Table 1.
Candidate regions for causal genes of 14 traits.
| Trait | QTL name | Year | Chr | Start | End | P value of peak | Number of significant genes | Annotated genes |
|---|---|---|---|---|---|---|---|---|
| Days to heading | qDTH1 | 2019 | 1 | 36,302,302 | 36,661,955 | 1.50E−05 | 9 | OsHESO1 (LOC_Os01g62780) |
| qDTH3 | 2018 | 3 | 33,075,629 | 33,082,634 | 5.71E−05 | 1 | Hd16 (LOC_Os03g57940) | |
| qDTH6-1 | 2019 | 6 | 2,867,939 | 4,105,198 | 3.50E−06 | 1 | ||
| qDTH6-2 | 2018 | 6 | 7,241,590 | 10,682,931 | 2.69E−09 | 19 | Hd1(LOC_Os06g16370) | |
| 2019 | 6 | 7,242,240 | 13,273,924 | 2.22E−07 | 14 | |||
| qDTH7-1 | 2019 | 7 | 3,857,839 | 5,220,414 | 3.50E−06 | 5 | ||
| qDTH7-2 | 2019 | 7 | 8,502,975 | 8,503,004 | 5.08E−05 | 1 | Ghd7 (LOC_Os07g15770) | |
| qDTH7-3 | 2019 | 7 | 28,815,689 | 29,549,433 | 3.47E−06 | 1 | Hd2(LOC_Os07g49460) | |
| Culm length | qCL1 | 2019 | 1 | 7,080,206 | 7,239,635 | 1.66E−05 | 1 | |
| qCL5-1 | 2018 | 5 | 3,796,606 | 5,731,804 | 1.21E−05 | 1 | ||
| 2019 | 5 | 3,796,606 | 4,504,388 | 1.69E−07 | 1 | |||
| qCL5-2 | 2019 | 5 | 29,126,924 | 29,928,598 | 3.41E−05 | 18 | ||
| qCL6-1 | 2018 | 6 | 2,867,939 | 4,564,993 | 8.08E−07 | 20 | ||
| 2019 | 6 | 2,867,939 | 4,564,993 | 3.06E−06 | 14 | |||
| qCL6-2 | 2018 | 6 | 13,137,626 | 13,573,334 | 1.34E−05 | 2 | ||
| 2019 | 6 | 9,907,766 | 13,752,138 | 1.22E−06 | 15 | |||
| qCL7 | 2018 | 7 | 3,857,839 | 5,462,601 | 1.01E−05 | 4 | ||
| 2019 | 7 | 3,791,728 | 5,462,601 | 5.69E−06 | 4 | |||
| qCL8 | 2018 | 8 | 17,002,605 | 18,113,848 | 1.54E−05 | 2 | ||
| 2019 | 8 | 18,113,848 | 18,113,848 | 7.75E−05 | 2 | |||
| Panicle number | qPN5 | 2018 | 5 | 27,940,991 | 29,363,499 | 9.42E−07 | 4 | |
| Panicle length | qPL11 | 2019 | 11 | 6,369,017 | 7,194,273 | 1.72E−05 | 1 | sp1(LOC_Os11g12740) |
| Spikelet number | qSPN7 | 2019 | 7 | 3,855,482 | 5,222,866 | 5.73E−06 | 4 | |
| qSPN8 | 2018 | 8 | 18,739,837 | 20,501,113 | 1.37E−05 | 1 | ||
| qSPN9 | 2019 | 9 | 18,970,742 | 20,488,878 | 4.35E−05 | 10 | ||
| Flag leaf length | qFLL3 | 2018 | 3 | 27,926,299 | 30,995,908 | 1.86E−08 | 9 | |
| 2019 | 3 | 27,929,416 | 31,512,460 | 5.78E−06 | 4 | Hd6(LOC_Os03g55389) | ||
| qFLL6 | 2018 | 6 | 27,217,182 | 27,418,688 | 4.26E−05 | 2 | ||
| qFLL11 | 2018 | 11 | 25,450,620 | 25,503,471 | 5.07E−05 | 2 | ||
| Flag leaf width | qFLW1 | 2018 | 1 | 6,618,896 | 6,724,386 | 2.87E−05 | 1 | |
| 2019 | 1 | 6,618,896 | 6,647,986 | 1.51E−05 | 1 | |||
| qFLW4 | 2018 | 4 | 30,746,467 | 31,502,547 | 7.00E−07 | 11 | NAL1 (LOC_Os04g52479) | |
| 2019 | 4 | 31,157,451 | 31,352,197 | 3.00E−05 | 6 | |||
