Rice Genetics IV - IRRI books - International Rice Research Institute

(case 3), one may infer that this gene is expressed when the plant starts to elongate. Itsexpression apparently reaches its peak in the middle phase of panicle differentiation,as suggested by its strongest effect on the upper third internode. QNnei3 (case 4) iseven more interesting. The mapping data suggest that this gene expresses strongly atthe early vegetative growth stage, indicated by its large effect on the number ofnonelongated internodes, which contributes strongly to heading date but weakly toheight. QGl3 and QGw5 (cases 5 and 6) represent the indirect effects on grain weightof two genes affecting grain length and width. In addition, the opposite effects of thetwo genes on grain density provide an appropriate explanation for the negative correlationbetween grain length and/or width and grain density. This is a good examplefor the clustered QTLs arising from correlated traits having physiological (causal)relationships (Xu et al 2001). It should be pointed out that QTLs affecting correlatedtraits tend to be mapped in clusters in most reported QTL mapping studies. On theother hand, it is common that QTLs for uncorrelated traits can also be mapped togetherin the same experiment. In these cases, caution should be taken in interpretingthe results because of the typical low resolution (5–15 cM) of most mapped QTLseven with the use of more advanced analytical methods (Wang et al 1999, Kao et al1999).Table 10. Some main-effect QTLs (M-QTLs) affecting correlated traits identified in the Lemont/Teqing recombinant inbred population.Case M-QTL Trait Marker interval LOD Effect1 QPbn3b Primary branch number RM227–RM85 12.77 –0.54Secondary branch number 19.83 –4.89Spikelets per panicle 20.26 –0.822 QPbn4 Primary branch number RM303–RM317 8.30 0.48Secondary branch number 3.54 2.14Spikelets per panicle 2.94 0.343 QLusi12 Length of upper 2nd internode (cm) RG20q–RG91q 6.70 –0.69Length of upper 3rd internode (cm) 12.34 –0.92Length of upper 4th internode (cm) 12.03 –0.68Plant height (cm) 5.81 –2.374 QNnei3 Nonelongated internode number RG348a–C636x 13.47 –1.02Elongated internode number 11.23 –0.21Heading date (d) 15.23 –3.60Length of upper 4th internode (cm) 4.11 –0.42Plant height (cm) 4.98 –1.965 QGl3 Grain length (mm) RD3.5–RD3.7 15.31 3.04Grain volume (mm 3 ) 3.97 11.80Grain density (mg mm –3 ) 5.43 –0.741,000-grain weight (g) 8.34 0.806 QGw5 Grain width (mm) Y1049–R569a 12.87 –1.07Grain thickness (mm) 7.20 –0.36Grain volume (mm 3 ) 7.56 –1.85Grain density (mg mm –3 ) 7.93 1.031,000-grain weight (g) 3.81 –0.62QTL mapping in rice: . . . 165