Developmental profiling of gene expression in soybean trifoliate leaves and cotyledons

BMC Plant Biology

Volumn 15, Issue 1, 2015, Pages

  Brown, Anne V ^a   Hudson, Karen A ^b  

^a PURDUE UNIVERSITY   (United States)

^b U S DEPARTMENT OF AGRICULTURE   (United States)

Author keywords

Cotyledon senescence; Glycine max; Leaf development; Leaf senescence

Indexed keywords

GLYCINE MAX;

COTYLEDON; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; MOLECULAR GENETICS; PHOTOSYNTHESIS; PLANT GENE; PLANT LEAF; SOYBEAN;

COTYLEDON; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; MOLECULAR SEQUENCE DATA; PHOTOSYNTHESIS; PLANT LEAVES; SEQUENCE ANALYSIS, DNA; SOYBEANS;

EID: 84935043987     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/s12870-015-0553-y     Document Type: Article

References (66)

1. ASA. SoyStats 2013. In: Association AS, editor. A reference guide to important soybean facts and figures. 2013.
2. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, et al. Genome sequence of the palaeopolyploid soybean. Nature. 2010;463(7278):178-83.
3. Hartman GL, Miles MR, Frederick RD. Breeding for resistance to soybean rust. Plant Dis. 2005;89(6):664-6.
4. Smith JR, Nelson RL. Selection for seed-filling period in soybean. Crop Sci. 1986;26(3):466-9.
5. Rivero RM, Kojima M, Gepstein A, Sakakibara H, Mittler R, Gepstein S, et al. Delayed leaf senescence induces extreme drought tolerance in a flowering plant. Proc Natl Acad Sci. 2007;104(49):19631-6.
6. Smith DL. Cotyledon anatomy in the Leguminosae. Bot J Linn Soc. 1983;86(4):325-55.
7. Harris M, Mackender RO, Smith DL. Photosynthesis of cotyledons of soybean seedlings. New Phytol. 1986;104(3):319-29.
8. Breeze E, Harrison E, McHattie S, Hughes L, Hickman R, Hill C, et al. High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. Plant Cell. 2011;23(3):873-94.
9. Li P, Ponnala L, Gandotra N, Wang L, Si Y, Tausta SL, et al. The developmental dynamics of the maize leaf transcriptome. Nat Genet. 2010;42(12):1060-7.
10. Watanabe M, Balazadeh S, Tohge T, Erban A, Giavalisco P, Kopka J, et al. Comprehensive dissection of spatiotemporal metabolic shifts in primary, secondary, and lipid metabolism during developmental senescence in Arabidopsis. Plant Physiol. 2013;162(3):1290-310.
11. Lohman KN, Gan S, John MC, Amasino RM. Molecular analysis of natural leaf senescence in Arabidopsis thaliana. Physiol Plant. 1994;92(2):322-8.
12. Gan S, Amasino RM. Making sense of senescence (molecular genetic regulation and manipulation of leaf senescence). Plant Physiol. 1997;113(2):313-9.
13. Gepstein S, Sabehi G, Carp MJ, Hajouj T, Nesher MFO, Yariv I, et al. Large-scale identification of leaf senescence-associated genes. The Plant Journal. 2003;36(5):629-42.
14. Balazadeh S, Riaño-Pachón D, Mueller-Roeber B. Transcription factors regulating leaf senescence in Arabidopsis thaliana. Plant Biol. 2008;10(s1):63-75.
15. Hinderhofer K, Zentgraf U. Identification of a transcription factor specifically expressed at the onset of leaf senescence. Planta. 2001;213(3):469-73.
16. Breeze E, Harrison E, Page T, Warner N, Shen C, Zhang C, et al. Transcriptional regulation of plant senescence: from functional genomics to systems biology. Plant Biol. 2008;10(s1):99-109.
17. Shamimuzzaman M, Vodkin L. Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling. Functional & Integrative Genomics. 2014;4:683-96.
18. Buchanan-Wollaston V, Earl S, Harrison E, Mathas E, Navabpour S, Page T, et al. The molecular analysis of leaf senescence-a genomics approach. Plant Biotechnol J. 2003;1(1):3-22.
19. Fischer AM. The complex regulation of senescence. Crit Rev Plant Sci. 2012;31(2):124-47.
