Organization of the prolamin gene family provides insight into the evolution of the maize genome and gene duplications in grass species.
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.
Xu
Jian-Hong
JH
Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8020, USA.
Messing
Joachim
J
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*
D010940:Plant Proteins; D055315:Prolamins
Genome Res. 2002 Oct;12(10):1549-55
12368247
Plant Mol Biol. 1989 Mar;12(3):245-56
24272860
Genome Res. 2006 Feb;16(2):251-9
16354755
Genome Dyn. 2008;4:41-56
18756076
Proc Natl Acad Sci U S A. 2003 Jul 22;100(15):9055-60
12853580
Plant J. 2007 May;50(4):574-85
17425713
Genome Res. 2004 Oct;14(10A):1924-31
15466290
Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13206-11
16141333
Proc Natl Acad Sci U S A. 2004 Oct 5;101(40):14349-54
15388850
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
9254694
Plant Mol Biol. 1993 May;22(2):323-36
8507833
PLoS Genet. 2007 Jul;3(7):e123
17658954
Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
9396791
Nature. 2000 Dec 14;408(6814):796-815
11130711
Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):7094-7
9192697
Genome Res. 2004 Oct;14(10A):1932-7
15466291
Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):6809-14
11038553
Plant Physiol. 2001 Mar;125(3):1198-205
11244101
BMC Plant Biol. 2008 Feb 19;8:18
18284697
Plant J. 1996 Sep;10(3):415-24
8811857
Trends Genet. 2002 May;18(5):232-6
12047939
Genome Res. 2004 Oct;14(10A):1916-23
15466289
Brief Bioinform. 2004 Jun;5(2):150-63
15260895
Plant Physiol. 2002 Dec;130(4):1626-35
12481046
Plant Cell. 2004 Jul;16(7):1667-78
15208399
Science. 2003 Nov 14;302(5648):1206-8
14615538
Genome Res. 2006 Oct;16(10):1241-51
16902087
Trends Genet. 2005 Apr;21(4):227-33
15797618
Proc Natl Acad Sci U S A. 1990 Oct;87(20):7809-13
2235998
Nucleic Acids Res. 2004 Dec 29;32(22):e189
15625231
Plant Mol Biol. 2005 Sep;59(2):363-74
16247562
Proc Natl Acad Sci U S A. 1994 May 24;91(11):4867-71
8197149
Plant Cell. 2001 Oct;13(10):2297-317
11595803
Plant Physiol. 2007 May;144(1):258-77
17384160
Trends Genet. 2007 Jun;23(6):270-2
17418444
Theor Appl Genet. 1989 Feb;77(2):217-26
24232532
Nature. 2005 Aug 11;436(7052):793-800
16100779