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Regional Differences in Recombination Hotspots Between Two Chicken Populations

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Regional Differences in Recombination Hotspots Between Two Chicken Populations

Martin G Elferink et al. BMC Genet.

Abstract

Background: Although several genetic linkage maps of the chicken genome have been published, the resolution of these maps is limited and does not allow the precise identification of recombination hotspots. The availability of more than 3.2 million SNPs in the chicken genome and the recent advances in high throughput genotyping techniques enabled us to increase marker density for the construction of a high-resolution linkage map of the chicken genome. This high-resolution linkage map allowed us to study recombination hotspots across the genome between two chicken populations: a purebred broiler line and a broiler x broiler cross. In total, 1,619 animals from the two different broiler populations were genotyped with 17,790 SNPs.

Results: The resulting linkage map comprises 13,340 SNPs. Although 360 polymorphic SNPs that had not been assigned to a known chromosome on chicken genome build WASHUC2 were included in this study, no new linkage groups were found. The resulting linkage map is composed of 31 linkage groups, with a total length of 3,054 cM for the sex-average map of the combined population. The sex-average linkage map of the purebred broiler line is 686 cM smaller than the linkage map of the broiler x broiler cross.

Conclusions: In this study, we present a linkage map of the chicken genome at a substantially higher resolution than previously published linkage maps. Regional differences in recombination hotspots between the two mapping populations were observed in several chromosomes near the telomere of the p arm; the sex-specific analysis revealed that these regional differences were mainly caused by female-specific recombination hotspots in the broiler x broiler cross.

Figures

Figure 1
Figure 1
Sex-average recombination rate for populations 1 and 2. Recombination rate was calculated for 500 kb nonoverlapping bins, and plotted using a sliding window of eight bins. Population 1 is shown in red and population 2 is shown in blue. On the x-axis, the genomic position is given in million base pairs. On the y-axis, the recombination rate is given in cM/Mb. If known, the position of the centromer is indicated by a solid black line. GGA16, GGA21--GGA28, LGE22, and LGE64 were not included in this figure, because the graphs of these 11 small chromosomes were uninformative. Note that the scale of the y-axis of GGA1 is twice as high as for the other chromosomes.
Figure 2
Figure 2
Sex-specific recombination rate for populations 1 and 2. Recombination rate was calculated for 500 kb nonoverlapping bins, and plotted using a sliding window of eight bins. The female map of population 1 is shown in blue, and the male map of population 1 is shown in red. The female map of population 2 is shown in purple, and the male map of population 2 is shown in green. On the x-axis, the genomic position is given in million basepairs. On the y-axis, the recombination rate is given in cM/Mb. If known, the position of the centromer is indicated by a solid black line. GGA16, GGA21--GGA28, LGE22, and LGE64 were not included in this figure, because the graphs of these 11 small chromosomes were uninformative. Note that the scale of the y-axis of GGA1 is twice as high as for the other chromosomes.

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