Genetic Control of Plasticity in Root Morphology and Anatomy of Rice in Response to Water Deficit

Elucidating the genetic control of rooting behavior under water-deficit stress is essential to breed climate-robust rice (Oryza sativa) cultivars. Using a diverse panel of 274 indica genotypes grown under control and water-deficit conditions during vegetative growth, we phenotyped 35 traits, mostly related to root morphology and anatomy, involving 45,000 root-scanning images and nearly 25,000 cross sections from the root-shoot junction. The phenotypic plasticity of these traits was quantified as the relative change in trait value under water-deficit compared with control conditions. We then carried out a genome-wide association analysis on these traits and their plasticity, using 45,608 high-quality single-nucleotide polymorphisms. One hundred four significant loci were detected for these traits under control conditions, 106 were detected under water-deficit stress, and 76 were detected for trait plasticity. We predicted 296 (control), 284 (water-deficit stress), and 233 (plasticity) a priori candidate genes within linkage disequilibrium blocks for these loci. We identified key a priori candidate genes regulating root growth and development and relevant alleles that, upon validation, can help improve rice adaptation to water-deficit stress.

Does morphological and anatomical plasticity during the vegetative stage make wheat more tolerant of water deficit stress than rice?

Water scarcity and the increasing severity of water deficit stress are major challenges to sustaining irrigated rice (Oryza sativa) production. Despite the technologies developed to reduce the water requirement, rice growth is seriously constrained under water deficit stress compared with other dryland cereals such as wheat (Triticum aestivum). We exposed rice cultivars with contrasting responses to water deficit stress and wheat cultivars well adapted to water-limited conditions to the same moisture stress during vegetative growth to unravel the whole-plant (shoot and root morphology) and organ/tissue (root anatomy) responses. Wheat cultivars followed a water-conserving strategy by reducing specific leaf area and developing thicker roots and moderate tillering. In contrast, rice 'IR64' and 'Apo' adopted a rapid water acquisition strategy through thinner roots under water deficit stress. Root diameter, stele and xylem diameter, and xylem number were more responsive and varied with different positions along the nodal root under water deficit stress in wheat, whereas they were relatively conserved in rice cultivars. Increased metaxylem diameter and lower metaxylem number near the root tips and exactly the opposite phenomena at the root-shoot junction facilitated the efficient use of available soil moisture in wheat. Tolerant rice 'Nagina 22' had an advantage in root morphological and anatomical attributes over cultivars IR64 and Apo but lacked plasticity, unlike wheat cultivars exposed to water deficit stress. The key traits determining the adaptation of wheat to dryland conditions have been summarized and discussed.

Biomarkers for grain yield stability in rice under drought stress

Crop yield stability requires an attenuation of the reduction of yield losses caused by environmental stresses such as drought. Using a combination of metabolomics and high-throughput colorimetric assays, we analysed central metabolism and oxidative stress status in the flag leaf of 292 indica rice (Oryza sativa) accessions. Plants were grown in the field and were, at the reproductive stage, exposed to either well-watered or drought conditions to identify the metabolic processes associated with drought-induced grain yield loss. Photorespiration, protein degradation, and nitrogen recycling were the main processes involved in the drought-induced leaf metabolic reprogramming. Molecular markers of drought tolerance and sensitivity in terms of grain yield were identified using a multivariate model based on the values of the metabolites and enzyme activities across the population. The model highlights the central role of the ascorbate-glutathione cycle, particularly dehydroascorbate reductase, in minimizing drought-induced grain yield loss. In contrast, malondialdehyde was an accurate biomarker for grain yield loss, suggesting that drought-induced lipid peroxidation is the major constraint under these conditions. These findings highlight new breeding targets for improved rice grain yield stability under drought.

