QTLs affecting leaf rolling and folding in rice

Leaf rolling (outward) and folding (inward) are two morphological characters for which tremendous genetic variation exists among different rice genotypes. Slightly rolled or folded leaves may allow rice plants to have greater effective leaf area per unit land without causing shading. In addition, genotypes with partially rolled or folded leaves may have better water use efficiency because leaf rolling or folding is expected to have reduced leaf area. Although several genes controlling the extreme phenotype of leaf rolling have been reported (cf. Nagato and Yoshimura 1998), leaf rolling and folding in rice appear to be a complex trait since varied degrees of leaf rolling and folding are often observed in progenies from crosses involving distantly related parents which show no leaf rolling or folding. In this study, we report identification of quantitative trait loci (QTLs) associated with leaf rolling and folding in 188 recombinant inbred lines (RILs) from a cross between Lemont (japonica) and Teqing (indica) using DNA markers. The 188 RILs were planted in the field at IRRI in two replications. Individual RILs in each replication were visually evaluated for their leaf rolling (outward) and folding (inward) based on a scale of I - 5 scores at booting stage, in which 1 indicated no folding or rolling, and 5 indicated rolling nearly into cylinder or nearly complete folding. A complete linkage map consisting of 256 markers including 179 well-distributed RFLP markers, three morphological markers gil, C and Ph (Li et a!. 1999), as well as 74 RAPD markers was used for QTL analysis. QTL mapping was performed using the QTLMapper Version 1.0 based on a threshold of LOD 3.0 (Wang et a!. 1999). Lemont bad slightly rolled leaves (score 2) while Teqing showed slightly folded leaves (score 2). However, the RILs exhibited considerable transgressive segregation in leaf rolling and folding, ranging from 1 - 5 for both traits. Four main-effect QTLs and a pair of epistatic loci influencing leaf rolling were mapped to 6 rice chromosomes (1, 3, 4, 5, 6, and 7) (Tables 1 and 2). Collectively, these QTLs explained 60% of the total phenotypic variation. Two QTLs, QR11 and QR13 were detected with LOD scores of 9.8 and 7.1, and explained 15.2% and 9.6% of the total phenotypic variation, respectively. The interaction between QR11 and QR13 explained an additional 14.5% of the variation. The other two main-effect QTLs had relatively small effects. The Lemont allele at 2 QTLs (QR11 and QRI7) resulted in increased degree of outward leaf rolling. Four main-effect QTLs and three pairs of epistatic loci causing leaf folding were mapped to chromosomes 1,3,4,5,6, 7,9, and 12. And collectively explained 57.6% of the total phenotypic variation (Tables 1 and 2). QF14, QF15, QF17 and QF19 explained 9.3%, 15.3%, 4.6% and 7.7% of the total genotypic variation in inward leaf folding. The Teqing alleles at 3 QTLs (QF14, QF17 and QF19) caused increased degree of inward leaf folding. It is interesting to note that QR15 and QF15 were mapped at the identical location. However, whether these two QTLs represent the same gene affecting leaf rolling and folding, remains to be tested.

Leaf rolling (outward) and folding (inward) are two morphological characters for which tremendous genetic variation exists among different rice genotypes. Slightly rolled or folded leaves may allow rice plants to have greater effective leaf area per unit land without causing shading. In addition, genotypes with partially rolled or folded leaves may have better water use efficiency because leaf rolling or folding is expected to have reduced leaf area. Although several genes controlling the extreme phenotype of leaf rolling have been reported (cf. Nagato and Yoshimura 1998), leaf rolling and folding in rice appear to be a complex trait since varied degrees of leaf rolling and folding are often observed in progenies from crosses involving distantly related parents which show no leaf rolling or folding. In this study, we report identification of quantitative trait loci (QTLs) associated with leaf rolling and folding in 188 recombinant inbred lines (RILs) from a cross between Lemont (japonica) and Teqing (indica) using DNA markers.

The 188 RILs were planted in the field at IRRI in two replications. Individual RILs in each replication were visually evaluated for their leaf rolling (outward) and folding (inward) based on a scale of I - 5 scores at booting stage, in which 1 indicated no folding or rolling, and 5 indicated rolling nearly into cylinder or nearly complete folding. A complete linkage map consisting of 256 markers including 179 well-distributed RFLP markers, three morphological markers gil, C and Ph (Li et a!. 1999), as well as 74 RAPD markers was used for QTL analysis. QTL mapping was performed using the QTLMapper Version 1.0 based on a threshold of LOD 3.0 (Wang et a!. 1999).

Lemont bad slightly rolled leaves (score 2) while Teqing showed slightly folded leaves (score 2). However, the RILs exhibited considerable transgressive segregation in leaf rolling and folding, ranging from 1 - 5 for both traits. Four main-effect QTLs and a pair of epistatic loci influencing leaf rolling were mapped to 6 rice chromosomes (1, 3, 4, 5, 6, and 7) (Tables 1 and 2). Collectively, these QTLs explained 60% of the total phenotypic variation. Two QTLs, QR11 and QR13 were detected with LOD scores of 9.8 and 7.1, and explained 15.2% and 9.6% of the total phenotypic variation, respectively. The interaction between QR11 and QR13 explained an additional 14.5% of the variation. The other two main-effect QTLs had relatively small effects. The Lemont allele at 2 QTLs (QR11 and QRI7) resulted in increased degree of outward leaf rolling.

Four main-effect QTLs and three pairs of epistatic loci causing leaf folding were mapped to chromosomes 1,3,4,5,6, 7,9, and 12. And collectively explained 57.6% of the total phenotypic variation (Tables 1 and 2). QF14, QF15, QF17 and QF19 explained 9.3%, 15.3%, 4.6% and 7.7% of the total genotypic variation in inward leaf folding. The Teqing alleles at 3 QTLs (QF14, QF17 and QF19) caused increased degree of inward leaf folding. It is interesting to note that QR15 and QF15 were mapped at the identical location. However, whether these two QTLs represent the same gene affecting leaf rolling and folding, remains to be tested.