Chromosomal-level genome assembly of the high-quality Xian/Indica rice (Oryza sativa L.) Xiangyaxiangzhan

Liang, Jiayan; Kong, Leilei; Hu, Xiaodan; Fu, Chongyun; Bai, Song

doi:10.1186/s12870-023-04114-0

BMC Plant Biology

Table 4 Some cloned genes containing complete LTR in their 1 kb flanking regions

From: Chromosomal-level genome assembly of the high-quality Xian/Indica rice (Oryza sativa L.) Xiangyaxiangzhan

Category	Relative position of LTR	Symbol	Gene function or phenotypic characteristics
A^a	Upstream	D35	Internode length
	Upstream	THIS1	Lipase; tillering, plant height, and spikelet fertility
	Upstream	ACL2	Abaxially curled leaf 2
	Upstream	Os4CL4	Lignin biosynthesis, plant cell wall modification
	Downstream	NAL1	Number of adventitious roots, internode length, chlorophyll content, leaf shape, leaf width, grain yield, spike type, Plant cell size
	Downstream	D10	Establishment of internode development model, biosynthesis of monocytolide, regulation of tiller formation
	Downstream	TIG1	Tiller angle, plant cell length
	Downstream	CYP714B1	Internode length
	Upstream	OsMADS4	Gene expression regulation, ear morphogenesis, stamen development
A/B^b	Upstream	DDX47	Number of lateral roots, plant height, root length, heat resistance
	Upstream	D1	internode length, leaf width, leaf length, grain size, and red-light sensitivity Gibberellin sensitivity, drought tolerance, stem diameter, 1000 grain weight, spike density
	Downstream	OsVAMP714	Rice blast resistance, plant height, shoot growth rate, leaf sheath length
	Downstream	HTD12	Internode length, tiller number, cold tolerance, drought tolerance, abscisic acid content, β- Carotene content, Osmotic regulation capacity, salt resistance
B^c	Upstream	OsDi19–4	Drought-induced 19 gene
	Upstream	OsGDI3	Response to fungi, anti-bacterial response, low temperature stress response, water stress response, insect resistance response, salt stress response
	Downstream	DEPG1	Bacterial leaf blight resistance, rice bacterial stripe disease resistance
	Downstream	OsCK1	Heading stage, osmotic stress sensitivity, abscisic acid sensitivity, salt tolerance
C^d	Upstream	OsYSL15	Iron (III)-deoxymugineic acid transporter
	Upstream	OsPht1;1	Phosphate transporter gene, phosphorus absorption, phosphate content
	Upstream	OsSPX4	Phosphate content
	Downstream	OsAAP3	Tiller number, spike number, amino acid content, grain number per plant, yield per plant, nitrogen utilization efficiency
	Downstream	OsNRT1.1A	Plant height, heading date, aboveground biomass, nitrate transport, yield per plant, nitrogen utilization rate
D^e	Upstream	AL1	Aleurone layer and/or transfer cell-specific gene
	Upstream	OsGS1;3	Interact with Nf-yc12 to regulat the synthesis of protein in the endosperm
	Upstream	OsPDIL1;1	Endosperm color, silty endosperm
	Downstream	OsPK2	Protein content, seed development characteristics, amylose content, starch content, total lipid content, chalky endosperm, Germination rate, 1000 grain weight
	Downstream	GGC2	Spike length, grain length, 1000 grain weight
E^f	Upstream	OsUGT707A2	UVB stress response, flavonoid biosynthesis
	Downstream	RFT1	Heading stage, photoperiod sensitivity, growth stage
	Downstream	OsNDPK2	Leaf color, chlorophyll content, chloroplast development
	Downstream	RSS3	Cell length, root

^aPlant morphogenesis
^bPlant morphogenesis/Stress response
^cStress response
^dNutrient utilization
^eRice quality
^fOther

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ISSN: 1471-2229

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