Table 2

Genes associated with Al tolerance in wheat, as identified by microarray profiling
A: Constitutively expressed genes associated with Al tolerance.

Gene number response type^a	Probeset IDs^b	Annotation^c	Representative GenBank/ Closest TIGR TC ID	Reference/fold change^d

84- Stress^a	Ta.30659.1.S1_at	Almt1-1 mRNA for aluminum-activated malate transporter	AB081803.1/TC275842	[33]/5.4
85- Unknown	TaAffx.11437.1.S1_at	Unknown	CD916477/TC237550	3.1
86- Unknown	Ta.6595.1.S1_at	Weak similarity to pinin	CA680476/TC239245	0.4
87- Metabolism	Ta.9190.2.S1_at	Putative Anaphase promoting complex subunit 10	BJ321280/TC237861	0.3
88- Unknown	Ta.7249.1.S1_at	Unknown	CA713200/TC238862	0.2
89- Signalling	TaAffx.16664.1.A1_at	F-box containing domain (IPR001810) and F-Box associated domain (IPR006527); Ubiquitination	CK205523/TC255586	0.2

B: Up-regulated genes associated with Al tolerance.

Response	Probeset IDs^a	Annotation^a	Representative GenBank/ Closest TIGR TC ID	Reference/fold change^d

90- Unknown	Ta.23271.1.S1_s_at	unknown	CA680274/TC249675	7.6
91- Stress	Ta.8545.1.S1_at	Glutathione S-transferase (GST)	BQ162041/TC259746	5.7
92- Pathogen	Ta.21314.1.S1_x_at	Similar to disease resistance response protein	CA669694/TC266782	5.2
93- Unknown	TaAffx.26343.1.S1_at	Unknown	CA689752/TC257163	4.9
94- Metabolism	Ta.8447.1.S1_a_at	Putative cytochrome P450 monooxygenase	CA669038/TC236876	[67]/4
95- Pathogen	Ta.24632.1.S1_at	Pathogen response serine-type endopeptidase inhibitor activity; putative protease inhibitor	BE405372/TC248320	4
96- Stress	Ta.3118.1.S1_at	Glutathione S-transferase	BE515437/TC238392	3.2
97- Unknown	TaAffx.86317.1.S1_at	Yippee-like protein IPR004910; role in cell division	CA611222/TC268232	3.2
98- Pathogen	Ta.24632.1.S1_x_at	Pathogen response serine-type endopeptidase inhibitor activity; putative protease inhibitor	BE405372/TC248320	3.1
99- Unknown	Ta.10326.1.S1_at	Unknown	BJ244180/TC238059	3.1
100- Unknown	Ta.14224.1.S1_at	Weak similarity to Protamine 1B or Zinc Knuckle domain	CK214385/TC252792	3.1
101- Metabolism	Ta.28890.1.A1_s_at	Fructose-1,6-bisphosphatase isozyme 2 (F1,6-BP)	CA686703/TC235271	2.9
102- Pathogen	Ta.24632.1.S1_a_at	Pathogen response serine-type endopeptidase inhibitor activity; putative protease inhibitor	BE405372/TC248320	2.9
103- Unknown	Ta.13302.1.S1_at	Unknown	BQ801428/TC258348	2.5
104- Unknown	Ta.23097.1.S1_x_at	Weak similarity to Adhesive/ proline-rich-like protein	CA699090/TC241038	2.4
105- Unknown	Ta.29761.1.A1_at	Similar to At2g31940	AJ609795/TC243334	2.4
106- Metabolism	Ta.4084.1.S1_at	Putative cellulose synthase-like protein OsCslE1 (cell wall metabolism)	BJ264002/TC253821	2.4
107- Signalling	TaAffx.12876.1.S1_at	Putative C2H2 type zinc finger transcription factor	BJ220837/TC275754	2.1
108- Pathogen	Ta.7883.1.S1_x_at	Putative disease resistance response protein	CK212322/TC267223	0.2

a: The gene are numbered consecutively to Table 1 to simplify presentation in the text and Figure 3. The response type is based on previous publications. b: According to Affymetrix Gene Chip^®wheat genome array description. The probesetIDs are presented in decreasing order of differential expression (most over-expressed to most down-regulated). The last 4 entries in Table 2A are more expressed in sensitive cultivars. The last entry in Table 2B is a down-regulated gene in the tolerant cultivars. For more details on gene expression level, see Additional file 2. Genes subsequently tested by qRT PCR are in bold. c: Annotations were made based on Affymetrix gene annotation complemented with BLAST results using the public representative ID provided with the Affymetrix Gene Chip^®wheat genome array. d: The fold change represents the mean ratio of gene expression in the two tolerant cultivar/the two sensitive cultivar (50% RGI).
Houde and Diallo BMC Genomics 2008 9:400 doi:10.1186/1471-2164-9-400