Genome-wide association reveals novel genomic loci controlling rice grain yield and its component traits under water-deficit stress during the reproductive stage

A diversity panel comprising of 296 indica rice genotypes was phenotyped under non-stress and water-deficit stress conditions during the reproductive stage in the 2013 and 2014 dry seasons (DSs) at IRRI, Philippines. We investigated the genotypic variability for grain yield, yield components, and related traits, and conducted genome-wide association studies (GWAS) using high-density 45K single nucleotide polymorphisms. We detected 38 loci in 2013 and 64 loci in 2014 for non-stress conditions and 69 loci in 2013 and 55 loci in 2014 for water-deficit stress. Desynchronized flowering time confounded grain yield and its components under water-deficit stress in the 2013 experiment. Statistically corrected grain yield and yield component values using days to flowering helped to detect 31 additional genetic loci for grain yield, its components, and the harvest index in 2013. There were few overlaps in the detected loci between years and treatments, and when compared with previous studies using the same panel, indicating the complexity of yield formation under stress. Nevertheless, our analyses provided important insights into the potential links between grain yield with seed set and assimilate partitioning. Our findings demonstrate the complex genetic architecture of yield formation and we propose exploring the genetic basis of less complex component traits as an alternative route for further yield enhancement.

Association mapping and genetic dissection of drought-induced canopy temperature differences in rice

Drought-stressed plants display reduced stomatal conductance, which results in increased leaf temperature by limiting transpiration. In this study, thermal imaging was used to quantify the differences in canopy temperature under drought in a rice diversity panel consisting of 293 indica accessions. The population was grown under paddy field conditions and drought stress was imposed for 2 weeks at flowering. The canopy temperature of the accessions during stress negatively correlated with grain yield (r= -0.48) and positively with plant height (r=0.56). Temperature values were used to perform a genome-wide association (GWA) analysis using a 45K single nucleotide polynmorphism (SNP) map. A quantitative trait locus (QTL) for canopy temperature under drought was detected on chromosome 3 and fine-mapped using a high-density imputed SNP map. The candidate genes underlying the QTL point towards differences in the regulation of guard cell solute intake for stomatal opening as the possible source of temperature variation. Genetic variation for the significant markers of the QTL was present only within the tall, low-yielding landraces adapted to drought-prone environments. The absence of variation in the shorter genotypes, which showed lower leaf temperature and higher grain yield, suggests that breeding for high grain yield in rice under paddy conditions has reduced genetic variation for stomatal response under drought.

Plant host and drought shape the root associated fungal microbiota in rice

Background and Aim

Water is an increasingly scarce resource while some crops, such as paddy rice, require large amounts of water to maintain grain production. A better understanding of rice drought adaptation and tolerance mechanisms could help to reduce this problem. There is evidence of a possible role of root-associated fungi in drought adaptation. Here, we analyzed the endospheric fungal microbiota composition in rice and its relation to plant genotype and drought.

Methods

Fifteen rice genotypes (Oryza sativa ssp. indica) were grown in the field, under well-watered conditions or exposed to a drought period during flowering. The effect of genotype and treatment on the root fungal microbiota composition was analyzed by 18S ribosomal DNA high throughput sequencing. Grain yield was determined after plant maturation.

Results

There was a host genotype effect on the fungal community composition. Drought altered the composition of the root-associated fungal community and increased fungal biodiversity. The majority of OTUs identified belonged to the Pezizomycotina subphylum and 37 of these significantly correlated with a higher plant yield under drought, one of them being assigned to Arthrinium phaeospermum.

Conclusion

This study shows that both plant genotype and drought affect the root-associated fungal community in rice and that some fungi correlate with improved drought tolerance. This work opens new opportunities for basic research on the understanding of how the host affects microbiota recruitment as well as the possible use of specific fungi to improve drought tolerance in rice.

