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Table 1 Summary statistics for the 251 SNPs analyzed in 12 biomass genes

From: Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.)

      Polymorphism Nucleotide diversity Tajima’s test
         Non Syn       
Gene Contig Chromosome No. of samples No. of sites (coding length bp) Stot Non Cod Syn Con Non Con d πtot × 10-3 (SD × 10-3) θw × 10-3 (SD ×  10-3) h Hd (SD) D
PHYC contig03093 Chr09N 353 3224 (2279) 20 7 6 2 5 0.620 1.68 (0.04) 0.87 (0.25) 91 0.963 (0.002) 0.362
TE contig99597 Chr05K 351 2088 (278) 21 21 0 0 0 1.006 3.43 (0.08) 1.40 (0.31) 84 0.883 (0.010) 0.138
TE contig04674 Chr05Na 334 2088 (278) 21 20 1 0 0 1.006 3.78 (0.09) 1.58 (0.34) 110 0.959 (0.003) 0.316
VRN3 contig07490 Chr03Na 337 2258 (1771) 12 1 4 2 5 0.531 1.30 (0.05) 0.74 (0.21) 22 0.759 (0.013) 0.723
VRN3 contigl6433 Chr03K 356 2258 (1773) 10 3 1 3 3 0.443 0.95 (0.03) 0.62 (0.19) 30 0.728 (0.016) 0.62
DW3 contig26301 Chr06K 327 2207 (2207) 5 2 0 2 1 0.227 0.56 (0.02) 0.32 (0.14) 10 0.629 (0.018) 1.267
DW3 contigll7938 Chr06N 337 2198 (2198) 4 2 0 1 1 0.182 0.55 (0.02) 0.25 (0.13) 14 0.714 (0.010) 0.793
FLD contigl02960 Chr07K 346 2329 (1395) 3 2 1 0 0 0.129 0.10 (0.01) 0.18 (0.10) 5 0.207 (0.020) −0.588
FLD contig01920 Chr07N 339 2330 (1395) 1 0 0 0 1 0.043 0.15 (0.01) 0.06 (0.06) 2 0.346 (0.017) 1.253
Gl contigl5400 Chr05K 342 3456 (1185) 20 13 2 1 4 0.608 1.71 (0.06) 0.81 (0.18) 83 0.904 (0.006) −0.264
Gl contig01489 Chr05N 312 3464 (1185) 10 7 0 1 2 0.289 1.05 (0.03) 0.40 (0.13) 22 0.757 (0.013) 1.655
FLT contig09545 Chr07K 365 1826 (195) 17 17 0 0 0 0.931 1.97 (0.05) 1.30 (0.31) 64 0.931 (0.005) −0.103
FLT contig08422 Chr07N 339 2181 (195) 21 21 0 0 0 0.963 2.85 (0.04) 1.34 (0.29) 62 0.899 (0.006) 0.63
PHYB contigl3571 Chr09N 350 3198 (2758) 4 1 0 1 2 0.125 0.55 (0.01) 0.17 (0.09) 7 0.697 (0.009) 3.265**
PHYB contig21054 Chr09K 342 3194 (2758) 7 6 1 0 0 0.219 0.49 (0.01) 0.30 (0.12) 12 0.666 (0.012) 0.771
HD1 contig03275 Chr04K 306 2220 (1104) 7 2 2 0 3 0.360 0.93 (0.44) 0.44 (0.17) 8 0.776 (0.008) 2.082
HD1 contig05584 Chr04N 363 2140 (1113) 17 17 0 0 0 0.280 1.66 (0.04) 1.11 (0.27) 30 0.901 (0.005) −0.142
PGM contigl7299 Chr09K 343 3120 (1634) 8 5 2 0 1 0.256 0.59 (0.36) 0.36 (0.13) 28 0.848 (0.008) 1.27
PGM contig200892 Chr09Na 315 696 (391) 7 4 3 0 0 1.006 3.3 (0.05) 1.40 (0.53) 13 0.780 (0.007) 1.328
TB1 contig06045 Chr09K 339 2428 (1109) 10 2 5 1 2 0.412 1.42 (0.03) 0.59 (0.21) 38 0.817 (0.010) 1.625
TB1 contig76312 Chr09N 314 2597 (1115) 26 16 5 3 2 1.001 2.53 (0.07) 1.41 (0.37) 84 0.926 (0.005) 0.037
Total     51,500 (28313) 251 169 33 17 32       
Sugenome Nb    372 6709 (2884) 106 73 12 9 13   1.61 (0.04) 0.65 (0.31) 610 0.99 (0.20) −0.353
Sugenome Nb    372 6709 (2884) 100 67 13 6 10   0.31 (0.03) 0.53 (0.11) 637 0.99 (0.10) −0.269
  1. Stot Total No. of polymorphic sites, Non Cod No. of SNPs in non-coding regions, Syn No. of synonymous SNPs, Con No. of conservative amino acid changes, Non Con No. of non-conservative amino acid changes, d Percentage polymorphism (SNP density), πtot Nucleotide diversity, θw Theta per site from Watterson estimator, D Tajima’s D, h No. of haplotypes, Hd Haplotype diversity, SD Standard deviation
  2. aChromosome and subgenome allocation were corrected according to mapping data (P Qi and KM Devos, unpublished data)
  3. bSubgenome comparisons were limited to overlapping regions