Dynamic rearrangements determine genome organization and useful traits in soybean

Plant Physiology

Volumn 151, Issue 3, 2009, Pages 1066-1076

  Kim, Kyung Do ^a   Shin, Jin Hee ^a   van, Kyujung ^a   Kim, Dong Hyun ^a   Lee, Suk Ha ^a,b  

^a Seoul National University   (South Korea)

^b Seoul National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); GLYCINE MAX; MEDICAGO TRUNCATULA;

EID: 70350655959     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.109.141739     Document Type: Article

References (60)

1. Adams KL, Wendel JF (2005) Polyploidy and genome evolution in plants. Curr Opin Plant Biol 8: 135-141
2. Axelsson T, Shavorskaya O, Lagercrantz U (2001) Multiple flowering time QTLs within several Brassica species could be the result of duplicated copies of one ancestral gene. Genome 44: 856-864
3. Bernard RL, Weiss MG (1973) Qualitative genetics. In BE Caldwell, ed, Soybeans: Improvement, Production, and Uses. American Society of Agronomy, Madison, WI, pp 117-154
4. Blanc G, Wolfe KH (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16: 1667-1678
5. Cai CM, Van K, Kim MY, Jun TH, Shin JH, Cho SY, Lee YS, Lee SH (2008a) SNP discovery, linkage analysis and microsynteny in tentative consensus sequences derived from roots cDNA in a supernodulating soybean mutant. Euphytica 164: 189-197
6. Cai CM, Van K, Kim MY, Lee SH (2005) Optimization of SNP genotyping assay with fluorescence polarization detection. Korean J Crop Sci 50: 361-367
7. Cai CM, Van K, Kim MY, Lee SH (2008b) Sequence divergence of recently duplicate genes in soybean (Glycine max L. Merr.). Genes Genom 30: 271-281
8. Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T, et al (2006) Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci USA 103: 14959-14964
9. Choi IY, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, Chase K, Lark KG, Reiter RS, Yoon MS, et al (2007) A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176: 685-696
10. Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, et al (2006) Widespread genome duplications throughout the history of flowering plants. Genome Res 16: 738-749
11. Eichler EE, Sankoff D (2003) Structural dynamics of eukaryotic chromosome evolution. Science 301: 793-797
12. Feaster CV (1951) Bacterial pustule disease in soybeans: artificial inoculation, varietal resistance, and inheritance of resistance. In Missouri Agricultural Experiment Station Research Bulletin 487. Missouri Agricultural Experiment Station, Columbia, MO, Research Bulletin 487
13. Gharbi K, Glover KA, Stone LC, MacDonald ES, Matthews L, Grimholt U, Stear MJ (2009) Genetic dissection of MHC-associated susceptibility to Lepeophtheirus salmonis in Atlantic salmon. BMC Genet 10: 20
14. Groth D, Braun E (1986) Growth kinetics and histopathology of Xanthomonas campestris pv. glycines in leaves of resistant and susceptible soybeans. Phytopathology 76: 959-965
15. Hadley HH, Hymowitz T (1973) Speciation and cytogenetics. In BE Caldwell, ed, Soybeans: Improvement, Production and Uses. American Society of Agronomy, Madison, WI, pp 96-116
16. Hall AE, Kettler GC, Preuss D (2006) Dynamic evolution at pericentromeres. Genome Res 16: 355-364
17. Hartwig EE, Johnson HW (1953) Effect of the bacterial pustule disease on yield and chemical composition of soybeans. Agron J 45: 22-23
18. Hartwig EE, Lehman SG (1951) Inheritance of resistance to the bacterial pustule disease in soybeans. Agron J 43: 226-229
19. Ilic K, SanMiguel PJ, Bennetzen JL (2003) A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes. Proc Natl Acad Sci USA 100: 12265-12270
