The metabolic changes that effect fruit quality during tomato fruit ripening

Zhu, Feng; Wen, Weiwei; Cheng, Yunjiang; Fernie, Alisdair R.

doi:10.1186/s43897-022-00024-1

Molecular Horticulture

Table 1 Validated structure and transcriptional genes of tomato fruit quality metabolism

From: The metabolic changes that effect fruit quality during tomato fruit ripening

Metabolite pathway or TF famaily	Gene name	Gene ID	Gene function validation method or regulation pathway	Reference
Chlorophyll degradation	SGR1	Solyc08g080090	Map-Based Cloning and transgene	(Barry et al. 2008; Luo et al. 2013)
	SGRL	Solyc04g063240	Transgene	(Yang et al. 2020)
	PPH	Solyc01g088090	Transgene	(Guyer et al. 2014)
Carotenoid biosynthesis	PSY1	Solyc03g031860	Transgene	(Bird et al. 1991)
	PSY2	Solyc02g081330	Bacterial mutant complementation	(Bartley and Scolnik 1993)
	CRTISO	Solyc10g081650	Map-Based Cloning and E.coli transformation	(Isaacson et al. 2002)
	ZDS	Solyc01g097810	Transgene	(McQuinn et al. 2020)
	PDS	Solyc03g123760	Virus-Induced Gene Silencing (VIGS)	(Naing et al. 2019)
	LCYE	Solyc12g008980	E.coli transformation	(Roessner-Tunali et al. 2003)
	LCYB	Solyc04g040190	Transgene	(Diretto et al. 2020)
	BCH2	Solyc03g007960	Map-Based Cloning and E.coli transformation	(Galpaz et al. 2006)
	ZEP	Solyc02g090890	Map-Based Cloning	(Galpaz et al. 2008)
	NSY	Solyc06g074240	E.coli transformation	(Bouvier et al. 2000)
	NXD	Solyc12g041880	Map-Based Cloning	(Neuman et al. 2014)
Cell wall metabolism	Exp1	Solyc06g051800	Transgene	(Brummell et al. 1999)
	PG	Solyc10g080210	Transgene	(Jiang et al. 2019)
	XTHs	Solyc01g099630	Transgene	(Miedes et al. 2010)
	PL	Solyc03g111690	Transgene	(Yang et al. 2017)
	PE1/PE2	Solyc03g123630/Solyc07g064170	Transgene	(Wen et al. 2013)
	TBG4	Solyc12g008840	Transgene	(Smith et al. 2002)
	Cel1/Cel2	Solyc08g081620/ Solyc09g010210	Transgene	(Flors et al. 2007)
	Xyl1/ Xyl2	Solyc11g044910/ Solyc01g079570	Transgene and enzyme assay	(Tateishi et al. 2014)
Central metabolism	Aco-1	Solyc12g005860	Mutant phenotype analysis	(Carrari et al. 2003)
	ICDH1	Solyc01g005560	Transgene	(Gamrasni et al. 2020)
	MDH	Solyc07g062650	Transgene	(Centeno et al. 2011)
	SWEET15	Solyc09g074530	Transgene	(Ko et al. 2020)
	SUT1/SUT2	Solyc11g017010/ Solyc05g007190	Transgene	(Hackel et al. 2006)
	SWEET 1a	Solyc04g0646410	Map-Based Cloning and Transgene	(Shammai et al. 2018)
	LIN5	Solyc09g010080	Map-Based Cloning and Transgene	(Fridman et al. 2000; Zanor et al. 2009)
	AgpL1	Solyc01g109790	Map-Based Cloning and enzyme assay	(Petreikov et al. 2006)
	VIF	Solyc12g099190	Transgene	(Qin et al. 2016)
	INVINH1	Solyc12g099200	Transgene	(Jin et al. 2009)
	TIV1	Solyc03g083910	Transgene	(Klann et al. 1996)
	SuSy1	Solyc12g009300	Transgene and enzyme assay	(D'Aoust et al. 1999)
