植物基因组学领域的140篇经典文献

植物基因组学研究我感兴趣的几个领域1.基因组的结构和变异2.分子标记连锁图谱构建和基因定位3.QTL定位的原理和方法4.QTL精细定位5.基因和QTL的克隆5.1插入突变方法5.2图位克隆的方法(含比较图位克隆)5.3候选基因法6.资源评估和利用7.分子标记辅助选择(含分子设计育种)8.转基因8.1转基因体系和实证研究8.2转基因的生态学安全研究9.比较基因组9.1标记水平的比较研究9.2序列水平的比较研究9.3性状水平的比较研究9.4功能比较研究10.杂种优势研究10.1遗传学解释10.2分子生物学解释11.分子进化(主要是玉米进化)12.基于连锁不平衡的关联分析12.1实证研究12.2方法学研究13.基因组研究中的一些新技术运用13.1DNA芯片技术13.2 DNA shuffling13.3 Gene Trap13.4 Gene therapy in plants13.5 TILLING 技术
1.植物基因组的结构和变异在越来越多的植物基因组被测完后,该研究的重要性逐渐显现,该方面的文章可以说是汗牛充栋.在玉米方面该领域的大牛是Buckler, ES; Messing, J, Dooner HK, Doebley J ; Gaut, BS.1. Buckler, E. S., Gaut, B. S. and McMullen, M. D. (2006)Molecular and functional diversity of maize. Curr. Opin. PlantBiol. 9, 172-176这是关于玉米基因组结构的REVIEW文章,先了解大概,在细读研究文章.其任何2个玉米自交系之间的遗传变异大于人和大猩猩之间的差异的经典论断充分说明玉米变异的广泛性.最近因为人类基因组研究的进展而似乎可以改写.2.Messing J, Dooner HK. Organization and variability of themaize genome. Curr Opin Plant Biol. 2006 Apr;9(2):157-63两位大牛的联合REVIEW, 值得一读.3.Goff S A, Ricke D, Lan T H, Presting G, Wang R, Dunn M,Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D,Martin C, Katagiri F, Lange B M, Moughamer T, Xia Y, Budworth P,Zhong J, Miguel T, et al. A Draft Sequence of the Rice Genome Oryzasativa L. ssp. japonica. Science, 2002, 296: 92-100大家或许都知道这篇文章,但我相信看完的不多,尽管全基因组测序的文章许多,强烈建议大家读这篇,讨论写的太好了.同期中国测序的文章就相形见拙许多,当然之后水稻精细图谱的公布,这篇文章也可以读读.4. International Rice Genome Sequencing Project. The map-basedsequence genome. nature, 2005, 436: 793-8005.Fu H H, Dooner H K. Intraspecific violation of geneticcolinearity and its implications in maize. Proc Natl Acad Sci USA,2002, 99: 9573-9578改文章给我的启示许多,基因的存在和缺失也是等位基因的一种形式就是其一,尽管后来该文章的结论不断被修正.6.Song R, Messing J: Gene expression of a gene family in maizebased on noncolinear haplotypes. Proc Natl Acad Sci USA 2003,100:9055-9060.宋任涛代表作之一,与Fu的文章有异曲同工之妙,给杂种优势提供了新的解释.7.Brunner S, Fengler K, Morgante M, Tingey S, Rafalski A:Evolution of DNA sequence non-homologies among maize inbreds. PlantCell 2005, 17:343-360.5,6工作的基础上提供了更多的数据8. Lai J, Li Y, Messing J, Dooner HK: Gene movement by Helitrontransposons contributes to the haplotype variability of maize. ProcNatl Acad Sci USA 2005, 102:9068-9073.赖锦盛的代表工作之一,为玉米基因组的扩张提供了全面的解释.9. Lai J, Ma J, Swigonova Z, Ramakrishna W, Linton E, Llaca V,Tanyolac B, Park YJ, Jeong OY, Bennetzen JL et al.: Gene loss andmovement in the maize genome. Genome Res 2004, 14:1924-1931部分阐述了玉米基因组的结构的成因,更多的是插入而不是缺失.10. Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A, RafalskiA:Gene duplication and exon shuffling by helitron-like transposonsgenerate intraspecies diversity in maize.Nat Genet 2005,37:997-1002与8讲的同一个故事.11.Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, GautBS: Patterns of DNA sequence polymorphism along chromosome 1 ofmaize (Zea mays ssp. mays L.). Proc Natl Acad Sci USA 2001,8:9161-9166该数据表明,在玉米基因组大约只保留了其祖先大刍草60%的遗传变异.12.Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, Yu Y,Wei F, Fuks G, Soderlund CA, Mayer KF et al.: Sequence compositionand genome organization of maize. Proc Natl Acad Sci USA 2004,101:14349-14354玉米有59000个基因的预测就出自此文.
13. Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S,
Pontaroli AC, Wei F, Haberer G, Fuks G, Du C, Raymond C, Estep MC,
Liu R, Bennetzen JL, Chan AP, Rabinowicz PD, Quackenbush J,
Barbazuk WB, Wing RA, Birren B, Nusbaum C, Rounsley S, Mayer KF,
Messing J.  Uneven chromosome contraction and
expansion in the maize genome. Genome Res. 2006
Oct;16(10):1241-5114.Emrich SJ, Li L, Wen TJ, Yandeau-Nelson MD, Fu Y, Guo L, Chou
HH, Aluru S, Ashlock DA, Schnable PS. Nearly Identical Paralogs:
Implications for Maize (Zea mays L.) Genome Evolution.Genetics.
2007 Jan;175(1):429-39
Schnable
提出的NIP概念给我们以后的关联分析和其他一系列研究提出了新的挑战,尽管在玉米基因组的频率只有1%.15. Fu Y, Emrich SJ, Guo L, Wen TJ, Ashlock DA, Aluru S,
Schnable PS.
Quality assessment of maize assembled genomic islands (MAGIs) and
large-scale experimental verification of predicted genes. Proc Natl
Acad Sci U S A. 2005  23;102(34):12282-7.
