Table 1.

Summary of functionally characterized plastid genes associated with cold and abiotic stress.

Categorya	Tissueb	Abioticc	Locus_ID	Gene symbol	Keywordd	Titlee
BAf	Ubi	Heat	LOC_Os06g50300	Hsp90|rHsp90|OSGrp94	abiotic stress	rHsp90 gene expression in response to several environmental stresses in rice (Oryza sativa L.)
BA	Leaf	Heat	LOC_Os08g29110	OsTRXZ	cold stress	TSV, a putative plastidic oxidoreductase, protects rice chloroplasts from cold stress during development by interacting with plastidic thioredoxin Z.
BA	Ubi	Heat	LOC_Os04g32950	OsCNX	drought tolerance	Heterologous expression of rice calnexin (OsCNX) confers drought tolerance in Nicotiana tabacum
BA	Leaf	Heat	LOC_Os03g19380	OsCP12	drought tolerance	The rice RING E3 ligase, OsCTR1, inhibits trafficking to the chloroplasts of OsCP12 and OsRP1, and its over-expression confers drought tolerance in Arabidopsis
BA	Ubi	Heat	LOC_Os07g34570	OsDR8	disease resistance	Dual function of rice OsDR8 gene in disease resistance and thiamine accumulation
MTg	Leaf	Heat	LOC_Os03g45400	OsNUS1|V1	leaf	A virescent gene V1 determines the expression timing of plastid genes for transcription/translation apparatus during early leaf development in rice
MT	Leaf	Heat	LOC_Os12g37610	TCD11	leaf	The rice TCD11 encoding plastid ribosomal protein S6 is essential for chloroplast development at low temperature
MT	Leaf	Heat	LOC_Os05g34040	TCD5|CSV1|TSV	leaf	Temperature-sensitive albino gene TCD5, encoding a monooxygenase, affects chloroplast development at low temperatures.
MT	Leaf	Heat	LOC_Os03g29810	VYL	leaf	A rice virescent-yellow leaf mutant reveals new insights into the role and assembly of plastid caseinolytic protease in higher plants
MT	Leaf	Heat	LOC_Os04g51280	WSP1	leaf	The RNA editing factor WSP1 is essential for chloroplast development in rice.
MT	Leaf	Heat	LOC_Os06g02580	ZN	leaf	ZEBRA-NECROSIS, a thylakoid-bound protein, is critical for the photoprotection of developing chloroplasts during early leaf development
MT	Leaf	Heat	LOC_Os02g33610	GRY79	seedling	GRY79 encoding a putative metallo-β-lactamase-trihelix chimera is involved in chloroplast development at early seedling stage of rice.
MT	Leaf	Heat	LOC_Os12g17910	OsCPn60alpha1|OsCPn60a1	seedling	OsCpn60alpha1, encoding the plastid chaperonin 60alpha subunit, is essential for folding of rbcL
MT	Ubi	Heat	LOC_Os11g09280	OsPDIL1;1	seedling	Formation of protein disulfide bonds catalyzed by OsPDIL1;1 is mediated by microRNA5144-3p in rice.
MT	Ubi	Heat	LOC_Os06g41990	SPP	root	A rice stromal processing peptidase regulates chloroplast and root development
MT	Leaf	Heat	LOC_Os05g48200	OsNADH-GOGAT2	spikelet number	Disruption of a novel NADH-glutamate synthase2 gene caused marked reduction in spikelet number of rice
MT	Ubi	Heat	LOC_Os06g08770	OIP30	pollen	OIP30, a RuvB-like DNA helicase 2, is a potential substrate for the pollen-predominant OsCPK25/26 in rice
PTh	Ubi	Heat	LOC_Os03g19510	OsClpP5	chloroplast	An active DNA transposon nDart causing leaf variegation and mutable dwarfism and its related elements in rice
PT	Ubi	Heat	LOC_Os01g16040	OsPAPST1	chloroplast	Identification of a dual-targeted protein belonging to the mitochondrial carrier family that is required for early leaf development in rice
PT	Ubi	Heat	LOC_Os03g60910	OspTAC2	chloroplast	OspTAC2 encodes a pentatricopeptide repeat protein and regulates rice chloroplast development.
PT	Ubi	Heat	LOC_Os07g06940	WP1|OsValRS2	chloroplast	WHITE PANICLE1, a Val-tRNA synthetase regulating chloroplast ribosome biogenesis in rice, is essential for early chloroplast development.
PT	Leaf	Heat	LOC_Os03g40550	OsFLN2|HSA1	chloroplast	FRUCTOKINASE-LIKE PROTEIN 1 interacts with TRXz to regulate chloroplast development in rice.
PT	Ubi	Heat	LOC_Os07g08340	OsPK2	grain	OsPK2 encodes a plastidic pyruvate kinase involved in rice endosperm starch synthesis, compound granule formation and grain filling.
PT	Ubi	Heat	LOC_Os01g52500	NADP-ME2|OsNADP-ME2	growth	Expression of an NADP-malic enzyme gene in rice (Oryza sativa L.) is induced by environmental stresses; over-expression of the gene in Arabidopsis confers salt and osmotic stress tolerance
PT	Leaf	Heat	LOC_Os07g43810	RNP29	phosphate	Identification and characterization of chloroplast casein kinase II from Oryzasativa (rice).
PT	Ubi	Heat	LOC_Os03g55090	Pho1	starch	Mutation of the plastidial alpha-glucan phosphorylase gene in rice affects the synthesis and structure of starch in the endosperm

^a Agronomic traits associated with functionally characterized genes out of candidate genes in this study.

^b Anatomical cluster information of the gene.

^c Abiotic cluster information of the gene.

^d Key trait of characterized role of the gene.

^e Title of research paper of the gene.

^f Biotic or abiotic stress related trait.

^g Morphological trait.

^h Physiological trait.