Assessment of candidate reference genes for expression studies in Vicia faba L. by real-time quantitative PCR

Molecular Breeding

Volumn 28, Issue 1, 2011, Pages 13-24

  Gutierrez, Natalia ^a   Giménez, María J ^b   Palomino, Carmen ^a   Avila, Carmen M ^a  

^a IFAPA CENTRO ALAMEDA DEL OBISPO   (Spain)

^b CSIC   (Spain)

Author keywords

Anti nutritional compounds; Disease resistance; Faba bean; qPCR; Reference genes

Indexed keywords

GENE EXPRESSION;

ANTI-NUTRITIONAL; ANTI-NUTRITIONAL COMPOUND; ANTINUTRITIONAL FACTORS; CANDIDATE GENES; DISEASE RESISTANCE; FABA BEANS; QPCR; REAL-TIME QUANTITATIVE PCR; REFERENCE GENES; VICIA FABA;

POLYMERASE CHAIN REACTION;

VICIA FABA;

EID: 79959662007     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-010-9456-7     Document Type: Article

References (48)

1. Ahn K, Huh JW, Park SJ, Kim DS, Ha HS, Kim YJ, Lee JR, Chang KT, Kim HS (2008) Selection of internal reference genes for SYBR green qRT-PCR studies of rhesus monkey (Macaca mulatta) tissues. BMC Mol Biol 9: 78.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
3. Andersen CL, Jensen JL, Orntoft TF (2004) Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res 64: 5245-5250.
4. Avila CM, Sillero JC, Rubiales D, Moreno MT, Torres AM (2003) Identification of RAPD markers linked to the Uvf-1 gene conferring hypersensitive resistance against rust (Uromyces viciae-fabae) in Vicia faba L. Theor Appl Genet 107: 353-358.
5. Avila CM, Satovic Z, Sillero JC, Rubiales D, Moreno MT, Torres AM (2004) Isolate and organ-specific QTLs for ascochyta blight resistance in faba bean (Vicia faba L). Theor Appl Genet 108: 1071-1078.
6. Avila CM, Nadal S, Moreno MT, Torres AM (2006) Development of a simple PCR-based marker for the determination of growth habit in Vicia faba L. using a candidate gene approach. Mol Breed 17: 185-190.
7. Avila CM, Atienza SG, Moreno MT, Torres AM (2007) Development of a new diagnostic marker for growth habit selection in faba bean (Vicia faba L.) breeding. Theor Appl Genet 115: 1075-1082.
8. Bennett MD, Leitch IJ (1995) Nuclear-DNA amounts in angiosperms. Ann Bot 76: 113-176.
9. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55: 611-622.
10. Choi HK, Kim D, Uhm T, Limpens E, Lim H, Mun JH, Kalo P, Penmetsa RV, Seres A, Kulikova O, Roe BA, Bisseling T, Kiss GB, Cook DR (2004a) A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M-sativa. Genetics 166: 1463-1502.
11. Choi HK, Mun JH, Kim DJ, Zhu HY, Baek JM, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR (2004b) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA 101: 15289-15294.
12. Cook DR (1999) Medicago truncatula-a model in the making! Commentary. Curr Opin Plant Biol 2: 301-304.
13. Cruz F, Kalaoun S, Nobile P, Colombo C, Almeida J, Barros LMG, Romano E, Grossi-de-Sa MF, Vaslin M, Alves-Ferreira M (2009) Evaluation of coffee reference genes for relative expression studies by quantitative real-time RT-PCR. Mol Breed 23: 607-616.
14. Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible WR (2005) Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol 139: 5-17.
15. Díaz-Ruiz R, Satovic Z, Ávila CM, Alfaro CM, Gutierrez MV, Torres AM, Román B (2009) Confirmation of QTLs controlling Ascochyta fabae resistance in different generations of faba bean (Vicia faba L.). Crop Pasture Sci 60: 353-361.
16. Die JV, Verdejo CIG, Dita MA, Nadal S, Roman B (2009) Gene expression analysis of molecular mechanisms of defense induced in Medicago truncatula parasitized by Orobanche crenata. Plant Physiol Biochem 47: 635-641.
17. Dos Santos CV, Letousey P, Delavault P, Thalouarn P (2003) Defense gene expression analysis of Arabidopsis thaliana parasitized by Orobanche ramosa. Phytopathology 93: 451-457.
18. Ellwood SR, Phan HTT, Jordan M, Hane J, Torres AM, Avila CM, Cruz-Izquierdo S, Oliver RP (2008) Construction of a comparative genetic map in faba bean (Vicia faba L.); conservation of genome structure with Lens culinaris. BMC Genomics 9: 380.
19. FAOSTAT (2010). http://faostat. fao. org/site/567/default. aspx#ancor.
20. Gutierrez N, Avila CM, Duc G, Marget P, Suso MJ, Moreno MT, Torres AM (2006) CAPs markers to assist selection for low vicine and convicine contents in faba bean (Vicia faba L.). Theor Appl Genet 114: 59-66.
21. Gutierrez N, Avila CM, Rodriguez-Suarez C, Moreno MT, Torres AM (2007) Development of SCAR markers linked to a gene controlling absence of tannins in faba bean. Mol Breed 19: 305-314.
22. Gutierrez N, Avila CM, Moreno MT, Torres AM (2008) Development of SCAR markers linked to zt-2, one of the genes controlling absence of tannins in faba bean. Aust J Agric Res 59: 62-68.
23. Hernandez-Bello MA, Chilvers MI, Akamatsu H, Peever TL (2006) Host specificity of Ascochyta spp. infecting legumes of the viciae and cicerae tribes and pathogenicity of an interspecific hibrid. Phytopathology 96: 1148-1156.
