Agricultural Institute

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

A simple and quantitative method for the determination of (1→3) (1→4)-β-D-glucan in barley flour and malt is described. The method allows direct analysis of β-glucan in flour and malt slurries. Mixed-linkage β-glucan is specifically depolymerized with a highly purified (1→3) (1→4)-β-D-glucanase (lichenase), from Bacillus subtilis, to tri-, tetra- and higher degree of polymerization (d.p.) oligosaccharides. These oligosaccharides are then specifically and quantitatively hydrolysed to glucose using purified β-D-glucosidase. The glucose is then specifically determined using glucose oxidase/peroxidase reagent. Since barley flours contain only low levels of glucose, and maltosaccharides do not interfere with the assay, removal of low d.p. sugars is not necessary. Blank values are determined for each sample allowing the direct measurement of β-glucan in maltsamples.α-Amylasedoes not interfere with the assay. The method issuitable for the routineanalysis of β-glucan in barley samples derived from breeding programs; 50 samples can be analysed by a single operator in a day. Evaluation of the technique on different days has indicated a mean standard error of 0–1 for barley flour samples containing 3–8 and 4–6% (w/w) β-glucan content.

Providing an adequate quantity and quality of food for the escalating human population under changing climatic conditions is currently a great challenge. In outdoor cultures, sunlight provides energy (through photosynthesis) for photosynthetic organisms. They also use light quality to sense and respond to their environment. To increase the production capacity, controlled growing systems using artificial lighting have been taken into consideration. Recent development of light-emitting diode (LED) technologies presents an enormous potential for improving plant growth and making systems more sustainable. This review uses selected examples to show how LED can mimic natural light to ensure the growth and development of photosynthetic organisms, and how changes in intensity and wavelength can manipulate the plant metabolism with the aim to produce functionalized foods.

Abstract Understanding the drivers of yield levels under climate change is required to support adaptation planning and respond to changing production risks. This study uses an ensemble of crop models applied on a spatial grid to quantify the contributions of various climatic drivers to past yield variability in grain maize and winter wheat of European cropping systems (1984–2009) and drivers of climate change impacts to 2050. Results reveal that for the current genotypes and mix of irrigated and rainfed production, climate change would lead to yield losses for grain maize and gains for winter wheat. Across Europe, on average heat stress does not increase for either crop in rainfed systems, while drought stress intensifies for maize only. In low-yielding years, drought stress persists as the main driver of losses for both crops, with elevated CO 2 offering no yield benefit in these years.

The survival of Mycobacterium avium subsp. paratuberculosis was studied by culture of fecal material sampled at intervals for up to 117 weeks from soil and grass in pasture plots and boxes. Survival for up to 55 weeks was observed in a dry fully shaded environment, with much shorter survival times in unshaded locations. Moisture and application of lime to soil did not affect survival. UV radiation was an unlikely factor, but infrared wavelengths leading to diurnal temperature flux may be the significant detrimental component that is correlated with lack of shade. The organism survived for up to 24 weeks on grass that germinated through infected fecal material applied to the soil surface in completely shaded boxes and for up to 9 weeks on grass in 70% shade. The observed patterns of recovery in three of four experiments and changes in viable counts were indicative of dormancy, a hitherto unreported property of this taxon. A dps-like genetic element and relA, which are involved in dormancy responses in other mycobacteria, are present in the M. avium subsp. paratuberculosis genome sequence, providing indirect evidence for the existence of physiological mechanisms enabling dormancy. However, survival of M. avium subsp. paratuberculosis in the environment is finite, consistent with its taxonomic description as an obligate parasite of animals.

Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information. Such techniques have the potential to generate phenotypically linked functional markers, especially when fingerprints are generated from the transcribed or expressed region of the genome. It is to be expected that these recently developed techniques will generate larger datasets, but their shortcomings should also be acknowledged and carefully investigated.

With the ever-increasing global demand for high quality rice in both local production regions and with Western consumers, we have a strong desire to understand better the importance of the different traits that make up the quality of the rice grain and obtain a full picture of rice quality demographics. Rice is by no means a 'one size fits all' crop. Regional preferences are not only striking, they drive the market and hence are of major economic importance in any rice breeding / improvement strategy. In this analysis, we have engaged local experts across the world to perform a full assessment of all the major rice quality trait characteristics and importantly, to determine how these are combined in the most preferred varieties for each of their regions. Physical as well as biochemical characteristics have been monitored and this has resulted in the identification of no less than 18 quality trait combinations. This complexity immediately reveals the extent of the specificity of consumer preference. Nevertheless, further assessment of these combinations at the variety level reveals that several groups still comprise varieties which consumers can readily identify as being different. This emphasises the shortcomings in the current tools we have available to assess rice quality and raises the issue of how we might correct for this in the future. Only with additional tools and research will we be able to define directed strategies for rice breeding which are able to combine important agronomic features with the demands of local consumers for specific quality attributes and hence, design new, improved crop varieties which will be awarded success in the global market.

