Positive correlation between recombination rate and nucleotide diversity is shown under domestication selection in the chicken genome |
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Authors: | Lin Fang,Jia Ye,Ning Li,Yong Zhang,SongGang Li,Gane Ka-Shu Wong,Jun Wang |
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Affiliation: | (1) Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China;(2) Beijing Genomics Institute, Beijing, 101300, China;(3) Department of Medicine, University of Washington Genome Center, Fluke Hall, M/C, 352145 Seattle, USA;(4) Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark;(5) The Institute of Human Genetics, University of Aarhus, DK-8000 Aarhus C, Denmark |
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Abstract: | Positive correlation between recombination rate and nucleotide diversity has been observed in a wide variety of eukaryotes on megabase scale. On the basis of genome-wide chicken genetic variation map generated by comparing three domestic breeds with wild ancestor and the positions of markers on the genetic linkage map, we found that SNPs rates were similar for all chromosomes while the recombina- tion rates increased in micro chromosomes. In other words no correlation exists in chromosome size. Nevertheless, when we scanned the genome by calculating the values of each characteristic within non-overlapping windows, instead of single value for each chromosomes, the nucleotide diversity was found to be significantly correlated with the recombination rate (r=0.27, P<0.0005). Furthermore, the significant association not only existed between these two features, but also existed between all 6 pairwise combinations of nucleotide diversity, recombination rate, GC content and average gene length. This co-variation is very meaningful for the studies of sequence evolution. |
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Keywords: | recombination rate nucleotide diversity positive correlation domestication selection chicken |
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