Table 2. Genes upregulated in T2 vs D3 and/or D4 under excess light that are involved in the water–water cycle and/or cyclic electron flow around photosystem I.

Pathway/ complex	Annotation	Gene	T2E vs D3E	T2E vs D4E	D3E vs D4E	T2E vs T2L	D3E vs D3L	D4E vs D4L
Water–water	CuZn-SOD	Glyma12g08650	++	++		++	−	−−
		Glyma12g30260	++	+		++	−−	−
		Glyma11g19840	+	++		+	−
	Peroxidase/APX	Glyma15g41280	++	++
		Glyma13g20170	++	−−	−−	++		++
		Glyma14g05850	++		−−
		Glyma01g36780	++		−	+
		Glyma20g30910	++		−−			++
		Glyma13g04410	++		−−
		Glyma17g20450	++
		Glyma13g23620		++	++		+
		Glyma14g35440		++			−−
		Glyma02g37160		++			−−	−−
CEF-PSI	NDF1	Glyma08g23400		++	++	++
		Glyma07g02610		++	++	++
	NDF4	Glyma13g43260	++	++		++
		Glyma15g02080		++	+	+		−
	NDF6	Glyma06g20990		++	+	+
	NDHN	Glyma18g05640		++
	CRR3	Glyma07g23800		++		++
	CRR21	Glyma06g23620		++			−	−
	CRR23	Glyma05g27080		++
	CRR31	Glyma03g01720		++	+
	PPL2	Glyma20g38370		++	+	+
		Glyma20g23100		++	++	+
	FKB16–2	Glyma08g14740		++	+			−
	NQR	Glyma04g27580	++		−−			++
	LhcA5	Glyma04g04110		++		+
	LhcA6	Glyma09g08260		++			−
		Glyma15g19810		++		+
	STN8	Glyma18g44800	++	++		+	−
		Glyma16g34620		++
	Fd	Glyma12g29110		++	+			−
		Glyma08g20110		++			−	−
PS I	PsaH	Glyma13g43370		++			−−	−−
	PsaN	Glyma04g39370		++	+		−−	−
	PsaO	Glyma12g09730	++	++		−	−−	−−
	PSI-P	Glyma16g02010	++		−		−
		Glyma03g42240		++
		Glyma19g44990		++	+
Cyt b6f	PetE/cupredoxin	Glyma06g10500	++			−	−
		Glyma14g35530	++
		Glyma19g25570	++		−		−−
		Glyma02g37210	++		−		−
		Glyma04g02240		++	+		−
	PetM	Glyma06g03920	++				−	−
	HCF107	Glyma07g36870	++		−		−	−

Abbreviations: APX, ascorbate peroxidase; CEF-PSI, cyclic electron flow around photosystem I; Fd, ferredoxin.

For each column, genes that are overexpressed in the first sample vs the second sample are indicated by ‘+' (unadjusted p-value <0.05) or ‘++' (false discovery rate (FDR)<0.05); genes that are underexpressed in the first sample vs the second sample are indicated by ‘−' (unadjusted p-value <0.05) or ‘−−' (FDR<0.05).