From genome to phenome and back in tomato

被引：13

作者：

Ichihashi, Yasunori ^{[1
,2
]}

Sinha, Neelima R. ^{[1
]}

机构：

[1] Univ Calif Davis, Dept Plant Biol, Davis, CA 95616 USA

[2] RIKEN, Ctr Sustainable Resource Sci, Yokohama, Kanagawa 2300045, Japan

来源：

CURRENT OPINION IN PLANT BIOLOGY | 2014年 / 18卷

基金：

美国国家科学基金会; 日本学术振兴会;

关键词：

SOLANUM-LYCOPERSICON L; MOLECULAR-GENETICS; NATURAL VARIATION; FRUIT SIZE; FUNCTIONAL ELEMENTS; LEAF MORPHOLOGY; ROOT-TIP; RNA-SEQ; ARABIDOPSIS; INTROGRESSION;

D O I：

10.1016/j.pbi.2013.12.004

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

The tomato is an ideal plant species for genomic and evolutionary studies. Thanks to recent technical advances, a plethora of information relating to tomato genomics has been generated. In addition, various phenotypes related to morphology, physiology and yield have been investigated in tomato and its wild relatives. In this review, we summarize recent key findings in tomato genomics that used both developmental and evolutionary approaches to link the genome to phenome. Combined, these perspectives allow us to look at the trends in tomato evolution in addition to providing insight into the future direction of research that can utilize this unique model species.

引用

页码：9 / 15

页数：7

共 70 条

[1] Fruit-localized phytochromes regulate lycopene accumulation independently of ethylene production in tomato [J].

Alba, R ;

Cordonnier-Pratt, MM ;

Pratt, LH .

PLANT PHYSIOLOGY, 2000, 123 (01) :363-370

[2] Resolution by recombination: breaking up Solanum pennellii introgressions [J].

Alseekh, Saleh ;

Ofner, Itai ;

Pleban, Tzili ;

Tripodi, Pasquale ;

Di Dato, Francesco ;

Cammareri, Maria ;

Mohammad, Ayed ;

Grandillo, Silvana ;

Fernie, Alisdair R. ;

Zamir, Dani .

TRENDS IN PLANT SCIENCE, 2013, 18 (10) :536-538

[3] Analysis of the genome sequence of the flowering plant Arabidopsis thaliana [J].

Kaul, S ;

Koo, HL ;

Jenkins, J ;

Rizzo, M ;

Rooney, T ;

Tallon, LJ ;

Feldblyum, T ;

Nierman, W ;

Benito, MI ;

Lin, XY ;

Town, CD ;

Venter, JC ;

Fraser, CM ;

Tabata, S ;

Nakamura, Y ;

Kaneko, T ;

Sato, S ;

Asamizu, E ;

Kato, T ;

Kotani, H ;

Sasamoto, S ;

Ecker, JR ;

Theologis, A ;

Federspiel, NA ;

Palm, CJ ;

Osborne, BI ;

Shinn, P ;

Conway, AB ;

Vysotskaia, VS ;

Dewar, K ;

Conn, L ;

Lenz, CA ;

Kim, CJ ;

Hansen, NF ;

Liu, SX ;

Buehler, E ;

Altafi, H ;

Sakano, H ;

Dunn, P ;

Lam, B ;

Pham, PK ;

Chao, Q ;

Nguyen, M ;

Yu, GX ;

Chen, HM ;

Southwick, A ;

Lee, JM ;

Miranda, M ;

Toriumi, MJ ;

Davis, RW .

NATURE, 2000, 408 (6814) :796-815

[4] Root elongation, water stress, and mechanical impedance: a review of limiting stresses and beneficial root tip traits [J].

Bengough, A. Glyn ;

McKenzie, B. M. ;

Hallett, P. D. ;

Valentine, T. A. .

JOURNAL OF EXPERIMENTAL BOTANY, 2011, 62 (01) :59-68

[5] Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [J].

Birney, Ewan ;

Stamatoyannopoulos, John A. ;

Dutta, Anindya ;

Guigo, Roderic ;

Gingeras, Thomas R. ;

Margulies, Elliott H. ;

Weng, Zhiping ;

Snyder, Michael ;

Dermitzakis, Emmanouil T. ;

Stamatoyannopoulos, John A. ;

Thurman, Robert E. ;

Kuehn, Michael S. ;

Taylor, Christopher M. ;

Neph, Shane ;

Koch, Christoph M. ;

Asthana, Saurabh ;

Malhotra, Ankit ;

Adzhubei, Ivan ;

Greenbaum, Jason A. ;

Andrews, Robert M. ;

Flicek, Paul ;

Boyle, Patrick J. ;

Cao, Hua ;

Carter, Nigel P. ;

Clelland, Gayle K. ;

Davis, Sean ;

Day, Nathan ;

Dhami, Pawandeep ;

Dillon, Shane C. ;

Dorschner, Michael O. ;

Fiegler, Heike ;

Giresi, Paul G. ;

Goldy, Jeff ;

Hawrylycz, Michael ;

Haydock, Andrew ;

Humbert, Richard ;

James, Keith D. ;

Johnson, Brett E. ;

Johnson, Ericka M. ;

Frum, Tristan T. ;

Rosenzweig, Elizabeth R. ;

Karnani, Neerja ;

Lee, Kirsten ;

Lefebvre, Gregory C. ;

Navas, Patrick A. ;

Neri, Fidencio ;

Parker, Stephen C. J. ;

Sabo, Peter J. ;

Sandstrom, Richard ;

Shafer, Anthony .

NATURE, 2007, 447 (7146) :799-816

[6] Variation Revealed by SNP Genotyping and Morphology Provides Insight into the Origin of the Tomato [J].

Blanca, Jose ;

Canizares, Joaquin ;

Cordero, Laura ;

Pascual, Laura ;

Jose Diez, Maria ;

Nuez, Fernando .

PLOS ONE, 2012, 7 (10)

[7] A Draft Genome Sequence of Nicotiana benthamiana to Enhance Molecular Plant-Microbe Biology Research [J].

Bombarely, Aureliano ;

Rosli, Hernan G. ;

Vrebalov, Julia ;

Moffett, Peter ;

Mueller, Lukas A. ;

Martin, Gregory B. .

MOLECULAR PLANT-MICROBE INTERACTIONS, 2012, 25 (12) :1523-1530

[8] Whole-genome sequencing of multiple Arabidopsis thaliana populations [J].

Cao, Jun ;

Schneeberger, Korbinian ;

Ossowski, Stephan ;

Guenther, Torsten ;

Bender, Sebastian ;

Fitz, Joffrey ;

Koenig, Daniel ;

Lanz, Christa ;

Stegle, Oliver ;

Lippert, Christoph ;

Wang, Xi ;

Ott, Felix ;

Mueller, Jonas ;

Alonso-Blanco, Carlos ;

Borgwardt, Karsten ;

Schmid, Karl J. ;

Weigel, Detlef .

NATURE GENETICS, 2011, 43 (10) :956-U60

[9] Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution [J].

Carroll, Sean B. .

CELL, 2008, 134 (01) :25-36

[10] A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines [J].

Chitwood, Daniel H. ;

Kumar, Ravi ;

Headland, Lauren R. ;

Ranjan, Aashish ;

Covington, Michael F. ;

Ichihashi, Yasunori ;

Fulop, Daniel ;

Jimenez-Gomez, Jose M. ;

Peng, Jie ;

Maloof, Julin N. ;

Sinha, Neelima R. .

PLANT CELL, 2013, 25 (07) :2465-2481

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