1. The B73 maize genome: complexity, diversity, and dynamics
- Author
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Kristi Collura, Nay Thane, Sanzhen Liu, Sharon Wei, Joshua C. Stein, Jason Waligorski, Shanmugam Rajasekar, Robert A. Martienssen, Patrick S. Schnable, Marc Cotton, Georgina Lopez, R. Kelly Dawe, Jennifer Sgro, Krista Delaney, Linda McMahan, Krishna L. Kanchi, Qi Sun, Jeffrey L. Bennetzen, Asif T. Chinwalla, Zhijie Liu, Gernot G. Presting, Jennifer S. Hodges, Jianwei Zhang, Doreen Ware, William Spooner, Melissa Kramer, Stephanie Muller, Kelly Mead, Jeffrey A. Jeddeloh, Peter Van Buren, W. Richard McCombie, Thomas J. Wang, Stephanie M. Jackson, Beth Miller, Ananth Kalyanaraman, Wolfgang Golser, Rene Lomeli, Aswathy Sebastian, Ara Ko, Alan M. Myers, Carol Soderlund, Kai Ying, Thomas K. Wolfgruber, Lixing Yang, Sunita Kumari, Yujun Han, Jayson Talag, John D. Nguyen, Shawn Leonard, Shiran Pasternak, Chad Tomlinson, Barbara Gillam, Angelina Angelova, Weizu Chen, Bryan W. Penning, Catrina Fronick, Apurva Narechania, Zeljko Dujmic, Matt Cordes, Tina Graves, Cheng Ting Yeh, Jennifer Currie, Michael S. Waterman, Seunghee Lee, Amy Denise Reily, Sandra W. Clifton, Jean-Marc Deragon, Matthew W. Vaughn, Jessica Ruppert, Chengzhi Liang, Dan Nettleton, Maureen C. McCann, Michele Braidotti, Scott Kruchowski, Shiguo Zhou, Ning Jiang, Feiyu Du, Cindy Strong, Thomas P. Brutnell, Scott J. Emrich, Nicholas C. Carpita, Michael J. Levy, Srinivas Aluru, Yi Jia, Liya Ren, Laura Courtney, Teri Mueller, Ruifeng He, Marco Cardenas, Fusheng Wei, Brandon Delgado, Lalit Ponnala, Robert S. Fulton, Elizabeth Applebaum, Jinke Lin, Kevin L. Schneider, Le Yan, Kelsi Rotter, Ben Faga, Susan M. Rock, Elizabeth Ingenthron, Adam Scimone, Andrea Zuccolo, Cristian Chaparro, Neha Shah, Qihui Zhu, Hye-Ran Lee, Richard P. Westerman, Chuanzhu Fan, Dave Kudrna, Rachel Abbott, Lidia Nascimento, Jer Ming Chia, Kerri Ochoa, Lindsey Phelps, Elizabeth Ashley, Damon Lisch, Lucinda Fulton, Gabriel Scara, Bill Courtney, Lori Spiegel, Kim D. Delehaunty, Anupma Sharma, Andrew Levy, Hyeran Kim, Richard K. Wilson, Patrick Minx, Rod A. Wing, Phillip SanMiguel, An-Ping Hsia, Yan Fu, Kyung Kim, Nathan M. Springer, Regina S. Baucom, Woojin Kim, Jason Falcone, Pinghua Li, David C. Schwartz, W. Brad Barbazuk, Jamey Higginbotham, Susan R. Wessler, T. K. Thane, Jessica Henke, Hao Wang, Jiming Jiang, Yeisoo Yu, Sara Kohlberg, Claude Ambroise, Kevin Crouse, Theresa Zutavern, Pamela Marchetto, David Campos, Lifang Zhang, James C. Estill, Dawn H. Nagel, Marina Wissotski, Eddie Belter, Center for Plant Genomics, Iowa State University (ISU), Cold Spring Harbor Laboratory (CSHL), Department of Genetics [Saint-Louis], Washington University in Saint Louis (WUSTL), Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, Department of Genetics, Development, and Cell Biology, Department of Electrical and Computer Engineering [Iowa], University of Iowa [Iowa City], University of Florida [Gainesville] (UF), Department of Genetics, University of Georgia [USA], Cornell University [New York], Department of Botany and Plant Pathology, Purdue University [West Lafayette], Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Department of Agronomy, NimbleGen, Department of Horticulture, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Biological Sciences [West Lafayette], and Department of plant Biology
- Subjects
0106 biological sciences ,MESH: Genome, Plant ,MESH: Sequence Analysis, DNA ,MESH: Zea mays ,MESH: Base Sequence ,MESH: RNA, Plant ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,01 natural sciences ,Genome ,Divergence ,MESH: Ploidies ,MESH: DNA Methylation ,MESH: Genes, Plant ,Nested association mapping ,Copy-number variation ,MESH: Genetic Variation ,MESH: Chromosomes, Plant ,2. Zero hunger ,Genetics ,0303 health sciences ,Multidisciplinary ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,[SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN] ,Arabidopsis-Thaliana ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,Retrotransposons ,MESH: DNA Transposable Elements ,Helitron ,MESH: Centromere ,MESH: Recombination, Genetic ,MESH: DNA Copy Number Variations ,Ploidy ,Transposable element ,Genome evolution ,Evolution ,[SDV.BC]Life Sciences [q-bio]/Cellular Biology ,Biology ,Methylation ,[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics ,03 medical and health sciences ,MESH: Retroelements ,MESH: Inbreeding ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Zea-Mays ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM] ,MESH: DNA, Plant ,Gene ,030304 developmental biology ,MESH: Molecular Sequence Data ,Transposable Elements ,[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,Plant ,15. Life on land ,MESH: Crops, Agricultural ,[SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding ,Genes ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,MESH: Chromosome Mapping ,MESH: MicroRNAs ,010606 plant biology & botany - Abstract
A-Maize-ing Maize is one of our oldest and most important crops, having been domesticated approximately 9000 years ago in central Mexico. Schnable et al. (p. 1112 ; see the cover) present the results of sequencing the B73 inbred maize line. The findings elucidate how maize became diploid after an ancestral doubling of its chromosomes and reveals transposable element movement and activity and recombination. Vielle-Calzada et al. (p. 1078 ) have sequenced the Palomero Toluqueño ( Palomero ) landrace, a highland popcorn from Mexico, which, when compared to the B73 line, reveals multiple loci impacted by domestication. Swanson-Wagner et al. (p. 1118 ) exploit possession of the genome to analyze expression differences occurring between lines. The identification of single nucleotide polymorphisms and copy number variations among lines was used by Gore et al. (p. 1115 ) to generate a Haplotype map of maize. While chromosomal diversity in maize is high, it is likely that recombination is the major force affecting the levels of heterozygosity in maize. The availability of the maize genome will help to guide future agricultural and biofuel applications (see the Perspective by Feuillet and Eversole ).
- Published
- 2009
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