Root angle modifications by the DRO1 homolog improve rice yields in saline paddy fields.

The root system architecture (RSA) of crops can affect their production, particularly in abiotic stress conditions, such as with drought, waterlogging, and salinity. Salinity is a growing problem worldwide that negatively impacts on crop productivity, and it is believed that yields could be improved if RSAs that enabled plants to avoid saline conditions were identified. Here, we have demonstrated, through the cloning and characterization of qSOR1 (quantitative trait locus for SOIL SURFACE ROOTING 1), that a shallower root growth angle (RGA) could enhance rice yields in saline paddies. qSOR1 is negatively regulated by auxin, predominantly expressed in root columella cells, and involved in the gravitropic responses of roots. qSOR1 was found to be a homolog of DRO1 (DEEPER ROOTING 1), which is known to control RGA. CRISPR-Cas9 assays revealed that other DRO1 homologs were also involved in RGA. Introgression lines with combinations of gain-of-function and loss-of-function alleles in qSOR1 and DRO1 demonstrated four different RSAs (ultra-shallow, shallow, intermediate, and deep rooting), suggesting that natural alleles of the DRO1 homologs could be utilized to control RSA variations in rice. In saline paddies, near-isogenic lines carrying the qSOR1 loss-of-function allele had soil-surface roots (SOR) that enabled rice to avoid the reducing stresses of saline soils, resulting in increased yields compared to the parental cultivars without SOR. Our findings suggest that DRO1 homologs are valuable targets for RSA breeding and could lead to improved rice production in environments characterized by abiotic stress.

Haplotype analysis from unmanned aerial vehicle imagery of rice MAGIC population for the trait dissection of biomass and plant architecture.

Unmanned aerial vehicles (UAVs) are popular tools for high-throughput phenotyping of crops in the field. However, their use for evaluation of individual lines is limited in crop breeding because research on what the UAV image data represent is still developing. Here, we investigated the connection between shoot biomass of rice plants and the vegetation fraction (VF) estimated from high-resolution orthomosaic images taken by a UAV 10 m above a field during the vegetative stage. Haplotype-based genome-wide association studies of multi-parental advanced generation inter-cross (MAGIC) lines revealed four quantitative trait loci (QTLs) for VF. VF was correlated with shoot biomass, but the haplotype effect on VF was better correlated with that on shoot biomass at these QTLs. Further genetic characterization revealed the relationships between these QTLs and plant spreading habit, final shoot biomass and panicle weight. Thus, genetic analysis using high-throughput phenotyping data derived from low-altitude, high-resolution UAV images during early stages of rice growing in the field provides insights into plant growth, architecture, final biomass, and yield.

Caregiver treatment satisfaction is improved together with children's asthma control: Prospective study for budesonide monotherapy in school-aged children with uncontrolled asthma symptoms.

BACKGROUND: If asthmatic children cannot obtain sufficient control of their disease, not only do they suffer from asthma symptoms, but the daily life activities of their caregivers are also disrupted. We investigated the effectiveness of an inhaled corticosteroid (ICS) for symptom control in previously ICS-untreated school-aged asthmatic children as well as caregiver treatment satisfaction (CTS). METHODS: A multicenter, open-label, single-arm study on 12-week ICS (budesonide Turbuhaler®) monotherapy was undertaken in subjects aged 5-15 years with bronchial asthma not treated with ICS during the previous 3 months. At 0, 4, 8, and 12 weeks after start of ICS administration, Japanese Pediatric Asthma Control Program (JPAC) scores, and CTS scores were summated and lung function measured. At weeks 0 and 12, questionnaires on caregiver anxiety were also assessed. RESULTS: Seventy-five patients were enrolled, and 69 assessed. Ninety percent of subjects had been treated with asthma controller medication except ICS before study enrollment. JPAC score and CTS score were improved significantly at weeks 4, 8, and 12 (p < 0.001). With regard to CTS, more than half of caregivers showed a perfect score at weeks 8 and 12. There was a significant correlation between JPAC score and CTS score. Lung function and caregiver anxiety were also improved, and good compliance with treatment was observed during the intervention. CONCLUSIONS: If treating ICS-untreated school-aged asthmatic children with uncontrolled symptoms, ICS monotherapy can improve CTS along with improving asthma control.

Genome-wide association study identifies HLA-DP as a susceptibility gene for pediatric asthma in Asian populations.

