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Genetic and root phenotype diversity in Sri Lankan rice landraces may be related to drought resistance.

ABSTRACT: BACKGROUND:The development of relatively cheap and high throughput methods of genotyping and phenotyping plants offers the opportunity to explore local germplasm more thoroughly than before and should accelerate the identification of sources of genetic variation suitable for breeding. In this study, 135 Sri Lankan accessions, mostly identified as landraces, for which data was available at the International Rice Research Institute on drought scores were genotyped using a 384 SNP array and assessed for root depth using a newly developed buried herbicide method. Roots of 36 accessions were assessed using hydroponics and 12 using soil-filled rhizotrons to establish if variation in herbicide score could be attributed to root traits. RESULTS:Population structure based on the SNPs using STRUCTURE revealed six groups, being tropical japonica, aus and four indica subpopulations. Three of these indica subpopulations do not seem to be represented in the Rice Diversity Panel I (RDP1) of 372 global rice accessions and appear to represent genetic diversity so far poorly studied by the global scientific community. The herbicide score was highly discriminatory between landraces and correlated very strongly with hydroponic and rhizotron root traits. The mean herbicide score strongly differentiated between landraces according to the province and the latitude from which they were collected. It also differed between subpopulations, being high in indica 2 and tropical japonica and low in indica 1 and aus. Drought scores suggest that indica 2 is more drought resistant than the other groups. Correlations indicate that those landraces with high herbicide scores are more drought resistant in the vegetative stage. The landrace Niyan Wee, whose name in Sinhalese means "drought rice" belongs to the indica 2 subgroup, has high herbicide scores and deep roots. CONCLUSIONS:Niyan Wee and other cultivars within the indica 2 subgroup should be a valuable source of breeding for drought resistance at least partly because of their superior root traits, not normally associated with the indica rice cultivars.

SUBMITTER: Munasinghe M

PROVIDER: S-EPMC5396129 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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Genetic and root phenotype diversity in Sri Lankan rice landraces may be related to drought resistance.

Munasinghe Mayuri M Price Adam H AH

Rice (New York, N.Y.) 20160517 1

<h4>Background</h4>The development of relatively cheap and high throughput methods of genotyping and phenotyping plants offers the opportunity to explore local germplasm more thoroughly than before and should accelerate the identification of sources of genetic variation suitable for breeding. In this study, 135 Sri Lankan accessions, mostly identified as landraces, for which data was available at the International Rice Research Institute on drought scores were genotyped using a 384 SNP array and ...[more]

PMID: 27189009

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Project description:Background and Aims Root hydraulic limitations (i.e. intra-plant restrictions to water movement) may be related to crop performance under drought, and groupings in the hydraulic function of drought-tolerant and drought-susceptible rice (Oryza sativa) varieties have been previously reported. This study aimed to better understand the environmental and physiological relationships with rice root hydraulics under drought. Methods Xylem sap bleeding rates in the field (gsap g-1shoot) were measured on seasonal and diurnal time frames, during which time environmental conditions were monitored and physiological measurements were conducted. Complementary experiments on the effects of vapour pressure deficit (VPD) on root hydraulic conductivity and on transpiration rates of de-rooted tillers were conducted in growth chambers. Key Results The diurnal effects on bleeding rate were more closely related to irradiance than VPD, and VPD effects on root hydraulic conductivity measured on 21-day-old plants were due to effects on plant growth including root surface area, maximum root depth and root:shoot ratio. Leaf osmotic potential was related to the grouping of drought-tolerant and drought-susceptible varieties in rice root hydraulics, and these groupings were independent of differences in phenology. Low single-tiller bleeding rates were observed under high evapo-transpirational demand, higher bleeding rates were observed at more negative leaf osmotic potentials in drought-susceptible varieties, and drought-tolerant and susceptible varieties differed in the VPD-induced increase in transpiration rates of de-rooted tillers. Low root suberin amounts in some of the drought-susceptible varieties may have resulted in higher ion transport, as evidenced by higher sap K+ concentration and higher bleeding rates in those varieties. Conclusions These results provide evidence of the environmental effects on shoots that can influence root hydraulics. The consistent groupings of drought-tolerant and susceptible varieties suggest that traits affecting plant osmotic status may regulate root hydraulic response to drought in rice.

