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Table 3 SNP identification (SNP ID), additive effect and allelic variants for the SNP, proportion of total variance explained by the SNPs significantly associated with cell wall traits (PCA, FA, DFAT, DFA 8–O–4, DFA 8–5 l, DFA 8–5, DFA 5–5), and significance values for the association between the SNP and the phenotype (P-value and RMIP)

From: Genome-wide association analysis for maize stem Cell Wall-bound Hydroxycinnamates

Traita

QTLb

Markerc

Chrd

Bine

Allelesf

(No)g

Add Effecth

P-value

RMIPi

R2j

PCA

qPCA_1_1

S1_174637686

1

1.05

C/T

108/147

568.75

4.3E-08

0.69

0.08

PCA

qPCA_1_2

S1_288696782

1

1.11

T/G

190/68

813.84

1.9E-07

0.85

0.09

PCA

qPCA_1_3

S1_108071292

1

1.05

T/G

147/100

851.22

6.5E-08

0.92

0.11

PCA

qPCA_1_3

S1_108071293

1

1.05

A/T

147/101

851.22

6.5E-08

0.92

0.11

PCA

qPCA_3_1

S3_20426421

3

3.04

C/G

79/170

697.11

6.9E-07

0.57

0.08

FA

qFA_1_1

S1_187590405

1

1.06

T/C

125/133

177.91

1.9E-06

0.52

0.08

FA

qFA_1_2

S1_220067811

1

1.07

C/T

23/239

304.04

1.6E-06

0.61

0.07

FA

qFA_1_2

S1_220067812

1

1.07

C/T

20/237

320.80

1.2E-06

0.54

0.08

FA

qFA_1_3

S1_295476338

1

1.11

T/C

35/222

269.14

1.5E-08

0.81

0.08

FA

qFA_1_3

S1_295476576

1

1.11

C/T

37/223

243.99

6.4E-08

0.66

0.09

FA

qFA_4_1

ss4_10220935

4

4.01

C/A

170/83

181.03

1.9E-07

0.66

0.08

FA

qFA_5_1

ss5_169927760

5

5.04

A/G

81/182

185.18

1.1E-06

0.51

0.08

FA

qFA_8_1

S8_138322127

8

8.05

T/C

22/240

280.72

3.2E-07

0.57

0.08

DFAT

qDFAT_10_1

S10_22521088

10

10.03

A/G

15/240

55.93

7.9E-07

0.51

0.07

DFAT

qDFAT_3_1

S3_184608458

3

3.06

C/T

15/245

55.34

8.4E-08

0.5

0.08

DFA 8–O–4

qDFA8o4_1_1

S1_220067811

1

1.07

C/T

23/239

15.07

8.1E-07

0.69

0.08

DFA 8–O–4

qDFA8o4_1_1

S1_220067812

1

1.07

C/T

20/237

15.49

4.7E-07

0.54

0.08

DFA 8–O–4

qDFA8o4_10_1

S10_22521088

10

10.03

A/G

15/240

16.70

3.2E-07

0.51

0.07

DFA 5–5

qDFA55_1_1

S1_297490295

1

1.11

A/G

99/161

5.81

2.0E-06

0.57

0.07

DFA 5–5

qDFA55_1_2

S1_220067811

1

1.07

C/T

23/239

10.78

3.1E-07

0.62

0.08

DFA 5–5

qDFA55_1_2

S1_220067812

1

1.07

C/T

20/237

11.94

9.1E-08

0.7

0.08

DFA 5–5

qDFA55_3_1

ss3_60941077

3

3.04

G/A

38/229

8.39

9.8E-07

0.52

0.07

DFA 5–5

qDFA55_3_2

S3_184608458

3

3.06

C/T

15/245

14.73

6.49E-08

0.77

0.10

DFA 5–5

qDFA55_10_1

S10_22521088

10

10.03

A/G

15/240

13.24

3.9E-07

0.75

0.08

DFA 8–5

qDFA85_1_1

S1_297490295

1

1.11

A/G

99/161

12.04

9.7E-07

0.51

0.07

DFA 8–5 l

qDFA85l_1_2

S1_297490295

1

1.11

A/G

99/161

4.69

3.9E-07

0.64

0.08

DFA 8–5 l

qDFA85l_1_1

S1_220067811

1

1.07

C/T

23/239

8.30

4.1E-07

0.56

0.08

  1. a: PCA: p-coumaric acid; FA: ferulic acid; DFA 8–5 l: 8–5 linear diferulic acid; DFA 5–5: 5–5 diferulic acid; DFA 8–O–4: 8–O–4 diferulic acid; DFA 8–5b: 8–5 benzofuran diferulic acid; DFA 8–5: sum (DFA 8–5 l + DFA 8–5b); DFAT: total diferulates sum (DFA 5–5 + DFA 8–O–4 + DFA 8–5b + DFA 8–5 l)
  2. b: The number before the underscores indicates the chromosome and the number after the underscores indicates the QTL within the chromosome
  3. c: The number before the underscores indicates the chromosome number and the number after the underscore indicates the physical position in bp within the chromosome
  4. d: Chromosome
  5. e: A bin is the interval that includes all loci from the leftmost or top Core Marker to the next Core Marker. The genetic maps are divided into 100 segments of approximately 20 centiMorgans designated with the chromosome number followed by a two-digit decimal [25]
  6. f: The letter before the diagonal is the nucleotide with the larger value; and the letter after the diagonal is the nucleotide with the smaller value
  7. g: No = Number of inbred lines homozygous for a determined allelic variant, The number before the diagonal represents the number of homozygous with the largest mean value; and the number after the diagonal the number of homozygous with the smaller mean value
  8. h: Additive effect (μg/g DW): the additive effect was calculated as half the difference between the mean of the homozygous for the allele with the largest value and the mean of the homozygous for the allele with the smallest value
  9. i: RMIP: resample model inclusion probability
  10. j: Phenotypic variance explained by each marker
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BMC Plant Biology

ISSN: 1471-2229

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