看看什么是MAGI，也是Schnable的贡献，其超大的课题组（在美国而言）和永不疲倦的精力让他文章如麻，而且牛文不断。2.分子标记连锁图谱构建和基因定位该领域的理论发展最大贡献者当然属于Lincoln,而玉米连锁图的构建,
全世界多个实验室都有重要贡献,比如Coe EH, 法国的Falque,
和访问过农大的Schnable.这尽管是一项非常基础的工作,但非常重要.从下面文章的清单不难看出,只要做的好有特色,同样能发好文章.其它各个重要的动植物都走过类似的历程，在植物里这一领域的研究，玉米应该还是比较靠前的，因为它不但重要，而且也算得上模式植物.16. Lincoln S, Daly M, Lander E. Mapping genetic mapping with
MAPMAKER/EXP3.0. Cambridge: MA: Whitehead institute Technical
Report, 1992
尽管新的方法不断涌现,但MAPMAKER
目前仍然是连锁图构建和基因定位的经典方法.17.Helentjaris T, Slocum M, Wright S, Schaefer A, Niehhuis J.
Construction of genetic linkage maps in maize and tomato using
restriction fragment length polymorphisms. Theor Appl Genet, 1986,
72: 761–769
玉米第一张分子标记连锁图18.Burr, B., Burr, F., Thompson, K.H., Albersten, M. and Stuber,
C. W. (1988) Gene mapping with recombinant inbreds in maize.
Genetics 118, 519–526
玉米第一张RIL图谱19.Beavis, W. D., and Grant, D. (1991) A linkage map based on
information from 4 F2 populations of Maize (Zea mays L.). Theor.
Appl. Genet. 82, 636–644
玉米的F2图谱20.Gardiner, J. M., Coe, E. H., Melia-Hancock, S., Hoisington,
D. A. and Chao, S. (1993) Development of a core RFLP map in maize
using an immortalized F2 population. Genetics 134, 917–930.
玉米第一张IF2图谱(注意不同于我们提到的IF2群体)21.Gardiner, J., Schroeder, S., Polacco, M. L., Sanchez-Villeda,
H., Fang, Z., Morgante, M., Landewe, T., Fengler, K., Useche, F.,
Hanafey, M., Tingey, S., Chou, H., Wing, R., Soderlund, C. and Coe
Jr., E. H. (2004) Anchoring 93 971 maize expressed sequence tagged
unigenes to the bacterial artificial chromosome contig map by
two-dimensional overgo hybridization. Plant Physiol. 134,
1317-1326.
遗传图谱和物理图谱的整合22.Davis, G. L., McMullen, M. D., Baysdorfer, C., Musket, T.,
Grant, D., Staebell, M., Xu, G., Polacco, M., Koster, L.,
Melia-Hancock, S., Houchins, K., Chao, S., and Coe Jr, E. H.
(1999). A maize map standard with sequenced core markers, grass
genome reference points and 932 expressed sequence tagged sites
(ESTs) in a 1736-locus map. Genetics 152, 1137–117223.Natalya S, McMullen M D, Schultz L, Schroeder S,
Sanchez-Villeda H, Gardiner J, Bergstrom D, Houchins K,
Melia-Hancock S, Musket T, Duru N, Polacco M, Edwards K, Ruff T,
Register J C, Brouwer C, Thompson R, Velasco R, Chin E, Lee M,
Woodman-Clikeman W, Long MJ, Liscum E, Cone K, Davis G, Coe EH.
Development and mapping of SSR markers for maize. Plant Mol Bio,
2002, 48: 463-481
几张玉米的高密度连锁图24.Falque, M., Décousset, L., Dervins, D., Jacob, A. M., Joets,
J., Martinant, J. P., Raffoux, X., Ribière, N., Ridel, C., Samson,
D., Charcosset, A. and Murigneux, A. (2005) Linkage Mapping of 1454
New Maize Candidate Gene Loci. Genetics 170, 1957-1966
玉米的大规模基因定位及连锁图谱25.Fu Y, Wen TJ, Ronin YI, Chen HD, Guo L, Mester DI, Yang Y,
Lee M, Korol AB, Ashlock DA, Schnable PS. Genetic dissection of
intermated recombinant inbred lines using a new genetic map of
maize.Genetics. 2006 Nov;174(3):1671-83.
玉米的大规模的IDP图谱
而目前各类标记(IDP, Gene, cDNA, SSR, RFLP,
SNP等)都被整合到IBM图谱,并有机与玉米物理图谱进行了整合,详细信息参考MAIZEGDB.3.QTL定位的原理和应用该领域让我们记住一个名字,那就是毕业于华中农业大学,现供职于北卡州立大学的曾昭邦教授.他1994年发表在Genetics的文章,已经是QTL定位领域不可超越的传奇,其正面引用应该接近或者超过1000次.他也是大陆动物遗传育种专业留学生中在美国唯一的正教授.他多次回国和母校讲学,2000年在华农讲学,在分子数量遗传学门外徘徊的我根本听不懂他在讲什么,错失良机.其发展的QTL定位软件几经改进,可以说在数量遗传学领域路人皆知.26. Zeng Z B. Precision mapping of quantitative trait loci.
