A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate

  1. Martien A.M. Groenen1,9,
  2. Per Wahlberg2,
  3. Mario Foglio4,
  4. Hans H. Cheng3,
  5. Hendrik-Jan Megens1,
  6. Richard P.M.A. Crooijmans1,
  7. Francois Besnier8,
  8. Mark Lathrop4,
  9. William M. Muir5,
  10. Gane Ka-Shu Wong6,7,
  11. Ivo Gut4 and
  12. Leif Andersson2,8
  1. 1 Animal Breeding and Genomics Centre, Wageningen University, 6700 AH Wageningen, The Netherlands;
  2. 2 Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 24 Uppsala, Sweden;
  3. 3 USDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, Michigan 48823, USA;
  4. 4 Centre National de Génotypage, 91057 Evry, France;
  5. 5 Department of Animal Sciences, Purdue University, West Lafayette, Indiana 47907, USA;
  6. 6 Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton AB, T6G 2E9, Canada;
  7. 7 Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China;
  8. 8 Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-751 24 Uppsala, Sweden

    Abstract

    The resolution of the chicken consensus linkage map has been dramatically improved in this study by genotyping 12,945 single nucleotide polymorphisms (SNPs) on three existing mapping populations in chicken: the Wageningen (WU), East Lansing (EL), and Uppsala (UPP) mapping populations. As many as 8599 SNPs could be included, bringing the total number of markers in the current consensus linkage map to 9268. The total length of the sex average map is 3228 cM, considerably smaller than previous estimates using the WU and EL populations, reflecting the higher quality of the new map. The current map consists of 34 linkage groups and covers at least 29 of the 38 autosomes. Sex-specific analysis and comparisons of the maps based on the three individual populations showed prominent heterogeneity in recombination rates between populations, but no significant heterogeneity between sexes. The recombination rates in the F1 Red Jungle fowl/White Leghorn males and females were significantly lower compared with those in the WU broiler population, consistent with a higher recombination rate in purebred domestic animals under strong artificial selection. The recombination rate varied considerably among chromosomes as well as along individual chromosomes. An analysis of the sequence composition at recombination hot and cold spots revealed a strong positive correlation between GC-rich sequences and high recombination rates. The GC-rich cohesin binding sites in particular stood out from other GC-rich sequences with a 3.4-fold higher density at recombination hot spots versus cold spots, suggesting a functional relationship between recombination frequency and cohesin binding.

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    This Article

    1. Published in Advance December 16, 2008, doi: 10.1101/gr.086538.108 Genome Res. 19: 510-519

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