A Systematic View Exploring the Role of Chloroplasts in Plant Abiotic Stress Responses

Table 1

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

Category	Tissue	Abiotic	Locus_ID	Gene symbol	Keyword	Title
BA	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
MT	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
PT	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

Agronomic traits associated with functionally characterized genes out of candidate genes in this study.
Anatomical cluster information of the gene.
Abiotic cluster information of the gene.
Key trait of characterized role of the gene.
Title of research paper of the gene.
Biotic or abiotic stress related trait.
Morphological trait.
Physiological trait.