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Background  The functional allele of the rice gene  DEEPER ROOTING 1  ( DRO1 ) increases the root growth angle (RGA). However, wide natural variation in RGA is observed among rice cultivars with the functional  DRO1  allele. To elucidate genetic factors related to such variation, we quantitatively measured RGA using the basket method and analyzed quantitative trait loci (QTLs) for RGA in three F 2  mapping populations derived from crosses between the large RGA–type cultivar Kinandang Patong and each of three accessions with varying RGA: Momiroman has small RGA and was used to produce the MoK-F2 population; Yumeaoba has intermediate RGA (YuK-F2 population); Tachisugata has large RGA (TaK-F2 population). All four accessions belong to the same haplotype group of functional  DRO1  allele.    Results  We detected the following statistically significant QTLs: one QTL on chromosome 4 in MoK-F2, three QTLs on chromosomes 2, 4, and 6 in YuK-F2, and one QTL on chromosome 2 in TaK-F2. Among them, the two QTLs on chromosome 4 were located near  DRO2 , which has been previously reported as a major QTL for RGA, whereas the two major QTLs for RGA on chromosomes 2 ( DRO4 ) and 6 ( DRO5 ) were novel. With the LOD threshold reduced to 3.0, several minor QTLs for RGA were also detected in each population.    Conclusion  Natural variation in RGA in rice cultivars carrying functional  DRO1  alleles may be controlled by a few major QTLs and by several additional minor QTLs.    Electronic supplementary material  The online version of this article (doi:10.1186/s12284-015-0049-2) contains supplementary material, which is available to authorized users.

QTLs underlying natural variation of root growth angle among rice cultivars with the same functional allele of DEEPER ROOTING 1