Some ethylene biosynthesis and AP2/ERF genes reveal a specific pattern of expression during somatic embryogenesis in Hevea brasiliensis

Piyatrakul, Piyanuch; Putranto, Riza-Arief; Martin, Florence; Rio, Maryannick; Dessailly, Florence; Leclercq, Julie; Dufayard, Jean-François; Lardet, Ludovic; Montoro, Pascal

doi:10.1186/1471-2229-12-244

Table 2 Identification of putative functions for somatic embryogenesis marker genes based on the reciprocical best hit analysis (BLASTX) using full cDNA sequences, and then co-orthology relationships, inferred by phylogeny, using the deduced amino acid sequences of the AP2 domain for each gene (see Additional file 1 : Figure S1, Additional file 2 : Figure S2, Additional file 3 : Figure S3, Additional file 4 : Figure S4, Additional file 5 : figure S5 and Additional file 6 : Figure S6)

From: Some ethylene biosynthesis and AP2/ERF genes reveal a specific pattern of expression during somatic embryogenesis in Hevea brasiliensis

Gene	Callus on ENT		Callus on EXP		Embryo	Reciprocal best hit analysis				Phylogenetic analysis
Gene	R/NE	R/E	R/NE	R/E	Nor/Ab	Homology gene	Putative function	Species	Reference	Orthologous gene	Accession No	Putative Function	Reference
HbSAMS	0.08	0.04	18.20	5.16		SAMS	Precursor for ethylene biosynthesis	Eucalyptus	[40, 41]	.
HbACS2	0.01	0.01				ACS	ACS synthase	Ricinus	[41, 42]	.
HbETR1	0.35	0.40				HbETR	Signal transduction	Hevea	[41, 42]	.
HbERF-Ia1	0.31	0.15			0.26	DREB	Freezing & dehydration tolerance	Glycine	[43–45]	ERF53	At2g20880	Regulates drought-responsive gene expression	[46]
HbERF-Ib1					0.24	DREB	Freezing & dehydration tolerance	Populus	[43–45]	.	At4g39780	Unknown
HbERF-Ib3					0.14	DREB	Freezing & dehydration tolerance	Populus	[43–45]	.	At4g39780	Unknown
HbERF-Ib6					0.18	DREB1p	Dwarfed phenotypes,freezing & dehydration tolerance	Hevea	[44]	.
HbERF-Ib7					0.19	DREB1p	Dwarfed phenotypes,freezing & dehydration tolerance	Hevea	[44]	.
HbERF-Ib8					0.35	DREB1p	Dwarfed phenotypes,freezing & dehydration tolerance	Hevea	[44]	.
HbERF-IIb5					0.09	TINY	Affects plant height, hypocotyl elongation, and fertility	Populus	[47, 48]	.	At1g44830	Unknown
HbERF-IIIa1			18.80	3.40		TINY	Affects plant height, hypocotyl elongation, and fertility	Populus	[47, 48]	.	At1g01250	Unknown
HbERF-IIIb2			10.70	6.44		ERF025	Control of ethylene-responsive transcription genes	Glycine	[49]	.	At1g63040	Unknown
HbERF-IIIc1			7.84	3.99		CRT/DRE	Heat stress tolerance	Hevea	[50, 51]	CBF3/DREB1A	At4g25480	Response to low temperature, abscisic acid	[52]
										CBF2/DREB1C	At4g25470	Response to low temperature, abscisic acid,	[53]
										CBF1/DREB1B	At4g25490	Response to low temperature, abscisic acid	[52]
										CBF4/DREB1D	At5g51990	Response to drought stress and abscisic acid	[54]
										DDF2	At1g63030	Regulates in GA biosynthesis and stress tolerance	[55]
										DDF1	At1g12610	Regulates in GA biosynthesis and stress tolerance	[55]
HbERF-IIIe3			16.20	8.62		TINY	Affects plant height, hypocotyl elongation, and fertility	Populus	[47, 48]	TINY	At5g25810	Suppresses cell proliferation and exhibits pleiotropic effects	[47]
HbERF-IVa1			6.31	9.87		DREB2	Enhances drought stress tolerance	Populus	[50, 51]	DREB2A	At5g05410	Drought-responsive gene expression	[50]
HbERF-IVa2			5.92	4.83	0.33	DREB2C	Heat stress tolerance	Ricinus	[51]	DREB2A	At5g05410	Drought-responsive gene expression	[50]
