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A QTL for root growth angle on rice chromosome 7 is involved in the genetic pathway of DEEPER ROOTING 1.

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

Bottom Line: By crossing IR64 (which has a non-functional allele of DRO1) with Kinandang Patong (which has a functional allele of DRO1), we developed 26 chromosome segment substitution lines (CSSLs) that carried a particular chromosome segment from Kinandang Patong in the IR64 genetic background.Using these CSSLs, we found only one chromosomal region that was related to RGA: on chromosome 9, which includes DRO1.DRO3 may only affect RGA in plants with a functional DRO1 allele, suggesting that DRO3 is involved in the DRO1 genetic pathway.

View Article: PubMed Central - PubMed

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

ABSTRACT

Background: Root growth angle (RGA) is an important trait that influences the ability of rice to avoid drought stress. DEEPER ROOTING 1 (DRO1), which is a major quantitative trait locus (QTL) for RGA, is responsible for the difference in RGA between the shallow-rooting cultivar IR64 and the deep-rooting cultivar Kinandang Patong. However, the RGA differences between these cultivars cannot be fully explained by DRO1. The objective of this study was to identify new QTLs for RGA explaining the difference in RGA between these cultivars.

Results: By crossing IR64 (which has a non-functional allele of DRO1) with Kinandang Patong (which has a functional allele of DRO1), we developed 26 chromosome segment substitution lines (CSSLs) that carried a particular chromosome segment from Kinandang Patong in the IR64 genetic background. Using these CSSLs, we found only one chromosomal region that was related to RGA: on chromosome 9, which includes DRO1. Using an F2 population derived from a cross between Kinandang Patong and the Dro1-NIL (near isogenic line), which had a functional DRO1 allele in the IR64 genetic background, we identified a new QTL for RGA (DRO3) on the long arm of chromosome 7.

Conclusions: DRO3 may only affect RGA in plants with a functional DRO1 allele, suggesting that DRO3 is involved in the DRO1 genetic pathway.

No MeSH data available.


Related in: MedlinePlus

LOD score curves for the QTLs for the ratio of deep rooting and root growth angle in the KD-F2 plants. Rectangles represent linkage maps, with the DNA marker positions shown as vertical lines. Chromosome numbers are indicated under each linkage map (short arms are on the left). 9S and 9 L indicate separate linkage maps for the short and long arms of chromosome 9, respectively, for the region around DRO1 that is homozygous for Kinandang Patong. Dotted lines indicate the LOD thresholds (6.20 for both the ratio of deep rooting and the root growth angle).
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Fig4: LOD score curves for the QTLs for the ratio of deep rooting and root growth angle in the KD-F2 plants. Rectangles represent linkage maps, with the DNA marker positions shown as vertical lines. Chromosome numbers are indicated under each linkage map (short arms are on the left). 9S and 9 L indicate separate linkage maps for the short and long arms of chromosome 9, respectively, for the region around DRO1 that is homozygous for Kinandang Patong. Dotted lines indicate the LOD thresholds (6.20 for both the ratio of deep rooting and the root growth angle).

Mentions: Among the 768 SNP markers, 273 (35.5%) were polymorphic between IR64 and Kinandang Patong. To resolve the linkage gaps and to saturate the regions around the LOD support intervals for the QTLs detected with the DNA markers, we added 33 polymorphic SSR markers in these regions. The linkage map for the KD-F2 plants, composed of 306 DNA markers, covered almost the entire rice genome (Additional file 2: Figure S2). The total map length was 1359.8 cM, and the average distance between markers was 4.63 cM. The linkage map of chromosome 9 was divided into two linkage groups near the region of DRO1 because Dro1-NIL has the same chromosome segment as Kinandang Patong in this region (Figure 4, Additional file 2: Figure S2).Figure 4


A QTL for root growth angle on rice chromosome 7 is involved in the genetic pathway of DEEPER ROOTING 1.

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

LOD score curves for the QTLs for the ratio of deep rooting and root growth angle in the KD-F2 plants. Rectangles represent linkage maps, with the DNA marker positions shown as vertical lines. Chromosome numbers are indicated under each linkage map (short arms are on the left). 9S and 9 L indicate separate linkage maps for the short and long arms of chromosome 9, respectively, for the region around DRO1 that is homozygous for Kinandang Patong. Dotted lines indicate the LOD thresholds (6.20 for both the ratio of deep rooting and the root growth angle).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384719&req=5

Fig4: LOD score curves for the QTLs for the ratio of deep rooting and root growth angle in the KD-F2 plants. Rectangles represent linkage maps, with the DNA marker positions shown as vertical lines. Chromosome numbers are indicated under each linkage map (short arms are on the left). 9S and 9 L indicate separate linkage maps for the short and long arms of chromosome 9, respectively, for the region around DRO1 that is homozygous for Kinandang Patong. Dotted lines indicate the LOD thresholds (6.20 for both the ratio of deep rooting and the root growth angle).
Mentions: Among the 768 SNP markers, 273 (35.5%) were polymorphic between IR64 and Kinandang Patong. To resolve the linkage gaps and to saturate the regions around the LOD support intervals for the QTLs detected with the DNA markers, we added 33 polymorphic SSR markers in these regions. The linkage map for the KD-F2 plants, composed of 306 DNA markers, covered almost the entire rice genome (Additional file 2: Figure S2). The total map length was 1359.8 cM, and the average distance between markers was 4.63 cM. The linkage map of chromosome 9 was divided into two linkage groups near the region of DRO1 because Dro1-NIL has the same chromosome segment as Kinandang Patong in this region (Figure 4, Additional file 2: Figure S2).Figure 4

Bottom Line: By crossing IR64 (which has a non-functional allele of DRO1) with Kinandang Patong (which has a functional allele of DRO1), we developed 26 chromosome segment substitution lines (CSSLs) that carried a particular chromosome segment from Kinandang Patong in the IR64 genetic background.Using these CSSLs, we found only one chromosomal region that was related to RGA: on chromosome 9, which includes DRO1.DRO3 may only affect RGA in plants with a functional DRO1 allele, suggesting that DRO3 is involved in the DRO1 genetic pathway.

View Article: PubMed Central - PubMed

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

ABSTRACT

Background: Root growth angle (RGA) is an important trait that influences the ability of rice to avoid drought stress. DEEPER ROOTING 1 (DRO1), which is a major quantitative trait locus (QTL) for RGA, is responsible for the difference in RGA between the shallow-rooting cultivar IR64 and the deep-rooting cultivar Kinandang Patong. However, the RGA differences between these cultivars cannot be fully explained by DRO1. The objective of this study was to identify new QTLs for RGA explaining the difference in RGA between these cultivars.

Results: By crossing IR64 (which has a non-functional allele of DRO1) with Kinandang Patong (which has a functional allele of DRO1), we developed 26 chromosome segment substitution lines (CSSLs) that carried a particular chromosome segment from Kinandang Patong in the IR64 genetic background. Using these CSSLs, we found only one chromosomal region that was related to RGA: on chromosome 9, which includes DRO1. Using an F2 population derived from a cross between Kinandang Patong and the Dro1-NIL (near isogenic line), which had a functional DRO1 allele in the IR64 genetic background, we identified a new QTL for RGA (DRO3) on the long arm of chromosome 7.

Conclusions: DRO3 may only affect RGA in plants with a functional DRO1 allele, suggesting that DRO3 is involved in the DRO1 genetic pathway.

No MeSH data available.


Related in: MedlinePlus