Table 2.
Stably expressed QTNs for the five traits among different multi-methods.
| Trait | Method (1, 2, 3, 4)a | Marker | Chromosome | Maker position (bp) | LOD score | r2 (%)b |
|---|---|---|---|---|---|---|
| CBR | 1, 3, 4 | PZE-102138070 | 2 | 186,820,524 | 5.68, 3.92, 6.73 | 9.48, 5.00, 11.56 |
| 1, 4 | PZE-108009888 | 8 | 10,298,512 | 5.78, 3.17 | 8.01, 4.60 | |
| 1, 3 | PZE-110088629 | 10 | 138,832,523 | 3.85, 3.35 | 5.43, 2.65 | |
| 1, 3 | PZE-103123331 | 3 | 181,066,730 | 3.29, 4.53 | 6.40, 3.58 | |
| 1, 2, 3 | SYN6514 | 3 | 196,351,287 | 3.56, 4.05, 7.36 | 3.63, 6.32, 8.30 | |
| 1, 3, 4 | SYN7221 | 2 | 6,200,684 | 3.75, 11.83, 5.94 | 7.76, 10.78, 6.22 | |
| 1, 2 | PZE-109067144 | 9 | 110,459,334 | 3.27, 3.14 | 2.59, 4.92 | |
| 1, 2, 3, 4 | SYNGENTA15901 | 7 | 5,038,808 | 3.69, 3.74 | 10.75,4.77 (13.19) | |
| (7.63),7.03, 5.84 | 12.35, 11.39 | |||||
| 1, 3 | PZE-102109721 | 2 | 141,363,433 | 4.18, 5.46 | 3.64, 4.91 | |
| 2, 3 | PZE-102151093 | 2 | 197,600,202 | 5.56, 6.37 | 10.24, 12.66 | |
| 2, 3, 4 | PZE-101213720 | 1 | 264,163,677 | 4.65, 6.84, 4.20 | 6.88, 11.24, 6.73 | |
| 2, 3, 4 | SYN8267 | 4 | 169,213,008 | 5.19, 3.14 | 8.43, 1.83 | |
| (5.35),7.29 | (10.05), 16.35 | |||||
| 2, 4 | PZE-101152052 | 1 | 19,548,4495 | 4.16, 6.94 | 6.30, 4.76 | |
| 2, 4 | PZE-108020924 | 8 | 19,855,121 | 3.75, 13.53 | 4.89, 9.52 | |
| 3, 4 | PZE-104067972 | 4 | 134,998,323 | 4.90, 9.53 | 4.89, 7.06 | |
| CDR | 1, 4 | PZE-106032634 | 6 | 75,630,749 | 16.15, 4.43 | 18.87, 5.68 |
| 1, 2, 3, 4 | SYN39155 | 3 | 2,446,145 | 4.73, 5.07, 4.59 | 4.85, 6.45, 3.10 | |
| (4.76), 4.05 | (4.68), 4.21 | |||||
| 1, 2, 3, 4 | SYN32084 | 1 | 256,515,262 | 4.04, 3.05, 8.87 | 5.89, 2.65, 6.09 | |
| (6.35), 8.74 | (7.25), 5.19 | |||||
| 1, 2, 3 | PZE-101216827 | 1 | 267,908,158 | 3.48, 4.33, 6.19 | 4.77, 4.23, 3.25 | |
| 1, 2 | SYN11739 | 9 | 9,965,031 | 4.92, 3.66 | 14.28, 8.27 | |
| 1, 3 | SYN31996 | 6 | 163,506,361 | 3.13, 3.86 | 9.16, 3.58 | |
| 1, 3 | PZE-108002411 | 8 | 2,512,300 | 16.25, 4.97 | 14.64, 6.03 | |
| 1, 4 | PZE-101096007 | 1 | 94,367,481 | 4.86, 4.45 | 3.72, 5.66 | |
| 1, 3 | PZE-102109640 | 2 | 141,173,773 | 7.67, 5.68 | 4.86, 5.53 | |
| 3, 4 | PZE-104025174 | 4 | 29,335,471 | 9.52, 3.01 | 7.33, 0.89 | |
| 3, 4 | PZE-106036875 | 6 | 84,672,851 | 4.31, 6.72 | 1.97, 4.40 | |
| 3, 4 | PUT-163a-31909945-2005 | 6 | 110,706,817 | 4.29, 3.58 | 2.04, 4.30 | |
| 3, 4 | SYN8144 | 10 | 142,358,869 | 4.21, 4.09 | 3.31, 5.42 | |
| CPN | 1, 3, 4 | PZE-106032634 | 6 | 75,630,749 | 7.88, 4.58, 4.56 | 14.66, 7.12, 0.62 |
| 1, 3 | PZE-101220149 | 1 | 271,749,865 | 4.42 (8.26), 4.96 | 8.27 (14.86), 6.35 | |
| 1, 3 | SYN39155 | 3 | 2,446,145 | 3.06 (3.85), 4.20 | 5.14 (5.86), 3.04 | |
| 1, 3, 4 | PZE-108105282 | 8 | 159,954,599 | 3.88, 6.55, 5.42 | 6.91, 5.57, 1.57 | |
