Table 3.

Candidate genes and corresponding primers used for qPCR experiments Coffee sequences were selected (E-value ≤1e⁻¹⁰) from public databases with the BLAST programs (Altschul et al., 1990). Gene names were assigned based on the best BLASTX hit obtained by comparing the selected coffee ESTs with public databases. GenBank (GB) accession numbers of coffee EST sequences are also given. Primers were designed using the Primer Express software (Applied Biosystems).

Protein name	Gene name	GB numbers	Primer name	Primer sequence	bp	CG
Ubiquitin	CcUBQ10	GW488515	BUBI-F	5′-AAGACAGCTTCAACAGAGTACAGCAT-3′	104	R*
			BUBI-R	5′-GGCAGGACCTTGGCTGACTATA-3′
Glyceraldehyde-3-phosphate dehydrogenase	CcGAPDH	GW445811	GAPDH-F	5′-TTGAAGGGCGGTGCAAA-3′	59	R*
			GAPDH-R	5′-AACATGGGTGCATCCTTGCT-3′
Cathepsin	CcCTS1	GW442860	CATHEP-F	5′-CCCATTATCGTTCTGGTGTTTACAA-3′	80	R
			CATHEP-R	5′-ACCCCATCCAATCAGCTTTACA-3′
Actin	CcACT1	GW428479	ACTIN-F	5′-GGATTTCCAGGGCTGAATATGA-3′	80	R
			ACTIN-R	5′-CGATACGATAGTAGCAGCTTAAAAGC-3′
ADP-ribosylation factor (ARF)	CcADP1	GW450736	ADP-F	5′-ATGAATGCTGCTGAAATAACTGATAAG-3′	80	R
			ADP-R	5′-GCACAGGTGCTTTGGATATACCA-3′
Cyclophilin	CcCYN1	GW488988	CYCLO-F	5′-TCTTCATCTGCACCGACAAGA 3′5′-CACATCCATACCCTCCGTGAT-3′	80	R
			CYCLO-R
WRKY transcription factor	CcWRKY2	GT647873	18089-F	5′-CATGATCCCAAAGCAGTTATTACG-3′	67	1
			18089-R	5′-TTCTGGCAGTTGGTACATCATGAT-3′
Photosystem I subunit XI	CcPSAL1	GT646615	ND			1
Early light-induced protein (ELIP)	CcELIP1	GT647659	**			1
Early light-induced protein (ELIP)	CcELIP2	GT647647	**			1
Unknown protein 1	CcUNK1	DV689820	182052-F	5′-TATAGTGTTTATGGTGTGGCTTTCAGT-3′	79	1
			182052-R	5′-GTACCACCGTAGGGAGACGTATG-3′
Catalase	CcCAT1	GT649488	18297-F	5′-TGACAGAACCTGCAGTAAAGACAGTATT-3′	146	2
			18297-R	5′-AACCAACCAAATGAACGAACAAT-3′
Catalase	CcCAT2	GT648692	SH3055G111-F	5′-GATACCCAGCGACACCGTCTT-3′	70	5
			SH3055G111-R	5′-GATGAGCACACTTGGGAGCAT-3′		CcCAT1
Acyl-CoA-binding protein	CcACBP1	GT646045	9158-F	5′-AATACTACCAATGCAAGCAAGCTTA-3′	128	2
			9158-R	5′-CCTTCCATGCATCCCACTTT-3′
Chlorophyll a/b-binding protein	CcCAB1	GT647358	18230-F	5′-CTCTGAACTTCACCAGCTCTTCAA-3′	140	2
			18230-R	5′-GAGCTCGTCGTCCAATGAAGA-3′
Metallothionein like protein	CcMET1	GT650680	**			2
GLB2-like non-symbiotic haemoglobin	CcNSH1	GT649198	RBCS3'-F	5′-CTAAGGGATACGGATGAAATTCCA-3′	102	2
			RBCS3'-R	5′-CTCTCGCAGCTGCACTACTGATT-3′
Glycine-rich protein	CcGRP1	GT650953	GC182-F	5′-AAGCCAGCTTCTAGCTATGTCATGA-3′	100	2
			GC182-R	5′-GATCCAGCACTTATTTGAGATCACA-3′
