Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling

Functional and Integrative Genomics

Volumn 14, Issue 4, 2014, Pages 683-696

  Shamimuzzaman, Md ^a   Vodkin, Lila ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Expression profiling; RNA Seq; Soybean seedling cotyledons; Transcription factors

Indexed keywords

RIBOSOME PROTEIN; GLYOXYLIC ACID DERIVATIVE; MESSENGER RNA; TRANSCRIPTION FACTOR; VEGETABLE PROTEIN;

ARTICLE; CARBOHYDRATE METABOLISM; COTYLEDON; DEVELOPMENTAL STAGE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FUNCTION; GENETIC TRANSCRIPTION; GLYOXYLATE CYCLE GENE; NONHUMAN; PHOTOSYNTHESIS; PLANT DEVELOPMENT; PLANT GENE; PLANT GROWTH; PLANT LEAF; RNA SEQUENCE; SOYBEAN; TRANSCRIPTION FACTOR GENE; CLUSTER ANALYSIS; GENE ONTOLOGY; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS; SEEDLING; SEQUENCE ANALYSIS;

GLYCINE MAX;

CARBOHYDRATE METABOLISM; CLUSTER ANALYSIS; COTYLEDON; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENE ONTOLOGY; GENES, PLANT; GLYOXYLATES; MOLECULAR SEQUENCE ANNOTATION; PHOTOSYNTHESIS; PLANT PROTEINS; RNA, MESSENGER; SEEDLING; SEQUENCE ANALYSIS, RNA; SOYBEANS; TRANSCRIPTION FACTORS;

EID: 84912032172     PISSN: 1438793X     EISSN: 14387948     Source Type: Journal    
DOI: 10.1007/s10142-014-0388-x     Document Type: Article

References (46)

1. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11:R106
2. Bewley JD (1997) Seed germination and dormancy. Plant Cell 9(7):1055–1066
3. Byrne ME (2009) A role for the ribosome in development. Trends Plant Sci 14:512–519
4. Chaumont F, Barrieu F, Wojcik E, Chrispeels MJ, Jung R (2001) Aquaporins constitutes a large and highly divergent protein family in maize. Plant Physiol 125:1206–1215
5. Du H, Yang SS, Feng BR, Liu L, Tang YX, Huang YB, Liang Z (2012) Genome-wide analysis of the MYB transcription factor superfamily in soybean. BMC Plant Biol 12:106
6. Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L (2010) MYB transcription factors in Arabidopsis. Trends Plant Sci 15:573–581
7. Eastmond PJ (2006) SUGAR-DEPENDENT1 encodes a patatin domain triacylglycerol lipase that initiates storage oil breakdown in germinating Arabidopsis seeds. Plant Cell 18:665–675
8. Eastmond PJ, Graham IA (2001) Re-examining the role of the glyoxylate cycle in oilseeds. Trends Plant Sci 6:72–78
9. Eulgem T, Rushton PJ, Robatzek S, Somssich IE (2000) The WRKY superfamily of plant transcription factors. Trends Plant Sci 5:199–206
10. Falk KL, Behal RH, Xiang C, Oliver DJ (1998) Metabolic bypass of the tricarboxylic acid cycle during lipid mobilization in germinating oilseeds. Plant Physiol 117:473–481
11. Gonzalez DO, Vodkin LO (2007) Specific elements of the glyoxylate pathway play a significant role in the functional transition of the soybean cotyledon during seedling development. BMC Genomics 8:468
12. Gonzalez A, Zhao M, Leavitt JM, Lloyd AM (2008) Regulation of the anthocyanin biosynthetic pathway by the TTG1/bHLH/Myb transcriptional complex in Arabidopsis seedlings. Plant J 53:814–827
13. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD et al (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:D1178–D1186
14. Guo Y, Qiu L-J (2013) Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics. PLoS One 8(9):e76809
15. Harada JJ, Baden CS, Comai L (1988) Spacially regulated genes expressed during seed germination and postgerminative development are activated during embryogeny. Mol Gen Genet 212:466–473
16. Harris M, Mackender RO, Smith DL (1986) Photosynthesis of cotyledons of soybean seedlings. New Piiytol 104:319–329
17. Huang F, Chi Y, Meng Q, Gai J, Yu D (2006) GmZFP1 encoding a single zinc finger protein is expressed with enhancement in reproductive organs and late seed development in soybean (Glycine max). Mol Biol Rep 33:279–285
18. Hunt M, Kaur N, Stromvik M, Vodkin L (2011) Transcript profiling reveals expression differences in wild-type and glabrous soybean lines. BMC Plant Biol 11:145
19. Jiang W, Yu D (2009) Arabidopsis WRKY2 transcription factor mediates seed germination and postgermination arrest of development by abscisic acid. BMC Plant Biol 9:96
20. Jiménez-López S, Mancera-Martínez E, Donayre-Torres A, Rangel C, Uribe L, March S et al (2011) Expression profile of maize (Zea mays L.) embryonic axes during germination: translational regulation of ribosomal protein mRNAs. Plant Cell Physiol 52:1719–1733
21. Jofuku KD, den Boer BG, Van Montagu M, Okamuro JK (1994) Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell 6:1211–1225
22. Jones SI, Vodkin LO (2013) Using RNA-Seq to profile soybean seed development from fertilization to maturity. PLoS One 8(3):e59270
23. Koornneef M, Bentsink L, Hilhorst H (2002) Seed dormancy and germination. Curr Opin Plant Biol 5(1):33–36
24. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25
25. Larkin JC, Hunsperger JP, Culley D, Rubenstein I, Silflow CD (1989) The organization and expression of a maize ribosomal protein gene family. Genes Dev 3:500–509
26. MacArthur S, Li XY, Li J, Brown JB, Chu HC et al (2009) Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol 10:R80
27. Maes T, Van de Steene N, Zethof J, Karimi M, D’Hauw M, Mares G, Van Montagu M, Gerats T (2001) Petunia AP2-like genes and their role in flower and seed development. Plant Cell 13:229–244
28. McCarty DR (1986) A simple method for extractions of RNA from maize tissue. Maize Genet Coop News Lett 60:61
29. Mortazavi A, William BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628
30. Olsen AN, Ernst HA, Leggio L, Skriver K (2005) NAC transcription factors: structurally distinct, functionally diverse. Trends Plant Sci 10:79–87
31. Ooka H, Satoh K, Doi K, Nagata T, Otomo Y, Murakami K, Matsubara K, Osato N, Kawai J, Carninci P et al (2003) Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res 10:239–247
32. Park W, Scheffler BE, Bauer PJ, Campbell BT (2010) Identification of the family of aquaporin genes and their expression in upland cotton (Gossypium hirsutum L.). BMC Plant Biol 10:142
33. Penfield S, Rylott EL, Gylday AD, Graham S, Larson TR, Graham IA (2004) Reserve mobilization in the Arabidopsis endosperm fuels hypocotyls elongation in the dark, is independent of abscisic acid, and requires phosphoenolpyruvate carboxykinase1. Plant Cell 16:2705–2718
34. Ritchie SW, Hanway JJ, Thompson HE, Benson GO (1994) How a soybean plant develops. Iowa State University of Science and Technology. Spec Rep 53:1–20
35. Rushton PJ, Somssich IE, Ringler P, Shen QJ (2010) WRKY transcription factors. Trends Plant Sci 15:247–258
36. Saeed AI, Sharov V, White J, Li J, Liang W et al (2003) TM4: a free, opensource system for microarray data management and analysis. Biotechniques 34:374–378
37. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183
38. Shamimuzzaman M, Vodkin L (2013) Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNA-Seq. BMC Genomics 14:477
39. Singh KB (1998) Transcriptional regulation in plants: the importance of combinatorial control. Plant Physiol 118:1111–1120
40. Soeda Y, Konings MCJM, Vorst O, van Houwelingen AMML, Stoopen GM, Maliepaard CA, Kodde J, Bino RJ, Groot SPC, van der Geest AHM (2005) Gene expression programs during Brassica oleraceae seed maturation, osmopriming, and germination are indicators of progression of the germination process and the stress tolerance level. Plant Physiol 137:354–368
41. Stracke R, Ishihara H, Huep G, Barsch A, Mehrtens F, Niehaus K, Weisshaar B (2007) Differential regulation of closely related R2R3-MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling. Plant J 50:660–677
42. Tran LS, Quach TN, Guttikonda SK, Aldrich DL, Kumar R, Neelakandan A, Valliyodan B, Nguyen HT (2009) Molecular characterization of stress-inducible GmNAC genes in soybean. Mol Genet Genomics 281:647–664
43. Udvardi MK, Kakar K, Wandrey M, Montanari O, Murray J, Andriankaja A, Zhang J-Y, Benedito V, Hofer JMI, Chueng F, Town CD (2007) Legume transcription factors: global regulators of plant development and response to the environment. Plant Physiol 144:538–549
44. Wang C, Wang H, Zhang J, Chen S (2008) A seed-specific AP2-domain transcription factor from soybean plays a certain role in regulation of seed germination. Sci China Ser C 51:336–345
45. Yanagisawa S (2004) Dof domain proteins: plant-specific transcription factors associated with diverse phenomena unique to plants. Plant Cell Physiol 45(4):386–391
46. Zhang G, Chen M, Chen X, Xu Z, Guan S, Li LC, Li A, Guo J, Mao L, Ma Y (2008) Phylogeny, gene structures, and expression patterns of the ERF gene family in soybean (Glycine max L.). J Exp Bot 59:4095–4107