Transcriptional profiling of root-knot nematode induced feeding sites in cowpea (Vigna unguiculata L. Walp.) using a soybean genome array

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Das, Sayan ^a   Ehlers, Jeffrey D ^a   Close, Timothy J ^a   Roberts, Philip A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; COWPEA; DOWN REGULATION; GENOTYPE; INFECTION SENSITIVITY; NEMATODIASIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PARASITISM; PLANT MICROORGANISM INTERACTION; PLANT ROOT; PROTEIN EXPRESSION; PROTEIN FUNCTION; ROOT KNOT NEMATODE; SOYBEAN; UPREGULATION; ANIMAL; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; IMMUNOLOGY; LEGUME; NEMATODE; PARASITOLOGY; PHYSIOLOGY; PLANT DISEASE; PLANT GENOME;

GLYCINE MAX; MELOIDOGYNE; MELOIDOGYNE INCOGNITA; MELOIDOGYNE JAVANICA; VIGNA UNGUICULATA;

ANIMALS; FABACEAE; GENE EXPRESSION PROFILING; GENOME, PLANT; NEMATODA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT DISEASES; PLANT ROOTS; SOYBEANS;

EID: 77955681498     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-480     Document Type: Article

References (51)

1. Ehlers JD. Cowpea (Vigna unguiculata L. Walp.). Field Crops Res 1997, 53(1-3):187-204.
2. Timko MP, Ehlers JD, Roberts PA, . eds Cowpea 2007, Berlin: Springer-Verlag, eds.
3. Trudgill DL, Blok VC. Apomictic, polyphagus, root-knot nematodes: exceptionally successful and damaging biotrophic root pathogens. Annu Rev Phytopathol 2001, 39:53-77. 10.1146/annurev.phyto.39.1.53, 11701859.
4. Jung C, Wyss W. New approaches to control plant parasitic nematodes. Appl Microbiol Biotechnol 1999, 51(4):439-446.
5. Roberts PA, Frate CA, Matthews WC, Osterli PP. Interactions of virulent Meloidogyne incognita and Fusarium wilt on resistant cowpea genotypes. Phytopathology 1995, 85(10):1288-1295.
6. Ehlers JD, Matthews WC, Hall AE, Roberts PA. Breeding and evaluation of cowpeas with high levels of broad-based resistance to root-knot nematodes. Proceedings of World Cowpea Conference III: 2002; International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria 2002, 41-51.
7. Fery RL, Dukes PD. Inheritance of root-knot nematode resistance in cowpea (Vigna unguiculata [L.] Walp.). J Am Soc Hortic Sci 1980, 105:671-674.
8. Das S, Demason DA, Ehlers JD, Close TJ, Roberts PA. Histological characterization of root-knot nematode resistance in cowpea and its relation to reactive oxygen species modulation. J Exp Bot 2008, 59(6):1305-1313. 10.1093/jxb/ern036, 18375605.
9. Williamson VM. Plant nematode resistance genes. Curr Opinion Plant Biol 1999, 2:327-331.
10. Pegard A, Brizzard G, Fazari A, Soucaze O, Abad P, Djian-Caporalino C. Histological characterization of resistance to different root-knot nematode species related to phenolics accumulation in Capsicum annuum. Phytopathology 2005, 95(2):158-165. 10.1094/PHYTO-95-0158, 18943985.
11. Kaplan DT, Thomason IJ, Van Gundy SD. Histological study of compatible and incompatible interaction of soybeans and Meloidogyne incognita. J Nematol 1979, 11(4):338-343. 2617977, 19300654.
12. Das S, Bhat PR, Sudhakar C, Ehlers JD, Wanamaker S, Roberts PA, Cui X, Close TJ. Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array. BMC Genomics 2008, 9:107. 10.1186/1471-2164-9-107, 2270837, 18307807.
13. Jammes F, Lecomte P, Almeida-Engler J, Bitton F, Martin-Magniette ML, Renou JP, Abad P, Favery B. Genome-wide expression profiling of the host response to root-knot nematode infection in Arabidopsis. Plant J 2005, 44(3):447-458. 10.1111/j.1365-313X.2005.02532.x, 16236154.
14. Fuller VL, Lilley CJ, Atkinson HJ, Urwin PE. Differential gene expression in Arabidopsis following infection by plant-parasitic nematodes Meloidogyne incognita and Heterodera schachtii. Mol Plant Pathol 2007, 8(5):595-609. 10.1111/j.1364-3703.2007.00416.x, 20507524.
15. Bar-Or C, Kapulnik Y, Koltai H. A broad characterization of the transcriptional profile of the compatible tomato response to the plant parasitic root knot nematode Meloidogyne javanica. Eur J Plant Pathol 2005, 111(2):181-192.