20. Innes RW, Ameline-Torregrosa C, Ashfield T, Cannon E, Cannon SB, Chacko B, Chen NW, Couloux A, Dalwani A, Denny R, et al (2008) Differential accumulation of retroelements and diversification of NBLRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean. Plant Physiol 148: 1740-1759
21. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-467
22. Kearsey MJ, Farquhar AG (1998) QTL analysis in plants: where are we now? Heredity 80: 137-142
23. Lackey JA (1980) Chromosome numbers in the Phaseoleae (Fabaceae: Faboideae) and their relation to taxonomy. Am J Bot 67: 595-602
24. Lai J, Ma J, Swigonova Z, Ramakrishna W, Linton E, Llaca V, Tanyolac B, Park YJ, Jeong OY, Bennetzen JL, et al (2004) Gene loss and movement in the maize genome. Genome Res 14: 1924-1931
25. Laviolette FA, Athow KL, Probst AH, Wilcox JR (1970) Effect of bacterial pustule on yield of soybeans. Crop Sci 10: 150-151
26. Leder EH, Danzmann RG, Ferguson MM (2006) The candidate gene, Clock, localizes to a strong spawning time quantitative trait locus region in rainbow trout. J Hered 97: 74-80
27. Lee JM, Bush AL, Specht JE, Shoemaker RC (1999) Mapping of duplicate genes in soybean. Genome 42: 829-836
28. Lee JM, Grant D, Vallejos CE, Shoemaker RC (2001) Genome organization in dicots. II. Arabidopsis as a 'bridging species' to resolve genome evolution events among legumes. Theor Appl Genet 103: 765-773
29. Lin JY, Jacobus BH, SanMiguel P, Walling JG, Yuan Y, Shoemaker RC, Young ND, Jackson SA (2005) Pericentromeric regions of soybean (Glycine max L. Merr.) chromosomes consist of retroelements and tandemly repeated DNA and are structurally and evolutionarily labile. Genetics 170: 1221-1230
30. Marek LF, Shoemaker RC (1997) BAC contig development by fingerprint analysis in soybean. Genome 40: 420-427
31. Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, Yu Y, Wei F, Fuks G, Soderlund CA, Mayer KF, et al (2004) Sequence composition and genome organization of maize. Proc Natl Acad Sci USA 101: 14349-14354
32. Moghadam HK, Poissant J, Fotherby H, Haidle L, Ferguson MM, Danzmann RG (2007) Quantitative trait loci for body weight, condition factor and age at sexual maturation in Arctic charr (Salvelinus alpinus): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar). Mol Genet Genomics 277: 647-661
33. Mudge J, Cannon SB, Kalo P, Oldroyd GE, Roe BA, Town CD, Young ND (2005) Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana. BMC Plant Biol 5: 15
34. Narvel JM, Jakkula LR, Phillips DV, Wang T, Lee SH, Boerma HR (2001) Molecular mapping of Rxp conditioning reaction to bacterial pustule in soybean. J Hered 92: 267-270
35. O'Malley KG, Sakamoto T, Danzmann RG, Ferguson MM (2003) Quantitative trait loci for spawning date and body weight in rainbow trout: testing for conserved effects across ancestrally duplicated chromosomes. J Hered 94: 273-284
36. Otto SP, Whitton J (2000) Polyploid incidence and evolution. Annu Rev Genet 34: 401-437
37. Pagel J, Walling JG, Young ND, Shoemaker RC, Jackson SA (2004) Segmental duplications within the Glycine max genome revealed by fluorescence in situ hybridization of bacterial artificial chromosomes. Genome 47: 764-768
38. Pfeil BE, Schlueter JA, Shoemaker RC, Doyle JJ (2005) Placing paleopolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families. Syst Biol 54: 441-454
39. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386
40. Schlueter JA, Dixon P, Granger C, Grant D, Clark L, Doyle JJ, Shoemaker RC (2004) Mining EST databases to resolve evolutionary events in major crop species. Genome 47: 868-876