Incorporating genome-wide association into eco-physiological simulation to identify markers for improving rice yields

We explored the use of the eco-physiological crop model GECROS to identify markers for improved rice yield under well-watered (control) and water deficit conditions. Eight model parameters were measured from the control in one season for 267 indica genotypes. The model accounted for 58% of yield variation among genotypes under control and 40% under water deficit conditions. Using 213 randomly selected genotypes as the training set, 90 single nucleotide polymorphism (SNP) loci were identified using a genome-wide association study (GWAS), explaining 42-77% of crop model parameter variation. SNP-based parameter values estimated from the additive loci effects were fed into the model. For the training set, the SNP-based model accounted for 37% (control) and 29% (water deficit) of yield variation, less than the 78% explained by a statistical genomic prediction (GP) model for the control treatment. Both models failed in predicting yields of the 54 testing genotypes. However, compared with the GP model, the SNP-based crop model was advantageous when simulating yields under either control or water stress conditions in an independent season. Crop model sensitivity analysis ranked the SNP loci for their relative importance in accounting for yield variation, and the rank differed greatly between control and water deficit environments. Crop models have the potential to use single-environment information for predicting phenotypes under different environments.

Laparoscopic management of neonatal gastric volvulus: a case report and review of the literature

We report a neonate who presented with failure to thrive, non-bilious vomiting and upper abdominal distension starting at one week of age. A barium upper GI study confirmed the diagnosis of organoaxial volvulus of the stomach, and the child underwent a successful laparoscopic gastropexy. At one year of follow-up the child is asymptomatic. We discuss the technique and review the literature.

Spontaneous expulsion of unusual tracheobronchial foreign body

An extremely rare case of long, thin and sharp pin in a young boy which was inhaled initially and defied removal at branchoscopy was eventually recovered in stool after a long and variable course through alimentary tract has been reported.

Development and validation of a predictive score, for identifying poor eastern cooperative oncology group performance status (performance status 3-4) advanced nonsmall cell lung cancer patients who are likely to benefit from tyrosine kinase inhibitors

BACKGROUND

One of the ten advanced lung cancer patients presents with poor eastern cooperative oncology group performance status (ECOG PS). There are no clear guidelines about management of these patients. The benefit of tyrosine kinase inhibitors (TKI) in this patient population remains questionable. Hence, in this study, we attempted to develop and validate a predictive score which would predict benefit from oral TKI.

METHODS

This was a prospective observational study done at Tata Memorial Hospital, India. Patients with nonsmall cell lung cancer with ECOG PS 3-4 were included in this study. All these patients had received oral TKI on compassionate grounds and were followed up till death. The overall survival (OS) was calculated from date of start of TKI to date of death. R software was used for development and validation of the predictive model.

RESULTS

The median survival duration of the discovery cohort and validation cohort were 170.5 and 115 days, respectively. The model predicted OS accurately, within ±2 months in 72.1% and within ±3 months in 81.7% of patients.

CONCLUSION

The current model can predict OS in poor PS patients treated with TKI within a satisfactory clinical range and can be used for decision-making of these patients.

Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance

BACKGROUND

Rice is the second most produced crop worldwide, but is highly susceptible to drought. Micro-organisms can potentially alleviate the effects of drought. The aim of the present study was to unravel the genetic factors involved in the rice-microbe interaction, and whether genetics play a role in rice drought tolerance. For this purpose, the composition of the root mycobiota was characterized in 296 rice accessions (Oryza sativa L. subsp. indica) under control and drought conditions. Genome wide association mapping (GWAS) resulted in the identification of ten significant (LOD > 4) single nucleotide polymorphisms (SNPs) associated with six root-associated fungi: Ceratosphaeria spp., Cladosporium spp., Boudiera spp., Chaetomium spp., and with a few fungi from the Rhizophydiales order. Four SNPs associated with fungi-mediated drought tolerance were also found. Genes located around those SNPs, such as a DEFENSIN-LIKE (DEFL) protein, EXOCYST TETHERING COMPLEX (EXO70), RAPID ALKALINIZATION FACTOR-LIKE (RALFL) protein, peroxidase and xylosyltransferase, have been shown to be involved in pathogen defense, abiotic stress responses and cell wall remodeling processes. Our study shows that rice genetics affects the recruitment of fungi, and that some fungi affect yield under drought. We identified candidate target genes for breeding to improve rice-fungal interactions and hence drought tolerance.

Thrombocytopenia in malaria--correlation with type and severity of malaria

AIM OF THE STUDY

Malaria is a major health problem in the tropics with increased morbidity and mortality. Thrombocytopenia is a common finding in malaria. Although a reliable diagnostic marker, prognostic implications could vary in the two types of malaria. This study was undertaken to correlate the presence and severity of thrombocytopenia with the type of malaria.