Asthma is a complex phenotype influenced by genetic and environmental factors. We conducted a genome-wide association study (GWAS) with 938 Japanese pediatric asthma patients and 2,376 controls. Single-nucleotide polymorphisms (SNPs) showing strong associations (P<1×10(-8)) in GWAS were further genotyped in an independent Japanese samples (818 cases and 1,032 controls) and in Korean samples (835 cases and 421 controls). SNP rs987870, located between HLA-DPA1 and HLA-DPB1, was consistently associated with pediatric asthma in 3 independent populations (P(combined) = 2.3×10(-10), odds ratio [OR] = 1.40). HLA-DP allele analysis showed that DPA1*0201 and DPB1*0901, which were in strong linkage disequilibrium, were strongly associated with pediatric asthma (DPA1*0201: P = 5.5×10(-10), OR = 1.52, and DPB1*0901: P = 2.0×10(-7), OR = 1.49). Our findings show that genetic variants in the HLA-DP locus are associated with the risk of pediatric asthma in Asian populations.

Prophylactic effectiveness of suplatast tosilate in children with asthma symptoms in the autumn: a pilot study.

BACKGROUND: Exacerbations of bronchial asthma usually occur in the autumn. To our knowledge, however, the effectiveness of drugs for preventing exacerbations of asthma in the autumn has not been studied previously, except for leukotriene receptor antagonists and Omalizmab. METHODS: This study compared the prophylactic effectiveness of suplatast tosilate with that of mequitazine in children with asthma symptoms, which is usually exacerbated in the autumn. The study group comprised 27 children aged 2 to 15 years who required treatment for asthmatic attacks during the past year and tested positive at least for mite allergen in the preceding autumn. The subjects were randomly assigned to receive either suplatast or mequitazine. The primary endpoint of this study was the number of days without symptoms during the 8 weeks of treatment. In addition, the Japanese Pediatric Asthma Control Program (JPAC) scores were also recorded every 2 weeks in each group. RESULTS: Overall, 14 patients received suplatast, and 13 received mequitazine for 8 weeks from September through early October. During follow-up, the number of days without symptoms and the total JPAC scores did not differ significantly between the groups. However, as compared with weeks 1 to 2 of treatment, the mean number of days without symptoms during weeks 7 to 8 increased significantly in only the suplatast group (8.6 vs. 11.5 days; p = 0.004). CONCLUSIONS: Our results suggest that short-term additional treatment with suplatast is useful for preventing asthma symptoms in children with asthma, which is usually exacerbated in the autumn.

Inhibition of common cold-induced aggravation of childhood asthma by leukotriene receptor antagonists.

BACKGROUND: Virus infection is an important risk factor for aggravation of childhood asthma. The objective of this study was to examine the effect of drugs on aggravation of asthma induced by a common cold. METHODS: Asthma control was examined in a survey of 1,014 Japanese pediatric patients with bronchial asthma. The occurrence of common cold, asthma control, and drugs used for asthma control were investigated using a modified Childhood Asthma Control Test (C-ACT) for patients aged <4 years old and 4 to 11 years old, and an Asthma Control Test (ACT) for patients aged 12 to 15 years old. RESULTS: The status of asthma control did not differ among the age groups. The prevalence of common cold and aggravation of asthma were significantly higher in patients aged <4 years old. Control of asthma following common cold-induced aggravation was significantly less effective in patients aged <4 years old compared to those aged ≥4 years old. In patients aged <4 years old with a common cold, asthma control was significantly more effective for those treated with leukotriene receptor antagonists (LTRAs) compared to treatment without LTRAs. Asthma control did not differ between patients who did or did not take inhaled corticosteroids or long-acting ß2 stimulants. CONCLUSIONS: These findings showed a high prevalence of common cold in younger patients with childhood asthma and indicated that common cold can induce aggravation of asthma. LTRAs are useful for long-term asthma control in very young patients who develop an asthma attack due to a common cold.

[Changes in treatment, symptoms and QOL of pediatric asthma patients at different ages for 7 years in Tochigi].