24. Hong SY, Seo PJ, Yang MS, Xiang F, Park CM (2008) Exploring valid reference genes for gene expression studies in Brachypodium distachyon by real-time PCR. BMC Plant Biol 8: 112.
25. Jain M, Nijhawan A, Tyagi AK, Khurana JP (2006) Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. Biochem Biophys Res Commun 345: 646-651.
26. Jian B, Liu B, Bi YR, Hou WS, Wu CX, Han TF (2008) Validation of internal control for gene expression study in soybean by quantitative real-time PCR. BMC Mol Biol 9: 59.
27. Kahl G, Winter P, Horres R, Rotter B, Jüngling R, LEGRESIST_Consortium (2009) Pathogenesis-related genes and genetic variation in potential resistance genes of major European legumes: the LEGRESIST project. Ascochyta 2009, Proceedings of the second international Ascochyta workshop, Pullman, Washington, USA, p 47.
28. Kalo P, Seres A, Taylor SA, Jakab J, Kevei Z, Kereszt A, Endre G, Ellis THN, Kiss GB (2004) Comparative mapping between Medicago sativa and Pisum sativum. Mol Genet Genom 272: 235-246.
29. Nicot N, Hausman JF, Hoffmann L, Evers D (2005) Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress. J Exp Bot 56: 2907-2914.
30. Olsvik P, Softeland L, Lie K (2008) Selection of reference genes for qRT-PCR examination of wild populations of Atlantic cod Gadus morhua. BMC Res Notes 1: 47.
31. Perez-de-Luque A, Gonzalez-Verdejo CI, Lozano MD, Dita MA, Cubero JI, Gonzalez-Melendi P, Risueno MC, Rubiales D (2006) Protein cross-linking, peroxidase and beta-1, 3-endoglucanase involved in resistance of pea against Orobanche crenata. J Exp Bot 57: 1461-1469.
32. Pflieger S, Lefebvre V, Causse M (2001) The candidate gene approach in plant genetics: a review. Mol Breed 7: 275-291.
33. Phan HTT, Ellwood SR, Ford R, Thomas S, Oliver R (2006) Differences in syntenic complexity between Medicago truncatula with Lens culinaris and Lupinus albus. Funct Plant Biol 33: 775-782.
34. Phan HTT, Ellwood SR, Hane JK, Ford R, Materne M, Oliver RP (2007) Extensive macrosynteny between Medicago truncatula and Lens culinaris ssp culinaris. Theor Appl Genet 114: 549-558.
35. Picard J (1976) Aperçu sur l'héredité du caractére absence de tannins dans les graines de féverole (Vicia faba L.). Annales de l'Amélioration des Plantes 26: 101-106.
36. Reid KE, Olsson N, Schlosser J, Peng F, Lund ST (2006) An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development. BMC Plant Biol 6: 27.
37. Remans T, Smeets K, Opdenakker K, Mathijsen D, Vangronsveld J, Cuypers A (2008) Normalisation of real-time RT-PCR gene expression measurements in Arabidopsis thaliana exposed to increased metal concentrations. Planta 227: 1343-1349.
38. Rispail N, Kaló P, Kiss GB, Ellis N, Gallardo K, Thompson RD, Prats E, Larrainzar E, Ladrera R, González EM, Arrese-Igor C, Ferguson BJ, Gresshoff PM, Rubiales D (2010) Model legumes contribute to faba bean breeding. Field Crops Res 115: 253-269.
39. Roman B, Satovic Z, Avila CM, Rubiales D, Moreno MT, Torres AM (2003) Locating genes associated with Ascochyta fabae resistance in Vicia faba. Aust J Agric Res 54: 85-90.
40. Román B, Torres AM, Rubiales D, Cubero JI, Satovic Z (2002) Mapping of quantitative trait loci controlling broomrape (Orobanche crenata Forsk.) resistance in faba bean (Vicia faba L.). Genome 45: 1057-1063.
41. Schmittgen TD, Zakrajsek BA (2000) Effect of experimental treatment on housekeeping gene expression: validation by real-time, quantitative RT-PCR. J Biochem Biophys Meth 46: 69-81.
42. Silberberg G, Baruch K, Navon R (2009) Detection of stable reference genes for real-time PCR analysis in schizophrenia and bipolar disorder. Anal Biochem 391: 91-97.
43. Sillero JC, Rubiales D (2002) Histological characterization of resistance to Uromyces viciae-fabae in faba bean. Phytopathology 92: 294-299.
44. Skovgaard K, Mortensen S, Poulsen KT, Angen O, Heegaard PMH (2007) Validation of putative reference genes for qRT-PCR normalization in tissues and blood from pigs infected with Actinobacillus pleuropneumoniae. Vet Immunol Immunopathol 118: 140-146.
45. Tivoli B, Baranger A, Avila CM, Banniza S, Barbetti M, Chen W, Davidson J, Lindeck K, Kharrat M, Rubiales D, Sadiki M, Sillero JC, Sweetingham M, Muehlbauer FJ (2006) Screening techniques and sources of resistance to foliar diseases caused by major necrotrophic fungi in grain legumes. Euphytica 147: 223-253.
46. Tong ZG, Gao ZH, Wang F, Zhou J, Zhang Z (2009) Selection of reliable reference genes for gene expression studies in peach using real-time PCR. BMC Mol Biol 10: 71.
47. Torres AM, Roman B, Avila CM, Satovic Z, Rubiales D, Sillero JC, Cubero JI, Moreno MT (2006) Faba bean breeding for resistance against biotic stresses: towards application of marker technology. Euphytica 147: 67-80.
48. Vandesompele J, De Preter K, Pattyn F, Poppe B, van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3: research0034. 0031-research0034. 0011.