Genetics, 1994, 136: 1457–1468
经典中的经典,但我估计认真读过的人不多,尤其新近入门的同学.同时在此基础上,
还发展了一系列分析方法.27. Cockerham CC and Z. B. Zeng Design III With Marker
Loci.Genetics 1996 143: 1437-1456
重新对Stuber的数据进行分析,认为超显性都是拟超显性.为我们的遗传设计提出了新的指导思想,但听从的不多
.28. Chen-Hung Kao, Zhao-Bang Zeng, and Robert D. Teasdale
Multiple Interval Mapping for Quantitative Trait Loci. Genetics
1999 152: 1203-1216
提出了MIM的算法,为我们估计总的遗传效应提供了方法.29.Chen-Hung Kao and Zhao-Bang Zeng Modeling Epistasis of
Quantitative Trait Loci Using Cockerham’s Model Genetics 2002 160:
1243-1261
提出了上位性的算法.30. Lander E S, Botstein S. Mapping Mendelian factors underlying
quantitative traits using RFLP linkage maps. Genetics, 1989, 121:
185–199
经典的区间作图法,
CIM是该基础上发展而来,贡献卓越,引用超过2000次.31. Wang D L, Zhu J, Li Z K, Paterson A H. Mapping QTLs with
epistatic effects and QTL  environment
interactions by mixed linear model approaches. Theor Appl Genet,
1999, 99: 1255-1264
浙江大学的朱军教授也是该领域的著名人物,在CIM基础上发展出MCIM(混合线性模型)的方法,也是一个重要的贡献,同时也提出条件QTL的定位方法,经典文章有下面2篇.32. Zhu J. Analysis of conditional genetic effects and variance
components in developmental genetics. Genetics, 1995, 141:
1633–1639
老鼠尾巴的长度和体重有什么关系?呵呵,这篇文章就研究这个,至少问题有趣.33. Yan J Q, Zhu J, He C X, Benmoussa M, Wu P. Molecular
dissection of developmental behavior of plant height in rice (Oryza
sativa L.). Genetics, 1998, 150: 1257-1265
株高发育性状的QTL定位,这篇文章给了我启示,而让我的论文有了点副产品,想了解改领域的基本知识,可以参考我2003科学通报的文章.34. Wei-Ren Wu, Wei-Ming Li, Ding-Zhong Tang, Hao-Ran Lu, and A.
J. Worland Time-Related Mapping of Quantitative Trait Loci
Underlying Tiller Number in Rice. Genetics 1999 151: 297-303
现在浙江大学的吴为人教授对时间序列的QTL分析也有贡献,但没有好的软件出来.关于QTL定位的应用文章枚不胜举,下面2篇文章是经典.35. Schon, C. C., Utz, H. F., Groh, S., Truberg, B., Openshaw,
S. and Melchinger, A. E. (2004) Quantitative trait locus mapping
based on resampling in a vast maize testcross experiment and its
relevance to quantitative genetics for complex traits. Genetics
167, 485-498
该研究用了超过1000个单株的超大群体,和19个环境的田间数据.
估计目前这2个数字仍然是无法超越的.36. Laurie, C. C., Chasalow, S. D., LeDeaux, J. R., McCarrol,
R., Rush, D., Hauge, B., Lai, C. Q., Clark, D., Rocheford, T. R.
and Dudley, J. W. (2004) The genetic architecture of response to
long-term artificial selection for oil concentration in the maize
kernel. Genetics 168, 2141-2155
该研究用了高油玉米长期选择的极端材料和大群体,所以对效应值小的QTL有很好的估计.37. 章元明. 作物QTL 定位方法研究进展. 科学通报, 19,
2223-2231.
我认为是迄今关于这方面最好的中文综述.尤其关于经典QTL的定位介绍的比较详细和到位,是对初进该领域的研究者最好的开门文章,几乎囊括了所有经典文章.我们常常知道QTL定位要选择显著标记对背景控制?原因是什么,多少合适?如果不选或者选多了会出现什么问题?如果理解了这些理论问题,大家对QTL 定位的结果就会有更深刻的认识,而不会简单堆积结果了.QTL定位下一步的一个发展方向将是:
1) Nested Association Mapping and Diallel Association
Mapping,
也就是结合连锁和连锁不平衡的分析方法,该方法有Buckler首先提出来并付诸实践,相信不久就有实际实验结果的文章出来,下一步是第一篇方法探讨文章.
38. Benjamin Stich, Jianming Yu, Albrecht E. Melchinger, Hans-Peter
Piepho, Friedrich Utz, Hans P Maurer, and Edward S Buckler Power to
detect higher-order epistatic interactions in a metabolic pathway
using a new mapping strategy. Genetics 2006: doi:
10.1534/genetics.106.0670332)
eQTL定位
这也是将来QTL定位的一个重要内容,也是联系遗传学上QTL定位和表达水平基因表达谱研究的桥梁.在动物方面（人，小鼠等）相关研究进展很多，下一波就是植物了。39 Gibson G, Weir B. The quantitative genetics of transcription.
Trends Genet, 2005, 21(11): 616—623
如何从转录水平认识数量性状40 Schadt E E, Monks S A, Drakes T A, et al. Genetics of gene
expression surveyed in maize, mouse and man.Nature, 2003,
422:297-302
eQTL定位的经典文章41  Brew R B, Yvert G, Clinton R, et al.
Genetic dissection of transcriptional regulation in budding yeast.
Science, 2002, 296: 752-755
虽然是酵母的数据但值得借鉴.3) PTL
差异表达蛋白和QTL位置的比较与分析(目前相关文章还比较少)42 Salvi S, Tuberosa R. To clone or not to clone plant QTLs:
present and future challenges. Trends Plant Sci, 2005, 10(6):
297-304
相关的综述文章43 Consoli L, Lefevre A, Zivy M, et al. QTL analysis of proteome
and transcriptome variations for dissecting the genetic
architecture of complex traits in maize. Plant Mol Biol, 2002,
48(5-6): 575-581
好象是仅有的研究文章,不过已经有一段时间没有追踪了4 QTL精细定位
毫无疑问,近年来发展而来的基于NIL的定位方法和策略取得了长足进步.
