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Positive correlation between recombination rate and nucleotide diversity is shown under domestication selection in the chicken genome

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分类：S831[农业科学—畜牧学;农业科学—畜牧兽医]
作者机构：[1]Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China, [2]Beijing Genomics Institute, Beijing 101300, China, [3]University of Washington Gen0me Center, Department of Medicine, Fluke Hall, M/C 352145, Seattle, USA, [4]Department of Biochemistry and Molecular Biology, University of Southem Denmark, DK-5230, Odense M, Denmark, [5]The Institute of Human Genetics, University of Aarhus, DK-8000 Aarhus C, Denmark
相关基金：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. 2006AAl0Al21 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. I）07030200740000）

作者： FANG Lin[2], YE Jia[2], LI Ning[1,2], ZHANG Yong[1,2], LI SongGang[1,2], GANE Ka-Shu WONG[3], WANG Jun[1,2,4,5]

关键词：小鸡, 基因组, 再结合率, 核苷多样性, 正相关性, recombination rate, nucleotide diversity, positive correlation, domestication selection, chicken

中文摘要：

在再结合率和核苷酸差异之间的积极关联在大基础规模上在许多优核质被观察了。根据基因变化地图由在基因连接地图上把三个国内品种与野祖先和标记的位置作比较产生了的染色体宽的鸡肉，当再结合率在微染色体增加了时，我们发现 SNP 率为所有染色体是类似的。换句话说，没有关联在染色体尺寸存在。但当我们由在非重叠的窗口以内计算每个特征的值扫描了染色体时，而不是为每个染色体的单个价值，核苷酸差异被发现显著地与再结合被相关，评价(r=0.27， P < 0.0005 ) 。而且，重要协会不仅在这二个特征之间存在，而且在所有 6 对之间存在核苷酸差异，再结合率， GC 内容和一般水准的明智的联合基因长度。这共变为顺序进化的研究是很有意义的。

英文摘要：

Positive correlation between recombination rate and nucleoUde 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 nucleoUde 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 nucleoUde 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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