Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars

Mofatto, Luciana Souto; Carneiro, Fernanda de Araújo; Vieira, Natalia Gomes; Duarte, Karoline Estefani; Vidal, Ramon Oliveira; Alekcevetch, Jean Carlos; Cotta, Michelle Guitton; Verdeil, Jean-Luc; Lapeyre-Montes, Fabienne; Lartaud, Marc; Leroy, Thierry; De Bellis, Fabien; Pot, David; Rodrigues, Gustavo Costa; Carazzolle, Marcelo Falsarella; Pereira, Gonçalo Amarante Guimarães; Andrade, Alan Carvalho; Marraccini, Pierre

doi:10.1186/s12870-016-0777-5

Table 1 Candidate genes and corresponding primers used for qPCR experiments

From: Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars

Gene	Protein name	C. canephora	GB	ATP	SGN	Primer	Primer sequences	bp
CaUBQ10	Ubiquitin	Cc02_g31600	GW488515	32782	U637098	BUBI-F BUBI-R	5’ AAGACAGCTTCAACAGAGTACAGCAT 3’ 5’ GGCAGGACCTTGGCTGACTATA 3’	104
CaAEP1 ^a	Putative aldose 1-epimerase	Cc07_g03170	GT005185	716	U637659	716-1 F 716-1R	5' CGGTGATGTCCTCTCTGATGAG 3’ 5’ GTTGGGATGAGCTGGTTGTTC 3’	75
CaCAB2 ^a	Chlorophyll a/b-binding protein	Cc09_g09030	GT003492	33540	U629601	48565-F 48565-R	5’ GTTCAAGGCTGGATCCCAAA 3’ 5’ GCAAGCCCAGATAGCCAAGA 3’	100
CaCHI1 ^a	Class III chitinase	Cc11_g00410	GT012279	32745	U637166	50103-F 50103-R	5’ AATCAAGCGACCGTCCATTC 3’ 5’ GTGTTTCCGCTGTGGATGTG 3’	70
CaCHI2 ^a	Putative chitinase	Cc00_g14300	GT011845	32737	U638035	53058-F 53058-R	5’ CCTGCTCGCGGTTTCTACAC 3’ 5’ TTGTTCCAAAAGCCCCATTG 3’	70
CaCHI3 ^a	Chitinase-like protein	Cc03_g13720	GW491433	32875	U645893	23638-F 23638-R	5’ AAACGGCCCGTCCAGAA 3’ 5’ GCTTTGTCCTGCTGGTCCAT 3’	130
CaDLP1 ^a	Dirigent-like protein	Cc00_g27410	GW477731	35149	nf	39577-F 39577-R	5’ TTGGTAGTCCGGCGAGAGAA 3’ 5’ GCATATCCCCGAGCAAACCT 3’	70
CaELIP3 ^a	Early light-induced protein (ELIP)	Cc03_g04300	GR985685	32771	U631550	32771-F 32771-R	5’ TCGGTTGCCATGCAATCTT 3’ 5’ GCAGATGAAGCCCACAGCTT 3’	100
CaGAS2 ^a	Glucosyltransferase arbutin synthase	Cc02_g39100	GT697284	3945	U632419	632419-F 632419-R	5’ GCTGACGACGTTAGGATTGAGA 3’ 5’ AACTTGGCGGTGTCAACCAA 3’	101
CaGRP2 ^a	Glycin-rich protein	Cc00_g16260	GW430980	32799	U635030	53139-1 F 53139-1R	5’ CACATATGCTGGTGAGCCAAA 3’ 5’ AGGCATTTAAGCGCCATGAT 3’	100
CaH2A ^a	Putative histone H2A	Cc01_g12440	GT723387	33557	U630412	53417-F 53417-R	5’ GCACTGGAGCTCCGGTCTAC 3’ 5’ AGCAGCATTTCCAGCCAATT 3’	80
CaHSP3 ^a	Heat schock protein (HSP) 70 kDa	Cc02_g08040	GR982512	33197	U636531	33197-1 F 33197-1R	5’ GGCGTCTGGCAACACGAT 3’ 5’ CGATGAGACGCTCGGTGTCT 3’	100
CaIPS1 ^a	Myo-inositol 1-phosphate synthase	Cc07_g15530	GT003538	10496	U632517	10496-1 F 10496-1R	5’ AAGCAACCTGAATTTGGCTGAT 3’ 5’ GAGAGGGACCATGGATTCCA 3’	100