DESIGN

A total of 1565 subjects were included in the study and identified positive for malaria parasites on peripheral smear examination with conventional microscopy. Platelet count was done on a fully automated, quantitative, hematology Coulter analyser.

RESULTS

Normal platelet count was noted in 21.6% cases. The mean platelet count in vivax malaria (n=973) was 1,15,390/microl (SD 64,580) with a range of 8000-5,73,000/microl, as against falciparum malaria (n=590) where the mean platelet count was 100,900/microl (SD 75,437) with a range of 2000-497,000/microl (Pearson coefficient 8.825, p < 0.0001). Platelet count < 20,000/microl was noted in only 1.5% cases in vivax malaria as against 8.5% cases of falciparum malaria, and none of the subjects with vivax malaria had a platelet count less than 5000/microl.

CONCLUSION

Although absence of thrombocytopenia is uncommon in malaria, its presence is not a distinguishing feature between the two types. Thrombocytopenia less than 20,000/microl can occur in P. vivax malaria although statistically more common with P. falciparum malaria. The above findings can have therapeutic implications in context of avoiding unnecessary platelet infusions with the relatively more benign course in P. vivax malaria.

Apolipoproteins: correlation with carotid intimamedia thickness and coronary artery disease

BACKGROUND

Lower levels of plasma apolipoprotein AI (Apo A-I) and higher levels of ApoB, and the ratio of ApoB to ApoA-I are considered to be independent risk factors for coronary heart disease, and may assume importance in the definite subset of Indian patients with normal levels of traditional lipid risk factors and an early-onset of coronary artery disease (CAD). Carotid intima-media thickness is considered as a marker of atherosclerosis and in prediction of clinical coronary events and coronary artery disease. With increasing interest in the role of non-traditional lipid risk factors in CAD and few studies reported in Indian subjects, we undertook this study to correlate the apolipoprotein levels with CAD and their impact on arterial thickening utilizing the carotid intima-media thickness as a surrogate marker.

METHODS AND RESULTS

Traditional lipid profile, apolipoprotein A-I and B and carotid artery Intima-media thickness (IMT) with a B-mode scan were measured in 309 patients recruited for the study (age group 36-64 years), which included 193 males and 116 females. Mean of maximal IMT exceeding 0.8 mm at the far wall of common carotid artery, excluding plaques, was selected as the higher values for comparison. One hundred and twenty two subjects had evidence for CAD as diagnosed by documented hospitalization with myocardial infarction or acute coronary syndrome, coronary angiography when feasible or noninvasive cardiac evaluation. Prevalence of subjects with increased IMT was higher among subjects with an apolipoprotein B: apolipoprotein A-I ratio exceeding one compared to those with a ratio less than one (30.6% vs 16.5%, p = 0.005). Prevalence of CAD was significantly higher among subjects with apolipoprotein B: apolipoprotein A-I ratio exceeding one as compared to those with a ratio less than one (53.7% vs 30.3%, p = 0.0002). Subjects with apolipoprotein B: apolipoprotein A-I ratio exceeding one and carotid IMT more than 0.8 mm had a 2.7-fold prevalence for CAD as against those with a ratio less than one and IMT less than 0.8 mm. On multivariate logistic regression analysis, apolipoprotein B: apolipoprotein A-I ratio exceeding one was significantly associated with increased IMT (odds ratio 2.27) and CAD (odds ratio 2.50) even after inclusion of sex, smoking, body mass index, total cholesterol, LDL-cholesterol, HDL-cholesterol, total cholesterol:HDL-cholesterol ratio and serum triglycerides into the model.

CONCLUSIONS

We conclude that apolipoprotein B to A-I ratio shows a strong association with carotid intimal medial thickening and coronary artery disease in this Western Indian population and may play an important role is assessment of coronary risk in addition to traditional coronary risk factors.

