Measurements and relationship of the traits
The receptor parent Jin23B is an indica variety with susceptible performance to rice blast, and the donor parents CR071 and QingGuAi with resistance performance to rice blast. The leaf blast resistance score of Jin23B were 4.17 and 4.11 at tillering stage, and 4.22 and 4.19 at heading stage in 2011 and 2012 respectively (Table 1). The neck blast resistance of Jin23B were 91.7% and 93.7% in 2011 and 2012 respectively (Table 1). The leaf blast resistance score of CR071 and QingGuAi were 0.83 and 1.06 at tillering stage in 2011, and 0.97 and 1.11 at tillering stage in 2012 (Table 1). The leaf blast resistance score of CR071 and QingGuAi were 1.00 and 1.14 at heading stage in 2011, and 1.00 and 1.19 at heading stage in 2012 (Table 1). For neck blast resistance, CR071 and QingGuAi were 3.33% and 6.67% in 2011, and 4.67% and 8.33% in 2012 (Table 1). The resistance score between CR071 and Jin23B, QingGuAi and Jin23B were significant different at the corresponding measurement stages (Table 1). The resistance control BL6 and susceptible control CO39 had leaf blast scores of 1.20 and 4.60 at tillering stage and 1.30 and 5.00 at heading stage in 2011. And those for neck blast of BL6 and CO39 at maturation stage were 10.11% and 96.53% in 2011, and 12.10% and 100% in 2012.
Table 1
Statistical description of the parents and the backcross population in two years
Trait | Year | Parent | | Jin23B/CR071 backcross population | | Jin23B/QingGuAi backcross population |
Jin23B | CR071 | QingGuAi | | Mean ± SD | Range | | Mean ± SD | Range |
RT | 2011 | 4.17 ± 0.38 | 0.83 ± 0.38 | 1.06 ± 0.47 | | 2.59 ± 1.12 | 0–5 | | 2.30 ± 1.16 | 0–5 |
2012 | 4.11 ± 0.32 | 0.97 ± 0.16 | 1.11 ± 0.40 | | 2.58 ± 1.14 | 0.17–4.5 | | 2.05 ± 1.05 | 0-4.75 |
RH | 2011 | 4.22 ± 0.42 | 1.00 ± 0.23 | 1.14 ± 0.35 | | 2.48 ± 1.25 | 0–5 | | 2.37 ± 1.30 | 0–5 |
2012 | 4.19 ± 0.40 | 1.00 ± 0.33 | 1.19 ± 0.40 | | 2.59 ± 1.16 | 0-4.5 | | 2.42 ± 1.08 | 0-4.58 |
RN | 2011 | 91.7%±2.08% | 3.33%±1.15 | 6.67%±0.58% | | 62.7%±40.7% | 0-100% | | 71.3%±36.91% | 0-100% |
2012 | 93.7%±2.31% | 4.67%±1.52 | 8.33%±0.58% | | 54.8%±33.6% | 0-100% | | 78.58 ± 32.23% | 0-100% |
Note: RT, leaf blast resistance at tillering stage. RH, leaf blast resistance at heading stage. RN, neck blast resistance at maturation stage. |
The distributions of lesion scores as measures of blast response at the six measurement stages for the BC3F1 population in 2011 and BC3F2 population in 2012 are shown in Fig. 2. There was transgressive segregation in both directions for all traits. The Pearson correlation coefficients showed significant correlation (p < 0.01) between all six traits in both years (Table S1). Blast resistance of the BC3F1 population at the tillering and heading stages in 2011 had a remarkable positive relationship with blast resistance of the BC3F2 population at the heading and maturation stages in 2012 (p < 0.01). Resistance during different stages also exhibited significant relationships (p < 0.01). Leaf blast at the tillering and heading stages and neck blast at the maturation stage were significantly correlated with each other, so we were able to predict the neck blast response level according to the leaf blast response at tillering under natural condition.