CaJAMT1 ^a	Jasmonate O-methyltransferase	Cc03_g07330	GR989151	33008	U631389	47327-F 47327-R	5’ CTGTGGCTGAACCCTTGCTT 3’ 5’ TCTTTGGACATGCGATCAGAAA 3’	100
CaMAS1 ^a	Momilactone-A synthase	Cc00_g13640	GW479615	33413	nf	33413-F 33413-R	5’ GGGCAGAGGCACGAAAAA 3’ 5’ GGTACCCTGCCGCAACTATG 3’	60
CaPP2 ^a	Putative phloem protein 2 (PP2)	Cc03_g13000	GR995691	33207	U633544	33207-F 33207-R	5’ GGTGTTGGCGATGTCGAGAT 3’ 5’ TTCCTTGGGTCGAAGCTCAA 3’	90
CaPSBB ^a	Photosystem II CP47 (psbB)-like protein	nf	GW447378	22102	U630312	55586-F 55586-R	5’ ATCGGAAATAATCCGGCAAA 3’ 5’ AACCATCCAATCGCTATTCCA 3’	80
CaSAMT1 ^a	S-adenosyl-methionine-methyltransferase	Cc03_g05630	DV672716	754	U629783	34318-F 34318-R	5’ AACGTTTGGGTGATGAATGTTG 3’ 5’ GTGCCAATAAGCCCTCTATCGT 3’	80
CaSDC1 ^a	S-adenosyl-L-methionine decarboxylase	Cc11_g11130	GT002431	8508	U629687	8508-1 F 8508-1R	5’ CTCGATTCCTCCCATCCTGAA 3’ 5’ TGACTGTGCCCCAGGGAATA 3’	100
CaSLP1 ^a	Subtilisin-like protein	Cc00_g19100	GW430663	1620	nf	7961-F 7961-R	5’ CCATCGTTCTCGGTGGTCTT 3’ 5’ GCATTGCTCCCCACATTCTT 3’	80
CaSTK1 ^a	Hypothetical S/T protein kinase	Cc00_g18670	GT687049	6301	U631794	6301-1 F 6301-1R	5’ CCACCCACAAGCTGTATTCTCA 3’ 5’ GACCCAATGGGATGTCATCAC 3’	80
CaUNK1 ^c	Unknown protein 1	Cc03_g08880	DV689820	33062	U614843	182052-F 182052-R	5’ TATAGTGTTTATGGTGTGGCTTTCAGT 3’ 5’ GTACCACCGTAGGGAGACGTATG 3’	79
CaUNK2 ^b	Unknown protein 2	Cc07_g01940	DV708962	31492	U637447	33353-F 33353-R	5’ GAACTTACAAACGCGCGTAACC 3’ 5’ CATGGTCGAATCCAGATTTCATT 3’	80
CaUNK3 ^b	Unknown protein 3	nf	nf	22823	nf	22823-F 22823-R	5’ GGAAGCATGCACACAGAAAATAGA 3’ 5’ TTCCTGTTTACGTCTTTTTCAATTGA 3’	80
CaUNK4 ^b	Unknown protein 4	Cc06_g11210	GW465088	39984	nf	55677-F 55677-R	5’ GCTGTGGTTTTAAAGTTTTGATGGA 3’ 5’ TGCAAAATTAAGGTCCCAACAGT 3’	81
CaUNK5 ^b	Unknown protein 5	Cc08_g09510	GW474926	4578	nf	4578-F 4578-R	5’ GGAGTTCCTGTCCGAAGTTGTT 3’ 5’ GGCATGCTGTCACCTGAAAA 3’	80
CaUNK6 ^b	Unknown protein 6	Cc03_g06850	GT002178	34993	U632634	34993-F 34993-R	5’ AAGCCAATGCCGATCGATT 3’ 5’ CGCCGCCGAAGATCTCTAG 3’	100
CaUNK7 ^b	Unknown protein 7	Cc03_g00560	GW444736	33613	U631416	25639-F 25639-R	5’ CGAGGAAGCTGAAGGAAAGGA 3’ 5’ TCCGACTGGCCTAACAAGGT 3’	61
CaUNK8 ^b	Unknown protein 8	Cc00_g04970	DV695331	33190	U640780	LP18101-F LP18100-R	5’ CTCGCGTGGCCGAGATC 3’ 5’ CCCTCACATTTCCACGTGAAT 3’	100
CaUNK9 ^b	Unknown protein 9	Cc03_g08920	GT649500	32762	U636808	30926-F 30926-R	5’ CGGAGGAGGCCATGGAGGT 3’ 5’ CCGTGTCCATAACCACCATGT 3’	123
CaUNK10 ^c	Unknown protein 10	nf	GT648004	14813	U645073	D18240-F D18240-R	5’ TAGCCTTGTTCTTTTAGGGAGTCTTATC 3’ 5’ AGAGCTTCGTCCAGGAAGAAGA 3’	134
