Journal Article

B73 Maize Genome: Complexity, Diversity, and Dynamics

Hsia, An-Ping, Wilson, Richard K, Jeddeloh, Jeffrey A, Yeh, Cheng-Ting, Nagel, Dawn Holligan, Sharma, Anupma, Jackson, Stephanie M, Chaparro, Cristian, Nguyen, John, Gillam, Barbara, Faga, Ben, Strong, Cindy, Abbott, Rachel M, Ambroise, Claude, Zhang, Lifang, Du, Feiyu, Kanchi, Krishna, Zuccolo, Andrea, Schnable, Patrick S, Lin, Jinke, Kumari, Sunita, Vaughn, Matthew W, Han, Yujun, Ying, Kai, Liang, Chengzhi, Tomlinson, Chad, Pasternak, Shiran, Rock, Susan M, Delgado, Brandon, Carpita, Nicholas C, Wissotski, Marina, Kramer, Melissa, Westerman, Richard, Thane, Nay, Mead, Kelly, Wing, Rod A, Nettleton, Dan, Courtney, Laura, Kudrna, Dave, Wang, Tom, Stein, Joshua C, Kim, HyeRan, Penning, Bryan W, He, Ruifeng, Narechania, Apurva, Waligorski, Jason, Zhang, Jianwei, Dujmic, Zeljko, Levy, Andy, Rajasekar, Shanmugam, Spiegel, Lori, Fulton, Lucinda, Zhu, Qihui, Marchetto, Pamela, Belter, Eddie, Martienssen, Robert A, Henke, Jessica, Ochoa, Kerri, Rotter, Kelsi, Ko, Ara, Lomeli, Rene, McMahan, Linda, Angelova, Angelina, Waterman, Michael, Aluru, Srinivas, Yang, Lixing, Liu, Zhijie, Campos, David, Ashley, Elizabeth, Clifton, Sandra

2009

Overview

We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

• Publisher: American Association for the Advancement of Science,The American Association for the Advancement of Science,American Association for the Advancement of Science (AAAS)
• Subject: Agronomy. Soil science and plant productions / allopolyploidy / Base Sequence / Biochemistry / Biochemistry, Molecular Biology / Biodiversity / Bioinformatics / Biological and medical sciences / Biological research / Cellular Biology / Centromere / Centromere - genetics / Centromeres / Cereal crops / Chromosome Mapping / Chromosomes / Chromosomes, Plant / Chromosomes, Plant - genetics / Computer Science / Corn / crops / Crops, Agricultural / Crops, Agricultural - genetics / Cytogenetics / diploidy / DNA Copy Number Variations / DNA Methylation / DNA Transposable Elements / DNA, Plant / DNA, Plant - genetics / Domestication / Evolutionary biology / Fundamental and applied biological sciences. Psychology / Generalities. Genetics. Plant material / Genes / Genes, Plant / Genetic recombination / Genetic resources, diversity / Genetic Variation / Genetics / Genetics and breeding of economic plants / Genome, Plant / Genomes / Genomics / Inbreeding / Life Sciences / MicroRNAs / MicroRNAs - genetics / Molecular biology / Molecular Networks / Molecular Sequence Data / Origin, evolution, domestication / Plant breeding / Plant material / Plants / Plants genetics / Ploidies / Populations and Evolution / Quantitative Methods / Recombination, Genetic / Research universities / Retroelements / Rice / RNA, Plant / RNA, Plant - genetics / Sequence Analysis, DNA / Sorghum / Structural Biology / Systematics, Phylogenetics and taxonomy / transposons / Vegetal Biology / Zea mays / Zea mays - genetics