title: Organization of the prolamin gene family provides insight into the evolution of the maize genome and gene duplications in grass species.
abstract: Zea mays, commonly known as corn, is perhaps the most greatly produced crop in terms of tonnage and a major food, feed, and biofuel resource. Here we analyzed its prolamin gene family, encoding the major seed storage proteins, as a model for gene evolution by syntenic alignments with sorghum and rice, two genomes that have been sequenced recently. Because a high-density gene map has been constructed for maize inbred B73, all prolamin gene copies can be identified in their chromosomal context. Alignment of respective chromosomal regions of these species via conserved genes allow us to identify the pedigree of prolamin gene copies in space and time. Its youngest and largest gene family, the alpha prolamins, arose about 22-26 million years ago (Mya) after the split of the Panicoideae (including maize, sorghum, and millet) from the Pooideae (including wheat, barley, and oats) and Oryzoideae (rice). The first dispersal of alpha prolamin gene copies occurred before the split of the progenitors of maize and sorghum about 11.9 Mya. One of the two progenitors of maize gained a new alpha zein locus, absent in the other lineage, to form a nonduplicated locus in maize after allotetraplodization about 4.8 Mya. But dispersed copies gave rise to tandem duplications through uneven expansion and gene silencing of this gene family in maize and sorghum, possibly because of maize's greater recombination and mutation rates resulting from its diploidization process. Interestingly, new gene loci in maize represent junctions of ancestral chromosome fragments and sites of new centromeres in sorghum and rice.
authors.affiliation: Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8020, USA.
authors.forename: Jian-Hong
authors.initials: JH
authors.lastname: Xu
authors.forename: Joachim
authors.initials: J
authors.lastname: Messing
mesh_terms: D002503:Centromere / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D019143:Evolution, Molecular; D017353:Gene Deletion; D018628:Gene Dosage; D020440:Gene Duplication; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D049810:Genetic Speciation; D018745:Genome, Plant / Q000235:genetics*; D010788:Photosynthesis / Q000502:physiology; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D011003:Ploidies; D006109:Poaceae / Q000235:genetics*; D055315:Prolamins; D003313:Zea mays / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D055315:Prolamins
references.citation: Genome Res. 2002 Oct;12(10):1549-55
references.pmid: 12368247
references.citation: Plant Mol Biol. 1989 Mar;12(3):245-56
references.pmid: 24272860
references.citation: Genome Res. 2006 Feb;16(2):251-9
references.pmid: 16354755
references.citation: Genome Dyn. 2008;4:41-56
references.pmid: 18756076
references.citation: Proc Natl Acad Sci U S A. 2003 Jul 22;100(15):9055-60
references.pmid: 12853580
references.citation: Plant J. 2007 May;50(4):574-85
references.pmid: 17425713
references.citation: Genome Res. 2004 Oct;14(10A):1924-31
references.pmid: 15466290
references.citation: Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13206-11
references.pmid: 16141333
references.citation: Proc Natl Acad Sci U S A. 2004 Oct 5;101(40):14349-54
references.pmid: 15388850
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Plant Mol Biol. 1993 May;22(2):323-36
references.pmid: 8507833
references.citation: PLoS Genet. 2007 Jul;3(7):e123
references.pmid: 17658954
references.citation: Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
references.pmid: 9396791
references.citation: Nature. 2000 Dec 14;408(6814):796-815
references.pmid: 11130711
references.citation: Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):7094-7
references.pmid: 9192697
references.citation: Genome Res. 2004 Oct;14(10A):1932-7
references.pmid: 15466291
references.citation: Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):6809-14
references.pmid: 11038553
references.citation: Plant Physiol. 2001 Mar;125(3):1198-205
references.pmid: 11244101
references.citation: BMC Plant Biol. 2008 Feb 19;8:18
references.pmid: 18284697
references.citation: Plant J. 1996 Sep;10(3):415-24
references.pmid: 8811857
references.citation: Trends Genet. 2002 May;18(5):232-6
references.pmid: 12047939
references.citation: Genome Res. 2004 Oct;14(10A):1916-23
references.pmid: 15466289
references.citation: Brief Bioinform. 2004 Jun;5(2):150-63
references.pmid: 15260895
references.citation: Plant Physiol. 2002 Dec;130(4):1626-35
references.pmid: 12481046
references.citation: Plant Cell. 2004 Jul;16(7):1667-78
references.pmid: 15208399
references.citation: Science. 2003 Nov 14;302(5648):1206-8
references.pmid: 14615538
references.citation: Genome Res. 2006 Oct;16(10):1241-51
references.pmid: 16902087
references.citation: Trends Genet. 2005 Apr;21(4):227-33
references.pmid: 15797618
references.citation: Proc Natl Acad Sci U S A. 1990 Oct;87(20):7809-13
references.pmid: 2235998
references.citation: Nucleic Acids Res. 2004 Dec 29;32(22):e189
references.pmid: 15625231
references.citation: Plant Mol Biol. 2005 Sep;59(2):363-74
references.pmid: 16247562
references.citation: Proc Natl Acad Sci U S A. 1994 May 24;91(11):4867-71
references.pmid: 8197149
references.citation: Plant Cell. 2001 Oct;13(10):2297-317
references.pmid: 11595803
references.citation: Plant Physiol. 2007 May;144(1):258-77
references.pmid: 17384160
references.citation: Trends Genet. 2007 Jun;23(6):270-2
references.pmid: 17418444
references.citation: Theor Appl Genet. 1989 Feb;77(2):217-26
references.pmid: 24232532
references.citation: Nature. 2005 Aug 11;436(7052):793-800
references.pmid: 16100779