Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken.
Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken.
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DOI：
10.1186/1471-2156-10-86
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发表时间：
2009-12-20
期刊：
影响因子：
2.9
通讯作者：
Groenen MA
中科院分区：
文献类型：
--
作者：
Megens HJ;Crooijmans RP;Bastiaansen JW;Kerstens HH;Coster A;Jalving R;Vereijken A;Silva P;Muir WM;Cheng HH;Hanotte O;Groenen MA
鸡（Gallus gallus），像大多数鸟类物种一样，具有非常独特的核型，由许多微小染色体和少数大型染色体组成。虽然已知微染色体的重组频率比大染色体高得多，但关于这两类染色体之间的连锁不平衡（LD）和单倍型多样性的差异的信息有限。在这项研究中，LD和单倍型多样性系统的特点是在371只鸟从8个鸡种群（商业线，花式品种，和红色原鸡）在宏观和微观染色体。为此，我们以每2kb 1个SNP的高密度（总共889个SNP）在大染色体（GGA 1和GGA 2）上采样了4个约1cM的区域，并且在小染色体（GGA 26和GGA 27）上采样了4个1.5 - 2cM的区域。在相似的物理距离，LD，单倍型纯合性，单块结构，和单倍型共享都较低的微相比，宏染色体。这些差异在人群中是一致的。微染色体的杂合性、遗传分化和衍生等位基因频率也较高。LD，单倍型变异，和单倍型共享种群之间的差异在很大程度上符合已知的人口统计学史的商品鸡。尽管LD的水平非常低，如测量的R2为大多数人口，观察到一些单块结构，特别是在大染色体，但单块大小通常小于10 kb。LD之间的差异微观和宏观染色体几乎完全解释了重组率的差异。微染色体和大染色体之间的单倍型多样性和单倍型共享的差异被解释为重组率和基因型变异的差异。单块结构是一致的鸡种群的人口统计学，和微观和宏观染色体之间的重组率的差异。有限的单倍体结构和LD表明，未来的全基因组标记分析将需要100+K SNP来利用单倍型信息。遗传参数的解释和可转移性需要考虑鸡染色体的大小，而且由于大多数鸟类都有微染色体，因此其他鸟类也有。
The chicken (Gallus gallus), like most avian species, has a very distinct karyotype consisting of many micro- and a few macrochromosomes. While it is known that recombination frequencies are much higher for micro- as compared to macrochromosomes, there is limited information on differences in linkage disequilibrium (LD) and haplotype diversity between these two classes of chromosomes. In this study, LD and haplotype diversity were systematically characterized in 371 birds from eight chicken populations (commercial lines, fancy breeds, and red jungle fowl) across macro- and microchromosomes. To this end we sampled four regions of ~1 cM each on macrochromosomes (GGA1 and GGA2), and four 1.5 -2 cM regions on microchromosomes (GGA26 and GGA27) at a high density of 1 SNP every 2 kb (total of 889 SNPs). At a similar physical distance, LD, haplotype homozygosity, haploblock structure, and haplotype sharing were all lower for the micro- as compared to the macrochromosomes. These differences were consistent across populations. Heterozygosity, genetic differentiation, and derived allele frequencies were also higher for the microchromosomes. Differences in LD, haplotype variation, and haplotype sharing between populations were largely in line with known demographic history of the commercial chicken. Despite very low levels of LD, as measured by r2 for most populations, some haploblock structure was observed, particularly in the macrochromosomes, but the haploblock sizes were typically less than 10 kb. Differences in LD between micro- and macrochromosomes were almost completely explained by differences in recombination rate. Differences in haplotype diversity and haplotype sharing between micro- and macrochromosomes were explained by differences in recombination rate and genotype variation. Haploblock structure was consistent with demography of the chicken populations, and differences in recombination rates between micro- and macrochromosomes. The limited haploblock structure and LD suggests that future whole-genome marker assays will need 100+K SNPs to exploit haplotype information. Interpretation and transferability of genetic parameters will need to take into account the size of chromosomes in chicken, and, since most birds have microchromosomes, in other avian species as well.
