A DNA-based method for studying root responses to drought in field-grown wheat genotypes

Root systems are critical for water and nutrient acquisition by crops. Current methods measuring root biomass and length are slow and labour-intensive for studying root responses to environmental stresses in the field. Here, we report the development of a method that measures changes in the root DNA concentration in soil and detects root responses to drought in controlled environment and field trials. To allow comparison of soil DNA concentrations from different wheat genotypes, we also developed a procedure for correcting genotypic differences in the copy number of the target DNA sequence. The new method eliminates the need for separation of roots from soil and permits large-scale phenotyping of root responses to drought or other environmental and disease stresses in the field.Chun Y. Huang, Haydn Kuchel, James Edwards, Sharla Hall, Boris Parent, Paul Eckermann, Herdina, Diana M. Hartley, Peter Langridge & Alan C. McKa

Identification of QTLs for relative root traits associated with phosphorus efficiency in two culture systems in Brassica napus

Modifications of root system morphology and architecture are considered important strategies of plant tolerance to phosphorus (P) deficiency. However, the effect of culture system on the responses of root traits to P deficiency is not well documented. In this study, the responses of root traits to P deficiency were recorded in a Brassica napus double haploid (DH) population consisting of 182 lines derived from a cross between cultivar ‘Tapidor’ and ‘Ningyou 7’ using an ‘agar’ system and a ‘pouch and wick’ system. Under P deficient conditions, more DH lines had greater total root length, primary root length, total lateral root length, mean lateral root length and less lateral root density in the ‘pouch and wick’ system than the ‘agar’ system. Ten and two quantitative trait loci (QTLs) were detected for the relative root traits in the ‘agar’ system and the ‘pouch and wick’ system, respectively. The QTL for the same trait in the ‘agar’ system did not overlap with that in the ‘pouch and wick’ system. Two and one QTL clusters identified in the ‘agar’ system were located on chromosome A09 (Cluster1 and Cluster2) and C04 (Cluster3), respectively. RLRN_A04b, RSDW_A09a and Cluster1 were found to affect the seed yield and/or yield-related traits in two field trials. Overall, this study demonstrated a significant impact of different culture systems on the responses of root traits to P deficiency and on the detection of QTLs for the relative root traits, and identified three major QTLs that could be employed for marker assisted selection of P efficient cultivars

Spatial variability in pH and key soil nutrients: Is this an opportunity to increase fertiliser and lime-use efficiency in grazing systems?

Nutrient-use efficiency is a key issue for grazing systems in Australia. Spatial variability in soil pH and nutrients at the sub-paddock scale may affect the efficiency of utilisation of, and provide an opportunity for, site-specific management (SSM) of fertiliser and soil ameliorants. However, there has been little research exploring the potential for SSM in grazing systems. This study examines the spatial variability of soil test pH, phosphorus (P), potassium (K) and sulfur (S) in two typical pasture fields (a native and an improved) on the Northern Tablelands of New South Wales and evaluates the potential for SSM based on a comparison with critical values. In both fields, the overall paddock mean from a grid survey containing >80 samples for pH, P, K and S (0-10cm) exceeded the critical values, suggesting that the addition of fertiliser or lime was not required. However, considerable sub-paddock-scale variability was observed, with CV ranging from 35% to 66% for the key nutrients (P, K and S). The Sprengel-Liebig Law of the Minimum was applied to evaluate the proportion of each field constrained by one or more soil characteristics. Up to 55% of the improved paddock and 78% of the native pasture was potentially responsive to amendments. The results of this study suggest that SSM of fertilisers and ameliorants could provide substantial improvements in productivity and possibly reductions in fertiliser use. The development and application of appropriate systems and tools to effectively quantify this spatial variability remain a challenge, coupled with management strategies that optimise the placement of amendments and account for the variability in other production limiting factors. © CSIRO 2014.Associated Grant:CRC for Spatial Information (CRCSI

