Abstract
BackgroundThe 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 F2 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.ResultsWe 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.ConclusionNatural 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 materialThe online version of this article (doi:10.1186/s12284-015-0049-2) contains supplementary material, which is available to authorized users.
Highlights
The functional allele of the rice gene DEEPER ROOTING 1 (DRO1) increases the root growth angle (RGA)
Phenotypic variation of the RGA and ratio of deep rooting (RDR) in three rice cultivars Sequence analysis of the DRO1 transcribed regions in 15 Japanese rice cultivars showed that 11 accessions had the same sequences as Kinandang Patong (Group I; Additional file 1: Figure S1)
Detection of QTLs for deep rooting in MoK-F2 The RDR50s in MoK-F2 were distributed between the values of the parental lines without considerable transgressive segregation, the RDR70s showed transgressive segregation, with values ranging from 3.5% to 43.3% (Figure 2)
Summary
The functional allele of the rice gene DEEPER ROOTING 1 (DRO1) increases the root growth angle (RGA). Wide natural variation in RGA is observed among rice cultivars with the functional DRO1 allele. All four accessions belong to the same haplotype group of functional DRO1 allele. The availability of water and nutrients in the soil strongly influences crop productivity (Herder et al 2010). These resources are heterogeneously distributed in the soil. An heterogeneous distribution of nutrients is caused by soil mobility and an uneven distribution of organic matter.
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