20. Buchanan-Wollaston V, Page T, Harrison E, Breeze E, Lim PO, Nam HG, et al. Comparative transcriptome analysis reveals significant differences in gene expression and signalling pathways between developmental and dark/starvation-induced senescence in Arabidopsis. The Plant Journal. 2005;42(4):567-85.
21. Guo Y, Gan S. AtNAP, a NAC family transcription factor, has an important role in leaf senescence. The Plant Journal. 2006;46(4):601-12.
22. Morales AM, O'Rourke JA, Van DE Mortel M, Scheider KT, Bancroft TJ, Borém A, et al. Transcriptome analyses and virus induced gene silencing identify genes in the Rpp4-mediated Asian soybean rust resistance pathway. Funct Plant Biol. 2013;40(10):1029-47.
23. Prioretti L, Gontero B, Hell R, Giordano M. Diversity and regulation of ATP sulfurylase in photosynthetic organisms. Frontiers in Plant Science. 2014;5.
24. Guo Y, Gan S. Leaf senescence: signals, execution, and regulation. Curr Top Dev Biol. 2005;71:83-112.
25. Himelblau E, Amasino RM. Nutrients mobilized from leaves of Arabidopsis thaliana during leaf senescence. J Plant Physiol. 2001;158(10):1317-23.
26. Leran S, Varala K, Boyer JC, Chiurazzi M, Crawford N, Daniel-Vedele F, et al. A unified nomenclature of NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family members in plants. Trends Plant Sci. 2014;19(1):5-9.
27. Fan SC, Lin CS, Hsu PK, Lin SH, Tsay YF. The Arabidopsis nitrate transporter NRT1.7, expressed in phloem, is responsible for source-to-sink remobilization of nitrate. Plant Cell. 2009;21(9):2750-61.
28. Yu T-S, Kofler H, Häusler RE, Hille D, Flügge U-I, Zeeman SC, et al. The Arabidopsis sex1 mutant is defective in the R1 protein, a general regulator of starch degradation in plants, and not in the chloroplast hexose transporter. Plant Cell. 2001;13(8):1907-18.
29. Rushton PJ, Somssich IE, Ringler P, Shen QJ. WRKY transcription factors. Trends Plant Sci. 2010;15(5):247-58.
30. Laurière C, Doyen C, Thévenot C, Daussant J. β-amylases in cereals a study of the maize β-amylase system. Plant Physiol. 1992;100(2):887-93.
31. Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, et al. mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. The Plant Journal. 2004;37(6):914-39.
32. Robatzek S, Somssich IE. A new member of the Arabidopsis WRKY transcription factor family, AtWRKY6, is associated with both senescence-and defence-related processes. The Plant Journal. 2001;28(2):123-33.
33. Eulgem T, Rushton PJ, Robatzek S, Somssich IE. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 2000;5(5):199-206.
34. Eulgem T, Somssich IE. Networks of WRKY transcription factors in defense signaling. Curr Opin Plant Biol. 2007;10(4):366-71.
35. Pysh LD, Wysocka-Diller JW, Camilleri C, Bouchez D, Benfey PN. The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes. The Plant Journal. 1999;18(1):111-9.
36. Lin JF, Wu SH. Molecular events in senescing Arabidopsis leaves. The Plant Journal. 2004;39(4):612-28.
37. Lin M, Pang C, Fan S, Song M, Wei H, Yu S. Global analysis of the Gossypium hirsutum L. transcriptome during leaf senescence by RNA-Seq. BMC Plant Biology. 2015;15:43.
38. Lijavetzky D, Carbonero P, Vicente-Carbajosa J. Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families. BMC Evol Biol. 2003;3(1):17.
39. Yanagisawa S, Sheen J. Involvement of maize Dof zinc finger proteins in tissue-specific and light-regulated gene expression. The Plant Cell Online. 1998;10(1):75-89.
40. Waters MT, Wang P, Korkaric M, Capper RG, Saunders NJ, Langdale JA. GLK transcription factors coordinate expression of the photosynthetic apparatus in Arabidopsis. Plant Cell. 2009;21(4):1109-28.
41. Jin J, Zhang H, Kong L, Gao G, Luo J. PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res. 2013;42(D1):D1182-7. gkt1016.
42. Ulmasov T, Murfett J, Hagen G, Guilfoyle TJ. Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements. The Plant Cell Online. 1997;9(11):1963-71.