BACKGROUND: A 7-year analysis of pediatric asthma in Tochigi was performed with the aim of improvement of future treatment. METHODS: Self-administered questionnaires were completed by pediatric asthma patients and their parents who visited pediatric clinics or hospitals in Tochigi at the same period of year in 2002, 2006, and 2008. Changes in asthma symptoms and in the QOL of the patients and their parents were analyzed. Data on the background and treatment of the patients were obtained from doctors. RESULTS: The questionnaires were answered by 1487, 1058, and 1014 patients or parents in 2002, 2006, and 2008, respectively. The results showed significant increases in the use of ICS and LTRA (p< 0.001, for each.) and significant decreases in the use of theophylline, DSCG, and LABA (p< 0.001, for each.). Frequency of wheezing, cough and sputum were significantly reduced in all age groups (p< 0.01, for each.). There were significant reductions of frequency of wheezing in patients under 2 years old; in wheezing and cough in patients aged 2-5 years old; and in wheezing, cough and sputum in patients aged 6-15 years old (p< 0.05 for each.). The QOL of the patients and their parents was significantly improved in all age groups (p< 0.05 for each.). CONCLUSION: These findings suggest that increased use of anti-inflammatory agents such as LTRA and ICS have contributed to a reduction in asthma symptoms and an improvement in the QOL of the pediatric patients and their parents, but more widespread use of these agents are still needed for residual uncontrolled asthma patients.

Development and validation of a nighttime sleep diary in asthmatic children.

The aim of this study was to derive a shorter version of the asthma diary, 'a nighttime sleep diary' from the traditional asthma diary (original version). The nighttime sleep diary mainly consisted of nighttime awakening that met the criteria of validity and practicality necessary for monitoring clinical control in infants and young children with asthma symptoms. Validation of the diary was performed in a 6-week prospective study of 40 children aged 6 months to 6 years treated with nebulized budesonide inhalation suspension or cromolyn sodium nebulized solution. The nighttime awakening score was significantly and positively associated with the nighttime asthma symptom score and daytime asthma symptom score along with the number of days with a cough. Therefore, the nighttime sleep diary is a simple and useful instrument to monitor day-to-day fluctuations in young children with asthma.

Remote-Sensing-Combined Haplotype Analysis Using Multi-Parental Advanced Generation Inter-Cross Lines Reveals Phenology QTLs for Canopy Height in Rice.

High-throughput phenotyping systems with unmanned aerial vehicles (UAVs) enable observation of crop lines in the field. In this study, we show the ability of time-course monitoring of canopy height (CH) to identify quantitative trait loci (QTLs) and to characterise their pleiotropic effect on various traits. We generated a digital surface model from low-altitude UAV-captured colour digital images and investigated CH data of rice multi-parental advanced generation inter-cross (MAGIC) lines from tillering and heading to maturation. Genome-wide association studies (GWASs) using the CH data and haplotype information of the MAGIC lines revealed 11 QTLs for CH. Each QTL showed haplotype effects on different features of CH such as stage-specificity and constancy. Haplotype analysis revealed relationships at the QTL level between CH and, vegetation fraction and leaf colour [derived from UAV red-green-blue (RGB) data], and CH and yield-related traits. Noticeably, haplotypes with canopy lowering effects at qCH1-4, qCH2, and qCH10-2 increased the ratio of panicle weight to leaf and stem weight, suggesting biomass allocation to grain yield or others through growth regulation of CH. Allele mining using gene information with eight founders of the MAGIC lines revealed the possibility that qCH1-4 contains multiple alleles of semi-dwarf 1 (sd1), the IR-8 allele of which significantly contributed to the "green revolution" in rice. This use of remote-sensing-derived phenotyping data into genetics using the MAGIC lines gives insight into how rice plants grow, develop, and produce grains in phenology and provides information on effective haplotypes for breeding with ideal plant architecture and grain yield.

[Investigation of factors childhood asthma persisting into adulthood].

BACKGROUND: A questionnaire survey was conducted to determine the percentages of patients with childhood-onset asthma persisting into adulthood and adult-relapse asthma in the adult asthmatic population, and to identify the factors the childhood-onset asthma persisting into adulthood. METHODS: The questionnaire survey included 822 adult asthmatic patients who visited out patient clinic at Nishikata Hospital. The characteristics of the three groups of adult asthmatics, namely, the childhood-onset asthma persisting into adulthood, adult-onset asthma and adult-relapse asthma, were compared with those of a group of 153 pediatric asthma patients with remission (control group). RESULTS: 1) The numbers of patients with adult-onset asthma, childhood-onset asthma persisting into adulthood and adult-relapse asthma in the survey population were 531 (64.7%), 168 (20.4%) and 123 (14.9%), respectively. 2) Comparison of the characteristics of the two groups of adult asthmatics (childhood-onset asthma persisting into adulthood and adult-relapse asthma) and control group revealed that the average age at onset and percentage of patients with a history of without preventive treatment, and delay in the start of early interventions were higher in the former groups than in the control group (p<0.01). Furthermore, the frequencies of severe asthma were significantly higher in the patients with childhood-onset asthma persisting into adulthood than in control group (p<0.01). The percentage of smokers was higher in the adult-relapse asthma group and childhood-onset asthma persisting into adulthood group than in control group. CONCLUSION: 1) In this adult asthmatic study population, the percentages of childhood-onset asthma persisting into adulthood and adult-relapse asthma in adult asthmatic population were 35.3%. 2) To prevent persistence of childhood-onset asthma into adulthood, it is important to prevent smoking, not keeping pets, and not delay in the onset of early interventions in childhood.

