A High-Density SNP-Based Linkage Map of the Chicken Genome Reveals Sequence Features Correlated With Recombination Rate

Authors: GROENEN, MARTIEN - Wageningen University; WAHLBERG, PER - UPPSALA UNIVERSITY; FOGLIO, MARIO - Centre National De Genotypage; Cheng, Hans; MEGENS, HENDRIK - Wageningen University; CROOIJMANS, RICHARD - Wageningen University; BESNIER, FRANCOIS - Swedish University Of Agricultural Sciences; LATHROP, MARK - Centre National De Genotypage; MUIR, WILLIAM - Purdue University; WONG, GANE - University Of Alberta; GUT, IVO - Centre National De Genotypage; ANDERSSON, LEIF - Uppsala University

Submitted to: Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/23/2008
Publication Date: 3/10/2009
Citation: Groenen, M.A., Wahlberg, P., Foglio, M., Cheng, H.H., Megens, H.J., Crooijmans, R.P., Besnier, F., Lathrop, M., Muir, W.M., Wong, G.K., Gut, I., Andersson, L. 2009. A High-Density SNP-Based Linkage Map of the Chicken Genome Reveals Sequence Features Correlated With Recombination Rate. Genome Research. 19(3):510-519.

Interpretive Summary: Genetic maps initiated modern molecular genetics and genomics. Specifically, these maps form the foundation for genome sequence assemblies, and the markers derived from them allow the identification of genes controlling simple and complex traits, especially those of agronomic importance. In this paper, a high density genetic map of the chicken genome was developed using single nucleotide polymorphisms (SNPs), the latest and most abundant class of genetic marker. Joint analysis of the chicken genetic map and genome sequence indicate the chicken genome has special characteristics that influence genetic recombination. As genetic composition and recombination is how plants and animals are selected in commercial breeding companies, the derived information is of fundamental importance, especially geneticists in academia and companies.

Technical Abstract: The resolution of the widely used chicken consensus linkage map was highly enlarged by genotyping a total of 12,945 SNPs on the three existing mapping populations in chicken; the Wageningen (WU), East Lansing (EL) and Uppsala (UPP) mapping populations. A total of 8608 SNPs could be included on the map bringing the total number of markers on the current consensus linkage map to 9285. The total length of the current sex average map is 3310 cM, which is considerably smaller then previous estimates of the map using the same populations, reflecting the higher quality of the new map. The current map consists of 37 linkage groups and covers at least 29 of the 38 autosomes. Assuming that the seven new linkage groups each represent an individual chromosome, the number of autosomes covered by the current map is 36. Sex specific analysis and comparisons of the maps based on the three individual populations show prominent heterogeneity in recombination rates between populations and no significant heterogeneity between sexes. Our data shows that recombination rates in the F1 Red Junglefowl/White Leghorn males and females from the UPP and EL populations are significantly lower compared with those in the WU broiler population, which appears to be consistent with a higher recombination rate in purebred domestic animals under strong artificial selection. Recombination rate varies considerably between the different chromosomes as well as along individual chromosomes and analysis of the sequence composition at recombination hot and cold spots clearly indicates a high correlation with GC rich sequences. From all specific GC-rich sequences analyzed, cohesin binding sites in particular stand out from the other GC- rich sequences with a 3.4 fold higher density at recombination hot spots versus recombination cold spots, suggesting a functional relationship between recombination frequency and cohesin binding.