该策略首先被Paterson提出来,然后被Zamir发扬广大,我们国家在这方面的研究应该说取得了长足的进步.其中Paterson（现在偏理论了），Zamir，Tanksley，McCouch以及日本和中国的多位科学家是这方面的领军科学家。44 Paterson AH, DeVerna JW, Lanini B et al. Fine mapping of
quantitative trait loci using selected overlapping recombinant
chromosomes, in an interspecies cross of tomato. Genetics, 1990,
124: 735-74245 Eshed Y, Zamir D．An introgression line population of
Lycopersicon pennellii in the cultivated tomato enables the
identification and fine mapping of yield-associated QTL. Genetics ,
1995, 141:1147-1162
较早的研究，现在看起来比较简单，但你要承认原创。46 Salvi S, Tuberosa R, Chiapparino E, Maccaferri M, Veillet
S,van Beuningen L, Isaac P, Edwards K, Phillips RL: Toward
positional cloning of Vgt1, a QTL controlling the transition from
the vegetative to the reproductive phase in maize. Plant Mol Biol
2002, 48:601-613
我一直以为这将是玉米中第一个被克隆的QTL,而追踪很久,但呼之欲出好多年终没有见到正式文章,但有消息表明已经拿到基因.Tuberosa是意大利的知名科学家,当时在武汉开会的时候希望我申请奖学金到他那里做博士后,还给我许多他发表的文章.47 Li JM, Thomson M, McCouch S R. Fine mapping of a grain-weight
quantitative trait locus in the pericentromeric region of rice
chromosome 3. Genetics, 2004 168: 2187-219548 Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q.
Related Articles, Links   GS3, a major QTL for grain length and weight and
minor QTL for grain width and thickness in rice, encodes a putative
transmembrane protein.
Theor Appl Genet. 2006, 112(6):1164-71
两篇文章做的同一个QTL位点，可见这个领域竞争的惨烈（事实上还有至少2个组在做这个位点）。但第二篇的遗传设计比较简单，第一篇太复杂了。但讨论起来是一套一套。49 Alpert K B, Tanksley S D. High-resolution mapping and
isolation of a yeast artificial chromosome contig containing fw2.2:
A major fruit weight quantitative trait locus in tomato. Proc Natl
Acad Sci USA, 1996, 93: 15503-15507
看看着篇定位的文章,你就知道Tanksley克隆第一个QTL是多么不容易.50 Ishimaru K.  Identification of a locus
increasing rice yield and physiological analysis of its function.
Plant Physiol. 2003 Nov;133(3):1083-90
这篇文章只有一个作者，可见日本人做研究有多么厉害了。这个人最近文章雪片般飘逸，绝对是后起之秀。5.基因和QTL的克隆51 Ashikari M, Matsuoka M. Identification, isolation and
pyramiding of quantitative trait loci for rice breeding. Trends
Plant Sci, 2006, 11(7): 344-35052 Bortiri E, Jackson D, Hake S. Advances in maize genomics: the
emergence of positional cloning.Curr Opin Plant Biol. 2006
Apr;9(2):164-71
这两篇综述告诉我们重要形状QTL的克隆将是未来竞争最为激烈的领域，同时已经克隆的QTL也尽收眼底，如果对这方面感兴趣，无疑给你做了很好的文献收集工作。5.1插入突变方法53 Bensen, R.J., G. S. Johal, V. C. Crane, J. T. Tossberg, P. S.
Schnable, R. B. Meeley, and S. P. Briggs. 1995. Cloning and
characterization of the maize An1 gene. The Plant Cell. 7:
75-84
与株高有关的一个突变体基因的克隆54 Doebley J, Stec A, Hubbard L. The evolution of apical
dominance in maize. Nature, 1997, 386: 485-488
玉米中克隆的第一个QTL55 Cui X, Wise RP, Schnable PS. The rf2 nuclear restorer gene of
male-sterile T-cytoplasm maize. Science. 1996 May
31;272(5266):1334-6
在17万株MU插入玉米中找到5个突变体，最终克隆了玉米的恢复基因Rf2,
从这也可以看出基于突变体的基因克隆与其说是个技术活不如说是一个体力活。应该是Schnable的成名作。56 Esteban B, George C, Erik V, et al. Ramosa2 encodes a lateral
organ boundary domain protein that determines the fate of stem
cells in branch meristems of maize. Plant Cell, 2006,
18:574-58557 Vollbrecht E, Springer PS, Goh L, et al. Architecture of
floral branch systems in maize and related grasses. Nature, 2005,
436:1119-1126
与玉米进化有关的2个QTL5.2图位克隆的方法(含比较图位克隆)58 Frary A, Nesbitt T C, Frary A, et al.  fw2.2: A quantitative trait locus key to the evolution of tomato
fruit size. Science, 2000, 289: 85-88
第一个被图位克隆的QTL，建议顺便看看Doebley对这篇文章的评论，就知道牛人站的高度在哪里。59 Ashikari M, Sakakibara H, Lin S, Yamamoto T, et al.
Cytokinin Oxidase Regulates Rice Grain Production. Science, 2005,
309: 741-7245
也是引起轰动的报道,因为可能是控制产量的基因被发现.记得文章刚发表后,Rocheford来访问问我跟进没有,呵呵.是准备跟进,但,相信不久会有后续报道出来.60 Wang H, Nussbaum-Wagler T, Li B, et al. The origin of the
naked grains of maize. Nature,  2005, 436:
714-719
第一个图位克隆的玉米QTL,用到比较基因组的策略61 Peng J, Richard E D, Hartley M N, et al. ‘Green
revolution’ genes encode mutant gibberellin reponse modulators.
Nature, 1999, 400: 256-261
比较图位克隆的经典62 Yan L, Loukoianov A, Blechl A, et al. The wheat VRN2 gene
is a flowering repressor down-regulated by vernalization. Science,
2004, 303: 1640 - 1644
小麦大基因组基因克隆的经典作品,毫无疑问该文章的联系作者已经是该领域的领军人物,目前在小麦中克隆的基因或QTL已经超过4个.63 Li C, Zhou A, Sang T.  Rice domestication
by reducing shattering. Science. 2006 31;311(5769):1936-9
水稻进化QTL的克隆,当年Science杂志还有另外一篇类似的文章,惊叹的是作者用的是F2群体,遗传设计大胆有效,常人不敢想象.Doebley的评论也是高屋建瓴.64 Ren ZH,Gao JP,Li LG, et al. A rice quantitive trait locus
for salt tolerance encodes a sodium transporter. Nature Genetics,
2005, 37:1141-1146
中国人的工作,也相当的不错.5.3候选基因法65 Ishimaru K, Ono K, Kashiwagi T. Identification of a new
gene controlling plant height in rice using the candidate-gene
strategy. Planta, 2004, 218: 388–395
我认为第一篇完全意义的侯选基因策略,参考其思路和生物信息学分析.66 Xiao WK, Xu ML et al. Genome-wide isolation of resistance
gene analogs in maize (Zea mays L.).Theor Appl Genet. 2006
Jun;113(1):63-72
徐明良老师工作,在没有精细定位或针对特定性状,这是一个很好的方法也构建了进一步深入研究的一个平台.6.资源评估和利用该领域的研究很重要,
几乎是上个世纪90年代许多农业大学的做作物遗传育种都要做的工作,但有趣的研究不多.