Surveillance of panicle positions by unmanned aerial vehicle to reveal morphological features of rice.

Rice plant architecture affects biomass and grain yield. Thus, it is important to select rice genotypes with ideal plant architecture. High-throughput phenotyping by use of an unmanned aerial vehicle (UAV) allows all lines in a field to be observed in less time than with traditional procedures. However, discrimination of plants in dense plantings is difficult, especially during the reproductive stage, because leaves and panicles overlap. Here, we developed an original method that relies on using UAV to identify panicle positions for dissecting plant architecture and to distinguish rice lines by detecting red flags attached to panicle bases. The plant architecture of recombinant inbred lines derived from Japanese cultivars 'Hokuriku 193' and 'Mizuhochikara', which differ in plant architecture, was assessed using a commercial camera-UAV system. Orthomosaics were made from UAV digital images. The center of plants was plotted on the image during the vegetative stage. The horizontal distance from the center to the red flag during the reproductive stage was used as the panicle position (PP). The red flags enabled us to recognize the positions of the panicles at a rate of 92%. The PP phenotype was related to but was not identical with the phenotypes of the panicle base angle, leaf sheath angle, and score of spreading habit. These results indicate that PP on orthomosaics could be used as an index of plant architecture under field conditions.

Discovery of QTL Alleles for Grain Shape in the Japan-MAGIC Rice Population Using Haplotype Information.

A majority of traits are determined by multiple quantitative trait loci (QTL) that can have pleiotropic effects. A multi-parent advanced generation inter-cross (MAGIC) population is well suited for genetically analyzing the effects of multiple QTL on traits of interest because it contains a higher number of QTL alleles than a biparental population. We previously produced the JAPAN-MAGIC (JAM) population, derived from eight rice (Oryza sativa L.) cultivars with high yield and biomass in Japan, and developed the method of genome-wide association study (GWAS) using haplotype information on the JAM lines. This method was effective for identifying major genes such as Waxy for eating quality and Sd1 for culm length. Here, we show that haplotype-based GWAS is also effective for the evaluation of multiple QTL with small effects on rice grain shape in the JAM lines. Although both the haplotype- and SNP-based GWAS identified multiple QTL for grain length and width, the sum of the estimated trait values of each allele for the QTL detected by haplotype-based GWAS had higher correlation with observed values than those detected by SNP-based GWAS, indicating high-accuracy QTL detection in the haplotype-based GWAS. Furthermore, the study revealed pleiotropic effects of some QTL regions in regulation of grain shape, suggesting that the haplotype-based GWAS using the JAM lines is an effective means to evaluate the main and side effects of haplotypes at each QTL. Information on the pleiotropic effects of haplotypes on various traits will be useful for designing ideal lines in a breeding program.

Haplotype-based allele mining in the Japan-MAGIC rice population.

Multi-parent advanced generation inter-cross (MAGIC) lines have broader genetic variation than bi-parental recombinant inbred lines. Genome-wide association study (GWAS) using high number of DNA polymorphisms such as single-nucleotide polymorphisms (SNPs) is a popular tool for allele mining in MAGIC populations, in which the associations of phenotypes with SNPs are investigated; however, the effects of haplotypes from multiple founders on phenotypes are not considered. Here, we describe an improved method of allele mining using the newly developed Japan-MAGIC (JAM) population, which is derived from eight high-yielding rice cultivars in Japan. To obtain information on the haplotypes in the JAM lines, we predicted the haplotype blocks in the whole chromosomes using 16,345 SNPs identified via genotyping-by-sequencing analysis. Using haplotype-based GWAS, we clearly detected the loci controlling the glutinous endosperm and culm length traits. Information on the alleles of the eight founders, which was based on the effects of mutations revealed by the analysis of next-generation sequencing data, was used to narrow down the candidate genes and reveal the associations between alleles and phenotypes. The haplotype-based allele mining (HAM) proposed in this study is a promising approach to the detection of allelic variation in genes controlling agronomic traits in MAGIC populations.

