The FAD2 gene family of soybean: Insights into the structural and functional divergence of a paleopolyploid genome

Crop Science

Volumn 47, Issue SUPPL. 1, 2007, Pages

  Schlueter, Jessica A ^a   Vasylenko Sanders, Iryna F ^b   Deshpande, Shweta ^b   Yi, Jing ^b   Siegfried, Mojesta ^b   Roe, Bruce A ^b   Schlueter, Shannon D ^c   Scheffler, Brian E ^d   Shoemaker, Randy C ^a  

^a U S DEPARTMENT OF AGRICULTURE   (United States)

^b UNIVERSITY OF OKLAHOMA   (United States)

^c IOWA STATE UNIVERSITY   (United States)

^d AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); GLYCINE MAX;

EID: 33847259161     PISSN: 0011183X     EISSN: None     Source Type: Journal    
DOI: 10.2135/cropsci2006.06.0382tpg     Document Type: Article

References (62)

1. Alt, J.L., W.R. Fehr, G.A. Welke, and D. Sandhu. 2005. Pheotypic and molecular analysis of oleate content in the mutant soybean line M23. Crop Sci. 45:1997-2000.
2. Altschul, S.F., W. Gish, W. Miller, E.W. Myers, and D.J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
3. The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature (London) 408:796-815.
4. Blanc, G., and K.H. Wolfe. 2004. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667-1678.
5. Bodenteich, A., S. Chissoe, Y.F. Wany, and B.A. Roe. 1993. Shotgun cloning as the stragety for choice to generate templates for high-throughput dideoxynucleotide sequencing, p. 42-50. In J.C. Venter (ed.) Automated DNA sequencing and analysis techniques. Academic Press, London.
6. Brudno, M., S. Malde, A. Poliakov, C.B. Do, O. Couronne, I. Dubchak, and S. Batzouglou. 2003. Glocal alignment: Finding rearrangements during alignment. Bioinformatics 19S1:i54-i62.
7. Burge, C., and S. Karlin. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268:78-94.
8. Chissoe, S.L., A. Bodenteich, Y.F. Wang, Y.P. Wang, D. Burian, S.W. Clifton, J. Crabtree, A. Freeman, K. Iyer, L. Jian, Y. May, H.J. McLaury, H.Q. Pan, O. Sharan, S. Toth, Z. Wong, G. Zhang, N. Heisterkamp, J. Groffen, and B.A. Roe. 1995. Sequence and analysis of the human ABL gene, the BCR gene, and regions involved in the Philadelphia chromosomal translocation. Genomics 27:67-82.
9. Diers, B.W., P. Keim, W.R. Fehr, and R.C. Shoemaker. 1992. RFLP analysis of soybean seed protein and oil content. Theor. Appl. Genet. 83:608-612.
10. Dong, Q., C.J. Lawrence, S.D. Schlueter, M.D. Wilkerson, S. Kurtz, C. Luschbough, and V. Brendel. 2005. Comparative plant genomics resources at PlantGDB. Plant Physiol. 139:610-618.
11. Force, A., M. Lynch, F.B. Pickett, A. Amores, Y.-L. Yan, and J. Postlethwait. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545.
12. Foster-Hartnett, D., J. Mudge, D. Danesh, H. Yan, D. Larsen, R. Denny, and N.D. Young. 2002. Comparative genomic analysis of sequences sampled from a small region on soybean molecular linkage group 'G'. Genome 45:634-645.
13. Frazer, K.A., L. Pachter, A. Poliakov, E.M. Rubin, and I. Dubchak. 2004. VISTA: Computational tools for comparative genomics. Nucleic Acids Res. 32:W273-W279.
14. Graham, M.A., L.F. Marek, and R.C. Shoemaker. 2002. Organization, expression and evolution of a disease resistance gene cluster in soybean. Genetics 162:1961-1977.
15. Grandbastien, M.A., S. Berry-Lowe, B.W. Shirley, and R. Meagher. 1986. Two soybean ribulose-1,5-bisphosphate carboxylase small subunit genes share extensive homology even in distant flanking sequences. Plant Mol. Biol. 7:451-465.
16. Grundy, S.M. 1986. Comparison of monounsaturated fatty acids and carbohydrates for lowering plasma cholesterol in man. N. Engl. J. Med. 314:745-748.
17. Haberer, G., S. Young, A.K. Bharti, H. Gundlach, C. Raymond, G. Fuks, E. Butler, R.A. Wing, S. Rounsley, B. Birren, C. Nusbaum, K.F.X. Mayer, and J. Messing. 2005. Structure and architecture of the maize genome. Plant Physiol. 139:1612-1624.
18. Hadley, H.H., and T. Hymowitz. 1973. Speciation and cytogenetics. p. 96-116. In B.E. Caldwell (ed.) Soybeans: Improvement, production, and uses. Agron. Monogr. 16. ASA, Madison, WI.
