QTLs underlying natural variation in stele and xylem structures of rice root

Rice cultivars show a wide range of variation in stele and xylem structures of the root as well as in root thickness (RTH). We identified quantitative trait loci (QTLs) for stele and xylem structures of the root by using 117 F-3 lines from a cross between the lowland rice cultivar IR64 (thin roots) and the upland rice cultivar Kinandang Patong (thick roots). QTL analysis was performed using genotype data consisting of 197 DNA markers in F-2 plants and phenotype data of the F-3 plants. Stele transversal area (STA), total area and number of late metaxylem vessels (MXA and MXN) and RTH were measured in basal cross sections of nodal roots. A total of 10 QTLs, 2 for STA, 4 for MXA, 2 for MXN and 2 for RTH, were detected on chromosomes 1, 2, 3, 9 and 10. The Kinandang Patong allele at all QTLs showed a positive additive effect on each trait, except for one QTL for MXA on chromosome 10. The phenotypic variance explained by each QTL ranged from 8.7% to 23.9%. A QTL for MXA on chromosome 9 showed the largest effect (23.9%) on total phenotypic variance. Although one QTL for STA, detected on chromosome 2, was mapped near a QTL for RTH, the other QTLs for stele and xylem structures did not map to the same chromosomal regions as the QTLs for RTH. We conclude that stele and xylem structures might be controlled by several genetic factors different from the QTLs for RTH.