16. Bhattarai KK, Xie Q-G, Mantelin S, Bishnoi U, Girke T, Navarre DA, Kaloshian I. Tomato susceptibility to root-knot nematodes requires an intact jasmonic acid signaling pathway. Mol Plant-Microbe Interact 2008, 21(9):1205-1214. 10.1094/MPMI-21-9-1205, 18700825.
17. Puthoff DP, Nettleton D, Rodermel SR, Baum TJ. Arabidopsis gene expression changes during cyst nematode parasitism revealed by statistical analyses of microarray expression profiles. Plant J 2003, 33(5):911-921. 10.1046/j.1365-313X.2003.01677.x, 12609032.
18. Puthoff DP, Ehrenfried ML, Vinyard BT, Tucker ML. GeneChip profiling of transcriptional responses to soybean cyst nematode, Heterodera glycines, colonization of soybean roots. J Exp Bot 2007, 58(12):3407-3418. 10.1093/jxb/erm211, 17977850.
19. Alkharouf NW, Klink VP, Chouikha IB, Beard HS, MacDonald MH, Meyer S, Knap HT, Khan R, Matthews BF. Timecourse microarray analyses reveal global changes in gene expression of susceptible Glycine max (soybean) roots during infection by Heterodera glycines (soybean cyst nematode). Planta 2006, 224(4):838-852. 10.1007/s00425-006-0270-8, 16575592.
20. Ithal N, Recknor J, Nettleton D, Hearne L, Maier T, Baum TJ, Mitchum MG. Parallel genome-wide expression profiling of host and pathogen during soybean cyst nematode infection of soybean. Mol Plant-Microbe Interact 2007, 20(3):293-305. 10.1094/MPMI-20-3-0293, 17378432.
21. Ithal N, Recknor J, Nettleton D, Maier T, Baum TJ, Mitchum MG. Developmental transcript profiling of cyst nematode feeding cells in soybean roots. Mol Plant-Microbe Interact 2007, 20(5):510-525. 10.1094/MPMI-20-5-0510, 17506329.
22. Tucker ML, Burke A, Murphy CA, Thai VK, Ehrenfried ML. Gene expression profiles for cell wall-modifying proteins associated with soybean cyst nematode infection, petiole abscission, root tips, flowers, apical buds, and leaves. J Experimental Bot 2007, 58(12):3395-3406.
23. Klink VP, Overall CC, Alkharouf NW, MacDonald MH, Matthews BF. A time-course comparative microarray analysis of an incompatible and compatible response by Glycine max (soybean) to Heterodera glycines (soybean cyst nematode) infection. Planta 2007, 226(6):1423-1447. 10.1007/s00425-007-0581-4, 17653570.
24. Klink VP, Overall CC, Alkharouf NW, MacDonald MH, Matthews BF. Laser capture microdissection (LCM) and comparative microarray expression analysis of syncytial cells isolated from incompatible and compatible soybean (Glycine max) roots infected by the soybean cyst nematode (Heterodera glycines). Planta 2007, 226(6):1389-1409. 10.1007/s00425-007-0578-z, 17668236.
25. Alvord WG, Roayaei JA, Quiñones OA, Schneider KT. A microarray analysis for differential gene expression in the soybean genome using Bioconductor and R. Briefings in Bioinformatics 2007, 8(6):415-431. 10.1093/bib/bbm043, 17906332.
26. Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP. Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res 2005, 15(5):674-680. 10.1101/gr.3335705, 1088295, 15867429.
27. Gilad Y, Oshlack A, Smyth GK, Speed TP, White KP. Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature 2006, 440(7081):242-245. 10.1038/nature04559, 16525476.
28. Voolstra C, Tautz D, Farbrother P, Eichinger L, Harr B. Contrasting evolution of expression differences in the testis between species and subspecies of the house mouse. Genome Res 2007, 17(1):42-49. 10.1101/gr.5683806, 1716265, 17038563.
29. Liao BY, Zhang JZ. Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol 2006, 23(3):530-540. 10.1093/molbev/msj054, 16280543.
30. Sartor MA, Zorn AM, Schwanekamp JA, Halbleib D, Karyala S, Howell ML, Dean GE, Medvedovic M, Tomlinson CR. A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus. Nucleic Acids Res 2006, 34(1):185-200. 10.1093/nar/gkj413, 1325202, 16397297.
31. Moehring AJ, Teeter KC, Noor MAF. Genome-wide patterns of expression in Drosophila pure species and hybrid males. II. Examination of multiple-species hybridizations, platforms, and life cycle stages. Mol Biol Evol 2007, 24(1):137-145. 10.1093/molbev/msl142, 17032727.
