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. 2013 Dec 6;201(4):1227–1239. doi: 10.1111/nph.12621

Table 3.

Markers with significant phenotypic associations (false discovery rate < 0.05) in 138 Miscanthus sinensis genotypes

Chromosomea Positionb Pc Qd MAFe PVEf Traitg Geneh Description/annotation
1 3 776 666 3.31E-06 0.03 0.01 0.12 TallestStem.9 Sb01g004700 ATVAMP725
1 3 789 996 2.98E-06 0.03 0.02 0.13 TallestStem.9 Sb01g004720 Aminoacyl-tRNA synthetase family
1 68 013 320 3.38E-06 0.03 0.01 0.12 TallestStem.9 Sb01g044850 Unknown protein
2 67 477 249 1.14E-06 0.03 0.01 0.16 StatureStemAngle.7 Sb02g032850 Unknown protein
2 67 477 259 1.14E-06 0.03 0.01 0.16 StatureStemAngle.7 Sb02g032850 Unknown protein
3 8 793 225 6.38E-07i,j,k 0.03 0.49 0.18 LeafLength.7 Sb03g008300 DNA binding/protein dimerization
3 65 293 238 2.79E-06 0.03 0.05 0.02 AvgeSen.9 Sb03g037310 ATCDPMEK
3 65 293 239 2.79E-06 0.03 0.05 0.02 AvgeSen.9 Sb03g037310 ATCDPMEK
4 4 150 586 1.57E-06 0.04 0.06 0.18 LeafLength.7 NA NA
6 50 249 485 3.35E-06 0.03 0.02 0.16 TallestStem.9 Sb06g020830 Protein kinase family protein
6 54 211 630 8.64E-07i,j,k 0.05 0.17 0.15 Lignin.8 Sb06g025250 Serine-type endopeptidase/serine-type peptidase
6 58 247 799 5.66E-07i,j 0.02 0.03 0.25 AvgeSen.9 Sb06g029670 ATP binding/protein kinase/protein serine/threonine kinase/protein tyrosine kinase/sugar binding
9 24 591 741 1.84E-06 0.03 0.03 0.26 AvgeSen.9 NA NA
9 46 480 666 4.07E-06 0.04 0.15 0.02 AvgeSen.9 Sb09g018620 Hydroxyproline-rich glycoprotein family protein
10 49 962 793 4.90E-07i,k 0.02 0.04 0.21 AvgeSen.9 Sb10g022360 Unknown protein
10 55 336 585 3.14E-06j 0.03 0.01 0.12 TallestStem.9 Sb10g026010 UBP19; cysteine-type endopeptidase/ubiquitin thiolesterase
10 59 574 096 1.50E-06j 0.03 0.05 0.19 TallestStem.9 Sb10g029835 Unknown protein

Associations with Bonferroni-corrected genome-wide significance (α = 0.05) are shown in bold. Only results for markers detected from alignments to the Sorghum bicolor genome are shown.

a

Chromosome, Sorghum bicolor chromosome to which the marker was aligned.

b

Position, Sorghum bicolor chromosome position to which the marker was aligned.

c

P,P value from genome-wide association studies (GWAS) analysis using the efficient mixed-model association expedited approach (EMMAX), including the kinship matrix and the first two eigenvectors of population structure (see the Materials and Methods section).

d

Q, false discovery rate calculated using the q-value R package (Dabney & Storey, 2013).

e

MAF, minor allele frequency.

f

PVE, naïve estimate of the proportion of variance explained based on simple linear regression (see the Materials and Methods section).

g

Trait, phenotypic trait as defined in Table 1.

h

Gene, Sorghum bicolor gene to which the marker was aligned.

i

Significant at genome-wide α = 0.05 after Bonferroni correction based on EMMAX analyses (see the Materials and Methods section).

j

Included in the optimal model according to the multiple Bonferroni criterion in multi-locus mixed-model (MLMM) analyses (see the Materials and Methods section).

k

Included in the optimal model according to the multiple Bonferroni criterion in MLMM analyses including the first two eigenvectors of population structure (see the Materials and Methods section).

NA, not applicable (markers aligning to putatively intergenic positions).