67 GS Khush. 2001, Green revolution: the way forward. Nature
Reviews Genetics, 2: 815-822
如果你知道Khush是谁,你就不难发现该文章的价值68 Liu K, Goodman M, Muse S, Smith JS, Buckler E, Doebley J:
Genetic structure and diversity among maize inbred lines as
inferred from DNA microsatellites. Genetics 2003,
165:2117-2128
玉米主要玉米材料遗传变异的分类和确定
69 Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S:
Genetic structure and diversity in Oryza sativa L. Genetics 2005,
169:1631-1638
如果了解McCouch的背景,你就知道她写的文章为什么这么优美,因为她本科念的是文学.70 Fukunaga K, Hill J,  Vigouroux Y, et al.
Genetic diversity and population structure of teosinte. Genetics,
2005, 169: 2241-2254
玉米祖先大刍草的遗传变异规律,将是重要的玉米遗传改良的潜在资源.71Jochen C.Reif, Sonia Hamrit et al. Trends in genetic
diversity among European maize cultivars and their parental
components during the past 50 years. Theor Appl Genet, 2005
先锋公司1930-1999共90年间推广杂交种的遗传基础进行了分析72 Stephen J, Smith C, Duvick D et al. Changes in pedigree
background of Pioneer brand maize hybrids widely grown from 1930 to
1999.  Crop Science. 2004, 44(6): 1935-1946
欧洲过去50年主要推广玉米品种遗传基础的变化规律7.分子标记辅助选择(含分子设计育种)这方面的综述和理论研究,远多于实证研究,也是一个有趣的现象.73 Xu, Y. (2003). Developing marker-assisted selection
strategies for breeding hybrid rice. Plant Breed. Rev. 23,
73–174
74 Li ZK, Fu BY, Gao YM, et al. Genome-wide introgression lines and
their use in genetic and molecular dissection of complex phenotypes
in rice (Oryza sativa L.).Plant Mol Biol. 2005 , 59(1):33-52
黎志康和徐云碧都是理论专家,对分子育种都有自己独到的理解,而目前他们都是这个领域的一线科学家.75 Andersen J R, Lübberstedt T. Functional markers in plants.
Trends Plant Sci, 2003, 8: 554-560
首次提出功能标记的概念,相信是分子育种的方向,尤其设计育种.76 Visscher P M，Haley C S, Thompson R. Marker-assisted
introgression in backcross breeding programs. Genetics, 1996, 144:
1923-1932
早期的理论探讨77 Bouchez A, Hospital F, Causse M, Gallais A, Charcosset
A.  Marker-assisted introgression of favorable
alleles at quantitative trait loci between maize elite lines.
Genetics, 2002, 162: 1945–1959
78 Yousef G G, Juvik. Comparison of phenotypic and marker-assisted
selection for quantitative traits in sweet corn. Crop Sci, 2001,
41: 645-655
上2篇文章是实证研究,但早期的结果好象有正有负.最近有一些进展,没有深入追踪.8.转基因
该领域是重要的发展方向,但不管你做不做这个研究都好象能说上几句.其实其科学问题还有许多值得探讨.如果你不从事这个工作,建议把大的概念和方向搞清楚.尤其以后准备当技术官员的,更应该多看正反两方面的意见,让自己更辨证.8.1转基因体系和实证研究
79 Meyer, P., and Saedler, H. (1996) Homology-dependent gene
silencing in plants. Annu.Rev. Plant Physiol. Plant Mol. Biol. 47,
23-48
转基因的沉默,较早的综述文章.80 Ye X, Al-Babili S, Kloti A , et al. Engineering the
provitamin A (beta-carotene) biosynthetic pathway into (
carotenoid) rice endosperm. Science, 2000, 287: 303-305
同时转多个基因,著名的金稻.81 Gordon-Kamm, W., Dilkes, B. P., Lowe, K., Hoerster, G.,
Sun, X., Ross, M., Church, L., Bunde, C., Farrell, J., Hill, P.,
Maddock, S., Snyder, J., Sykes, L., Li, Z., Woo, Y., Bidney, D. and
Larkins, B. A. (2002) Stimulation of the cell cycle and maize
transformation by disruption of the plant retinoblastoma pathway.
Proc. Natl. Acad. Sci. USA  99, 11975-11980.
经典的玉米转基因文章82 Ishida, Y., Saito, H., Hiei, Y. and Komari, T. (2003)
Improved protocol for transformation of maize (Zea mays L.)
mediated by Agrobacterium tumefaciens. Plant Biotech. 20,
57-66
改进的玉米转基因技术8.2转基因的生态学安全研究
83 Quist, D. and Chapela, I. H. (2001) Transgenic DNA
introgressed into traditional maize landraces in Oaxaca, Mexico.
Nature 414, 41-543
转基因的飘逸,但后来该研究也被质疑.
84 Bellin, M. R. and Berthaud, J. (2004) Transgenic maize and the
evolution of landrace diversity in Mexico. The importance of
farmers’ behavior. Plant Physiol.134, 883-888
转基因玉米能减少物种多样性?