32. Nieto-Diaz M, Pita-Thomas W, Nieto-Sampedro M. Cross-species analysis of gene expression in non-model mammals: reproducibility of hybridization on high density oligonucleotide microarrays. BMC Genomics 2007, 8:89. 10.1186/1471-2164-8-89, 1853087, 17407579.
33. Hudson ME, Bruggink T, Chang SH, Yu W, Han B, Wang X, van der Toorn P, Zhu T. Analysis of gene expression during Brassica seed germination using a cross-species microarray platform. Crop Sci 2007, 47(S2):S-96-112.
34. Bagnaresi P, Moschella A, Beretta O, Vitulli F, Ranalli P, Perata P. Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening. BMC Genomics 2008, 9:176. 10.1186/1471-2164-9-176, 2358903, 18416834.
35. Mitchell HJ, Hall JL, Barber MS. Elicitor-induced cinnamyl alcohol-dehydrogenase activity in lignifying wheat (Triticum aestivum L) leaves. Plant Physiol 1994, 104(2):551-556. 159230, 12232105.
36. Tarchini R, Biddle P, Wineland R, Tingey S, Rafalski A. The complete sequence of 340 kb of DNA around the rice Adh1-Adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell 2000, 12(3):381-391. 10.1105/tpc.12.3.381, 139838, 10715324.
37. Schweighofer A, Kazanaviciute V, Scheikl E, Teige M, Doczi R, Hirt H, Schwanninger M, Kant M, Schuurink R, Mauch F, Buchala A, Francesca C, Meskiene I. The PP2C-type phosphatase AP2C1, which negatively regulates MPK4 and MPK6, modulates innate immunity, jasmonic acid, and ethylene levels in Arabidopsis. Plant Cell 2007, 19(7):2213-2224. 10.1105/tpc.106.049585, 1955703, 17630279.
38. Van Damme EJM, Peumans WJ, Barre A, Rouge P. Plant lectins: A composite of several distinct families of structurally and evolutionary related proteins with diverse biological roles. Critical Rev Plant Sci 1998, 17(6):575-692.
39. Apel K, Hirt H. Reactive oxygen species: metabolism, oxidative stress and signal transduction. Annu Rev Plant Biol 2004, 55:373-399. 10.1146/annurev.arplant.55.031903.141701, 15377225.
40. Shi C, Thummler F, Melchinger AE, Wenzel G, Lubberstedt T. Comparison of transcript profiles between near-isogenic maize lines in association with SCMV resistance based on unigene-microarrays. Plant Sci 2006, 170(1):159-169.
41. Hulbert SH, Bai J, Fellers JP, Pacheco MG, Bowden RL. Gene expression patterns in near isogenic lines for wheat rust resistance gene Lr34/Yr18. Phytopathology 2007, 97(9):1083-1093. 10.1094/PHYTO-97-9-1083, 18944173.
42. Szakastis D, Heinen P, Krzysztof W, Hofmann J, Wagner F, Kreil DP, Sykacek P, Grundler FMW, Bohlman H. The transcriptome of syncytia induced by the cyst nematode Heterodera schachtii in Arabidopsis roots. Plant J 2009, 57(6):771-784. 10.1111/j.1365-313X.2008.03727.x, 2667683, 18980640.
43. Hussey RS, Barker KR. A comparison of methods of collecting inocula for Meloidogyne spp. including a new technique. Plant Dis Rep 1973, 57:1025-1028.
44. Ehlers JD, Matthews WC, Hall AE, Roberts PA. Inheritance of a broad-based form of root-knot nematode resistance in cowpea. Crop Sci 2000, 40:611-618.
45. Byrd DW, Kirkpatrick T, Barker KR. An improved technique for clearing and staining plant tissue for detection of nematodes. J Nematol 1983, 15:142-143. 2618249, 19295781.
46. Zhu HY, Choi HK, Cook DR, Shoemaker RC. Bridging model and crop legumes through comparative genomics. Plant Physiol 2005, 137(4):1189-1196. 10.1104/pp.104.058891, 1088312, 15824281.
47. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249-264. 10.1093/biostatistics/4.2.249, 12925520.
48. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 2003, 19(2):185-193. 10.1093/bioinformatics/19.2.185, 12538238.
49. Knudsen S. A biologist's guide to analysis of DNA microarray data. 2002, New York: Wiley-Interscience.
50. Li C, Wong WH. Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc Nat Acad Sci USA 2001, 98(1):31-36. 10.1073/pnas.011404098, 14539, 11134512.
51. Bender R, Lange S. Adjusting for multiple testing-when and how?. J Clinical Epidemiol 2001, 54:343-349.