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影响因子：
64.8
作者：
Frazer, Kelly A.;Ballinger, Dennis G.;Cox, David R.;Hinds, David A.;Stuve, Laura L.;Gibbs, Richard A.;Belmont, John W.;Boudreau, Andrew;Hardenbol, Paul;Leal, Suzanne M.;Pasternak, Shiran;Wheeler, David A.;Willis, Thomas D.;Yu, Fuli;Yang, Huanming;Zeng, Changqing;Gao, Yang;Hu, Haoran;Hu, Weitao;Li, Chaohua;Lin, Wei;Liu, Siqi;Pan, Hao;Tang, Xiaoli;Wang, Jian;Wang, Wei;Yu, Jun;Zhang, Bo;Zhang, Qingrun;Zhao, Hongbin;Zhao, Hui;Zhou, Jun;Gabriel, Stacey B.;Barry, Rachel;Blumenstiel, Brendan;Camargo, Amy;Defelice, Matthew;Faggart, Maura;Goyette, Mary;Gupta, Supriya;Moore, Jamie;Nguyen, Huy;Onofrio, Robert C.;Parkin, Melissa;Roy, Jessica;Stahl, Erich;Winchester, Ellen;Ziaugra, Liuda;Altshuler, David;Shen, Yan;Yao, Zhijian;Huang, Wei;Chu, Xun;He, Yungang;Jin, Li;Liu, Yangfan;Shen, Yayun;Sun, Weiwei;Wang, Haifeng;Wang, Yi;Wang, Ying;Xiong, Xiaoyan;Xu, Liang;Waye, Mary M. Y.;Tsui, Stephen K. W.;Wong, J. Tze-Fei;Galver, Luana M.;Fan, Jian-Bing;Gunderson, Kevin;Murray, Sarah S.;Oliphant, Arnold R.;Chee, Mark S.;Montpetit, Alexandre;Chagnon, Fanny;Ferretti, Vincent;Leboeuf, Martin;Olivier, Jean-Franccois;Phillips, Michael S.;Roumy, Stephanie;Sallee, Clementine;Verner, Andrei;Hudson, Thomas J.;Kwok, Pui-Yan;Cai, Dongmei;Koboldt, Daniel C.;Miller, Raymond D.;Pawlikowska, Ludmila;Taillon-Miller, Patricia;Xiao, Ming;Tsui, Lap-Chee;Mak, William;Song, You Qiang;Tam, Paul K. H.;Nakamura, Yusuke;Kawaguchi, Takahisa;Kitamoto, Takuya;Morizono, Takashi;Nagashima, Atsushi;Ohnishi, Yozo;Sekine, Akihiro;Tanaka, Toshihiro;Tsunoda, Tatsuhiko;Deloukas, Panos;Bird, Christine P.;Delgado, Marcos;Dermitzakis, Emmanouil T.;Gwilliam, Rhian;Hunt, Sarah;Morrison, Jonathan;Powell, Don;Stranger, Barbara E.;Whittaker, Pamela;Bentley, David R.;Daly, Mark J.;de Bakker, Paul I. W.;Barrett, Jeff;Chretien, Yves R.;Maller, Julian;McCarroll, Steve;Patterson, Nick;Pe'er, Itsik;Price, Alkes;Purcell, Shaun;Richter, Daniel J.;Sabeti, Pardis;Saxena, Richa;Schaffner, Stephen F.;Sham, Pak C.;Varilly, Patrick;Altshuler, David;Stein, Lincoln D.;Krishnan, Lalitha;Smith, Albert Vernon;Tello-Ruiz, Marcela K.;Thorisson, Gudmundur A.;Chakravarti, Aravinda;Chen, Peter E.;Cutler, David J.;Kashuk, Carl S.;Lin, Shin;Abecasis, Goncalo R.;Guan, Weihua;Li, Yun;Munro, Heather M.;Qin, Zhaohui Steve;Thomas, Daryl J.;McVean, Gilean;Auton, Adam;Bottolo, Leonardo;Cardin, Niall;Eyheramendy, Susana;Freeman, Colin;Marchini, Jonathan;Myers, Simon;Spencer, Chris;Stephens, Matthew;Donnelly, Peter;Cardon, Lon R.;Clarke, Geraldine;Evans, David M.;Morris, Andrew P.;Weir, Bruce S.;Tsunoda, Tatsuhiko;Johnson, Todd A.;Mullikin, James C.;Sherry, Stephen T.;Feolo, Michael;Skol, Andrew
通讯作者：
Skol, Andrew
影响因子：
4.4
作者：
DEVLIN, B;RISCH, N
通讯作者：
RISCH, N
影响因子：
1.7
作者：
Griffin, D. K.;Robertson, L. B. W.;Skinner, B. M.
通讯作者：
Skinner, B. M.
影响因子：
2.6
作者：
Nishida, Chizuko;Ishijima, Junko;Matsuda, Yoichi
通讯作者：
Matsuda, Yoichi
影响因子：
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作者：
Fang Lin;Ye Jia;Wang Jun
通讯作者：
Wang Jun