19. Heppard, E.P., A.J. Kinney, K.L. Stecca, and G.-H. Miao. 1996. Developmental and growth temperature regulation of two different microsomal ω-6 desaturase genes in soybeans. Plant Physiol. 110:311-319.
20. Hightower, R., and R. Meagher. 1985. Divergence and differential expression of soybean actin genes. EMBO J. 4:1-8.
21. Lackey, J.A. 1980. Chromosome numbers in the Phaseoleae (Fabaceae:Faboideae) and their relation to taxonomy. Am. J. Bot. 67:595-602.
22. Lander, E., P. Green, J. Abrahamson, A. Barlow, M. Daly, S. Lincoln, and L. Newberg. 1987. MAPMAKER: An interactive computer package for transcripting primary genetic linkage maps of experimental and natural populations. Genomics 1:174-181.
23. Lee, J.M., A. Bush, J.E. Specht, and R.C. Shoemaker. 1999. Mapping duplicate genes in soybean. Genome 42:829-836.
24. Lee, J.M., D. Grant, C.E. Vallejos, and R.C. Shoemaker. 2001. Genome organization in dicots. II. Arabidopsis as a 'bridging species' to resolve genome evolution events among legumes. Theor. Appl. Genet. 103:765-773.
25. Lee, J.S., and D.P.S. Verma. 1984. Chromosomal arrangement of leghemoglobin genes in soybean. Nucleic Acids Res. 11:5541-5553.
26. Lin, J.-Y., B.H. Jacobus, P. SanMiguel, J.G. Walling, Y. Yuan, J. Doyle, R.C. Shoemaker, N.D. Young, and S.A. Jackson. 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.
27. Lockton, S., and B.S. Gaut. 2005. Plant conserved non-coding sequences and paralogue evolution. Trends Genet. 21:60-65.
28. Lukashin, A., and M. Borodovsky. 1998. GeneMark.hmm: New solutions for gene finding. Nucleic Acids Res. 26:1107-1115.
29. Marek, L.F., J. Mudge, L. Darnielle, D. Grant, N. Hanson, M. Paz, Y. Huihuang, R. Denny, K. Larson, D. Foster-Hartnett, A. Cooper, D. Danesh, D. Larsen, T. Schmidt, R. Staggs, J.A. Crow, E. Retzel, N.D. Young, and R.C. Shoemaker. 2001. Soybean genomic survey: BAC-end sequences near RFLP and SSR markers. Genome 44:572-581.
30. Marek, L.F., and R.C. Shoemaker. 1997. BAC contig development by fingerprint analysis in soybean. Genome 40:420-427.
31. Masterson, J. 1994. Stomatal size in fossil plants: Evidence for polyploidy in majority of angiosperms. Science (Washington, DC) 264:421-424.
32. Mattson, F.H., and S.M. Grundy. 1985. Comparison of effects of dietary saturated, monounsaturated, and polyunsaturated fatty acids on plasma lipids and lipoproteins in man. J. Lipid Res. 26:194-202.
33. Mattson, J.W., C. Sun, and W.W. Koo. 2004. Analysis of the world oil crops market. Rep. No. 529. Dep. of Agribusiness and Applied Economics, North Dakota State Univ., Fargo.
34. McCarthy, E.M., and J.F. McDonald. 2003. LTR_STRUC: A novel search and identification program for LTR retrotransposons. Bioinformatics 19:362-367.
35. Messing, J., A.K. Bharti, W.M. Karlowski, H. Gundlach, H.R. Kim, Y. Yu, E Wei, G. Fuks, C.A. Soderlund, K.F.X. Mayer, and R.A. Wing. 2004. Sequence composition and genome organization of maize. Proc. Natl. Acad. Sci. USA 101:14349-14354.
36. Miquel, M.F., and J.A. Browse. 1994. High-oleate oilseeds fail to develop at low temperature. Plant Physiol. 106:421-427.
37. Mudge, J., S.B. Cannon, P. Kalo, G.E.D. Oldroyd, B.A. Roe, C.D. Town, and N.D. Young. 2005. Highly syntenic regions in the genomes of soybean, Medicago truncatula and Arabidopsis thaliana. BMC Plant Biol. 5:15.
38. Neidleman, S.L. 1987. Effects of temperature on lipid unsaturation. Biotechnol. Genet. Eng. Rev. 5:245-268.
39. Nielsen, N.C., C. Dickinson, T.J. Cho, V.H. Thanh, B.J. Scallon, R.L. Fischer, T.L. Sims, G.N. Drews, and R.B. Goldberg. 1989. Characterization of the glycinin gene family in soybean. Plant Cell 1:313-328.
40. Okuley, J., J. Lightner, K. Feldmann, N. Yadav, and J. Browse. 1994. The Arabidopsis FAD2 gene encodes the enzyme that is essential for polyunsaturated lipid synthesis. Plant Cell 6:147-158.
