. 2016 Mar 29;9:15. doi: 10.1186/s12284-016-0083-8

Table 2.

Association of SNPs with different salt related traits at 10 days of treatment with HKT genes (with R2 > 5 % and p < 0.01)

Gene	Trait	SNP	Site	p	R2 (%)	SNP type	MAF	Gene	Trait	SNP	Site	p	R2 (%)	SNP type	MAF
HKT 1;1	N_R	S0231	30724332	0.003	34.43	Int	37	HKT 1;5	N_S	S0077	11459042	0.002	31.57	Int	36
	K_S	S1955	30726056	0.003	30.75	Syn	5		N_S	S3893	11462858	0.005	33.00	P/A₁₄₀	20
	SPAD	S2094	30726195	0.003	31.90	S/N₂₅₈	32		K_S	S0077	11459042	0.003	30.92	Int	36
	SPAD	S2331	30726432	0.003	31.90	S/F₁₇₉	30		N_R	S0887	11459852	0.003	34.12	Int	13
	SPAD	S2546	30726647	0.003	31.90	Syn	30		N_R	S0919	11459884	0.009	34.42	Int	35
HKT 1;2	K_S	S0221	30545988	0.003	31.83	5’ NC	36		N_R	S0958	11459923	0.009	34.65	Int	35
	K_S	S1430	30547197	0.009	25.16	Int	21		N_R	S0959	11459924	0.003	34.12	Int	13
	K_S	S2282	30548049	0.003	31.54	Int	31		N_R	S0974	11459939	0.008	35.09	Int	6
HKT 1;3	N_R	S0337	4103487	0.005	33.93	C/R₁₆	30		N_R	S1036	11460001	0.002	37.37	Int	5
	SPAD	S0091	4103241	0.009	27.83	5’ NC	12		K_R	S1036	11460001	0.008	26.80	Int	5
	N_R	S0744	4103894	0.008	38.19	Syn	22		N_R	S1379	11460344	0.003	34.44	K/Q₄₂₉	49
	SPAD	S0744	4103894	0.008	35.21	Syn	22		N_R	S1913	11460878	0.003	34.62	Int	43
	SPAD	S1682	4104832	0.009	27.83	Int	10		N_R	S2043	11461008	0.004	33.62	Int	29
	SPAD	S1762	4104912	0.005	31.75	Int	45		K_S	S2146	11461111	0.002	34.93	Int	45
	SPAD	S2347	4105497	0.003	34.78	A/V₄₈₈	23		K_S	S2347	11461312	0.006	27.43	Int	28
	SPAD	S2374	4105524	0.004	32.49	R/Q₄₉₇	46		K_S	S2865	11461830	0.001	36.63	Int	14
	SPAD	S2392	4105542	0.009	27.68	T/M₅₀₃	13		K_S	S3893	11462858	0.009	31.17	Int	20
HKT 1;4	SPAD	S0886	30734275	0.003	34.72	3’NC	32	HKT 2;1	K_S	S3062	29541671	0.008	32.35	5’ NC	7
	SPAD	S1267	30734656	0.003	34.72	3’NC	32		N_R	S3062	29541671	0.004	39.70	5’ NC	7
	SPAD	S2284	30735673	0.002	37.42	Int	32		SPAD	S4153	29542762	0.009	25.80	5’ NC	38
	SPAD	S2804	30736193	0.003	34.72	Int	32		SPAD	S4377	29542986	0.002	33.96	5’ NC	36
	SPAD	S2974	30736363	0.002	37.03	Int	33		K_S	S5815	29544424	0.002	40.52	5’ NC	21
	SPAD	S3185	30736574	0.002	37.03	Int	32		K_S	S5817	29544426	0.007	32.66	5’ NC	7
	SPAD	S3228	30736617	0.007	36.36	Int	33	HKT 2;3	K_S	S0356	19241884	0.002	34.84	Int	10
	SPAD	S3307	30736696	0.003	34.87	Int	28		SPAD	S0761	19242289	0.003	31.88	I/T₇₇	34
	SPAD	S3544	30736933	0.003	34.72	Int	32		K_S	S1001	19242529	0.009	25.08	I/T₁₅₇	5
	SPAD	S4678	30738067	0.003	35.09	Int	35		SPAD	S2053	19243581	0.003	31.79	Syn	34
								HKT 2;4	K_S	S0334	29534433	0.004	37.20	Int	37

(N_S sodium concentration in shoot, K_S potassium concentration in shoot, N_R sodium concentration in root, K_S potassium concentration in root, Int intron, Syn synonymous, NC non-coding, MAF minor allele frequency in %)