are available, but the linkage map lacks gene-specific markers needed to identify genes underlying the QTL, and the gene-rich RH map lacks associations with marker genotypes needed to define the QTL. Integrating the maps will provide information to further explore the QTL as well as refine the comparative map between BTA 15 and HSA 11. A recently developed approach to integrating linkage and RH maps uses both linkage and RH data to resolve a consensus marker order, rather than aligning independently constructed maps. Automated map construction procedures employing this maximum-likelihood approach were developed to integrate BTA RH and linkage data, and establish comparative positions of BTA 15 markers with HSA 11 homologs.

Results

The integrated BTA 15 map represents 145 markers; 42 shared by both data sets, 36 unique to the linkage data and 67 unique to RH data. Sequence alignment yielded comparative positions for 77 bovine markers with homologs on HSA 11. The map covers approximately 32% of HSA 11 sequence in five segments of conserved synteny, another 15% of HSA 11 is shared with BTA 29. Bovine and human order are consistent in portions of the syntenic segments, but some rearrangement is apparent. Comparative positions of gene markers near the meat tenderness QTL indicate the region includes separate segments of HSA 11. The two microsatellite markers flanking the QTL peak are between defined syntenic segments.

Conclusions

Combining data to construct an integrated map not only consolidates information from different sources onto a single map, but information contributed from each data set increases the accuracy of the map. Comparison of bovine maps with well annotated human sequence can provide useful information about genes near mapped bovine markers, but bovine gene order may be different than human. Procedures to connect genetic and physical mapping data, build integrated maps for livestock species, and connect those maps to more fully annotated sequence can be automated, facilitating the maintenance of up-to-date maps, and providing a valuable tool to further explore genetic variation in livestock.