Table 6.

High impact SNP variants in cold-sensitive aus line Carolino 164 compared to cold-tolerant japonica line Krasnodarskij 3352.

Chr.	Gene annotation	Locus ID	SNP ID	Nucleotide change	Impact
1	OsACA6	LOC_Os01g71240	na	na	na
3	OsANK	LOC_Os03g47640	vg03_26984941	C>T	Arg355*
3	OsANK	LOC_Os03g47686	vg03_27020751	C>G	Tyr518*
3	OsANK	LOC_Os03g47693	vg03_27022097	G>A	Trp56*
3	OsANK	LOC_Os03g47720	vg03_27044642	CAA>CAAA	Glu86fs
3	OsGST3	LOC_Os03g50130	vg03_28595867	A>G	start_lost;Met1?
7	OsWAK38	LOC_Os04g29680	na	na	na
4	OsWAK40	LOC_Os04g29790	vg04_17752550	A>AAC	Ile158fsa
			vg04_17752554	TTG>T	Lys157fsa
6	OsRLK-803	LOC_Os06g04370	vg06-01867369	A>T	Ser529Cys
6	Transferase	LOC_Os06g04380	vg06_01875711	A>AC	Ser56fs
6	OsNAPL2	LOC_Os06g05660	vg06_02560533	G>T	Gly126Cys
6	Transferase	LOC_Os06g05790	vg06_02633463	T>TA	Leu483fs
6	OsFBL27	LOC_Os06g06050	vg06_02780806	A>AGAG	Glu6dup
			vg06_02781107	TGCGGCGGCGGCG>TGCGGCGGCGGCGGCG	Glu110dup
6	Esterase	LOC_Os06g06080	vg06_02803110	TCC>T	Arg25fs
6	OsMPK6	LOC_Os06g06090	vg06_02812762	GCCC>G	Gly29delb
6	OsFKBP13	LOC_Os06g45340	vg06_27403638	CGG>N/C	Ala4fs (if C)
6	CYP59A	LOC_Os06g45900	vg06_27783122	C>CGGGG	Leu43fs
			vg06_27791008	T>C	Ter549Argext*?
6	OsNAC011	LOC_Os06g46270	vg06_28037986	GCGGGCGGCG>C	Ala38_Ala50del
6	Hydrolase	LOC_Os06g46284	vg06_28057827	A>T	Tyr74*
8	RF6	LOC_Os08g01870	vg08_00538004	T>C	Cys484Arg
8	OsbHLH070	LOC_Os08g08160	vg08_04647095	T>TAA	Ile333fs
			vg08_04648125	CT>C	Splice variant
8	LTPL130	LOC_Os08g27674	vg08_16869517	TG>T	Thr61fs
8	OsRLCK253	LOC_Os08g28710	vg08_17559305	T>TCGC	Ala256 dup
11	OsPDIL1-1	LOC_Os11g09280	vg11_04974896	C>CG	Gly35fs
			vg11_04974890	GCATC>G	Asp36fs
11	OsFBX398	LOC_Os11g09360	vg11_05026584	G>A	Splice variant

na, not available; ext^*?, stop codon lost, reading frame extended; fs, frameshift.

^*Premature stop codon.

^aVariant in Krasnodarskij 3352; Carolino 164 same as the Nipponbare reference genome.

^bTotal of 233 variants between Krasnodarskij 3352 and Carolino 164.