Project description:BACKGROUND:Antimicrobial resistance (AMR) is a major challenge for global health care. Pharmacists play a key role in the health care setting to help support the quality use of medicines. The education, training, and experiences of pharmacy students have the potential to impact on patterns of antibiotic use in community and hospital settings. The aim of this study was to investigate antibiotic use, knowledge of antibiotics and AMR among undergraduate pharmacy students at Sri Lankan universities and to compare this between junior and senior pharmacy student groups. METHODS:A cross-sectional study was conducted at the six universities in Sri Lanka that offer pharmacy undergraduate programmes. All pharmacy students in each university were invited to participate in this study using a self-administered questionnaire with ethics approval. The study instrument comprised five major sections: demographic information, self-reported antibiotic use, knowledge of antibiotic uses in human health, knowledge of AMR and antibiotic use in agriculture. Descriptive data analyses were conducted and Chi-squared analysis was used to explore associations between different variables and level of pharmacy education. RESULTS:Four hundred sixty-six pharmacy students completed the questionnaire. A majority of participants (76%) reported antibiotic use in the past year. More than half (57%) of the junior pharmacy students incorrectly indicated that antibiotic use is appropriate for the management of cold and flu conditions. Senior pharmacy students (n?=?206) reported significantly better antibiotic knowledge than junior students (n?=?260), p?<?0.05. Overall pharmacy students showed good understanding of AMR and their knowledge level increased as the year of pharmacy study increased. CONCLUSIONS:This study found that pharmacy students commonly report using antibiotics. Junior students report some misconceptions about antimicrobials. A comparison between junior and senior pharmacy students suggests that pharmacy education is associated with improved understanding of appropriate antibiotic use and AMR among undergraduate pharmacy students in Sri Lanka.

Project description:BACKGROUND: Bacterial leaf blight (BLB) caused by the vascular pathogen Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious diseases leading to crop failure in rice growing countries. A total of 37 resistance genes against Xoo has been identified in rice. Of these, ten BLB resistance genes have been mapped on rice chromosomes, while 6 have been cloned, sequenced and characterized. Diversity analysis at the resistance gene level of this disease is scanty, and the landraces from West Bengal and North Eastern states of India have received little attention so far. The objective of this study was to assess the genetic diversity at conserved domains of 6 BLB resistance genes in a set of 22 rice accessions including landraces and check genotypes collected from the states of Assam, Nagaland, Mizoram and West Bengal. RESULTS: In this study 34 pairs of primers were designed from conserved domains of 6 BLB resistance genes; Xa1, xa5, Xa21, Xa21(A1), Xa26 and Xa27. The designed primer pairs were used to generate PCR based polymorphic DNA profiles to detect and elucidate the genetic diversity of the six genes in the 22 diverse rice accessions of known disease phenotype. A total of 140 alleles were identified including 41 rare and 26 null alleles. The average polymorphism information content (PIC) value was 0.56/primer pair. The DNA profiles identified each of the rice landraces unequivocally. The amplified polymorphic DNA bands were used to calculate genetic similarity of the rice landraces in all possible pair combinations. The similarity among the rice accessions ranged from 18% to 89% and the dendrogram produced from the similarity values was divided into 2 major clusters. The conserved domains identified within the sequenced rare alleles include Leucine-Rich Repeat, BED-type zinc finger domain, sugar transferase domain and the domain of the carbohydrate esterase 4 superfamily. CONCLUSIONS: This study revealed high genetic diversity at conserved domains of six BLB resistance genes in a set of 22 rice accessions. The inclusion of more genotypes from remote ecological niches and hotspots holds promise for identification of further genetic diversity at the BLB resistance genes.

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Genetic and root phenotype diversity in Sri Lankan rice landraces may be related to drought resistance.

Publications

Genetic and root phenotype diversity in Sri Lankan rice landraces may be related to drought resistance.

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