Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study

Rice

Table 4 Fifteen promising candidate genes for rice salt tolerance and their associations with the targeted traits identified by haplotype analysis

MSU.ID ^a	Function	GWAS ^b		ANOVA ^c		Trait ^d	Env ^e
MSU.ID ^a	Function	P value	R²(%)	P value	R²(%)
Os09g28910	carbonic anhydrase, chloroplast precursor	6.60E-05	3.5	0.0007	5.3	TSN	Y17
Os02g49700	homeobox associated leucine zipper	5.20E-07	11.8	1.10E-18	32.7	GY	Y17
Os06g42130	leucoanthocyanidin dioxygenase	7.90E-05	5.2	1.30E-05	8.1	SSD	Hydroponics
Os01g18240	MYB family transcription factor	4.00E-05	5.1	1.50E-07	8.6	PN	Y16
Os01g59660	MYB family transcription factor	7.70E-05	3.5	4.10E-07	10.6	TSN	Y17
Os08g06240	MYB family transcription factor	8.30E-05	4.4	4.70E-15	24.6	HD	Y17
Os04g51830	OsHKT1;4 - Na + transporter	1.60E-05	10.8	1.90E-05	14.1	PN	Y16
Os04g51830	OsHKT1;4 - Na + transporter	1.80E-05	7.6	2.20E-05	10.9	PN	Y17
Os01g18210	peptidyl-prolyl cis-trans isomerase, FKBP-type	6.30E-05	4.8	9.10E-06	6.3	PN	Y16
Os03g28300	protein kinase domain containing protein	1.40E-05	6	3.90E-06	10.6	SSR	Y16
Os04g52140	protein kinase domain containing protein	4.70E-05	9.6	1.40E-06	13.7	PN	Y16
Os04g52140	protein kinase domain containing protein	9.70E-05	6.2	2.00E-07	13.3	PN	Y17
Os04g56120	protein kinase domain containing protein	8.80E-05	3.8	2.40E-08	9.7	FGN	Y17
Os03g07480	sucrose transporter	3.10E-05	8	6.40E-14	26.4	GY	Y17
Os01g23530	terpene synthase	5.30E-05	3.7	0.0004	7.1	SN	Y17
Os05g31730	transporter, monovalent cation:proton antiporter-2 family	2.10E-07	6.2	5.40E-06	9.7	SSI	Hydroponics
Os05g31730	transporter, monovalent cation:proton antiporter-2 family	2.00E-05	6.1	2.90E-05	12.2	SSD	Hydroponics
Os01g06590	zinc finger, C3HC4 type domain containing protein	8.20E-05	7.2	4.90E-06	13.4	FGN	Y17

^aGene names from the MSU Rice Genome Annotation Project Database; ^b GWAS statistics for peak SNP within the gene; ^c ANOVA for haplotypes of the gene with target traits; ^d For trait name abbreviations see Fig.