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)
| 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 |
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)
b: The number before the underscores indicates the chromosome and the number after the underscores indicates the QTL within the chromosome
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
d: Chromosome
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]
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
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
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
i: RMIP: resample model inclusion probability
j: Phenotypic variance explained by each marker