Table 4.
Marker loci associated with dry matter and starch content of storage roots (P < 0.01).
| Marker | Model used | Based on phenotypic data Y2011 | Based on phenotypic data Y2012 | Based on phenotypic data Y2013 | Based on phenotypic data 3 years | ||||
|---|---|---|---|---|---|---|---|---|---|
| P-value | R2 | P-value | R2 | P-value | R2 | P-value | R2 | ||
| SIP002 | 1–4 | 0.00546 | 0.08354 | 3.39E-04 5.58E-04 | 0.05346 0.04972 | ||||
| SIP029 | 1–4 | 0.00761 | 0.07734 | 9.37E-06 | 0.28505 | 0.00281 | 0.2169 | 1.95E-04 | 0.07096 |
| 6.65E-04 | 0.12268 | 5.01E-04 | 0.06222 | ||||||
| 3.70E-10 | 0.18804 | ||||||||
| 0.0086 | 0.03596 | ||||||||
| SIP098 | 1 | 4.73E-04 | 0.12894 | 0.00987 | 0.10758 | 5.54E-06 | 0.10372 | ||
| 4.73E-04 | 0.12894 | 0.00987 | 0.10758 | 5.54E-06 | 0.10372 | ||||
| SIP125 | 1, 2 | 0.0032 | 0.11122 | 2.35E-05 | 0.07346 | ||||
| 5.23E-04 | 0.0502 | ||||||||
| 0.00452 | 0.034 | ||||||||
| SIP127 | 1, 2 | 0.00496 | 0.0333 | ||||||
| 0.00808 | 0.02967 | ||||||||
| SIP137 | 1–4 | 3.62E-04 | 0.13386 | 0.00117 | 0.16491 | 3.27E-06 | 0.10851 | ||
| 0.00236 | 0.09917 | 2.81E-04 | 0.20182 | 1.32E-04 | 0.07461 | ||||
| 5.84E-05 | 0.16682 | 0.00122 | 0.16364 | 7.86E-08 | 0.14187 | ||||
| 3.35E-04 | 0.13527 | 0.00265 | 0.14312 | 0.00115 | 0.05452 | ||||
| 0.00377 | 0.09046 | 1.15E-07 | 0.13852 | ||||||
| 1.42E-04 | 0.07393 | ||||||||
| 1.02E-05 | 0.09818 | ||||||||
| SIP151 | 1–4 | 0.0014 | 0.14032 | 0.00174 | 0.04596 | 0.00977 | 0.04987 | 3.79E-06 | 0.0506 |
| 0.0014 | 0.14032 | 0.00174 | 0.04596 | 3.79E-06 | 0.0506 | ||||
| 0.00132 | 0.02476 | ||||||||
| SIP160 | 1–4 | 0.00253 | 0.02155 | ||||||
| 0.00315 | 0.02062 | ||||||||
| SIP173 | 1, 2 | 0.00289 | 0.04194 | 0.0064 | 0.01776 | ||||
| 1.91E-04 | 0.03299 | ||||||||
| SIP178 | 1 | 0.00785 | 0.01678 | ||||||
| SIP183 | 1, 2 | 0.00783 | 0.09545 | 0.002 | 0.04463 | 0.00802 | 0.05205 | 1.32E-05 | |
| 0.00112 | 0.13975 | 0.00302 | 0.04121 | 0.00705 | |||||
| 0.00607 | 0.03538 | 6.78E-04 | 0.04432 | ||||||
| 0.00321 | 0.01719 | ||||||||
| 3.56E-06 | 0.02719 | ||||||||
| 8.01E-05 | 0.02053 | ||||||||
| 0.05001 | |||||||||
| 0.03646 | |||||||||
| SIP187 | 1–4 | 7.32E-04 | 0.05283 | 0.00557 | 0.0218 | ||||
| 6.64E-04 | 0.03268 | ||||||||
| SIP192 | 1, 2 | 6.33E-04 | 0.02739 | ||||||
| SIP195 | 1, 2 | 4.02E-04 | 0.16063 | 6.19E-04 | 0.05389 | 0.00881 | 0.05027 | 2.22E-07 | 0.06182 |
| SIP200 | 1, 2 | 0.00727 | 0.09031 | 0.00148 | 0.02389 | ||||
| SIP202 | 1–4 | 0.00138 | 0.1296 | 3.26E-04 | 0.09535 | 2.32E-05 | 0.04253 | ||
| 0.00754 | 0.09244 | 2.57E-04 | 0.03191 | ||||||
| SIP213 | 1–4 | 8.63E-06 | 0.23066 | 0.0086 | 0.03247 | 6.63E-04 | 0.08407 | 2.74E-05 | 0.04122 |
| 0.00133 | 0.12819 | 0.00384 | 0.03916 | 1.55E-06 | 0.05373 | ||||
| 0.00218 | 0.11767 | 0.00182 | 0.04544 | 0.00817 | 0.0166 | ||||
| 2.44E-04 | 0.06232 | 4.06E-04 | 0.02948 | ||||||
