title: Genome-wide expression analysis of soybean MADS genes showing potential function in the seed development.
abstract: The MADS family is an ancient and best-studied transcription factor and plays fundamental roles in almost every developmental process in plants. In the plant evolutionary history, the whole genome duplication (WGD) events are important not only to the plant species evolution, but to expansion of members of the gene families. Soybean as a model legume crop has experience three rounds of WGD events. Members of some MIKC(C) subfamilies, such as SOC, AGL6, SQUA, SVP, AGL17 and DEF/GLO, were expanded after soybean three rounds of WGD events. And some MIKC(C) subfamilies, MIKC* and type I MADS families had experienced faster birth-and-death evolution and their traces before the Glycine WGD event were not found. Transposed duplication played important roles in tandem arrangements among the members of different subfamilies. According to the expression profiles of type I and MIKC paralog pair genes, the fates of MIKC paralog gene pairs were subfunctionalization, and the fates of type I MADS paralog gene pairs were nonfunctionalization. 137 out of 163 MADS genes were close to 186 loci within 2 Mb genomic regions associated with seed-relative QTLs, among which 115 genes expressed during the seed development. Although MIKC(C) genes kept the important and conserved functions of the flower development, most MIKC(C) genes showed potentially essential roles in the seed development as well as the type I MADS.
authors: MOA Key Lab of Soybean Biology Beijing, National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors: Cheng-Ming
authors: CM
authors: Fan
authors: Xu
authors: X
authors: Wang
authors: Yan-Wei
authors: YW
authors: Wang
authors: Rui-Bo
authors: RB
authors: Hu
authors: Xiao-Mei
authors: XM
authors: Zhang
authors: Jian-Xin
authors: JX
authors: Chen
authors: Yong-Fu
authors: YF
authors: Fu
mesh_terms: D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D026161:MADS Domain Proteins / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*; D040641:Quantitative Trait Loci; D012639:Seeds / Q000235:genetics* / Q000254:growth & development*; D013025:Glycine max / Q000235:genetics* / Q000254:growth & development*
chemical_list: D026161:MADS Domain Proteins; D010940:Plant Proteins
references: Nature. 2007 Sep 27;449(7161):463-7
references: 17721507
references: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37
references: 21593126
references: J Exp Bot. 2011 Oct;62(14):4719-30
references: 21914655
references: Curr Opin Genet Dev. 2005 Aug;15(4):454-60
references: 15964755
references: Plant J. 2012 May;70(3):409-20
references: 22176531
references: Mol Biol Evol. 2012 Dec;29(12):3793-806
references: 22821009
references: Nature. 2011 Nov 16;480(7378):520-4
references: 22089132
references: Ann Bot. 2007 Sep;100(3):603-19
references: 17670752
references: Plant J. 2013 Jan;73(1):143-53
references: 22974547
references: New Phytol. 2010 Apr;186(1):175-83
references: 20409177
references: Mol Biol Evol. 2006 Nov;23(11):2245-58
references: 16926244
references: Nucleic Acids Res. 2012 Apr;40(7):e49
references: 22217600
references: Plant Physiol. 2010 Sep;154(1):287-300
references: 20631316
references: BMC Genomics. 2010 Feb 17;11:113
references: 20163715
references: Nature. 2010 Jan 14;463(7278):178-83
references: 20075913
references: Proc Natl Acad Sci U S A. 2000 May 9;97(10):5328-33
references: 10805792
references: J Mol Evol. 1996 Nov;43(5):484-516
references: 8875863
references: Genome. 2012 Mar;55(3):245-56
references: 22376137
references: Gene. 2005 Mar 14;347(2):183-98
references: 15777618
references: Plant Cell. 2011 Sep;23(9):3129-36
references: 21917551
references: Mol Biol Evol. 2003 Dec;20(12):1963-77