QTL mapping for blast resistance in Jin23B/CR071 population
A total of 16 QTLs for blast resistance were identified on chromosomes 1, 2, 3, 4, 6, 7, 8, 11 and 12 in the Jin23B/CR071 population in two years (Table 2; Fig. 3). The phenotypic variance explained by each QTL ranged from 3.50–34.08%.
Table 2
QTL mapping results from Jin23B/CR071 background population in two years
Trait | Chr | QTL | Position | LOD | Add | R2 (%) | Trait | Chr | QTL | Position | LOD | Add | R2 (%) |
11RT | | | | | | | 12RT | 1 | qBR1 a | RM237-RM486 | 7.39 | -0.73a | 6.09 |
2 | qBR2-1 | RM236-RM452 | 5.32 | 1.42 | 6.64 | 2 | qBR2-1 | RM236-RM452 | 6.17 | 1.63 | 8.17 |
| | | | | | 2 | qBR2-2 | RM324-RM341 | 4.73 | 1.20 | 5.77 |
| | | | | | 2 | qBR2-3 | RM530-RM213 | 4.13 | 0.92 | 9.15 |
3 | qBR3-3 | SR49-RM426 | 20.15 | 1.58 | 25.42 | 3 | qBR3-3 | SR49-RM426 | 30.08 | 1.81 | 34.08 |
6 | qBR6 | RM539-R19951 | 4.05 | 0.92 | 8.89 | 6 | qBR6 | RM539-R19951 | 10.02 | 1.92 | 20.40 |
| | | | | | 7 | qBR7-1 | RM501-RM542 | 3.47 | 1.51 | 10.09 |
| | | | | | 8 | qBR8 | RM72-RM404 | 4.04 | 1.31 | 6.29 |
12 | qBR12 | RM179-YP6213 | 2.80 | 0.57 | 4.25 | 12 | qBR12 | RM179-YP6213 | 3.57 | 0.58 | 4.48 |
11RH | 1 | qBR1 a | RM237-RM486 | 9.34 | -0.93 | 7.99 | 12RH | 1 | qBR1 a | RM237-RM486 | 8.35 | -0.80 | 7.25 |
2 | qBR2-1 | RM236-RM452 | 3.90 | 1.41 | 4.51 | 2 | qBR2-1 | RM236-RM452 | 5.75 | 1.41 | 6.38 |
2 | qBR2-2 | RM324-RM341 | 4.03 | 1.12 | 4.89 | 2 | qBR2-2 | RM324-RM341 | 3.91 | 1.13 | 5.21 |
2 | qBR2-3 | RM530-RM213 | 4.51 | 0.96 | 8.68 | 2 | qBR2-3 | RM530-RM213 | 3.23 | 0.84 | 7.47 |
3 | qBR3-3 | SR49-RM426 | 23.67 | 1.76 | 25.83 | 3 | qBR3-3 | SR49-RM426 | 28.23 | 1.78 | 31.33 |
6 | qBR6 | RM539-R19951 | 8.94 | 0.85 | 7.79 | 6 | qBR6 | RM539-R19951 | 7.80 | 0.95 | 10.40 |
8 | qBR8 | RM72-RM404 | 6.78 | 1.71 | 7.00 | 8 | qBR8 | RM72-RM404 | 4.20 | 1.30 | 4.83 |
12 | qBR12 | RM179-YP6213 | 3.28 | 0.59 | 3.90 | 12 | qBR12 | RM179-YP6213 | 2.93 | 0.53 | 3.50 |
11RN | 1 | qBR1 a | RM237-RM486 | 10.70 | -0.36 | 8.12 | 12RN | 1 | qBR1 a | RM237-RM486 | 10.55 | -0.35 | 9.48 |
2 | qBR2-3 | RM530-RM213 | 3.61 | 0.28 | 7.10 | | | | | | |
3 | qBR3-1 | RM282-RM411 | 4.74 | 0.31 | 7.19 | 3 | qBR3-1 | RM282-RM411 | 7.50 | 0.23 | 7.02 |
3 | qBR3-2 | RM411-RM487 | 4.12 | 0.23 | 3.91 | | | | | | |
4 | qBR4 | RM252-RM470 | 3.04 | 0.22 | 4.16 | | | | | | |
7 | qBR7-1 | RM501-RM542 | 28.26 | 0.54 | 28.48 | 7 | qBR7-1 | RM501-RM542 | 20.27 | 0.36 | 18.94 |
7 | qBR7-2 | RM214-M5543 | 25.26 | 0.48 | 22.00 | 7 | qBR7-2 | RM214-M5543 | 17.44 | 0.37 | 18.94 |
8 | qBR8 | RM72-RM404 | 3.33 | 0.37 | 4.06 | | | | | | |
11 | qBR11-1 | RM181-RM120 | 27.25 | 0.58 | 28.16 | 11 | qBR11-1 | RM181-RM120 | 21.57 | 0.47 | 26.19 |