Association of microalbuminuria with carotid intima-media thickness and coronary artery disease--a cross-sectional study in Western India

OBJECTIVE

Microalbuminuria, a slightly elevated albumin excretion in the urine, is considered a novel atherosclerotic risk factor, both in diabetics subjects and in general population. Carotid intima-media thickness assessed non-invasively by a B-mode ultrasound has been recently shown to be an early marker for atherosclerosis. This study aims at determining the role of microalbuminuria as an atherosclerotic risk factor and its association with coronary artery disease.

METHODS

We measured the urine microalbumin excretion and carotid intima-media thickness (IMT) in 301 subjects, with or without evidence for coronary artery disease (CAD). Microalbuminuria was diagnosed if urinary excretion of albumin exceeded 20 microgm/ml.

RESULTS

Of the 301 subjects (age group--30-80 years) recruited for the study, 194 were males, 107 females. One hundred amd eighteen subjects had evidence of CAD as diagnosed by documented hospitalization with myocardial infarction or acute coronary syndrome, coronary angiography when feasible or non-invasive cardiac evaluation. One hundred and sixty three subjects had diabetes mellitus. Microalbuminuria was detected in 74 subjects (24.6%). Prevalence of subjects with increased IMT was higher among subjects with microalbuminuria compared to normoalbuminuria (42% vs 21.4%, p < 0.003). Prevalence of CAD was significantly higher among diabetic subjects with microalbuminuria compared to those with normoalbuminuria (Diabetic subjects: 58% vs 31.9%, p = 0.002, Non-diabetic subjects: 41.7% vs 37.7%, p = 0.718). Multivariate logistic regression analysis using carotid intimal medial thickness as a dependent variable revealed a statistically significant association with microalbuminuria in diabetic subjects (p = 0.027).

CONCLUSION

We conclude that microalbuminuria shows a strong association with increased carotid intimal medial thickening and coronary artery disease in diabetic subjects in this Western Indian population.

Noninvasive assessment of endothelial dysfunction by brachial artery flow-mediated dilatation in prediction of coronary artery disease in Indian subjects

BACKGROUND

A noninvasive technique for testing endothelial function by ultrasound measurement of flow-mediated dilatation has recently generated considerable interest as a marker of atherosclerosis, and in the prediction of clinical coronary events and coronary artery disease.

METHODS AND RESULTS

We measured the flow-mediated dilatation of the brachial artery (endothelium-dependent vasodilatation) in 136 subjects, with or without evidence of coronary artery disease. Endothelial dysfunction was diagnosed if flow-mediated dilatation was less than 4.5%. Of the 136 subjects (age group 40-70 years) recruited for the study, 94 were males and 42 females. Sixty-eight subjects had evidence of coronary artery disease as diagnosed by documented hospitalization due to myocardial infarction or acute coronary syndrome, proved by coronary angiography when feasible or noninvasive cardiac evaluation. Endothelial dysfunction was detected in 90 subjects (66.2%). Prevalence of coronary artery disease was higher among subjects with endothelial dysfunction compared to those without (57.5% v. 34.7%, p=0.013). Prevalence of endothelial dysfunction was significantly higher among subjects with coronary artery disease as compared to those without coronary artery disease (76.4% v. 55.8%, p=0.012). The present study showed a sensitivity of 76%, specificity of 44%, positive predictive value of 58% and negative predictive value of 65% for endothelial dysfunction in the prediction of coronary artery disease. Multiple regression analysis using coronary artery disease as a dependent variable revealed a statistically significant association with endothelial dysfunction (p=0.033) even after the inclusion of traditional risk factors into the model.

CONCLUSIONS

We conclude that endothelial dysfunction shows a strong association with coronary artery disease and can be a useful noninvasive tool for the evaluation of coronary artery disease.

Carotid intima-media thickness as an independent predictor of coronary artery disease

BACKGROUND

A noninvasive technique of measuring carotid artery intima-media thickness has recently generated considerable interest as a marker of atherosclerosis and in the prediction of clinical coronary events and coronary artery disease. The present study evaluated the association of carotid artery intima-media thickness in the prediction of coronary artery disease in a western Indian population.

