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

Kitomi Y, Kanno N, Kawai S, Mizubayashi T, Fukuoka S, Uga Y - Rice (N Y) (2015)

Bottom Line: 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.With the LOD threshold reduced to 3.0, several minor QTLs for RGA were also detected in each population.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.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan.

ABSTRACT

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 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.

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.

No MeSH data available.


Related in: MedlinePlus

Frequency distributions of the ratio of deep rooting (RDR) in three F2populations. RDR50 (a) and RDR70 (b) were calculated as the numbers of roots that penetrated the mesh at an angle of >50° and >70° from the soil surface, respectively, divided by the total number of roots that penetrated the whole mesh (see Figure S8). MoK-F2, Momiroman × Kinandang Patong; YuK-F2, Yumeaoba × Kinandang Patong; TaK-F2, Tachisugata × Kinandang Patong. Vertical and horizontal lines above the bars indicate the mean and SD of each parental line.
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Fig2: Frequency distributions of the ratio of deep rooting (RDR) in three F2populations. RDR50 (a) and RDR70 (b) were calculated as the numbers of roots that penetrated the mesh at an angle of >50° and >70° from the soil surface, respectively, divided by the total number of roots that penetrated the whole mesh (see Figure S8). MoK-F2, Momiroman × Kinandang Patong; YuK-F2, Yumeaoba × Kinandang Patong; TaK-F2, Tachisugata × Kinandang Patong. Vertical and horizontal lines above the bars indicate the mean and SD of each parental line.

Mentions: 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). The other four accessions belonged to the haplotype group VII. Among the 11 accessions, we selected three accessions showing different RGA (Figure 1). The mean RGA increased in the following order: Momiroman, Yumeaoba, Tachisugata, and Kinandang Patong. Among the parental lines, Momiroman showed the smallest RDR50 and RDR70 (Figure 2), which is consistent with the lowest RGA in this cultivar.Figure 1


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

Kitomi Y, Kanno N, Kawai S, Mizubayashi T, Fukuoka S, Uga Y - Rice (N Y) (2015)

Frequency distributions of the ratio of deep rooting (RDR) in three F2populations. RDR50 (a) and RDR70 (b) were calculated as the numbers of roots that penetrated the mesh at an angle of >50° and >70° from the soil surface, respectively, divided by the total number of roots that penetrated the whole mesh (see Figure S8). MoK-F2, Momiroman × Kinandang Patong; YuK-F2, Yumeaoba × Kinandang Patong; TaK-F2, Tachisugata × Kinandang Patong. Vertical and horizontal lines above the bars indicate the mean and SD of each parental line.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4385264&req=5

Fig2: Frequency distributions of the ratio of deep rooting (RDR) in three F2populations. RDR50 (a) and RDR70 (b) were calculated as the numbers of roots that penetrated the mesh at an angle of >50° and >70° from the soil surface, respectively, divided by the total number of roots that penetrated the whole mesh (see Figure S8). MoK-F2, Momiroman × Kinandang Patong; YuK-F2, Yumeaoba × Kinandang Patong; TaK-F2, Tachisugata × Kinandang Patong. Vertical and horizontal lines above the bars indicate the mean and SD of each parental line.
Mentions: 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). The other four accessions belonged to the haplotype group VII. Among the 11 accessions, we selected three accessions showing different RGA (Figure 1). The mean RGA increased in the following order: Momiroman, Yumeaoba, Tachisugata, and Kinandang Patong. Among the parental lines, Momiroman showed the smallest RDR50 and RDR70 (Figure 2), which is consistent with the lowest RGA in this cultivar.Figure 1

Bottom Line: 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.With the LOD threshold reduced to 3.0, several minor QTLs for RGA were also detected in each population.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.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan.

ABSTRACT

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 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.

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.

No MeSH data available.


Related in: MedlinePlus