Gene expression profiling by cDNA-AFLP reveals potential candidate genes for partial resistance of ‘Président Roulin’ against Venturia inaequalis

Bastiaanse, Héloïse; Muhovski, Yordan; Parisi, Olivier; Paris, Roberta; Mingeot, Dominique; Lateur, Marc

doi:10.1186/1471-2164-15-1043

Table 3 Gene expression analysis of selected TDFs by qRT-PCR in ‘Président Roulin’ (resistant) and ‘Gala’ (susceptible)

From: Gene expression profiling by cDNA-AFLP reveals potential candidate genes for partial resistance of ‘Président Roulin’ against Venturia inaequalis

TDF	Annotation (blastx)	Exp.^a	Fold induction/repression
			cDNA-AFLP samples		Biological repetition
			Resistant cv.	Susceptible cv.	Resistant cv.	Susceptible cv.
	Defense response
43DU149’	cc-nbs-lrr resistance protein	IIb +	+7.9 ± 2.6*^b	+1.9 ± 0.0	+2.8 ± 1.1	+1.4 ± 0.3
56AU33’	cc-nbs-lrr resistance protein	IIb +	+2.6 ± 0.1*	+1.5 ± 0.1	+2.9 ± 0.5	+1.3 ± 0.5
42BUHcrVf	HcrVf paralog	IIb +	+1.0 ± 0.1	−1.9 ± 0.2*	−1.2 ± 0.1	−1.2 ± 0.2
43CU118	TMV resistance protein	IIb -	+1.6 ± 0.1	+1.5 ± 0.2	-	-
44AU9	LRR receptor kinase-like protein	IIb +	+ 5.1 ± 1.7*	+1.4 ± 0.4	+2.2 ± 0.4*	+1.7 ± 0.0*
44GU169	2-cys peroxiredoxin	IIb +	+10.3 ± 0.1*	+2.2 ± 0.1*	+1.4 ± 0.5	+1.2 ± 0.0
54CU21	Phi class glutathione transferase	IIb +	+3.5 ± 0.0*	−1.2 ± 0.5	+1.1 ± 0.1	−1.5 ± 0.1
	Signal transduction
2EU181	Putative MAP kinase	IIb +	+2.2 ± 0.0*	+1.4 ± 0.2	+2.1 ± 0.3*	−1.3 ± 0.0
39AU13	MAP kinase phosphatase	IIb +	+1.4 ± 0.0	+1.1 ± 0.2	−1.0 ± 0.1	−1.6 ± 0.0*
	Transporter
46EU122	ABC transporter	IIb -	−2.4 ± 0.1*	+1.3 ± 0.0	−1.5 ± 0.1	+2.4 ± 0.0*
	Oxidation reduction process
51DU17	Cytochrome P450	IIb +	+2.0 ± 0.3*	+1.1 ± 0.3	+1.0 ± 0.2	+1.1 ± 0.0
53DU34	Cytochrome P450	IIb -	−4.8 ± 0.0*	+1.5 ± 0.2	−1.9 ± 0.0*	−2.6 ± 0.1*
	Photosyntesis
56AU5’	Uroporphyrinogen decarboxylase	IIb +	+6.5 ± 1.3*	+3.9 ± 1.1	−1.0 ± 0.0	−1.4 ± 0.2
	Response to environmental stress
43DU149	Peroxidase 12	IIb +	+3.4 ± 0.2*	+1.2 ± 0.1	+4.0 ± 0.2*	+1.9 ± 0.2*
51HU129’	Tocopherol cyclase	IIb +	+8.1 ± 0.0*	+2.0 ± 0.1*	+6.9 ± 0.0*	+1.5 ± 0.0*
	Metabolism
Consensus 44EU122/44EU118	Cysteine protease	IIa -	- 12.7 ± 4.5*	- 4.1 ± 1.2*	−68.8 ± 0.0*	−3.2 ± 0.3
37DU41	Cysteine protease inhibitor	IIb +	+ 2.4 ± 0.1*	+1.2 ± 0.1	+2.9 ± 0.0*	+1.4 ± 0.1
1AU61’	Sumo ligase	IIb +	+1.5 ± 0.3	+1.6 ± 0.1	-	-
56AU29	Chitinase	IIb +	+2.3 ± 0.1*	+1.4 ± 0.1	+2.7 ± 0.2*	+1.2 ± 0.1*
44GU182	Lysosomal Pro-X carboxypeptidase	IIb -	- 28.4 ± 4.9*	+ 1.4 ± 0.1	−22.0 ± 0.0*	−1.9 ± 0.1*
	Transcription factor
53HU89	Zinc finger homeodomain protein1	IIb +	+10.3 ± 0.2*	+1.7 ± 0.1	+3.3 ± 0.1*	+1.8 ± 0.1*
	Cell wall organization
44GU173	Pectin methylesterase inhibitor	IIb +	+3.3 ± 0.8*	+1.1 ± 0.1	+3.6 ± 0.9*	+1.2 ± 0.2*
	Unknown functions
55FU102	No homology	IIa +	+3.0 ± 0.1*	+1.4 ± 0.5	+3.8 ± 0.2*	+1.3 ± 0.0
55HU125’	No homology	IIb +	+4.8 ± 0.0*	- 1.5 ± 0.1	+1.7 ± 0.0	+1.5 ± 0.2

^aExpression pattern according to the cDNA-AFLP. Group IIa represents pathogen-responsive TDFs expressed in common by both genotypes and group IIb pathogen-responsive and genotype specific TDFs. “+” = induced and “–” = repressed TDF.
^bMeans and SD of fold induction (+) or repression (−) calculated by the ΔΔCt method applied using qRT-PCR. Significant fold changes were judged considering the following criteria: statistical significance of individual ΔCt values at P <0.01 (*) and biological significance at fold change ≥2.

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