11 | qBR11-2 | RM120-RM536 | 24.09 | 0.44 | 20.26 | 11 | qBR11-2 | RM120-RM536 | 18.69 | 0.34 | 17.93 |
11 | qBR11-3 | RM21-RM590 | 8.02 | 0.53 | 17.48 | 11 | qBR11-3 | RM21-RM590 | 5.07 | 0.41 | 15.94 |
Note: a, the resistance effect of QTL come from Jin23B. 11RT and 12RT, leaf blast resistance at tillering stage in 2011 and 2012. 11RH and 12RH, leaf blast resistance at heading stage in 2011 and 2012. 11RN and 12RN, neck blast resistance at maturation stage in 2011 and 2012. |
For leaf blast resistance at tillering stage, nine QTLs were detected on chromosome 1, 2, 3, 6, 7, 8 and 12 (Table 2; Fig. 3). Among them, four QTLs, qBR2-1, qBR3-3, qBR6 and qBR12 were detected in both year, five QTLs, qBR1, qBR2-2, qBR2-3, qBR7-1 and qBR8 were detected only in 2012 (Table 2; Fig. 3). The QTLs flanked by SR49 and RM426 on chromosome 3, qBR3-3, was detected in both year and explained 25.42% of the phenotypic variation in 2011 and 34.08% of the phenotypic variation in 2012. A QTLs, qBR6, located between RM539 and R19951 on chromosome 6, was also detected in two years and explained 8.89% and 20.40% of the phenotypic variation, respectively. Two QTLs, qBR2-1 and qBR12, were located flanked by RM236-RM451 on chromosome 2, and RM179-YP6213 on chromosome 12, respectively. qBR2-1 was detected in both years and accounted for 6.64% and 8.17% of the phenotypic variation, respectively. Whereas qBR12 was detected in both year and accounted for 4.25% and 4.48% of the phenotypic variation.
For leaf blast resistance at heading stage, eight QTLs were detected on chromosome 1, 2, 3, 6, 8 and 12 (Table 2; Fig. 3), and all the QTLs were detected in both year. These QTLs explained the phenotypic variance ranged from 3.90–25.83% in 2011, and from 3.50–31.33% in 2012. Among them, the QTL, qBR3-3, flanked by SR49 and RM426 on chromosome 3, have the largest effect which explained 25.83% of the phenotypic variation in 2011 and 31.33% of the phenotypic variation in 2012.
For neck blast resistance at maturation stage, eleven QTLs were detected on chromosome 1, 2, 3, 4, 7, 8 and 11 (Table 2; Fig. 3). Among them, seven QTLs, qBR1, qBR3-1, qBR7-1, qBR7-2, qBR11-1, qBR11-2 and qBR11-3 were detected in both year, four QTLs, qBR2-3, qBR3-2, qBR4 and qBR8 were detected only in 2011 (Table 2; Fig. 3). These QTLs explained the phenotypic variance ranged from 3.91–28.48% in 2011, and from 7.02–26.19% in 2012. A QTL, qBR7-1, located between RM501 and RM542 on chromosome 7, explained 28.48% of the phenotypic variation, which have the largest effect in 2011. Whereas the QTL qBR11-1, located between RM181 and RM120 on chromosome 11, accounted for 26.19% of the phenotypic variation, which have the largest effect in 2012.