上面2篇是关于生态安全研究的文章,好象都是负面的,主要上一想让大家有理性和批评的思想,正面的文章很多.中国学者的如中科院黄季琨在Science和Nature就有好几篇.9.比较基因组
炙手可热,也是我感兴趣的领域,下面的划分当然也是我一家之言,
不一定正确,而且目光主要集中在禾本科.该领域的牛人比较多,如Gale,
Bennetzen, Paterson, Messing, Dooner等等.9.1标记水平比较基因组85 Gale M D, Devos K M. Comparative genetics in the grasses.
Proc Natl Acad Sci USA, 1998, 95: 1971–1974
著名的8卦图就出自这里86 Ahn S N, Tanksley S D. Comparative linkage maps of the rice
and maize genomes. Proc Natl Acad Sci USA, 1993, 90:
7980-7984
最早的玉米和水稻比较图谱87 Wilson W A, Harrington S E, Woodman W L, Lee M, Sorrells M
E, McCouch S R. Inferences on the genome structure of progenitor
maize through comparative analysis of rice, maize and the
domesticated panicoids. Genetics, 1999, 153: 453-473
改进的玉米和水稻比较图谱9.2序列水平的比较研究88 Bennetzen J L. Comparative sequence analysis of plant
nuclear genomes: microcolinearity and its many exceptions. Plant
Cell, 2000, 12: 1021-1030
89 Chen M, SanMiguel P, De Oliveira AC, Woo S S, Zhang H, Wing R A,
Bennetzen J L. Microcollinearity in sh2-homologous regions of the
maize, rice and sorghum genomes. Proc Natl Acad Sci USA, 1997, 94:
3431–3435
90 Swigonova Z, Lai, Jinsheng, Ma, J, et al. Close split of the
ancestor genomes of sorghum and maize. Genome Research, 2004, 14:
1916-1923
简单策略就是,找几个不同作物的保守区域,同时测几个BAC,看看发生什么?呵呵,我其实也早想到了,可没有银子,没有人支持.91 Salse J, B Piegu, R Cooke, M Delseny. New in silico insight
into the synteny between rice (Oryza sativa L.) and maize (Zea mays
L.) highlights reshuffling and identifies new duplications in the
rice genome. Plant J. 2004, 38(3):396-409
这个在水稻序列完成后作为桥梁与玉米大规模的比较,也是我的思路9.3性状水平的比较研究92 Paterson A H, Lin Y R, Li Z, Schertz K F, Doebley J F,
Pinson S R M, Liu S C, Stansel J W, Irvine J E. Convergent
domestication of cereal crops by independent mutations at
corresponding genetic loci. Science, 1995, 269: 1714–1718
种子大小和开花期等与进化有关的农艺性状的QTL具有同源性93 Chen H L, Wang S P, Xing Y Z, Xu C G, Hayes P M, Zhang Q.
Comparative analyses of genomic locations and race specificities of
loci for quantitative resistance to Pyricularia grisea in rice and
barley. Proc Natl Acad Sci USA, 2003, 100：2544–2549
部分抗稻瘟病的QTL在水稻和大麦中都具有同源性,
发现数量性状也有小种专化性94 Chardon F, Virlon B, Moreau L, Falque M, Joets J, Decousset
L, Murigneux A, Charcosset A.  Genetic
architecture of flowering time in maize as inferred from
quantitative trait loci meta-analysis and synteny conservation with
the rice genome. Genetics. 2004 Dec;168 (4):2169-85
这个大规模的比较有意思,我们的目标是与91结合,最终是实现大规模的QTL比较克隆.9.4功能比较研究95 Volker B, Stefan K, Virginia W. Comparative genomics of
Arabidopsis and maize: prospects and limitations. Genome Biology,
2002, 3(3): 1005.1–1005.6
序列的微线性老被打破,但基因的功能应该大都一样,这个就是检测这个预测的.96 Mural R J, Adams M D, Myers E W, Smith H O, Gabor Miklos G
L, Wides R, Halpern A, Li P W, Sutton G G, Nadeau J, Salzberg S L,
Holt R A, Kodira C D, Lu F, Chen L et al. A comparison of
whole-genome shotgun-derived mouse chromosome 16 and the human
genome. Science, 2002, 296: 1661-1671
全基因组大规模比较97 Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES.
Sequencing and comparison of yeast species to identify genes and
regulatory elements.Nature. 2003 May 15;423(6937):241-54
这篇文章我认为好在,提出了可以基于比较基因组的策略进行功能预测的概念.
10.杂种优势研究这个领域我认为是可能产生诺贝尔奖的领域,但过去100年我们几乎都在与数学打交道.所以这方面的文章都难以读懂,不容易理解.尽管离目标还遥遥无期,但我们要充满信心.这个领域在遗传学水平的领军人物中国有一大部分.最为出名的是张启发,
黎志康等.10.1遗传学解释98 Duvick, D. N. (1999) in The Genetics and Exploitation of
Heterosis in Crops eds. Coors, J. G. & Pandey, S. (Crop Sci.
Soc. Amer., Madison, WI), pp. 19–29
更早的文章就不推荐，这篇综述里面有全面引用和阐述，Duvick是先锋公司资深科学家，位至副总裁，对这个问题的认识，少有人望其项背，许多观点值得借鉴。99 Stuber CW, Lincoln S E, Wolff D W, et al. Identification of
genetic factors contributing to heterosis in a hybrid from 2 elite
maize inbred lines using molecular markers. Genetics, 1992, 132:
823-839
其超显性假说目前仍然被不断质疑和证明。100 Xiao J, Li J, Yuan L et al. Dominance is the major genetic
basis of heterosis in rice as revealed by QTL analysis using
molecular markers. Genetics, 1995, 140: 745-754
这篇文章让Tanksley
SD（水稻杂种优势理论）和袁隆平（水稻杂种优势应用）分享了沃尔夫粮食奖.