HbERF-IVa3			2.85	2.52		DREB2B	Water deprivation stimulus	Arabidopsis	[56]	.
HbERF-Vb2			3.24	7.39		RAP2.2	Response to hypoxic stress	Arabidopsis	[57]	.
HbERF-VI1					3.03	CRF2		Vitis	[58]	CRF2/TMO3	At4g23750	Related to root initiation at later embryonic stages	[58, 59]
HbERF-VI2	0.10	0.06				CRF2	Development of embryos and response to cytokin	Arabidopsis	[58]	CRF2/TMO3	At4g23750	Related to root initiation at later embryonic stages	[58, 59]
HbERF-VI-L1			5.81	4.97		ERF	Control of ethylene-responsive transcription genes	Ricinus	[60, 61]	.
HbERF-VIIa1					3.65	AP2/ERF	Response to biotic and abiotic stress conditions	Populus	[45]	.
HbERF-VIIa3			4.23		7.07	AP2/ERF	Response to biotic and abiotic stress conditions	Populus	[45]	.
HbERF-VIIa4	0.22	0.21	4.62		5.29	AP2/ERF	Response to biotic and abiotic stress conditions	Populus	[45]	.
HbERF-VIIa17			49.10	9.81		ERF-2	Control of ethylene-responsive transcription genes	Gossypium	[60, 61]	.
HbERF-VIIIa3	0.15	0.10		017		ERF3	Control of ethylene-responsive transcription genes	Arabidopsis	[62]	.
HbERF-VIIIa7			4.83	4.32		ATERF-4	Modulates ethylene and abscisic acid responses	Arabidopsis	[62]	.
HbERF-VIIIa11					0.16	ATERF-4	Modulates ethylene and abscisic acid responses	Arabidopsis	[62]	.
HbERF-IXb2			2.65	5.07		ERF	Control of ethylene-responsive transcription genes	Olimarabidopsis	[60, 61]		At5g07580	Unknown
HbERF-IXb4					0.17	ERF	Control of ethylene-responsive transcription genes	Ricinus	[60, 61]	.
HbERF-IXb8					0.07	ERF1	Drought, salt and freezing tolerances	Malus	[60, 61]	.	At5g51190	Unknown
HbERF-IXc4			57.10	10.50		ERF1	Drought, salt and freezing tolerances	Ricinus	[60, 61]	.
HbERF-Xb1					0.02	AP2/ERF	Response to biotic and abiotic stress conditions	Populus	[45]	RRTF1	At4g34410	Regulates redox homeostasis related to photosynthetic stress	[63]
HbAP2-1	0.14	0.11				ANT	Regulates up-regulation of genes establishing organ polarity and those specifying organ identity	Ricinus	[19, 64]	BBM	At5g17430	Promotes cell proliferation and morphogenesis during embryogenesis	[18, 65]
HbAP2-3			5.74	4.78		BBM	Cell proliferation and morphogenesis during embryogenesis	Ricinus	[18]	AIL7/PLT7	At5g65510	Regulates radial pattern formation process of a shoot apical meristem.	[66]
HbAP2-3			5.74	4.78		BBM	Cell proliferation and morphogenesis during embryogenesis	Ricinus	[18]	AIL6/PLT3	At5g10510	Regulation of floral meristem growth	[67]
HbAP2-5	0.13	0.10				AP2/ERF	Response to biotic and abiotic stress conditions	Ricinus	[45]	.	At2g41710	Unknown
HbAP2-7			24.90	12.90		AIL	Related to floral development	Vitis	[64]	ANT/DRG/CKC/CKC1	At4g37750	Regulates up—regulation of genes establishing organ polarity and those specifying organ identity	[19, 64]
HbAP2-12	0.13	0.10				AP2	Meristem maintenance and cell differentiation	Arabidopsis	[68, 69]	AP2/FLO2/FL1	At4g36920	Meristem maintenance and cell differentiation	[68, 69]
HbAP2-18	0.22	0.16				AP2	Meristem maintenance and cell differentiation	Vitis	[68, 69]	AP2/FLO2/FL1	At4g36920	Meristem maintenance and cell differentiation	[68, 69]
HbRAV-3			43.60	16.40		RAV1	Leaf maturation and senescence	Ricinus	[70]	.

The ratios between the relative transcript abundance of the regenerant and non-embryogenic lines (R/NE), the regenerant and embryogenic lines (R/E), of the normal and abnormal embryos (Nor/Ab) are presented for only significant down-regulated genes (< 1) and up-regulated (> 1).

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