Fine Mapping of QUICK ROOTING 1 and 2, Quantitative Trait Loci Increasing Root Length in Rice.

The volume that the root system can occupy is associated with the efficiency of water and nutrient uptake from soil. Genetic improvement of root length, which is a limiting factor for root distribution, is necessary for increasing crop production. In this report, we describe identification of two quantitative trait loci (QTLs) for maximal root length, QUICK ROOTING 1 (QRO1) on chromosome 2 and QRO2 on chromosome 6, in cultivated rice (Oryza sativa L.). We measured the maximal root length in 26 lines carrying chromosome segments from the long-rooted upland rice cultivar Kinandang Patong in the genetic background of the short-rooted lowland cultivar IR64. Five lines had longer roots than IR64. By rough mapping of the target regions in BC4F2 populations, we detected putative QTLs for maximal root length on chromosomes 2, 6, and 8. To fine-map these QTLs, we used BC4F3 recombinant homozygous lines. QRO1 was mapped between markers RM5651 and RM6107, which delimit a 1.7-Mb interval on chromosome 2, and QRO2 was mapped between markers RM20495 and RM3430-1, which delimit an 884-kb interval on chromosome 6. Both QTLs may be promising gene resources for improving root system architecture in rice.

Efficacy of a leukotriene receptor antagonist for pediatric cedar pollen allergy complicated by asthma.

Leukotriene receptor antagonists (LTRAs) are identified as a monotherapy for asthma and allergic rhinitis; however, their use in children for treatment of these diseases has not been examined. Accordingly, the present study investigated the efficacy of pranlukast dry syrup for children with both pollinosis and asthma. The subjects were children receiving treatment for asthma who were also diagnosed with cedar pollen allergy. Patients were divided into a group that received continuous treatment with pranlukast (group A; n=20) and a group that commenced add-on treatment for pollinosis following the onset of symptoms (group B; n=20). Patients in group B were randomly allocated to subgroup B1 (add-on treatment with pranlukast dry syrup) or subgroup B2 (add-on treatment with a second-generation antihistamine). In both groups, nasal and ocular symptoms were evaluated every day and recorded in a diary. Exacerbation of nasal obstruction was demonstrated in group B; however, not in group A. There was a significant difference in symptoms observed between the two groups during the late peak pollen period (P<0.05). The incidence of nasal obstruction (defined as a nasal obstruction score ≥3 or use of a nasal steroid spray) was significantly lower in group A compared with group B (P<0.05). The maximum scores for sneezing and nasal obstruction during the late peak of the pollen season were lowest in group A, followed by subgroup B1 and subgroup B2. The present study demonstrated that long-term administration of LTRA for the management of asthma may improve nasal symptoms of pollinosis during the pollen season in children with pollinosis and asthma.

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

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.

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

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.

A major QTL controlling deep rooting on rice chromosome 4.

Drought is the most serious abiotic stress that hinders rice production under rainfed conditions. Breeding for deep rooting is a promising strategy to improve the root system architecture in shallow-rooting rice cultivars to avoid drought stress. We analysed the quantitative trait loci (QTLs) for the ratio of deep rooting (RDR) in three F2 mapping populations derived from crosses between each of three shallow-rooting varieties ('ARC5955', 'Pinulupot1', and 'Tupa729') and a deep-rooting variety, 'Kinandang Patong'. In total, we detected five RDR QTLs on chromosomes 2, 4, and 6. In all three populations, QTLs on chromosome 4 were found to be located at similar positions; they explained from 32.0% to 56.6% of the total RDR phenotypic variance. This suggests that one or more key genetic factors controlling the root growth angle in rice is located in this region of chromosome 4.

Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions.

The genetic improvement of drought resistance is essential for stable and adequate crop production in drought-prone areas. Here we demonstrate that alteration of root system architecture improves drought avoidance through the cloning and characterization of DEEPER ROOTING 1 (DRO1), a rice quantitative trait locus controlling root growth angle. DRO1 is negatively regulated by auxin and is involved in cell elongation in the root tip that causes asymmetric root growth and downward bending of the root in response to gravity. Higher expression of DRO1 increases the root growth angle, whereby roots grow in a more downward direction. Introducing DRO1 into a shallow-rooting rice cultivar by backcrossing enabled the resulting line to avoid drought by increasing deep rooting, which maintained high yield performance under drought conditions relative to the recipient cultivar. Our experiments suggest that control of root system architecture will contribute to drought avoidance in crops.