当然Tanksley的主要贡献我认为还不是这，在番茄研究上更有建树比如第一个QTL就是他克隆的。而该文的第一作者也是袁先生的弟子101 Yu S B, Li J X, Xu C G., et al. Importance of epistasis as
the genetic basis of heterosis in an elite rice hybrid. Proc Natl
Acad Sci USA, 1997, 94: 9226-9231
张启发的经典之作,我花了3年才读懂这篇文章,重复打印了几次.102 Li Z K, Luo L J, Mei H W, Wang D L, Shu Q Y, Tabien R,
Zhong D B, Ying C S, Stansel J W, Khush G S, Paterson A H.
Overdominant epistatic loci are the primary genetic basis of
inbreeding depression and heterosis in rice. I. biomass and grain
yield. Genetics, 2001, 158: 1737-1753
103 Luo L J, Li Z K, Mei H W,  Shu Q Y, Tabien R,
Zhong D B, Ying C S, Stansel J W, Khush GS, Paterson A H.
Overdominant Epistatic Loci Are the Primary Genetic Basis of
Inbreeding Depression and Heterosis in Rice. II. Grain Yield
Components. Genetics, 2001, 158: 1755-1771
这两篇文章都是黎志康的杰作,看看超长的讨论就知道这个人理论水平高,呵呵.104 Hua J P, Xing Y , Wu W R, et al. Single-locus heterotic
effects and dominance by dominance interactions can adequately
explain the genetic basis of heterosis in an elite rice hybrid.
Proc Natl Acad Sci USA, 2003,100: 2574–2579
运用了IF2创新遗传设计上面6篇文章把杂种优势的各种效应都说了一遍，基于2个材料构建群体的各种遗传设计基本上都用到。其中中国科学家张启发和黎志康。105 Yaniv Semel, Jonathan Nissenbaum, Naama Menda, Michael
Zinder, Uri Krieger, Noa Issman, Tzili Pleban, Zachary Lippman,
Amit Gur, and Dani Zamir. From the Cover: Overdominant quantitative
trait loci for yield and fitness in tomato
PNAS 2006 103: 12981-12986
遗传学水平杂种优势研究的新思路，PNAS封面文章,值得一看,当然也有许多人有不同声音,比如张院士.同时5,6
2篇文章也从基因组学水平解决这个问题提供了新的视野.10.2分子生物学解释106 Swanson-Wagner RA, Jia Y, DeCook R, Borsuk LA, Nettleton
D, Schnable PS.  All possible modes of gene action
are observed in a global comparison of gene expression in a maize
F1 hybrid and its inbred parents. Proc Natl Acad Sci U S A. 2006
May 2;103(18):6805-10.
芯片技术在杂种优势研究中的成功应用107 Cis-transcriptional Variation in Maize Inbred Lines B73
and Mo17 Leads to Additive Expression Patterns in the F1 Hybrid.
Genetics, 2006; 173(4): 2199 - 2210.
做玉米研究一定要记住这2个自交系B73 and Mo17108 Guo M, Rupe MA, Zinselmeier C, Habben J, Bowen BA, Smith
OS:Allelic variation of gene expression in maize hybrids. Plant
Cell 2004, 16:1707-1716
为等位变异提供了转录表达水平的证据,为杂种优势研究提供了另一种思路.
其实先锋公司在这方面的工作一直走在前列.109 He G, Luo X, Tian F, Li K, Zhu Z, Su W, Qian X, Fu Y, Wang
X, Sun C, Yang J.    Haplotype variation in structure and expression
of a gene cluster associated with a quantitative trait locus for
improved yield in rice. Genome Res. 2006 May;16(5):618-26
中国农大孙传清和复旦大学杨金水的联袂表演,好象让我们看到了解决这个问题的曙光,尽管很弱.
11.分子进化(主要是玉米进化)玉米的分子进化研究可以说是Doelbley
J一个人的表演，其系统性，前瞻性无不让我佩服的五体投地。详细的参考我上一篇文章（从John
Doebley的研究历程谈如何读参考文献）这里就不多做解释.110 Doebley JF, Gaut BS, Smith BD.  The
molecular genetics of crop domestication. Cell. 2006 Dec
29;127(7):1309-21
这是这方面最新和最经典的综述111 Piperno DR, Flannery KV. The earliest archaeological maize
(Zea mays L.) from highland  Mexico: new
accelerator mass spectrometry dates and their implications. Proc
Natl Acad  Sci USA, 2001, 98: 2101-2103
玉米进化考古证据112 Doebley J, Stec A, Hubbard L. The evolution of apical
dominance in maize. Nature, 1997, 386: 485-488
113 Vollbrecht E, Springer PS, Goh L, et al. Architecture of floral
branch systems in maize and related grasses. Nature, 2005,
436:1119-1126
114 Wang R L, Stec A, Hey J, Lukens L, Doebley J. The limits of
selection during maize domestication. Nature, 1999, 398:
236-239
115 Esteban B, George C, Erik V, et al. Ramosa2 encodes a lateral
organ boundary domain protein that determines the fate of stem
cells in branch meristems of maize. Plant Cell, 2006,
18:574-585
116 Gallavotti A, Zhao Q, Kyozuka J, et al. The role of barren
stalk1 in the architecture of maize. Nature, 2004,
432:630-635
一系列有进化相关基因或QTL被克隆，进化的方式也是越来越清晰，当然这个清单显然不完整。117 Yamasaki M, Tenaillon MI, Vroh Bi I, Schroeder S,
Sanchez-Villeda H, Doebley JF, Gaut BS, McMullen MD: A large scale
screen for artificial selection in maize identifies candidate
agronomic loci for domestication and crop improvement. Plant Cell
2005, 17:2859-2872
118 Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF,
McMullen MD, Gaut BS: The effects of artificial selection on the
maize genome. Science 2005, 308:1310-1314
基因组水平的研究，让进化上升到一个新的高度，上2篇文章是最新的进展。而玉米进化一共大约有1200个基因受到选择就出自下一篇文章。12.基于连锁不平衡的关联分析我预测5年内中国也会在植物学领域开始热炒这个领域,
尽管目前我也做这个领域但知道的东西还很少.
