种田农民

 

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.

 

 

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.

 

 

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

 

 

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.

 

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.

 

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

 

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.

 

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.

 

 

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

 

 

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:)

 

 

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.

 

 

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.

 

 

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.

 

 

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 Mo17

 

108 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.