Combining QTL-seq and linkage mapping to fine map a candidate gene in qCTS6 for cold tolerance at the seedling stage in rice

Table 3 Identification of SNPs in putative candidate genes for CTS

Gene ID	Position	Amino_acid^a	DF-104 base	DN-430 base	T-pool base	S-pool base	Δ (SNP-index)	G-Value	ED	Fisher exact test	Structure_type	Function
Os06g0717400	30484096	L/S(-)	G	A	G	A	0.71	55.54	1.02	4.97E-13	exonic	hypothetical conserved gene
Os06g0717800	30499155	T/T(-)	A	G	A	G	0.47	21.54	0.44	9.03E-06	exonic exonic	protein phosphatase 2C
Os06g0717800	30499218	I/M(-)	C	T	C	T	0.58	33.47	0.68	1.73E-08	exonic exonic
Os06g0718000	30512105	Q/R(-)	C	T	C	T	0.29	8.52	0.17	0.004493	exonic	Hypothetical protein
Os06g0719500	30563973	F/Y(+)	A	T	A	T	0.60	18.83	0.72	4.71E-05	exonic	bZIP transcription factor

^a "/" indicates the amino acid before the mutation, the letter after the "/" indicates the amino acid after the mutation, "-" indicates the transcript located on the antisense strand, and "+" indicates the transcript located on the reference genome

ISSN: 1471-2229