METHODS AND RESULTS

Carotid artery intima-media thickness was measured with a B-mode scan in an ongoing study of 266 patients, who were further subdivided into 4 subgroups: those with non-insulin dependent diabetes mellitus; hypertension; diabetes mellitus with hypertension; and those without diabetes or hypertension (labeled as controls). The maximal intima-media thickness greater than 0.8 mm at the far wall of the common carotid artery, excluding raised lesions and plaques, was selected as the highest value for comparison. The subgroups were further divided into those with and without apparent coronary artery disease. A statistically significant intima-media thickness greater than 0.8 mm was observed in 59.2% of the subjects with coronary artery disease as against 40.8% in those without the disease on univariate analysis. A higher incidence of intima-media thickness of more than 0.8 mm was observed in all subgroups with coronary artery disease as against those without the disease, which was most marked in the hypertensive group (22.2% v. 3.6%) and contributed to the increased arterial thickness in diabetics with concomitant hypertension. Multivariate regression analysis revealed carotid artery intima-media thickness to be associated with coronary artery disease with an odds ratio of 2.40.

CONCLUSIONS

Carotid artery intima-media thickness is a simple, noninvasive and reproducible clinical tool to evaluate atherosclerosis and predict coronary artery disease in Indian subjects. Prospective studies in a larger number of subjects, particularly in those undergoing coronary angiography, will help in establishing the role of this technique.

Non-invasive assessment of arterial stiffness by pulse-wave velocity correlates with endothelial dysfunction

BACKGROUND

Pulse-wave velocity is the speed of the blood pressure wave to travel a given distance between two sites of the arterial system and is determined by the elasticity, wall thickness and blood density. Pulse-wave velocity correlates well with arterial distensibility and stiffness and is a useful non-invasive index to assess arteriosclerosis. Arterial endothelial dysfunction is one of the key early events in atherogenesis, preceding structural atherosclerotic changes. This study sought to establish the correlation of non-invasive estimation of arterial wall stiffness by pulse-wave velocity and its association with endothelial dysfunction in subjects at higher risk for atherosclerosis.

METHODS AND RESULTS

A total of 102 subjects (60 males and 42 females, mean age 51 years), including those with hypertension (n = 39), type 2 diabetes mellitus (n = 26), concomitant type 2 diabetes mellitus and hypertension (n = 29) and primary dyslipidemia without diabetes mellitus and hypertension (n = 8). Pulse-wave velocity was measured by the Vascular Profiler 1000 (VP-1000) waveform analysis and vascular evaluation system, an automated, non-invasive, screening device. Endothelial function was assessed by flow-mediated dilation of the brachial artery. The brachial-artery diameter was measured on B-mode ultrasound images, with the use of a 7.0 MHz linear-array transducer. Mean brachial artery pulse-wave velocity on the right extremity was 1699 cm/s and on the left 1694 cm/s. Mean flow-mediated dilation in the study subjects was 3.6 +/- 8.4%. Mean brachial artery pulse-wave velocity in the right and left extremities and the higher value of brachial artery pulse-wave velocity of the two extremities showed a negative and significant correlation with flow-mediated dilation of the brachial artery (correlation coefficient r = -0.32, p = 0.001; r = -0.40 p < 0.0001; r = -0.37, p = 0.001, respectively). Mean heart-brachial pulse-wave velocity also showed a negative and significant correlation with flow-mediated dilation of the brachial artery (r = -0.23, p = 0.022). Mean arterial stiffness was 36.2 +/- 22%. Arterial stiffness in the right extremity and the higher value of the two extremities showed a negative and significant correlation with flow-mediated dilation of the brachial artery (correlation coefficient r = -0.31, p = 0.002; r = -0.32, p = 0.001, respectively).

CONCLUSIONS

Increased values of pulse-wave velocity reflecting upon arterial stiffness show an excellent correlation with reduced values of brachial artery flow-mediated dilation. We propose that the non-invasive modalities of estimation of the pulse-wave velocity and endothelial function estimation by flow-mediated dilation of brachial artery be used in clinical practice in assessment of pre-clinical atherosclerosis.