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 recombination 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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Supported by the Chinese Academy of Sciences (Grant Nos. GJHZ0701-6 and KSCX2-YW-N-023), Ministry of Science and Technology under high-tech program 863 (Grant Nos. 2006AA10A121 and 2006AA02Z334), Chinese 973 Program (Grant Nos. 2007CB815703 and 2007CB815705), Ministry of Education (Grant No. XXBKYHT2006001), National Natural Science Foundation of China (Grant Nos. 30725008, 90608010, 90403130 and 90612019), and Chinese Municipal Science and Technology Commission (Grant No. D07030200740000)
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Fang, L., Ye, J., Li, N. et al. Positive correlation between recombination rate and nucleotide diversity is shown under domestication selection in the chicken genome. Chin. Sci. Bull. 53, 746–750 (2008). https://doi.org/10.1007/s11434-008-0159-y
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DOI: https://doi.org/10.1007/s11434-008-0159-y