41. Schlueter JA, Lin JY, Schlueter SD, Vasylenko-Sanders IF, Deshpande S, Yi J, O'Bleness M, Roe BA, Nelson RT, Scheffler BE, et al (2007a) Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing. BMC Genomics 8: 330
42. Schlueter JA, Scheffler BE, Jackson S, Shoemaker RC (2008) Fractionation of synteny in a genomic region containing tandemly duplicated genes across Glycine max, Medicago truncatula, and Arabidopsis thaliana. J Hered 99: 390-395
43. Schlueter JA, Scheffler BE, Schlueter SD, Shoemaker RC (2006) Sequence conservation of homeologous bacterial artificial chromosomes and transcription of homeologous genes in soybean (Glycine max L. Merr.). Genetics 174: 1017-1028
44. Schlueter JA, Vaslenko-Sanders IF, Deshpande S, Yi J, Siegfried M, Roe BA, Schlueter SD, Scheffler BE, Shoemaker RC (2007b) The FAD2 gene family of soybean: insights into the structural and functional divergence of a paleopolyploid genome. Crop Sci 47: S14-S26
45. Schranz ME, Quijada P, Sung SB, Lukens L, Amasino R, Osborn TC (2002) Characterization and effects of the replicated flowering time gene FLC in Brassica rapa. Genetics 162: 1457-1468
46. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W (2003) Human-mouse alignments with BLASTZ. Genome Res 13: 103-107
47. Shin JH, Van K, Kim DH, Kim KD, Jang YE, Choi BS, Kim MY, Lee SH (2008) The lipoxygenase gene family: a genomic fossil of shared polyploidy between Glycine max and Medicago truncatula. BMC Plant Biol 8: 133
48. Shoemaker RC, Polzin K, Labate J, Specht J, Brummer EC, Olson T, Young N, Concibido V, Wilcox J, Tamulonis JP, et al (1996) Genome duplication in soybean (Glycine subgenus soja). Genetics 144: 329-338
49. Shoemaker RC, Schlueter J, Doyle JJ (2006) Paleopolyploidy and gene duplication in soybean and other legumes. Curr Opin Plant Biol 9: 104-109
50. Somorjai IM, Danzmann RG, Ferguson MM (2003) Distribution of temperature tolerance quantitative trait loci in Arctic charr (Salvelinus alpinus) and inferred homologies in rainbow trout (Oncorhynchus my-kiss). Genetics 165: 1443-1456
51. Song QJ, Marek LF, Shoemaker RC, Lark KG, Concibido VC, Delannay X, Specht JE, Cregan PB (2004) A new integrated genetic linkage map of the soybean. Theor Appl Genet 109: 122-128
52. Van K, Ha BK, Kim MY, Moon JK, Paek NC, Heu S, Lee SH (2004) SSR mapping of genes conditioning soybean resistance to six isolates of Xanthomonas axonopodis pv. glycines. Genes Genom 26: 47-54
53. Van K, Kim DH, Cai CM, Kim MY, Shin JH, Graham MA, Shoemaker RC, Choi BS, Yang TJ, Lee SH (2008) Sequence level analysis of recently duplicated regions in soybean [Glycine max (L.) Merr.] genome. DNA Res 15: 93-102
54. Walling JG, Shoemaker R, Young N, Mudge J, Jackson S (2006) Chromosome-level homeology in paleopolyploid soybean (Glycine max) revealed through integration of genetic and chromosome maps. Genetics 172: 1893-1900
55. Weber CR, Dunleavy JM, Fehr WR (1966) Effect of bacterial pustule on closely related soybean lines. Agron J 58: 544-545
56. Wendel JF (2000) Genome evolution in polyploids. Plant Mol Biol 42: 225-249
57. Yan HH, Mudge J, Kim DJ, Larsen D, Shoemaker RC, Cook DR, Young ND (2003) Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana. Theor Appl Genet 106: 1256-1265
58. Yan HH, Mudge J, Kim DJ, Shoemaker RC, Cook DR, Young ND (2004) Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana. Genome 47: 141-155
59. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556
60. Young ND, Mudge J, Ellis TH (2003) Legume genomes: more than peas in a pod. Curr Opin Plant Biol 6: 199-204