CaUNK11 ^b	Unknown protein 11	Cc03_g14330	GR991912	8598	U637116	32792-F 32792-R	5’ GCTGGGAAAGCTACAGAAACCA 3’ 5’ GAACTCCAACGCCAAGCATT 3’	100
CaUNK12 ^b	Unknown protein 12	Cc10_g12840	nf	53029	nf	53029-F 53029-R	5’ CTTCACACCATTCAGACAATCGA 3’ 5’ GACCGTAATTGGGCGTCAAT 3’	100
CaUNK13 ^b	Unknown protein 13	Cc00_g17760	GT673421	14198	U639484	33980-F 33980-R	5’ ATTGCCCTGTTTGCATGCAT 3’ 5’ CTGCATGGTGATTGTCCTCAGT 3’	100
CaUNK14 ^b	Unknown protein 14	Cc00_g16260	GT672564	48325	U635030	11524-F 11524-R	5’ GGCGGTTGTCATGGATACG 3’ 5’ TTTGGCTCACCAGCATATGTG 3’	119
CaUNK15 ^b	Unknown protein 15	Cc00_g04970	GR983286	33190	U636790	05517-F 05517-R	5’ AAAATTTCACCACGGCAAGCT 3’ 5’ TTGCCTCCCTCACATTTCCA 3’	72
CaUNK16 ^b	Unknown protein 16	nf	GW464209	9761	U639049	18112-F 18112-R	5’ TGTGAACTGCCATCCCAAGA 3’ 5’ AAGACTACCATGTCCAACAACTTCAG 3’	88
CaUNK17 ^b	Unknown protein 17	Cc03_g08920	GT685623	32762	U636800	42747-F 42747-R	5’ AGGTGGCTGCCAAGTCAGTT 3’ 5’ ATGGTACTTGGCTTCTCCTTCCTC 3’	71
CaLTP1 ^d CaLTP2 ^d	Non-specific lipid transfer protein (nsLTP)	Cc11_g09700	HG008739 HG008740	46897	U632702	LTP-R2 LTP-FT	5’ CACCATTACATGGGAACGTTGC 3’ 5’ CTGTGGTCTGAAATGGCCAACT 3’	120
CaLTP3 ^d	Non-specific lipid transfer protein (nsLTP)	Cc04_g06890	HG008741	33368	U632702	LTP-R1 LTP-FT	5’ ATTCAACACCATTACTAGTTTTCGAGC 3’ 5’ CTGTGGTCTGAAATGGCCAACT 3’	113
LTP ^d	Non-specific lipid transfer protein (nsLTP)	nf		-	U632702	LTP-F100 LTP-R100	5’ TGCAATTTTATCAAAGATCCAGC 3’ 5’ AGTTGGCCATTTCAGACCACA 3’	93

Gene names were assigned based on the best BLAST hit obtained by comparing the coffee ESTs with public databases. C. canephora means coffee sequences that aligned with the candidate genes using BLASTx searches against NR/NCBI and filtration (http://coffee-genome.org [59]). GenBank (GB: http://blast.ncbi.nlm.nih.gov/Blast.cgi), ATP (http://www.lge.ibi.unicamp.br/cirad/) and SGN (Sol Genomics Network, http://solgenomics.net/) accession numbers of coffee ESTs are also given, as well as the length of base pairs (bp) of amplicons. nf: no-hits found (SGN: tools/blast/SGN Clusters [current version] / Coffee species Clusters, GB: BLASTn/Nucleotide collection [nr/nt]). The size of amplicons is based on the unigene. (^a): candidate genes (n = 20) identified during this study. (^b): orphan genes (n = 14) previously described [35] and analysed in this study. (^c): orphan genes (n = 3) with expression already been studied in leaves of D^T and D^S clones of C. canephora conilon [10, 11, 36]. (^d): LTP-encoding genes were previously described [37]

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ISSN: 1471-2229

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