Dynamic rearrangements determine genome organization and useful traits in soybean.
Soybean (Glycine max) is a paleopolyploid whose genome has gone through at least two rounds of polyploidy and subsequent diploidization events. Several studies have investigated the changes in genome structure produced by the relatively recent polyploidy event, but little is known about the ancient polyploidy due to the high frequency of gene loss after duplication. Our previous study, regarding a region responsible for bacterial leaf pustule, reported two homeologous Rxp regions produced by the recent whole-genome duplication event. In this study, we identified the full set of four homeologous Rxp regions (ranging from 1.96 to 4.60 Mb) derived from both the recent and ancient polyploidy events, and this supports the quadruplicated structure of the soybean genome. Among the predicted genes on chromosome 17 (linkage group D2), 71% of them were conserved in a recently duplicated region, while 21% and 24% of duplicated genes were retained in two homeologous regions formed by the ancient polyploidy. Furthermore, comparative analysis showed a 2:1 relationship between soybean and Medicago truncatula, since M. truncatula did not undergo the recent polyploidy event that soybean did. Unlike soybean, M. truncatula homeologous regions were highly fractionated and their synteny did not exist, revealing different rates of diploidization process between the two species. Our data show that extensive synteny remained in the four homeologous regions in soybean, even though the soybean genome experienced dynamic genome rearrangements following paleopolyploidy events. Moreover, multiple Rxp quantitative trait loci on different soybean chromosomes actually comprise homeologous regions produced by two rounds of polyploidy events.
Kim
Kyung Do
KD
Department of Plant Science, Seoul National University, Seoul 151-921, Korea.
Shin
Jin Hee
JH
Van
Kyujung
K
Kim
Dong Hyun
DH
Lee
Suk-Ha
SH
D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D055028:Comparative Genomic Hybridization; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D017343:Genes, Plant; D018745:Genome, Plant; D046913:Medicago truncatula / Q000235:genetics; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D011123:Polyploidy; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics*; D026801:Synteny
D018744:DNA, Plant
Nature. 2007 Sep 27;449(7161):463-7
17721507
Genome. 2004 Aug;47(4):764-8
15284882
Genome. 1997 Aug;40(4):420-7
18464837
Plant Mol Biol. 2000 Jan;42(1):225-49
10688139
DNA Res. 2008 Apr 30;15(2):93-102
18334514
BMC Genet. 2009 Apr 27;10:20
19397823
Plant Cell. 2004 Jul;16(7):1667-78
15208399
Genome Res. 2004 Oct;14(10A):1924-31
15466290
Theor Appl Genet. 2003 May;106(7):1256-65
12748777
Genetics. 2006 Oct;174(2):1017-28
16888343
Genetics. 2002 Nov;162(3):1457-68
12454088
Methods Mol Biol. 2000;132:365-86
10547847
Science. 2003 Aug 8;301(5634):793-7
12907789
Heredity (Edinb). 1998 Feb;80 ( Pt 2):137-42
9503632
Genetics. 1996 Sep;144(1):329-38
8878696
Mol Genet Genomics. 2007 Jun;277(6):647-61
17308931
Curr Opin Plant Biol. 2005 Apr;8(2):135-41
15752992
J Hered. 2008 Jul-Aug;99(4):390-5
18316321
J Hered. 2003 Jul-Aug;94(4):273-84
12920098
Curr Opin Plant Biol. 2006 Apr;9(2):104-9
16458041
Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12265-70
14530400
Genome Res. 2006 Mar;16(3):355-64
16461884
Genome. 2004 Feb;47(1):141-55
15060611
Genome Res. 2003 Jan;13(1):103-7
12529312
Genetics. 2003 Nov;165(3):1443-56
14668393
J Hered. 2001 May-Jun;92(3):267-70
11447243
Genome Res. 2006 Jun;16(6):738-49
16702410
Annu Rev Genet. 2000;34:401-437
11092833
Proc Natl Acad Sci U S A. 2006 Oct 3;103(40):14959-64
17003129
Comput Appl Biosci. 1997 Oct;13(5):555-6
9367129
Plant Physiol. 2008 Dec;148(4):1740-59
18842825
Genome. 2001 Oct;44(5):856-64
11681610
Proc Natl Acad Sci U S A. 2004 Oct 5;101(40):14349-54
15388850
BMC Genomics. 2007 Sep 19;8:330
17880721
BMC Plant Biol. 2008 Dec 23;8:133
19105811
J Hered. 2006 Jan-Feb;97(1):74-80
16407529
Curr Opin Plant Biol. 2003 Apr;6(2):199-204
12667879
Genetics. 2005 Jul;170(3):1221-30
15879505
Genome. 2004 Oct;47(5):868-76
15499401
Genetics. 2006 Mar;172(3):1893-900
16361231
Genetics. 2007 May;176(1):685-96
17339218
BMC Plant Biol. 2005 Aug 15;5:15
16102170
Theor Appl Genet. 2004 Jun;109(1):122-8
14991109
Syst Biol. 2005 Jun;54(3):441-54
16012110