Among the sixteen QTLs in the Jin23B/CR071 population, the gene effect of fifteen QTLs come from donor parent CR071, in contrast, the gene effect of qBR1 come from Jin23B. The QTLs, qBR1, flanked by RM237 and RM486 on chromosome 1, was detected in both year at five measuring stage and explained phenotypic variations of 6.09% in 12RT, 7.99% in 11RH, 7.25% in 12RH, 8.12% in 11RN and 9.48% in 12RN, respectively (Table 2). Six QTLs, qBR2-1, qBR2-3, qBR3-3, qBR6, qBR8 and qBR12 were detected in both year at four measuring stage; two QTLs qBR2-2 and qBR7-1 were detected in both year at three measuring stage; five QTLs qBR3-1, qBR7-2, qBR11-1, qBR11-2 and qBR11-3 were detected in both year at two measuring stage and these QTLs only have the effect to neck blast in maturation stage; two QTLs, qBR3-2 and qBR4 were only detected in 11RN.
QTL mapping for blast resistance in Jin23B/QingGuAi population
A total of 13 QTLs for blast resistance were identified on chromosomes 1, 2, 3, 4, 6, 7, 8, 11 and 12 in the Jin23B/QingGuAi population in two years (Table 3; Fig. 4). The phenotypic variance explained by each QTL ranged from 2.42–28.95%.
Table 3
QTL mapping results from Jin23B/QingGuAi background population in two years
Trait | Chr | QTL | Position | LOD | Add | R2 (%) | Trait | Chr | QTL | Position | LOD | Add | R2 (%) |
11RT | 6 | qBR6 | L6ID3F-ZH6111 | 19.39 | 1.40 | 24.93 | 12RT | 1 | qBR1-1 | RM297-RM486 | 2.98 | 0.54 | 3.95 |
7 | qBR7-1 | RM214-RM5543 | 7.83 | 0.89 | 8.87 | 6 | qBR6 | L6ID3F-ZH6111 | 13.73 | 1.14 | 19.91 |
11 | qBR11-1 | RM229-RM457 | 5.17 | 1.08 | 6.57 | 7 | qBR7-1 | RM214-RM5543 | 3.18 | 0.55 | 4.12 |
| | | | | | 11 | qBR11-2 | RM457-YH43 | 6.94 | 34.7 | 5.49 |
11RH | | | | | | | 12RH | 4 | qBR4-2 | RM241-RM317 | 3.44 | 0.49 | 2.51 |
6 | qBR6 | ZH6111-RM20069 | 28.39 | 1.90 | 36.48 | 6 | qBR6 | L6ID3F-ZH6111 | 28.35 | 1.31 | 25.27 |
7 | qBR7-1 | RM214-RM5543 | 14.98 | 1.36 | 16.47 | 7 | qBR7-1 | RM214-RM5543 | 29.33 | 1.43 | 26.31 |
| | | | | | 11 | qBR11-1 | RM229-RM457 | 3.2 | 0.61 | 2.42 |
11RN | | | | | | | 12RN | 1 | qBR1-2 | RM5-RM488 | 10.9 | 24.76 | 8.55 |
| | | | | | 2 | qBR2 | ZH282-RM71 | 2.59 | 44.12 | 8.92 |
| | | | | | 3 | qBR3 | RM3441-RM232 | 4.46 | 50.77 | 12.72 |
4 | qBR4-1 | RM471-RM241 | 3.69 | 42.68 | 12.31 | 4 | qBR4-1 | RM471-RM241 | 7.64 | 40.01 | 18.47 |
4 | qBR4-2 | RM241-RM317 | 2.53 | 45.94 | 8.82 | 4 | qBR4-2 | RM241-RM317 | 6.76 | 46.65 | 16.92 |
6 | qBR6 | L6ID3F-ZH6111 | 33.94 | 50.47 | 31.91 | 6 | qBR6 | L6ID3F-ZH6111 | 29.23 | 42.24 | 28.95 |
7 | qBR7-1 | RM214-RM5543 | 30.17 | 50.02 | 27.94 | 7 | qBR7-1 | RM214-RM5543 | 20.75 | 35.94 | 18.71 |
| | | | | | 7 | qBR7-2 | RM432-RM21691 | 4.61 | 17.06 | 3.43 |
8 | qBR8 | RM404-RM210 | 7.80 | 38.08 | 18.89 | | | | | | |
| | | | | | 12 | qBR12 | RM5927-RM6296 | 8.02 | -33.18 a | 9.58 |