| Basal culm diameter | qBCD4 | 2019 | 4 | 2,691,755 | 2,691,755 | 1.02E−05 | 2 | |
| qBCD5-1 | 2019 | 5 | 3,796,606 | 4,504,388 | 1.94E−06 | 1 | ||
| qBCD5-2 | 2018 | 5 | 27,940,991 | 29,890,589 | 7.86E−06 | 4 | ||
| 2019 | 5 | 27,505,030 | 29,928,598 | 3.39E−07 | 20 | |||
| qBCD6-1 | 2019 | 6 | 9,907,766 | 13,752,138 | 6.32E−07 | 14 | ||
| qBCD6-2 | 2019 | 6 | 19,093,132 | 19,093,132 | 7.76E−05 | 2 | ||
| qBCD8 | 2019 | 8 | 23,677,530 | 23,962,828 | 3.55E−05 | 2 | ||
| qBCD11 | 2019 | 11 | 27,724,930 | 29,015,100 | 3.49E−05 | 19 | ||
| Breaking moment | qBM6 | 2019 | 6 | 22,823,316 | 23,019,186 | 6.47E−07 | 1 | |
| Bending stress | qBS4 | 2019 | 4 | 1,283,779 | 1,283,779 | 2.56E−06 | 1 | |
| qBS5-1 | 2019 | 5 | 3,796,606 | 5,463,605 | 3.13E−07 | 6 | ||
| qBS5-2 | 2019 | 5 | 29,126,924 | 29,928,598 | 4.29E−06 | 19 | ||
| qBS6 | 2018 | 6 | 9,925,796 | 10,075,483 | 3.64E−06 | 3 | ||
| 2019 | 6 | 9,907,766 | 12,107,939 | 4.68E−07 | 12 | |||
| qBS7 | 2018 | 7 | 757,788 | 2,705,676 | 6.98E−06 | 1 | ||
| qBS8 | 2019 | 8 | 2,143,950 | 6,043,554 | 4.29E−07 | 2 | ||
| qBS10-1 | 2019 | 10 | 1,113,943 | 3,297,222 | 3.90E−08 | 4 | ||
| qBS10-2 | 2019 | 10 | 9,718,000 | 11,691,675 | 1.90E−07 | 1 | ||
| qBS11 | 2018 | 11 | 27,812,322 | 27,828,581 | 4.54E−05 | 1 | ||
| 2019 | 11 | 25,790,142 | 28,446,869 | 1.85E−05 | 19 | |||
| Young’s modulus | qYM4 | 2019 | 4 | 2,840,514 | 3,546,128 | 2.03E−05 | 3 | |
| qYM5-1 | 2018 | 5 | 3,796,606 | 5,312,775 | 2.05E−05 | 1 | ||
| 2019 | 5 | 3,796,606 | 5,312,775 | 3.43E−08 | 2 | |||
| qYM5-2 | 2018 | 5 | 21,334,298 | 23,321,036 | 5.10E−06 | 2 | ||
| 2019 | 5 | 22,307,597 | 23,321,036 | 2.23E−06 | 1 | |||
| qYM5-3 | 2018 | 5 | 29,126,924 | 29,928,598 | 6.01E−05 | 4 | ||
| 2019 | 5 | 27,398,408 | 29,928,598 | 1.88E−08 | 20 | |||
| qYM6 | 2019 | 6 | 9,907,766 | 13,752,138 | 3.56E−07 | 17 | ||
| qYM8-1 | 2019 | 8 | 3,469,204 | 4,596,332 | 3.95E−07 | 3 | ||
| qYM8-2 | 2019 | 8 | 23,677,530 | 24,784,308 | 1.76E−07 | 3 | ||
| qYM10 | 2019 | 10 | 1,113,943 | 3,297,222 | 3.02E−07 | 4 | ||
| qYM11 | 2018 | 11 | 27,670,642 | 28,857,992 | 1.24E−07 | 4 | ||
| 2019 | 11 | 27,724,930 | 29,015,100 | 9.78E−07 | 45 | |||
| Flexural rigidity | qFR6 | 2019 | 6 | 22,823,316 | 22,994,705 | 3.13E−06 | 1 | |
| Culm tissue density | qCTD2 | 2019 | 2 | 33,208,146 | 34,879,419 | 5.80E−06 | 2 | |
| qCTD6 | 2018 | 6 | 8,197,078 | 10,452,678 | 1.69E−05 | 5 | ||
| qCTD9 | 2019 | 9 | 20,466,533 | 21,189,653 | 5.61E−05 | 8 | ||
| Culm diameter (3rd) | q3CD5 | 2019 | 5 | 27,505,030 | 29,682,002 | 8.40E−08 | 11 |