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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

Chromosomal positions and allelic effects of QTLs for the ratio of deep rooting (RDR) detected on chromosome 4 in the MoK-F2 population.(a) Peaks of the LOD curves indicate the putative positions of QTLs for RDR. Vertical lines in each linkage map indicate the genetic positions (cM) of DNA markers. Red bar on the linkage map indicates 1.8-LOD support interval of RDR50, calculated by using the lodint function within the R/qtl software. DNA markers are shown under the linkage maps; the numbers in parentheses indicate their physical map positions (Mb) in the Nipponbare genome. The nearest DNA marker to the LOD peak of putative QTL for RDR50 (red) is shown. (b) Frequency distribution of RDR in the MoK-F2 population showing three genotype classes of the DNA markers closest to the QTLs for RDR50. For each allele, an inverted triangle indicates the mean and a horizontal bar indicates SD. The same shading is used for triangles and corresponding bars. The means labeled with different letters differ significantly (P < 0.05, Tukey’s multiple comparison test).
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Fig4: Chromosomal positions and allelic effects of QTLs for the ratio of deep rooting (RDR) detected on chromosome 4 in the MoK-F2 population.(a) Peaks of the LOD curves indicate the putative positions of QTLs for RDR. Vertical lines in each linkage map indicate the genetic positions (cM) of DNA markers. Red bar on the linkage map indicates 1.8-LOD support interval of RDR50, calculated by using the lodint function within the R/qtl software. DNA markers are shown under the linkage maps; the numbers in parentheses indicate their physical map positions (Mb) in the Nipponbare genome. The nearest DNA marker to the LOD peak of putative QTL for RDR50 (red) is shown. (b) Frequency distribution of RDR in the MoK-F2 population showing three genotype classes of the DNA markers closest to the QTLs for RDR50. For each allele, an inverted triangle indicates the mean and a horizontal bar indicates SD. The same shading is used for triangles and corresponding bars. The means labeled with different letters differ significantly (P < 0.05, Tukey’s multiple comparison test).

Mentions: One significant QTL for RDR50 was detected on chromosome 4 with an LOD threshold of 5.76, but no statistically significant QTLs for RDR70 were found with a LOD threshold of 5.79 (Figures 3 and 4a). The QTL for RDR50 showed a large contribution to the phenotypic variance, explaining 20.3% of the total (Table 1). The mean RDR50s of lines homozygous for the Kinandang Patong allele at the SNP marker AE04005953 closest to this QTL were significantly higher than those of the lines homozygous for the Momiroman allele (Figure 4b). When we decreased the LOD threshold to 3.0, we found evidence of three minor QTLs for RDR50 and four minor QTLs for RDR70 (Table 1, Figure 3). Comparison of the map positions of these eight QTLs showed that the QTLs for RDR50 on chromosomes 2, 4, and 7 were located in the same regions as the QTLs for RDR70. One QTL for RDR50 and one for RDR70 were detected on chromosomes 1 and 10, respectively. A two-dimensional scan revealed no significant epistatic interactions in the whole genome in this population (Additional file 3: Figure S3).Figure 3


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)

Chromosomal positions and allelic effects of QTLs for the ratio of deep rooting (RDR) detected on chromosome 4 in the MoK-F2 population.(a) Peaks of the LOD curves indicate the putative positions of QTLs for RDR. Vertical lines in each linkage map indicate the genetic positions (cM) of DNA markers. Red bar on the linkage map indicates 1.8-LOD support interval of RDR50, calculated by using the lodint function within the R/qtl software. DNA markers are shown under the linkage maps; the numbers in parentheses indicate their physical map positions (Mb) in the Nipponbare genome. The nearest DNA marker to the LOD peak of putative QTL for RDR50 (red) is shown. (b) Frequency distribution of RDR in the MoK-F2 population showing three genotype classes of the DNA markers closest to the QTLs for RDR50. For each allele, an inverted triangle indicates the mean and a horizontal bar indicates SD. The same shading is used for triangles and corresponding bars. The means labeled with different letters differ significantly (P < 0.05, Tukey’s multiple comparison test).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Chromosomal positions and allelic effects of QTLs for the ratio of deep rooting (RDR) detected on chromosome 4 in the MoK-F2 population.(a) Peaks of the LOD curves indicate the putative positions of QTLs for RDR. Vertical lines in each linkage map indicate the genetic positions (cM) of DNA markers. Red bar on the linkage map indicates 1.8-LOD support interval of RDR50, calculated by using the lodint function within the R/qtl software. DNA markers are shown under the linkage maps; the numbers in parentheses indicate their physical map positions (Mb) in the Nipponbare genome. The nearest DNA marker to the LOD peak of putative QTL for RDR50 (red) is shown. (b) Frequency distribution of RDR in the MoK-F2 population showing three genotype classes of the DNA markers closest to the QTLs for RDR50. For each allele, an inverted triangle indicates the mean and a horizontal bar indicates SD. The same shading is used for triangles and corresponding bars. The means labeled with different letters differ significantly (P < 0.05, Tukey’s multiple comparison test).
Mentions: One significant QTL for RDR50 was detected on chromosome 4 with an LOD threshold of 5.76, but no statistically significant QTLs for RDR70 were found with a LOD threshold of 5.79 (Figures 3 and 4a). The QTL for RDR50 showed a large contribution to the phenotypic variance, explaining 20.3% of the total (Table 1). The mean RDR50s of lines homozygous for the Kinandang Patong allele at the SNP marker AE04005953 closest to this QTL were significantly higher than those of the lines homozygous for the Momiroman allele (Figure 4b). When we decreased the LOD threshold to 3.0, we found evidence of three minor QTLs for RDR50 and four minor QTLs for RDR70 (Table 1, Figure 3). Comparison of the map positions of these eight QTLs showed that the QTLs for RDR50 on chromosomes 2, 4, and 7 were located in the same regions as the QTLs for RDR70. One QTL for RDR50 and one for RDR70 were detected on chromosomes 1 and 10, respectively. A two-dimensional scan revealed no significant epistatic interactions in the whole genome in this population (Additional file 3: Figure S3).Figure 3

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