尽管目前这个领域有很多人质疑,也确实有许多不成熟的地方,但必须承认其发展之势不可以阻挡.植物领域的领军人物当然是Buckler.118 Yu J, Buckler ES. Genetic association mapping and genome
organization of maize.Curr Opin Biotechnol. 2006
Apr;17(2):155-60
简单清晰的综述文章,如果要做这个领域,当然是必读的.119 杨小红，严建兵，郑艳萍，等。植物数量性状关联分析研究进展.
作物学报. 2006(on line first)
扫盲和入门文章,尽管还有不足之处,但也是迄今能找到这个领域的唯一中文综述.12.1实证研究120 Remington DL, Thornsberry JM,Matsuoka Y,Wilson LM,Whitt
SR,Doebley J, Kresovich S, 121Goodman MM, Buckler ES: Structure of
linkage disequilibrium and phenotypic associations in the maize
genome. Proc Natl Acad Sci USA 2001, 98:11479-11484.
早期的探讨122 Thornsberry JM, Goodman MM, Doebley J, Kresovich S,
Nielsen D, Buckler ES IV: Dwarf8 polymorphisms associate with
variation in flowering time. Nat Genet 2001, 28:286-289.
看山之作,尽管后来不断有文章出来修订和赶紧,但动摇不了其地位.123 Palaisa KA, Morgante M, Williams M, Rafalski A:
Contrasting effects of selection on sequence diversity and linkage
disequilibrium at two phytoene synthase loci. Plant Cell
2003,15:1795-1806
124 Wilson LM, Whitt SR, Ibanez-Carranza AM, Goodman MM, Rocheford
TR, Buckler ES: Dissection of maize kernel composition and starch
production by candidate gene association. Plant Cell 2004,
16:2719-2733.
几个实证研究, 都是相当的不错,当然这个清单可以很长.12.2方法学研究
125 Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley
JF,McMullen MD, Gaut BS, Holland JB, Nielsen D et al.: A unified
mixed-model method for association mapping accounting for multiple
levels of relatedness. Nat Genet 2005, 38: 203–208.
方法学的奠基之作,关键有界面友好的分析软件问世.126 Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick
NA, et al. Principal components analysis corrects for
stratification in genome-wide association studies. Nat Genet.
2006;38:904–909
当然也会有人推荐这种方法,而不承认上面的论断.127 Patterson N, Price AL, Reich D. Population Structure and
Eigenanalysis. PLoS Genet. 2006 Dec 22;2(12):e190
群体结构的分析方法讨论,如果从事该研究必须读.
  128 Aranzana MJ, Kim S, Lister C, Shindo C, Tang C, Toomajian C,
Zheng H, Dean C, Marjoram P, Nordborg M. An Arabidopsis Example of
Association Mapping in Structured Samples.Zhao K. PLoS Genet. 2007
Jan 19;3(1):e4
哪种方法更好,呵呵这是深入的比较和分析,值得读这篇文章.
13.基因组研究中的一些新技术运用
新技术总是不断涌现,呵呵,我也不是一个擅长的追跑者.但要明确的是技术是工具,要我所用,而不能为他所累.所以就不做详细介绍了.自己看吧13.1DNA芯片技术
129 Rensink WA, Buell CR. Microarray expression profiling
resources for plant genomics. Trends Plant Sci. 2005, 10(12):
603-609
130 Ma J, Morrow DJ, Fernandes J, et al. Comparative profiling of
the sense and antisense transcriptome of maize lines. Genome Biol,
2006 , 13: 7(3): R22
131 Jiang K, Zhang S, Lee S, et al. Transcription profile analyses
identify genes and pathways central to root cap functions in maize.
Plant Mol Bio, 2006, 60(3): 343-363
这仅是在玉米中的应用,该领域的文章和综述可以用多如牛毛来形容.13.2 DNA shuffling
呵呵,
某年考博士的题目,这里提供最早的文献,然后大家如果有兴趣,就可以用google从牛毛去了解牛喜欢吃什么草.
132 Stemmer WP. Rapid evolution of a protein in vitro by DNA
shuffling.
Nature. 1994 Aug 4;370(6488):389-9113.3Gene Trap
这个领域的文章多如牛毛,随便挑了一篇.
133 Springer PS. Gene traps: tools for plant development and
genomics.Springer PS. Plant Cell. 2000 Jul;12(7):1007-20.13.4 Gene therapy in plants
本来我很看好的,但好象发展并不快,先锋公司最早的参与者之一.
134 Hohn B, Puchta H.Gene therapy in plants. Proc. Natl. Acad.
Sci. USA,8321–8323, 1999
135 Yoon K, Cole-Strauss A, Kmiec EB. Proc Natl Acad Sci U S A 1996
Mar 5;93(5):2071-6  136 Zhu T, Peterson DJ, Tagliani L, St Clair G, Baszczynski CL,
Bowen B. Proc Natl Acad Sci U S A 1999 Jul 20;96(15):8768-73
137 Beetham PR, Kipp P.B, Sawycky XL, Arntzen CJ, May GD. Proc Natl
Acad Sci U S A 1999.96(15):8774-813.5 TILLING 技术
不依赖转基因的检测点突变的方法,反向遗传学研究中的新贵,
有相当的应用潜力
138 An G, Jeong DH, Jung KH et al. Reverse genetic approaches
for functional genomics of rice. Plant Mol Biol. 2005
Sep;59(1):111-123
关于反向遗传学研究的综述
139 Gilchrist, E. J., and Haughn, G. W. (2005). TILLING without a
plough: a new method with applications for reverse genetics. Curr.
Opin. Plant Biol. 8, 1–5
140 Till, B. J., Reynolds, S. H., Weil, C., Springer, N., Burtner,
C., Young, K., Bowers, E., Codomo, C. A., Enns, L. C., Odden, A.
R., Greene, E. A., Comai, L., and Henikoff, S. (2004). Discovery of
induced point mutations in maize by TILLING. BMC Plant Biol. 4,
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