Table 4.
QTLs mapped of agronomic traits in F2, F3, and F4 populations.
| Traita | QTL | Chr | QTL peak (cM) | Flanking markerb | SNP (P1/P2)c | Genetic distance between loci and trait cM | Left flanking marker (cM) | Right flanking marker (cM) | Genomic positiond | LOD | Expl% |
|---|---|---|---|---|---|---|---|---|---|---|---|
| BRN | VaBrn4.1 (F2,F3) | 4 | 18.455 | s690-144110,s856-165880 | (T/G) | 0.0593 | 17.862 | 18.455 | 2728770–2973972 | 5.91 | 20.4 |
| VaBrn4.2 (F3) | 4 | 17.862 | s165-116310 | (G/A) | 0.974 | 16.888 | 16.888 | 2466844 | 4.55 | 20.8 | |
| ST1l_ST10l | VaST1-10I9.1 (F2) | 9 | 57.735 | s249-3204596 | (C/A) | 0 | 57.735 | 57.735 | 28712717 | 4.92 | 17.3 |
| SDNPPD | VaSnp3.1 (F2) | 3 | 16.847 | s624-5207,s624-5245 | (A/C) | 0.0120 | 16.835 | 16.847 | 5754076–5754114 | 4.89 | 17.3 |
| VaSnp4.1 (F2) | 4 | 19.37 | s80-1776704 | (G/A) | 0 | 19.37 | 19.37 | 5393066 | 3.98 | 11.8 | |
| SD100WT | VaSd100wt11.1 (F2) | 11 | 57.237 | s268-1701932,s268-1618129 | (C/T) | 0.0420 | 57.195 | 57.237 | 31820598–31904338 | 6.00 | 20.7 |
| VaSd100wt1.1 (F2,F3) | 1 | 92.683 | s244-1339845,s244-641945 | (A/G) | 2.143,13.457 | 90.54 | 106.14 | 32224913–32922813 | 4.34 | 12.2 | |
| VaSd100wt1.2 (F3) | 1 | 88.54 | s168-1117751 | (G/A) | 19.429 | 88.54 | 88.54 | 30134755 | 4.16 | 19.2 | |
| VaSd100wt1.3(F2) | 1 | 90.683 | s244-641945,s384-495870 | (G/A) | 0.5457 | 90.683 | 96.14 | 32922813–36773639 | 4.06 | 11.5 | |
| PDDM25 | VaFld4.1 (F2) | 4 | 17.862 | s690-144110 | (A/C) | 0 | 17.862 | 17.862 | 2728770 | 20.00 | 55.4 |
| PDDM50 | VaFld4.1 (F2) | 4 | 17.862 | s690-144110 | (A/C) | 0 | 17.862 | 17.862 | 2728770 | 25.5 | 64.9 |
| PDDM75 | VaGp4.1 (F2,F3) | 4 | 20.113 | s80-1776704,s80-1939896 | (C/T) | 0.7431 | 19.37 | 21.113 | 5556258 | 14.46 | 47 |
| FLD | VaFld4.1 (F2/F4,F2) | 4 | 17.862 | s165-116310,s690-144110 | (A/C) | 0.9740 | 16.888 | 17.862 | 2466844–2728770 | 32.29 | 71.3 |
| VaFld4.2 (F2,F2) | 4 | 17.862 | s690-144110,s856-165880 | (A/C) | 0.0593 | 17.862 | 18.455 | 2728770–2973972 | 32.29 | 25.9 | |
| VaFld4.3(F4,F4) | 4 | 16.888 | s58-238422,s165-116310 | (G/A) | 5.4490 | 12.407 | 16.888 | 238422–2466844 | 6.19 | 30.3 | |
| VaFld7.1 (F2) | 7 | 45.625 | s57-1742194 | (G/T) | 0 | 45.625 | 45.462 | 8738088 | 4.00 | 4.1 | |
| FLD50 | VaFld4.1 (F2,F2) | 4 | 17.862 | s165-116310, s690-144110 | (A/C) | 0 | 16.888 | 17.862 | 2466844–2728770 | 33.96 | 73.1 |
| VbFld4.1 (F3,F4) | 4 | 22.272 | s80-940518,s80-1199058 | (C/A) | 0.6330 | 21.639 | 22.272 | 4556880–4815420 | 4.69 | 24.2 | |
| VaFld10.1 (F2) | 10 | 62.007 | s20-880363, s356-1554658 | (A/C) | 0 | 62.007 | 62.007 | 35805580–37408870 | 4.05 | 3.9 | |
| VaFld10.2(F2) | 10 | 62.738 | s356-1554658 | (T/G) | 0 | 62.735 | 62.735 | 37408870 | 4.00 | 3.9 | |
| LFMW | VaLfmw2.1 (F4) | 2 | 50.877 | s536-414880 | (C/G) | 0 | 50.877 | 50.877 | 22751890 | 4.1 | 21.2 |
| SDT | VaSdt4.1 (F2) | 4 | 9.641 | s58-1489334,s58-345785 | (G/T) | 9.6410 | 0 | 9.641 | 345785,1489334 | 2.84 | 9.11 |
The Permutation Test is used to calculate the significant threshold for subsequent Interval mapping and MQM mapping; “Expl(%)” denotes the percentage of the variance (Van Ooijen, 2009); “QTL Peak” presents a loci with the largest LOD value. This loci identifies the most likely location that is located within a gene or near a gene affected by a relative trait.
QLT names: BRN, number of branches on the main stem; ST1l_ST10l, stem Internode length (first to tenth); SDNPPD, seed number per Pod; SD100WT, 100-seed weight of pod; PDDM25, days to maturity of 25% pod; PDDM50, days to maturity of 50% pod; PDDM75, days to maturity of 75% pod; FLD, days to first flowering; FLD50, days of 50% flowering.
The left flanking marker, the right flanking marker: if there is only one marker at a site, only one marker met our criterion (LOD > threshold value of the Permutation Test).
P1 is the abbreviation of parent 1 which is one of the parents of the QLT group, P2 represents another parent.
Genomic position: genomic position of the left flanking marker, genomic position of the right flanking marker.