	TRAMP	Solyc08g081190	Transgene	(Chen et al. 2001)
	Frk1/Frk2	Solyc03g006860/ Solyc06g073190	Transgene	(Odanaka et al. 2002)
	ALMT9	Solyc06g072910	GWAS and transgene	(Ye et al. 2017)
Secondary metabolism	PAL	Solyc10g086180	Map-Based Cloning and transgene	(Brog et al. 2019)
	CL	Solyc08g083110	Map-Based Cloning and transgene	(Brog et al. 2019)
	C4H		Transgene	(Millar et al. 2007)
	4CL	Solyc12g094520	Introgression line and enzyme activity	(Rigano et al. 2016)
	CHS1	Solyc09g091510	Transgene	(Schijlen et al. 2007)
	CHI	Solyc05g010320	Map-Based Cloning and transgene	(Kang et al. 2014)
	F3H	Solyc02g083860	Map-Based Cloning and transgene	(Maloney et al. 2014)
	F3’5’H	Solyc11g066580	Enzyme assay	(Olsen et al. 2010)
	DFR	Solyc02g085020	Transgene	(Andrew et al. 1994)
	CTOMT1	Solyc10g005060	Transgene and enzyme assay	(Mageroy et al. 2012)
	AnthOMT	Solyc06g06450	Transgene	(Gomez Roldan et al. 2014)
	MOMT1	Solyc06g083450	Enzyme assay	(Schmidt et al. 2011)
	MOMT4		Map-Based Cloning and enzyme assay	(Kim et al. 2014)
	UGT78-a	Solyc10g083440	Enzyme assay and transgene	(Tohge et al. 2020)
	UGTs	Solyc12g096870 /Solyc12g098600	Map-Based Cloning and transgene	(Alseekh et al. 2020)
	F3HL	Solyc03g080190	Transgene	(Meng et al. 2015)
	FdAT1	Solyc12g088170	Transgene and enzyme assay	(Tohge et al. 2015)
	GORKY	Solyc03g120570	Map-Based Cloning and Transgene	(Kazachkova et al. 2021)
	GAME31	Solyc02g062460	Map-Based Cloning and Transgene	(Cardenas et al. 2019)
	GAME5	Solyc10g085230	Map-Based Cloning and Transgene	(Szymanski et al. 2020)
	GAME4/ GAME6/ GAME11/ GAME12/ GAME17/ GAME18/ GAME2	Solyc12g006460/ Solyc07g043460/Solyc07g043420/Solyc12g006470/ Solyc07g043480/ Solyc07g043500/ Solyc07g043410	Transgene and enzyme assay	(Itkin et al. 2013; Alseekh et al. 2015)
	GAME1	Solyc07g043490	Transgene and enzyme assay	(Itkin et al. 2011)
	SAMT	Solyc09g091550	QTL mapping and enzyme assay	(Tieman et al. 2010)
	Lecithin:cholesterol acyltransferase/ LIP1 / LIP2	Solyc05g050710/ Solyc12g055730/ Solyc03g123750	Map-Based Cloning and Transgene	(Garbowicz et al. 2018)
	TomLoxC	Solyc01g006540	pan-genome analysis and Transgene	(Chen et al. 2004; Gao et al. 2019)
	GAUT10	Solyc04g064490	GWAS	(Bauchet et al. 2017)
	PPEAT	Solyc02g079490	GWAS	(Dominguez et al. 2020)
	COI1	Solyc05g052620	Transgene	(Li et al. 2004)
	AAT1	Solyc08g005770	Transgene	(Goulet et al. 2015)
	CCD1A	Solyc01g087250	Transgene and enzyme assay	(Simkin et al. 2004)
	CCD1B	Solyc01g087260	Transgene and enzyme assay	(Ilg et al. 2014)
	FLORAL4	Solyc04g063350	Map-Based Cloning and Transgene	(Tikunov et al. 2020)
	LIP8	Solyc09g091050	Map-Based Cloning and Transgene	(Li et al. 2020a)
	AADC1/2	Solyc08g068610/ Solyc08g006750	Transgene and enzyme assay	(Tieman et al. 2006)