Mannose 6-phosphate reductase	CcMPR1	GT648734	LPSH3069F05-F	5′-AATCAGCAATTACAGCGTTTTGC-3′	100	2,3
			LPSH3069F05-R	5′-AGTGACACAGATGCCGTGCTT-3′
Aldose-phosphate reductase	CcAPR1	GT649483	LPSH3060G02-F	5′-TGAAGCCAGCTGTGAATCAACT-3′	100	5
			LPSH3060G02-R	5′-GTGTGGGCAGTGACACAGATG-3′		CcMPR1
Unknown protein 10	CcUNK10	GT648004	D18240-F	5′-TAGCCTTGTTCTTTTAGGGAGTCTTATC-3′	134	2
			D18240-R	5′-AGAGCTTCGTCCAGGAAGAAGA-3′
TNF-associated factor (TRAF)	CcTRAF1	GT652792	LP-12677-FLP-12677-R	5′-GACTCTGGGCACATCGTGATAG-3′5′-TGCGAAGGGAAAGAATGGAA-3′	100	3
Prephenate dehydrogenase	CcPDH1	GT655248	LP175502-F	5′-GCAGGGACATGGACGAATTT-3′	100	3
			LP175502-R	5′-TGAAACGGCATGGACTTGAC-3′
Unknown protein 8	CcUNK8	DV695331	LP18100-F	5′-CTCGCGTGGCCGAGATT-3′	100	3
			LP18100-R	5′-CCCTCACATTTCCACGTGAAT-3′
Dehydrin	CcDH3	DV689895	18390-F	5′-TTAATAGCAGCTTTCCAGTGTGTCA-3′	100	3
			18390-F	5′-GATCCCCCAAAAAGCAGAAAA-3′
EDR1-like MAPKK kinase	CcEDR1	GW457961	LPSH3054B02-F	5′-TGTCAAATTGATGAAAAGCGAAGA-3′	100	3
			LPSH3054B02-R	5′-AAGGAAAAGTAGGAAATCAGCCAAA-3′
EDR1-like MAPKK kinase	CcEDR2	DV681462	EDR13-FEDR13-R	5′ CGGCATAAGAGCGAGTGGAA 3′5′ ATGCAATCGCTGGTGTAGAAAA 3′	70	6
Small heat shock protein (sHSP)	CcHSP1	GW447897	LPSH3056B04-F	5′-GGTAGGACGCCATGGGAGAT-3′	100	3, 4
			LPSH3056B04-R	5′-CCTCAACCCACACCTTCACAT-3′
Carbonic anhydrase	CcCA1	GT008701	HRAM1-F	5′-AAGGCCATTGTCGGACTTCA-3′	100	4
			HRAM1-R	5′-TTGTTTGCAACTCTGCAGTGATT-3′
Type-2C protein phosphatase (PP2C)	CcPP2C	GW435032	HRAM2-F	5′-CGAAGAAATCAGGCGTATCAGAG-3′	101	4
			HRAM2-R	5′-TAAACCGCACGTCACCAAAAG-3′
Oxygen-evolving complex PSII (psbO)	CcPSBO	GT647517	HRAM12-F	5′-TGAATTTCTCGTGCCATCATACA-3′	101	4
			HRAM12-R	5′-CTCCAGCAGGCAATGCAACT-3′
Oxygen-evolving complex PSII (psbP)	CcPSBP	GW488995	HRAM7-F	5′-AGCTGTCGATTCCCTCAAAATG-3′	100	4
			HRAM7-R	5′-GAGACACTGCTGTTGCTATCGAA-3′
Oxygen-evolving complex PSII (psbQ)	CcPSBQ	GT645658	HRAM36-F	5′-CAGGGCAATCAAGGTTGGA-3′	102	4
			HRAM36-R	5′-CGGTCCTTGAGTGGCAAATC-3′
Rubisco small chain (RbcS)	CcRBCS1	GT649534	18244-F	5′-CACCAACTGGAAAGTTGAAGAA-3′	169	6
			18244-R	5′-TATCCCGGTGACCTGTGGTATT-3′
Subtilisin-like serine protease	CcSDD1	GT659840	SDD1-F	5′-GAGCCCCGATTGATCTTCTG-3′	101	6
			SDD1-R	5′-ACTCAGCCCCAAAAGGGTTAA−3′
Glucosyltransferase arbutin synthase	CcGAS1	GT721173	ARBU09-F	5′-AAAGCGTTGCAGGAGCAAGA-3′	80	6
			ARBU09-R	5′-CTGTCCCCTGAGCCCATCT-3′
Abscisic acid receptor	CcPYL3	GT720590	PYL31-F	5′-CGGTGACGACTGTCCATGAG-3′	80	6
			PYL31-R	5′-CGGCACGTCAACGATATACG-3′
Abscisic acid receptor	CcPYL7	DV704550	PYL72-F	5′-GAGAAGCACATTCTTGGGATCAA-3′	80	6