43. Liu L, Zhou Y, Zhou G, Ye R, Zhao L, Li X, et al. Identification of early senescence-associated genes in rice flag leaves. Plant Mol Biol. 2008;67(1-2):37-55.
44. Mueller-Roeber B, Balazadeh S. Auxin and its role in plant senescence. J Plant Growth Regul. 2014;33(1):21-33.
45. Gregersen PL, Holm PB. Transcriptome analysis of senescence in the flag leaf of wheat (Triticum aestivum L.). Plant Biotechnol J. 2007;5(1):192-206.
46. Hickman R, Hill C, Penfold CA, Breeze E, Bowden L, Moore JD, et al. A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves. The Plant Journal. 2013;75(1):26-39.
47. Hudson ME, Quail PH. Identification of promoter motifs involved in the network of phytochrome A-regulated gene expression by combined analysis of genomic sequence and microarray data. Plant Physiol. 2003;133(4):1605-16.
48. Li Y, Swaminathan K, Hudson ME. Rapid, organ-specific transcriptional responses to light regulate photomorphogenic development in dicot seedlings. Plant Physiol. 2011;156(4):2124-40.
49. Alvarez-Canterbury AMR, Flores DJ, Keymanesh K, To K, Brusslan JA. A double SORLIP1 element is required for high light induction of ELIP genes in Arabidopsis thaliana. Plant Mol Biol. 2014;84(3):259-67.
50. Giuliano G, Pichersky E, Malik V, Timko M, Scolnik P, Cashmore AR. An evolutionarily conserved protein binding sequence upstream of a plant light-regulated gene. Proc Natl Acad Sci. 1988;85(19):7089-93.
51. Guiltinan MJ, Marcotte WR, Quatrano RS. A plant leucine zipper protein that recognizes an abscisic acid response element. Science. 1990;250(4978):267-71.
52. Ulmasov T, Hagen G, Guilfoyle TJ. ARF1, a transcription factor that binds to auxin response elements. Science. 1997;276(5320):1865-8.
53. Hagen G, Guilfoyle T. Auxin-responsive gene expression: genes, promoters and regulatory factors. Plant Mol Biol. 2002;49(3-4):373-85.
54. Izawa T, Foster R, Chua N-H. Plant bZIP protein DNA binding specificity. J Mol Biol. 1993;230(4):1131-44.
55. Kim SY, Ma J, Perret P, Li Z, Thomas TL. Arabidopsis ABI5 subfamily members have distinct DNA-binding and transcriptional activities. Plant Physiol. 2002;130(2):688-97.
56. Jakoby M, Weisshaar B, Dröge-Laser W, Vicente-Carbajosa J, Tiedemann J, Kroj T, et al. bZIP transcription factors in Arabidopsis. Trends Plant Sci. 2002;7(3):106-11.
57. Harris JC, Hrmova M, Lopato S, Langridge P. Modulation of plant growth by HD-Zip class I and II transcription factors in response to environmental stimuli. New Phytol. 2011;190(4):823-37.
58. Bao X, Franks RG, Levin JZ, Liu Z. Repression of AGAMOUS by BELLRINGER in floral and inflorescence meristems. Plant Cell. 2004;16(6):1478-89.
59. Meng Y, Li H, Wang Q, Liu B, Lin C. Blue light-dependent interaction between Cryptochrome2 and CIB1 regulates transcription and leaf senescence in soybean. Plant Cell. 2013;25(11):4405-20.
60. Yin G, Xu H, Xiao S, Qin Y, Li Y, Yan Y, et al. The large soybean (Glycine max) WRKY TF family expanded by segmental duplication events and subsequent divergent selection among subgroups. BMC Plant Biology. 2013;13(1):148.
61. Hudson KA. The circadian clock-controlled transcriptome of developing soybean seeds. The Plant Genome. 2010;3(1):3-13.
62. Fehr WR, Caviness CE. Stages of Soybean Development. Iowa, USA: Iowa State University Cooperative Extension Service; 1977. vol. Special Report 80.
63. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-9.
64. Severin AJ, Woody JL, Bolon Y-T, Joseph B, Diers BW, Farmer AD, et al. RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biology. 2010;10(1):160.
65. Anders S, Huber W. Differential expression of RNA-Seq data at the gene level-the DESeq package. Heidelberg, Germany: EMBL; 2012.
66. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139-40.