	ASAT1	Solyc12g006330	In vitro enzyme assay	(Fan et al. 2016)
	ASAT2	Solyc04g012020	In vitro enzyme assay	(Fan et al. 2016)
	ASAT3	Solyc11g067270	Map-Based Cloning and Transgene	(Schilmiller et al. 2015)
	ASAT4	Solyc01g105580	Map-Based Cloning and Transgene	(Schilmiller et al. 2012)
	IPMS3	Solyc08g014230	Map-Based Cloning and enzyme assay	(Ning et al. 2015)
MADS TFs	CMB1	Solyc04g005320	Pigmentation	(Zhang et al. 2018a)
	RIN	Solyc05g012020	Carotenoid, cell wall and secondary metabolism	(Fujisawa et al. 2013)
	TDR4	Solyc06g069430	Secondary metabolism	(Zhao et al. 2019)
	MBP8	Solyc12g087830	Cell wall	(Yin et al. 2017)
	MBP15	Solyc12g087810	Carotenoid	(Yin et al. 2018)
	MADS1	Solyc03g114840	Carotenoid	(Dong et al. 2013)
NAC TFs	NOR	Solyc10g006880	Pigmentation and cell wall	(Gao et al. 2020)
	NOR-like1	Solyc07g063420	Pigmentation and cell wall	(Gao et al. 2018b)
	NAC1	Solyc04g009440	Pigmentation and cell wall	(Ma et al. 2014)
	NAC4	Solyc11g017470	Pigmentation	(Zhu et al. 2014)
	NAP2	Solyc04g005610	Pigmentation and fruit softening	(Kou et al. 2018; Ma et al. 2018)
MYB TFs	MYBATV	Solyc10g086290	Anthocyanin	(Yan et al. 2020b)
	ANT1	Solyc10g086260	Anthocyanin	(Schreiber et al. 2012)
	MIXTA-like	Solyc02g088190	Primary metabolism	(Ying et al. 2020)
	MYB72	Solyc07g055000	Chlorophylls, carotenoids and flavonoids	(Wu et al. 2020)
	MYB12	Solyc01g079620	Flavonoid	(Ballester et al. 2010)
	MYB111	Solyc06g009710	SGA	(Chen et al. 2019a)
	AN2	Solyc10g086250	Anthocyanin and volatile	(Jian et al. 2019; Zhi et al. 2020)
WD40 TFs	AN11	Solyc03g097340	Secondary metabolism	(Gao et al. 2018a)
ERF TFs	ERF.G3-like	Solyc02g077790	Flavonoid	(Li et al. 2020b)
	AP2a	Solyc03g044300	Pigmentation and cell wall	(Karlova et al. 2011)
	ERF.B3	Solyc05g052030	Pigmentation	(Liu et al. 2014)
	GAME9	Solyc01g090340	GWAS and transgene	(Cardenas et al. 2016; Zhu et al. 2018)
GRAS TFs	GRAS38	Solyc07g052960	Pigmentation, secondary metabolism and cell wall	(Shinozaki et al. 2018)
ABF TFs	AREB1	Solyc04g078840	Primary metabolic	(Bastias et al. 2014)
ARF TFs	ARF6A	Solyc12g006340	Starch and soluble sugars	(Yuan et al. 2019)
	ARF4	Solyc11g069190	Cell wall	(Sagar et al. 2013)
	ARF10	Solyc11g069500	Sugar accumulation	(Yuan et al. 2018)
BLH TFs	BL4	Solyc08g065420	Cell wall metabolism	(Yan et al. 2020a)
bHLH TFs	GL3		Anthocyanin	(Nukumizu et al. 2013)
	TT8	Solyc09g065100	Anthocyanin	(Qiu et al. 2016)
	bHLH114	Solyc01g096370	SGA	(Li et al. 2020b)
	PRE2	Solyc02g067380	Pigmentation	(Zhu et al. 2017)
bZIP TFs	bZIP1	Solyc01g079480	Amino acid metabolism	(Sagor et al. 2016)
HD-zip TFs	HZ24	Solyc04g005800	d-mannose/l-galactose pathway	(Hu et al. 2016)
E3 ubiquitin ligase	PPSR1	Solyc01g006810	Carotenoid	(Wang et al. 2020)

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