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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)

From: High levels of nucleotide diversity and fast decline of linkage disequilibrium in rye (Secale cerealeL.) genes involved in frost response

CG Fragment length (bp) Gene coverage a No. of lines b No. of SNPs c(non-synonymous) d N /d S 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     
  1. a E: exon; UTR: untranslated region; I: intron
  2. 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.
  3. c Minor allele frequency (MAF) > 0.05
  4. d SNPs are silent since they were all located in the first intron of the gene.
  5. Significance levels: * P < 0.05, ** P < 0.01, *** P < 0.001
  6. n.a.: not available