41. Pan, H.Q., Y.P. Wang, S.L. Chissoe, A. Bodenteich, Z. Wang, K. Iyer, S.W. Chifton, J.S. Crabtree, and B.A. Roe. 1994. The complete nucleotide sequence of the SacBII domain of the P1 pAD10-SacBII Cloning vetor and three cosmid cloning vectors: PTCF, svPHEP, and LAWRIST16. GATA 11:181-186.
42. Roe, B.A. 2004. Shotgun library transcription for DNA sequencing, p. 171-187. In X. Zhao and M. Stodolsky (ed.) Methods in molecular biology. Vol. 255. Bacterial artificial chromosomes, Vol. 1. Library transcription, physical mapping, and sequencing. Human Press, Totowa, NJ.
43. Roe, B., J. Crabtree, and A. Khan. 1996. In D. Rickwood (ed.) DNA isolation and sequencing: Essential techniques series. J. Wiley & Sons, NY.
44. SanMiguel, P., and J.L. Bennetzen. 1998. Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann. Bot. (Lond.) 82:37-44.
45. Schlueter, J.A., P. Dixon, C. Granger, D. Grant, L. Clark, J.J. Doyle, and R.C. Shoemaker. 2004. Mining EST databases to resolve evolutionary events in major crop species. Genome 47:868-876.
46. Schlueter, J.A., B.E. Scheffler, and R.C. Shoemaker. 2006. Sequence conservation of homeologous BACs and expression of homeologous genes in soybean (Glycine max L. Merr). Genetics (in press) doi:10.1534/genetics.105. 055020.
47. Schlueter, S.D., Q. Dong, and V. Brendel. 2003. GeneSeqer@PlantGDB: Gene structure predication in plant genomes. Nucleic Acids Res. 31:3597-3600.
48. Schlueter, S.D., M.D. Wilkerson, E. Huala, S.Y. Rhee, and V. Brendel. 2005. Community-based gene structure annotation for the Arabidopsis thaliana genome. Trends Plant Sci. 10:9-14.
49. Shoemaker, R., K. Polzin, J. Labate, J. Specht, E.C. Brummer, T. Olson, N. Young, V. Concibido, J. Wilcox, J. Tamulonis, G. Kochert, and H.R. Boerma. 1996. Genome duplication in soybean (Glycine subgenus soja). Genetics 144:329-338.
50. Song, Q.J., L.F. Marek, R.C. Shoemaker, K.G. Lark, V.C. Concibido, X. Delannay, J.E. Specht, and P.B. Cregan. 2004. A new integrated genetic linkage map of the soybean. Theor. Appl. Genet. 109:122-128.
51. Su, Z., J. Wang, J. Yu, X. Huang, and X. Gu. 2006. Evolution of alternative splicing after gene duplication. Genome Res. 16:182-189.
52. Tang, G.-Q., W.P. Novitzky, H.C. Griffing, S.C. Huber, and R.E. Dewey. 2005. Oleate desaturase enzymes of soybean: Evidence of regulation through differential stability and phosphorylation. Plant J. 44:433-446.
53. Thomas, J.M.G., K.J. Boote, L.H. Allen, M. Gallo-Meagher, and J.M. David. 2003. Seed physiology and metabolism: Elevated temperature and carbon dioxide effects on soybean seed composition and transcript abundance. Crop Sci. 43:1548-1577.
54. Thompson, G.A. 1993. Response of lipid metabolism to developmental change and environmental perturbation, p. 591-619. In T.S. Moore (ed.) Lipid metabolism in plant. CRC Press, Boca Raton, FL.
55. Walling, J.G., R. Shoemaker, N. Young, J. Mudge, and S. Jackson. 2006. Chromosome-level homeology in paleopolyploid soybean (Glycine max) revealed through integration of genetic and chromosome maps. Genetics 172:1893-1900.
56. Warner, K., P. Orr, L. Parrot, and M. Glynn. 1994. Effects of frying oil composition on potato chip stability. J. Am. Oil Chem. Soc. 71:1117-1121.
57. Wilkerson, M.D., S.D. Schlueter, and V. Brendel. 2006. yrGATE: A web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes. Genome Biol. 7:R58.
58. Wolfe, K.H. 2001. Yesterday's polyploids and the mystery of diploidization. Nat. Rev. Genet. 2:333-341.
59. Yan, H.H., J. Mudge, D.J. Kim, D. Larsen, R.C. Shoemaker, D.R. Cook, and N.D. Young. 2003. Estimates on conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana. Theor. Appl. Genet. 106:1256-1265.
60. Yan, H.H., J. Mudge, D.J. Kim, R.C. Shoemaker, D.R. Cook, and N.D. Young. 2004. Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana. Genome 47:141-155.
61. Yang, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 15:555-556.
62. Young, N.D., J. Mudge, and Y.N. Ellis. 2003. Legume genomes: More than peas in a pod. Curr. Opin. Plant Biol. 6:199-204.