Table 1.

Summary information of candidate gene (CG) sequences: Analyzed fragment length, gene coverage, number of lines, number of SNPs, rate ratio of non-synonymous to synonymous substitutions (d_N/d_S), number of Indels and haplotypes, haplotype (Hd) and nucleotide diversity (π), Tajima's D, and linkage disequilibrium (LD)

CG	Fragment length (bp)	Gene coverage a	No. of lines b	No. of SNPs c (non-synonymous)	dN/dS	No. of Indels	No. of haplotypes	Hd ± SD	π ± SD × 10-3 (only exon)	Tajima's D	Intra-genic LD (r2)
ScCbf2	619	5'UTR/E	169	2 (0)	0.001	1	7	0.67 ± 0.02	1.5 ± 0.1 (1.4 ± 0.1)	1.17	0.13
ScCbf6	495	E	197	3 (0)	0.023	0	9	0.44 ± 0.04	3.6 ± 0.3	-0.35	0.77
ScCbf9b	1,371	5'UTR/E/3'UTR	183	30 (10)	0.174***	1	95	0.98 ± 0.03	7.1 ± 0.3 (11.5 ± 0.2)	1.71	0.14
ScCbf11	623	E	128	27 (12)	0.165	0	12	0.65 ± 0.02	14.5 ± 0. 9	1.74	0.51
ScCbf12	754	5'UTR/E/3'UTR	141	25 (8)	0.286***	1	48	0.89 ± 0.02	8.8 ± 1.0 (7.7 ± 0.1)	0.40	0.38
ScCbf14	560	E	185	5 (3)	0.606**	0	4	0.17 ± 0.04	1.5 ± 0.3	-0.27	0.92
ScCbf15	502	E	172	3 (3)	1.490***	1	9	0.68 ± 0.04	3.0 ± 0.2	2.14*	0.30
ScDhn1	435	5'UTR/E	138	4 (1)	0.128**	2	12	0.33 ± 0.05	2.7 ± 0.5 (4.4 ± 0.1)	-1.86*	0.48
ScDhn3	514	I/E/3'UTR	130	12 (2)	0.229***	2	21	0.73 ± 0.03	8.1 ± 0.6 (8.9 ± 0.1)	0.008	0.25
ScIce2	1,224	I/E	189	36d	n.a.	0	32	0.80 ± 0.02	11.2 ± 0.6 (0)	2.34*	0.36
ScVrn1	542	5'UTR/E	198	0	n.a.	1	2	0.11 ± 0.03	0.4 ± 0.1 (0)	-0.33	n.a.
Total	7,639			147 (39)		9	251

^a E: exon; UTR: untranslated region; I: intron

^b Failure of amplification in some of the lines may be due to the presence of SNPs/Indels in the binding sites of the sequences and/or the absence of some of the Cbf genes in some particular lines.

^c Minor allele frequency (MAF) > 0.05

^d SNPs are silent since they were all located in the first intron of the gene.

Significance levels: * P < 0.05, ** P < 0.01, *** P < 0.001

n.a.: not available