references: 12949148
references: Protein Sci. 1995 Aug;4(8):1618-32
references: 8520488
references: Plant Cell. 1995 Aug;7(8):1271-82
references: 7549483
references: Nature. 2000 May 11;405(6783):200-3
references: 10821278
references: Nature. 2003 Jul 3;424(6944):85-8
references: 12840762
references: Plant Cell. 2010 Aug;22(8):2562-78
references: 20807882
references: Nucleic Acids Res. 2003 Aug 1;31(15):4401-9
references: 12888499
references: Proc Natl Acad Sci U S A. 1996 May 14;93(10):4793-8
references: 8643482
references: Mol Biol Evol. 2007 Mar;24(3):679-86
references: 17179139
references: PLoS Genet. 2010 May 13;6(5):e1000949
references: 20485521
references: Mol Biol Evol. 2002 Jun;19(6):801-14
references: 12032236
references: Mol Biol Evol. 2011 Oct;28(10):2731-9
references: 21546353
references: BMC Plant Biol. 2004 Jun 01;4:10
references: 15171794
references: Plant J. 2008 Jun;54(6):1037-48
references: 18346189
references: Bioinformatics. 2002 Jan;18(1):207-8
references: 11836235
references: Cell. 1988 Dec 23;55(6):989-1003
references: 3203386
references: BMC Mol Biol. 2009 Sep 28;10:93
references: 19785741
references: Mol Genet Genomics. 2003 Feb;268(5):598-606
references: 12589434
references: Plant Mol Biol. 2005 May;58(1):89-107
references: 16028119
references: Science. 2008 Jun 6;320(5881):1344-9
references: 18451266
references: Mol Biol Evol. 2012 Jan;29(1):293-302
references: 21813465
references: Genome Biol. 2007;8(11):R249
references: 18034896
references: Annu Rev Plant Biol. 2009;60:433-53
references: 19575588
references: BMC Genomics. 2007 Jul 18;8:242
references: 17640358
references: PLoS One. 2011;6(12):e28150
references: 22164235
references: Plant Physiol. 2009 Jan;149(1):354-69
references: 18997115
references: Plant Cell. 1995 Aug;7(8):1259-69
references: 7549482
references: Plant Cell. 2006 Aug;18(8):1862-72
references: 16798889
references: Plant Cell. 1996 Nov;8(11):1977-89
references: 8953767
references: Nat Methods. 2008 Jul;5(7):621-8
references: 18516045
references: Genome Biol. 2010;11(6):214
references: 20587009
references: J Mol Biol. 1988 Dec 5;204(3):593-606
references: 3066908
references: Plant Physiol. 2008 Apr;146(4):1663-72
references: 18305206
references: Plant Cell. 2011 Mar;23(3):865-72
references: 21378131
references: Plant Physiol. 2007 Jan;143(1):447-60
references: 17071640
references: Plant Cell. 2003 Jul;15(7):1538-51
references: 12837945
references: Plant Cell. 2005 May;17(5):1424-33
references: 15805477
references: Nature. 2000 Apr 13;404(6779):766-70
references: 10783890
references: Proc Natl Acad Sci U S A. 2010 May 4;107(18):8063-70
references: 20385809
references: Gene. 2006 Aug 15;378:84-94
references: 16831523
references: J Mol Evol. 2003 May;56(5):573-86
references: 12698294
references: Development. 2012 Sep;139(17):3081-98
references: 22872082
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D843-6
references: 20008513
references: Curr Biol. 2004 Nov 9;14(21):1935-40
references: 15530395
references: Nature. 1990 Jul 5;346(6279):35-9
references: 1973265
references: Mol Biol Evol. 2007 Oct;24(10):2298-309
references: 17670808
references: Plant Physiol. 2007 Apr;143(4):1467-83
references: 17293439
references: J Exp Bot. 2006;57(13):3445-55
references: 17023564
references: Nucleic Acids Res. 2009 Apr;37(6):e45
references: 19237396
references: Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):1910-5
references: 14764899
references: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8
references: 19458158
references: Science. 1990 Nov 16;250(4983):931-6
references: 17746916
references: Plant Cell. 2008 Mar;20(3):635-47
references: 18334668
references: Mol Phylogenet Evol. 2003 Dec;29(3):464-89
references: 14615187