Tracking and capturing of bioorthogonal labelled RNA carried by extracellular vesicles during maternal–embryo communication

Background: During implantation window, the uterine epithelium acquires a receptive phenotype and is being prepared for the initial blastocyst attachment. This unique phenomenon may stem from embryonic–maternal crosstalk utilizing an intricate language. Extracellular vesicles (EV) could be a logical mean for maternal–embryo communication. The current investigation was aimed at deciphering the main signals exchanged between the mother and the baby. Methods: The 5-ethynyl uridine (EU)-labelled trophoblast spheroids were cultivated with an endometrial cell line in a non-contact co-culturesystem.ThetrophoblastEU-labelledRNAwastrackedandcaptured in endometrial cells. The transferred labelled RNA was affinity-precipitated and purified using biotin-azide click chemistry. Total RNA-sequencing was conducted with synthesized cDNA from captured labelled and non-EU labelled RNA (background) (n=4).Differential expression analysis of RNA-seq data was performed using edgeR and limma packages to identify the transferred transcripts using differential enrichment as a proxy. The Integrative Genomics Viewer was used to validate the coverage of differentially enriched transcripts. The results were confirmed by quantitative PCR (qPCR).To establish the route of candidate RNA transfer, EVs were isolated from co-culture media using size-exclusion chromatography. Total RNA was extracted from EVs, EU-labelled RNA was affinity-precipitated and the absolute copy number of putatively transferred RNA sequences was quantified. Results: Differential enrichment analysis demonstrated that the majority of putatively transferred transcripts were non-coding RNAs derived from the mir99alet7c cluster (Chromosome 21: LINC00478). The presence of non-coding sequences from this chromosomal region in the RNA extracted from EVs was confirmed by qPCR. This suggests that these sequences are carried by throphoblast EVs. Summary/Conclusion: In this study, we showed that biorthogonal RNA labelling chemistry can be used for the deciphering trophoblast–endometrial communications. These are the initial steps towards decoding the earliest stages of the mother–offspring language/crosstalk

Relationship between combat-related traumatic injury and its severity to predicted cardiovascular disease risk: ADVANCE cohort study

Background This study investigated the relationship between combat-related traumatic injury (CRTI) and its severity and predicted cardiovascular disease (CVD) risk. Material and methods This was an analysis of comparative 10-year predicted CVD risk (myocardial infarction, stroke or CVD-death) using the QRISK®3 scoring-system among adults recruited into the Armed Services Trauma Rehabilitation Outcome (ADVANCE) cohort study. Participants with CRTI were compared to uninjured servicemen frequency-matched by age, sex, rank, deployment (Afghanistan 2003–2014) and role. Injury severity was quantified using the New Injury Severity Score (NISS). Results One thousand one hundred forty four adult combat veterans were recruited, consisting of 579 injured (161 amputees) and 565 uninjured men of similar age ethnicity and time from deployment/injury. Significant mental illness (8.5% vs 4.4%; p = 0.006) and erectile dysfunction (11.6% vs 5.8%; p < 0.001) was more common, body mass index (28.1 ± 3.9 vs 27.4 ± 3.4 kg/m2; p = 0.001) higher and systolic blood pressure variability (median [IQR]) (1.7 [1.2–3.0] vs 2.1 [1.2–3.5] mmHg; p = 0.008) lower among the injured versus uninjured respectively. The relative risk (RR) of predicted CVD (versus the population expected risk) was higher (RR:1.67 [IQR 1.16–2.48]) among the injured amputees versus the injured non-amputees (RR:1.60 [1.13–2.43]) and uninjured groups (RR:1.52 [1.12–2.34]; overall p = 0.015). After adjustment for confounders CRTI, worsening injury severity (higher NISS, blast and traumatic amputation) were independently associated with QRISK®3 scores. Conclusion CRTI and its worsening severity were independently associated with increased predicted 10-year CVD risk