Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data

Jung, Ki-Hong; Gho, Hyun-Jung; Giong, Hoi-Khoanh; Chandran, Anil Kumar Nalini; Nguyen, Quynh-Nga; Choi, HeeBak; Zhang, Tian; Wang, Wen; Kim, Jin-Hyun; Choi, Hong-Kyu; An, Gynheung

doi:10.1186/1939-8433-6-19

Rice

Table 1 Summary of functionally characterized japonica or indica preferred genes from OGRO ( http://qtaro.abr.affrc.go.jp/ogro )

From: Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data

MSU_ ID^a	Gene name	Major category	Detailed function	Method^b	log2 ja/in^c	Reference
LOC_Os01g18860	OsSAMS3	Morphological trait	Dwarf	Kd^d	−4.46 (in^g)	(Li et al. 2011)
LOC_Os01g18860	OsSAMS3	Physiological trait	Flowering	Kd	−4.46 (in)	(Li et al. 2011)
LOC_Os01g18860	OsSAMS3	Physiological trait	Germination dormancy	Kd	−4.46 (in)	(Li et al. 2011)
LOC_Os01g18860	OsSAMS3	Physiological trait	Sterility	Kd	−4.46 (in)	(Li et al. 2011)
LOC_Os09g35980	TAC1	Morphological trait	Culm leaf	Nv^e	−2.90 (in)	(Yu et al. 2007)
LOC_Os01g71930	Osg1	Physiological trait	Sterility	Kd	3.96 (ja^h)	(Wan et al. 2011)
LOC_Os02g12380	HDA710	Morphological trait	Culm leaf	Kd	4.89 (ja)	(Hu et al. 2009)
LOC_Os02g12380	HDA710	Morphological trait	Dwarf	Kd	4.89 (ja)	(Hu et al. 2009)
LOC_Os02g12380	HDA710	Morphological trait	Panicle flower	Kd	4.89 (ja)	(Hu et al. 2009)
LOC_Os02g43370	OsYSL2	Physiological trait	Eating quality	Kd/Ox^f	−3.03 (in)	(Ishimaru et al. 2010)
LOC_Os02g43370	OsYSL2	Resistance/Tolerance	Other soil stress tolerance	Kd/Ox	−3.03 (in)	(Ishimaru et al. 2010)
LOC_Os03g55389	Hd6	Physiological trait	Flowering	Nv	−4.13 (in)	(Takahashi et al. 2001)
LOC_Os05g25770	OsWRKY45	Resistance/Tolerance	Bacterial blight resistance	Kd/Ox	3.07 (ja)	(Tao et al. 2009)
LOC_Os05g25770	OsWRKY45	Resistance/Tolerance	Bacterial blight resistance	Kd/Ox	3.07 (ja)	(Shimono et al. 2012)
LOC_Os05g25770	OsWRKY45	Resistance/Tolerance	Blast resistance	Kd/Ox	3.07 (ja)	(Tao et al. 2009)
LOC_Os05g25770	OsWRKY45	Resistance/Tolerance	Blast resistance	Kd/Ox	3.07 (ja)	(Shimono et al. 2012)
LOC_Os05g25770	OsWRKY45	Resistance/Tolerance	Blast resistance	Ox	3.07 (ja)	(Shimono et al. 2007)
LOC_Os05g25770	OsWRKY45	Resistance/Tolerance	Cold tolerance	Kd/Ox	3.07 (ja)	(Tao et al. 2011)
LOC_Os05g25770	OsWRKY45	Resistance/Tolerance	Drought tolerance	Kd/Ox	3.07 (ja)	(Tao et al. 2011)
LOC_Os05g25770	OsWRKY45	Resistance/Tolerance	Salinity tolerance	Kd/Ox	3.07 (ja)	(Tao et al. 2011)
LOC_Os05g25770	OsWRKY45	Resistance/Tolerance	Sheath blight resistance	Kd/Ox	3.07 (ja)	(Shimono et al. 2012)
LOC_Os06g22460	Pi25	Resistance/Tolerance	Blast resistance	Nv	−3.38 (in)	(Shang et al. 2009)
LOC_Os06g22460	Pid3	Resistance/Tolerance	Blast resistance	Nv	−3.38 (in)	(Chen et al. 2011)
LOC_Os07g45570	OsBLE2	Morphological trait	Culm leaf	Kd	3.62 (ja)	(Yang et al. 2003)
LOC_Os07g45570	OsBLE2	Morphological trait	Dwarf	Kd	3.62 (ja)	(Yang et al. 2003)
LOC_Os07g45570	Aldolase	Morphological trait	Root	Kd	3.62 (ja)	(Konishi et al. 2004)
LOC_Os11g11810	Pia	Resistance/Tolerance	Blast resistance	Nv	5.56 (ja)	(Okuyama et al. 2011)

^a indicates the locus id provided from Rice Genome Annotation Project team at Michigan State University.
^b indicates methods used for the functional analysis.
^c indicates log2 fold change (averaged japonica intensity/averaged indica intensity).
^d indicates knockdown analysis through transgenic approaches or T-DNA insertion.
^e indicates natural variation.
^f indicates overexpression analysis through transgenic approaches.
^g indicates indica eQTLs.
^h indicates japonica eQTLs.

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