The B73 Maize Genome: Complexity, Diversity, and Dynamics
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).
Abstract
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.
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Published In
Science
Volume 326 | Issue 5956
20 November 2009
20 November 2009
Copyright
Copyright © 2009, American Association for the Advancement of Science.
Submission history
Received: 1 July 2009
Accepted: 13 October 2009
Published in print: 20 November 2009
Acknowledgments
The Maize Genome Sequencing Project supported by NSF award DBI-0527192 (R.K.W., S.W.C., R.S.F., R.A.W., P.S.S., S.A., L.S., D.W., W.R.M., R.A.M.). The Maize Transposable Element Consortium and the Maize Centromere Consortium supported by NSF awards DBI-0607123 (S.R.W., J.L.B., R.K.D., N.J., P.S.M.) and DBI-0421671 (R.K.D., J.J., G.G.P.). Also supported by NSF grants DBI-0321467 (D.W.), DBI-0321711 (P.S.S.), DBI-0333074 (D.W.), DBI-0501818 (D.C.S.), DBI-0501857 (Y.Y.), DBI-0701736 (T.P.B., Q.S.), DBI-0703273 (R.A.M.), and DBI-0703908 (D.W.), and by USDA National Research Initiative Grants 2005-35301-15715 and 2007-35301-18372 from the USDA Cooperative State Research, Education, and Extension Service (P.S.S.) and from the USDA-ARS (408934 and 413089) to D.W., and from the Office of Science (Biological and Environmental Research), U.S. Department of Energy, grant DE-FG02-08ER64702 to N.C.C. and M.C.M. Sequences of the reference chromosomes have been deposited in GenBank as accession numbers CM000777 to CM000786. RNA-sequence reads have been deposited in the Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo) as accession numbers GSE16136, GSE16868, and GSE16916. Centromeric sequences have been deposited in the National Center for Biotechnology Information, NIH, Trace Archive as accessions 1757396377 to 1757412600 and 2185189231 to 2185200942.
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