Genomic and transcriptomic analysis reveal molecular basis of salinity tolerance in a novel strong salt-tolerant rice landrace Changmaogu

Sun, Bing-Rui; Fu, Chong-Yun; Fan, Zhi-Lan; Chen, Yu; Chen, Wen-Feng; Zhang, Jing; Jiang, Li-Qun; Lv, Shuwei; Pan, Da-Jian; Li, Chen

doi:10.1186/s12284-019-0360-4

Rice

Table 5 The candidate genes for salt tolerance based on the index and ED of SNP and InDel

From: Genomic and transcriptomic analysis reveal molecular basis of salinity tolerance in a novel strong salt-tolerant rice landrace Changmaogu

Mutation type	Gene ID	Position	Fuctional annotation
nonsynonymous coding SNP	Os01g0655400	26,608,476–26,601,904	Transposon protein, putative
	Os01g0733200	30,582,485–30,583,743	HSF-type DNA-binding domain containing protein
	Os01g0656200	26,652,944–26,658,313	Protein phosphatase 2C, putative, expressed
	Os01g0655500	26,611,799–26,618,704	Serine/threonine-protein kinase stt7
	Os01g0647800	26,114,190–26,111,942	Hypothetical protein
	Os01g0655600	26,619,462–26,620,234	Hypothetical protein
	Os01g0729800	30,422,055–30,422,387	Hypothetical protein
	Os01g0658300	26,769,190–26,767,671	Microneme protein Sm70 putative, expressed
	Os01g0715100	30,516,831–30,517,430	Ubiquitin-related 4 (Precursor)
	Os01g0715100	29,740,123–29,742,527	Conserved hypothetical protein
	Os01g0733100	30,585,423–30,585,100	Hypothetical protein
	Os01g0655700	26,622,829–26,624,411	Hypothetical protein
	Os01g0656600	26,706,158–26,699,189	Hypothetical protein
	Os01g0665500	27,200,990–27,196,417	Probable WRKY transcription factor 71
	Os01g0714700	29,717,779–29,718,346	Hypothetical protein
	Os01g0659900	26,872,217–26,875,033	F-box domain and kelch repeat containing protein
	Os01g0727600	30,341,594–30,340,015	Conserved hypothetical protein
	Os01g0712250	29,590,343–29,589,249	Arginine/serine-rich protein
	Os01g0722100	30,102,785–30,107,361	Bacterial transferase hexapeptide domain containing protein
	Os01g0732100	30,533,818–30,536,908	Hypothetical protein
	Os01g0655250	26,592,688–26,593,702	PWWP domain containing protein
	Os01g0655300	26,599,136-26,599,632	Similar to Trithorax 4
	Os01g0719150	29,971,297-29,971,882	Hypothetical protein
Frameshift mutation	Os01g0733200	30,582,485–30,583,743	HSF-type DNA-binding domain containing protein
	Os01g0659400	26,823,851–26,822,203	Non-protein coding transcript
	Os01g0655700	26,622,829–26,624,411	Hypothetical protein
	Os01g0655600	26,619,462–26,620,234	Hypothetical protein
	Os01g0733100	30,585,423–30,585,100	Cortical cell-delineating protein (Precursor)
	Os01g0712250	29,590,343–29,589,249	Arginine/serine-rich protein 45
	Os01g0655250	26,592,688–26,593,702	PWWP domain containing protein
	Os01g0655300	26,599,136-26,599,632	Similar to Trithorax 4

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