			PYL72-R	5′-GGATGCACGGTAAGGATGGA-3′
Amidase (IAA synthesis)	CcAMI1	GT651356	HD141612-F	5′-AGATGTCTGCCACAGTGTGAAGA-3′	80	6
			HD141612-R	5′-GGAGTGCAAGGATGCCAAAA-3′
RD29-like protein	CcRD29	GT660256	RD29-F	5′-TGATGATCAAGATCCCCAACAC-3′	100	6
			RD29-R	5′-CTTCGCTTTCGCCTTCACTT-3′
AP2/ERF DREB-like	CcDREB1	GW463524	DREBA09-F	5′-CAATGCCTGCAAAGCCAATTA-3′	80	6
			DREBA09-R	5′-TTTTCCTGCCTGCACGTTTC-3′
NAC-RD26-like	CcRD26	GT003652	NACRD26-F	5′-TTTGGCCCTGCGCTCTAGT-3′	98	6
			NACRD26-R	5′-AAGCGGGTCAGTTTCTCGAA-3′
MYB-type 2 transcription factor	CcMYB1	GT689406	MYB61-F	5′-CCCGGCAATCTTCCAGCTA−3′	100	6
			MYB61-R	5′-TCAAGCGTGGCAACTTCACT−3′
Caffeoyl-CoA 3-O methyltransferase	CcCCoAOMT1	GT715419	CCOAOMT-F	5′-GACACACCAGCCCTTTCGAT-3′	100	6
			CCOAOMT-R	5′-CAGCTCTCGCTCTTCCAGAAG-3′
Clp protease ATP-binding subunit	CcCLP1	GT651512	CLP1-F	5′-CCACCCCAGTAGGACCAGAAA-3′	80	6
			CLP1-R	5′-CATTCGTCGTGCTCGTGTTG-3′
Ascorbate peroxidase	CcAPX1	GT697455	ASCPER1-F	5′-GACCTGAACAATGCCCAGAAG-3′	70	6
			ASCPER1-R	5′-CGTAAATGAGCAGCAGGTGATG-3′
Ascorbate peroxidase	CcAPX2	EE193467	ASCPER6-F	5′-AGACCGTGTCTCAAACCGACTAC-3′	80	5 CcAPX1
			ASCPER6-R	5′ GTTGATCTGTTGGCCCAAAGA 3′
Leucine zipper (ABA signalling)	CcABI5	GT645781	ABI52-F	5′-GCCGCTGCAGCCTCTATTT-3′	99	6
			ABI52-R	5′-AGCTGAGCGTTGTTCCCTATCT-3′
Leucine zipper (ABA signalling)	CcAREB1	EE198828	AREB11-F	5′-TGTTGTAAGGGAGGATGCTCAA-3′	100	6
			AREB11-R	5′-TCCAAACCCAAAAGCCTGAT-3′
Homeobox leucine zipper hypothetical protein	CcHDZ1	GT724869	HD68272-F	5′-GACGTTGACGGACGAGAACA−3′	100	6
			HD68272-R	5′-TGTAGCCGCTGGCAACTG−3′
Homeobox leucine zipper hypothetical protein	CcHDZ2	GW447493	HD111162-F	5′-AGTGCCAGGGAAAAGAATTCC-3′	100	6
			HD111162-R	5′-TCCGGCTGTCTCTTTCTCATG-3′

R, reference genes tested, with CcUBQ10 and CcGAPDH being used as reference genes in qPCR experiments (*, **. gene expression tested by northern blot but not by qPCR); ND, gene expression not determined.

The size of the amplicon in bp is also indicated. The selected candidate genes (CGs) corresponded to (1) genes exclusively overexpressed in the leaf SH3 cDNA library of drought-tolerant clone 14 of C. canephora var. Conilon subjected to drought (Fig. 1A); (2) genes mainly overexpressed in the SH3 cDNA library (Fig. 1B); (3) genes identified by the macroarray experiment (Fig. 2); (4) genes encoding proteins showing differential accumulation by 2-DE (Fig. 3); (5) genes homologous to other CGs; and (6) genes selected from the literature. CGs are ordered as presented in the text.