| 1, 4 | PZE-108057325 | 8 | 102,454,042 | 3.07, 6.36 | 5.32, 0.47 | |
| 1, 3 | PZE-104066682 | 4 | 131,771,972 | 7.49, 3.31 | 17.57, 8.73 | |
| 1, 3 | PZE-106043314 | 6 | 93,212,668 | 6.64, 3.46 | 9.61, 4.20 | |
| 1, 2, 3 | PZE-102186765 | 2 | 230,884,488 | 9.11, 7.26, 6.50 | 12.45, 0.30, 9.41 | |
| 2, 3 | PZE-109062403 | 9 | 104,884,301 | 6.36, 13.00 | 16.33, 14.58 | |
| 3, 4 | PZE-103049772 | 3 | 54,177,469 | 6.93, 12.72 | 14.03, 12.98 | |
| 1, 3 | SYN29447 | 5 | 213,294,101 | 3.29, 6.18 | 5.79, 6.17 | |
| CRR | 2, 3 | SYN18315 | 1 | 252,377,691 | 7.13, 7.27 | 12.37, 9.45 |
| 2, 3 | PZE-106008760 | 6 | 25,291,385 | 6.76, 4.44 | 13.33, 6.04 | |
| 2, 4 | PZE-101085779 | 1 | 75,627,286 | 4.81, 7.65 | 10.52, 6.47 | |
| 2, 3 | SYN28088 | 5 | 68,653,887 | 4.18, 6.13 | 6.74, 5.74 | |
| 2, 3 | PZE-106000504 | 6 | 1,234,387 | 3.04, 4.17 | 4.13, 2.57 | |
| 2, 3, 4 | PZE-107005556 | 7 | 3,824,391 | 4.13, 3.90 (6.29) | 9.14, 3.76 (7.74) | |
| 3.43(4.47) | 2.00(4.80) | |||||
| 3, 4 | SYN35026 | 5 | 1,946,471 | 4.72 (3.28) | 4.09 (3.07) | |
| 9.40 (7.37) | 6.53 (17.27) | |||||
| 3, 4 | PZE-105122012 | 5 | 179,270,149 | 5.07, 7.25 | 4.17, 4.70 | |
| 3, 4 | SYN18708 | 1 | 21,466,619 | 5.18, 4.33 | 4.15, 3.11 | |
| GCR | 1, 3 | SYN32084 | 1 | 256,515,262 | 3.99, 4.08 | 6.10, 4.35 |
| 1, 3 | SYNGETA13688 | 2 | 5,681,488 | 4.08 (4.26), 4.96 | 9.82 (7.55), 5.25 | |
| 1, 3, 4 | PZE-109121058 | 9 | 154,807,596 | 8.07, 7.71, 5.76 | 13.73, 11.26, 8.20 | |
| 1, 3, 4 | PZE-103123331 | 3 | 181,066,730 | 3.42, 4.03, 7.25 | 6.67, 7.75, 5.46 | |
| 1, 3 | PZE-108010908 | 8 | 11,504,308 | 4.61, 6.26 | 6.88, 6.58 | |
| 1, 4 | SYN37974 | 2 | 10,782,867 | 3.25, 6.41 | 7.78, 10.77 | |
| 2, 3 | PZE-103108199 | 3 | 169,053,554 | 3.28, 5.74 | 4.47, 6.96 | |
| 2, 3 | PZE-104024889 | 4 | 28,985,737 | 3.66 (3.31), 4.93 | 5.99 (6.48), 5.90 | |
| 2, 4 | PZE-104069507 | 4 | 138,153,696 | 5.14, 4.45 | 10.42, 14.05 | |
| 2, 4 | PZE-101106628 | 1 | 110,914,630 | 4.86, 5.53 | 15.03, 9.59 | |
| 3, 4 | SYN7221 | 2 | 6,200,684 | 4.70, 3.42 | 3.57, 3.82 | |
| 3, 4 | PZE-109081358 | 9 | 129,514,761 | 5.86, 6.96 | 3.98, 9.62 | |
| 3, 4 | PZE-101223466 | 1 | 274,722,612 | 9.02, 7.28 | 12.32, 8.94 | |
| 3, 4 | PZE-102138070 | 2 | 186,820,524 | 6.33 (9.02), 6.42 | 10.12 (12.43), 9.73 | |
| 3, 4 | SYN21743 | 9 | 1,347,687 | 7.10, 5.60 | 9.66, 7.20 | |
| 3, 4 | PZE-108021239 | 8 | 20,231,393 | 4.19, 4.09 | 4.87, 5.42 |
Traits include CBR (callus browning rate), CDR (callus differentiating rate), CPN (callus plantlet number), CRR (callus rooting rate), and GCR (green callus rate).
a
Method numbers correspond to (1) mrMLM, (2) FASTmrEMMA, (3) ISIS EM-BLASSO, and (4) pLARmEB.
b
r2 (%), phenotypic variation of traits explained by each QTN.
The values in parentheses denote the means for QTNs in different environments.