Note: a, the resistance effect of QTL come from Jin23B. 11RT and 12RT, leaf blast resistance at tillering stage in 2011 and 2012. 11RH and 12RH, leaf blast resistance at heading stage in 2011 and 2012. 11RN and 12RN, neck blast resistance at maturation stage in 2011 and 2012. |
For leaf blast resistance at tillering stage, four QTLs were detected on chromosome 1, 6, 7 and 11 (Table 3; Fig. 4). Among them, three QTLs, qBR1-1, qBR6 and qBR7-1 were detected in both year, one QTLs, qBR11-2 was detected only in 2012 (Table 3; Fig. 4). A QTL, qBR1-1, located between RM297 and RM486 on chromosome 1, was detected in two years and explained 24.93% and 3.95% of the phenotypic variation, respectively. The QTL flanked by L6ID3F and ZH6111 on chromosome 6, qBR6, was also detected in both year and explained 8.87% of the phenotypic variation in 2011 and 19.91% of the phenotypic variation in 2012. The QTL, qBR7-1, flanked by RM214 and RM5543 on chromosome 7 was detected in both years and accounted for 6.57% and 4.12% of the phenotypic variation, respectively. Whereas qBR11-2 was detected only in 2012 and accounted for 5.49% of the phenotypic variation.
For leaf blast resistance at heading stage, four QTLs were detected on chromosome 4, 6, 7 and 11 (Table 3; Fig. 4). Two QTLs, qBR6 and qBR7-1, were detected in both year and the QTLs explained the phenotypic variance were 36.48% and 16.47% in 2011, respectively, and 25.27% and 26.31 in 2012, respectively. Two QTL, qBR4-2 and qBR11-1, were located flanked by RM241-RM317 on chromosome 4, and RM229-RM547 on chromosome 11, respectively. The QTLs qBR4-2 and qBR11-1 were detected only in 2012 and accounted for 2.51% and 2.42% of the phenotypic variation, respectively.
For neck blast resistance at maturation stage, ten QTLs were detected on chromosome 1, 2, 3, 4, 6, 7 and 12 (Table 3; Fig. 4). Among them, four QTLs, qBR4-1, qBR4-2, qBR6 and qBR7-1 were detected in both year, and explained the phenotypic variance were 12.31%, 8.82%, 31.91% and 27.94%, respectively, in 2011, and were 18.47%, 16.92%, 28.95% and 18.71%, respectively, in 2012. Six QTLs, qBR1-2, qBR2, qBR3, qBR7-2, qBR8 and qBR12 were detected only in one year (Table 3; Fig. 4), and explained the phenotypic variance were 8.55%, 8.92%, 12.72%, 3.43%, 18.89% and 9.58%, respectively.
Among the thirteen QTLs in the Jin23B/QingGuAi population, the gene effect of twelve QTLs come from donor parent QingGuAi, in contrast, the gene effect of qBR12 come from Jin23B. The QTLs, qBR12, flanked by RM5927 and RM6296 on chromosome 12, was detected only in 2012 at maturation stage and explained phenotypic variations of 9.58% (Table 2). Two QTLs, qBR6 and qBR7 were detected in both year at six measuring stage; one QTL, qBR4-2, was detected in both year at three measuring stage; two QTLs, qBR4-1 and qBR11-2 were detected in both year at two measuring stage; eight QTLs, qBR1-1, qBR1-2, qBR2, qBR3, qBR7-2, qBR8, qBR11-1 and qBR12 were only detected in one measuring stage.