Table 1.
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