| 1.35E-04 | 0.03425 | ||||||||
| 2.34E-04 | 0.03188 | ||||||||
| 8.72E-07 | 0.05624 | ||||||||
| SIP214 | 1–4 | 4.58E-04 | 0.05675 | 0.00324 | 0.0245 | ||||
| 4.81E-04 | 0.05634 | 0.00175 | 0.02763 | ||||||
| 3.38E-04 | 0.05928 | 9.41E-04 | 0.03083 | ||||||
| 4.01E-04 | 0.05786 | 2.26E-04 | 0.03819 | ||||||
| 3.71E-04 | 0.05851 | 0.00248 | 0.02586 | ||||||
| 0.00788 | 0.03303 | 0.00647 | 0.021 | ||||||
| 0.00927 | 0.01919 | ||||||||
| 0.00351 | 0.0241 | ||||||||
| SIP222 | 1–4 | 0.00314 | 0.06444 | 2.59E-04 | 0.03187 | ||||
| 0.00799 | 0.05192 | 1.36E-04 | 0.03471 | ||||||
| 0.00185 | 0.02326 | ||||||||
| SIP235 | 1–4 | 0.00369 | 0.0395 | 0.00996 | 0.04951 | 6.87E-04 | 0.03367 | ||
| 0.00369 | 0.0395 | 0.00996 | 0.04951 | 6.87E-04 | 0.03367 | ||||
| 4.52E-05 | 0.04824 | ||||||||
| 4.52E-05 | 0.04824 | ||||||||
| SIP237 | 1–4 | 0.00307 | 0.04123 | 0.00206 | 0.04452 | 3.50E-06 | 0.05059 | ||
| 0.00151 | 0.024 | ||||||||
| 0.00151 | 0.024 | ||||||||
| SIP240 | 3, 4 | 0.00802 | 0.05568 | ||||||
| SIP245 | 1–3 | 2.67E-04 | 0.15966 | 0.00525 | 0.01843 | ||||
| 0.00943 | 0.08474 | 0.00846 | 0.01649 | ||||||
| 6.71E-04 | 0.02737 | ||||||||
| 0.00273 | 0.02131 | ||||||||
| SIP250 | 1–4 | 0.00581 | 0.10368 | 0.00109 | 0.04994 | 0.00539 | 0.02193 | ||
| 0.00336 | 0.1164 | 0.00562 | 0.02188 | ||||||
| 0.00702 | 0.02085 | ||||||||
| 2.31E-04 | 0.03835 | ||||||||
| SIP252 | 1–4 | 0.00318 | 0.11767 | 0.0065 | 0.03473 | 0.00561 | 0.0183 | ||
| 0.00359 | 0.11488 | 0.00732 | 0.01716 | ||||||
| 0.00484 | 0.10792 | ||||||||
| SIP254 | 1–4 | 1.03E-04 | 0.19263 | 1.61E-04 | 0.03361 | ||||
| SIP261 | 1–4 | 0.00349 | 0.10755 | 0.00591 | 0.0558 | 0.00207 | 0.0225 | ||
| 0.00439 | 0.05963 | 0.00316 | 0.02068 | ||||||
| 0.00115 | 0.02502 | ||||||||
| SIP263 | 1–4 | 0.00218 | 0.11762 | 0.00379 | 0.01995 | ||||
| SIP265 | 1–4 | 8.27E-04 | 0.1383 | 0.00184 | 0.02307 | ||||
| SIP285 | 1–4 | 0.00276 | 0.12097 | 0.00879 | 0.03224 | 0.00797 | 0.05213 | 0.00128 | 0.02465 |
| 9.41E-04 | 0.05088 | 0.00991 | 0.01592 | ||||||
| 0.00983 | 0.03146 | 0.0048 | 0.01901 | ||||||
| 4.12E-06 | 0.04988 | ||||||||
| SIP288 | 1–4 | 0.00659 | 0.03487 | 0.00502 | 0.02249 | ||||
| SIP300 | 1–4 | 0.00391 | 0.10988 | 0.00522 | 0.03656 | 5.68E-05 | 0.03816 | ||
| 2.06E-04 | 0.06365 | ||||||||
These markers were found to be associated with the corresponding traits when four models were used: 1, the naive model-without controlling for Q and K; 2, GLM used after controlling the population structure (Q); 3, MLM used after controlling the population structure (Q+K); and 4, MLM used without controlling for the population structure (K). When detected using various models, the P-values were obtained using model 2 or 3, which controlled for the population structure. The model information was the same as for Tables 5, 6, and Supplementary Materials 7, 9, 11.