A total of 256 beef heifers, in 2 experiments, was used to establish fertilization rate and subsequent embryo survival rates. Fertilization rate following a single artificial insemination was 90%. Pooled estimates of embryo survival showed high survival rates up to Day 8 (93%) but markedly reduced (P < 0.001) survival at Days 12 (56%), 16 (66%) and 42 (58%). It is suggested that most embryonic mortality occurs between Days 8 and 16.

For many years, probiotic bacteria have been known to confer health benefits to the consumer. One possible mechanism for this may be the ability of probiotic bacteria to modulate immune responses. Oral administration of Lactobacillus casei strain Shirota (LcS) has been found to enhance innate immunity by stimulating the activity of splenic NK cells. Oral feeding with killed LcS was able to stimulate the production of Th1 cytokines, resulting in repressed production of IgE antibodies against Ovalbumin in experimental mice. The ability to switch mucosal immune responses towards Th1 with probiotic bacteria provides a strategy for treatment of allergic disorders. Growth of Meth A tumour cells in the lungs was also inhibited by intrapleural injection of LcS. Oral administration of other probiotic bacteria, such as Streptococcus thermophilus (St), Lactobacillus fermentum (Lf) and yeast (Y), elicited different immune responses. Mice that were prefed yeast or Lf followed by feeding with ovalbumin (OVA) responded better to vaccination with OVA than mice not given either probiotic or OVA or mice that had been prefed only OVA. However, antibody responses were significantly suppressed in response to vaccination with OVA in mice that had been prefed yeast followed by yeast and OVA as well as mice prefed Lf followed by Lf and OVA. Prefeeding St followed by OVA feeding enhanced cellular immune responses against ovalbumin. In contrast, mice prefed St followed by St + OVA were hyporesponsive against OVA. While antigen feeding alone appears to prime for an immune response, cofeeding antigen with probiotic bacteria can suppress both antibody and cellular immune responses and may provide an efficacious protocol to attenuate autoimmune diseases, such as experimental allergic encephalomyelitis, by jointly dosing with myelin basic protein and probiotic bacteria.

Methods for generalized linear models are extended to provide estimates of location and variance parameters for mixed models fitted to binomial data formed by classifying samples from an underlying normal distribution. The method estimates the parameters directly on the underlying scale. For a balanced one-way random effects model, the variance estimator simplifies to the usual analysis of variance one. The estimation of variances and the prediction of random effects for binomial traits is required by animal breeders. The predictors given are analogous to best linear unbiased predictors (Henderson, 1973) but differ from those presented by Harville & Mee (1984).

ABSTRACT Chalk is an important quality characteristic in rice and occurs most commonly when high temperatures are experienced during grain development. The aims of this report are to determine whether chalk affects cooking quality and to attempt to explain the effects on the basis of starch and protein in chalky and translucent grains. Three cultivars of rice were grown in the glasshouse at either 38/21°C or 26/15°C (day/night temperatures). Rice grown at the higher temperature contained more chalky grains. Grains in the inferior position were more susceptible to forming chalk than were those in the superior position. The presence or absence of chalk affected cooking quality but neither amylose content, amylopectin structure nor protein composition explained the differences in cooking quality. However, the shape, size, and packing of amyloplasts and cells in chalky grains differed from those in translucent grains and might offer an explanation for the differences in cooking quality. It seems likely that the processes involved in the initiation or packing of amyloplasts are susceptible to high temperatures.

A multiplex PCR was developed for the rapid detection of genes encoding Shiga toxins 1 and 2 (stx1 and stx2), intimin (eaeA), and enterohemolysin A (hlyA) in 444 fecal samples derived from healthy and clinically affected cattle, sheep, pigs, and goats. The method involved non-solvent-based extraction of nucleic acid from an aliquot of an overnight culture of feces in EC (modified) broth. The detection limit of the assay for both fecal samples and pure cultures was between 18 and 37 genome equivalents. stx1 and hlyA were the most commonly encountered virulence factors.

OBJECTIVE: To review and interpret aspects of the pathogenesis and epidemiology of paratuberculosis (Johne's disease) for veterinarians involved in current Johne's disease control programs. PROCEDURE: An electronic and manual search was undertaken to identify published information which, together with limited unpublished data, was interpreted and summarised. CONCLUSIONS: Paratuberculosis, a chronic enteropathy of ruminants, is caused by Mycobacterium avium subsp paratuberculosis and is transmitted mainly in faeces to young animals by infected adults, some of which may not have clinical signs. The incubation period is inversely related to the size of the challenge dose but can be extremely prolonged. Clinical cases may not be seen within the economic lifespan of farm animals, particularly when stocking rates are low, pasture is spelled, or when animals are culled at a relatively young age. Other as yet unknown influences may determine the rate of progression or recovery from infection. Paratuberculosis appears in a range of forms from a disease with high prevalence and significant mortality through to one with very low prevalence and little obvious morbidity or mortality. Detection of infected flocks and herds relies on use of laboratory tests. Bacteriological culture of faeces is the most sensitive herd-level test. The passage of time and repeated testing are the greatest allies in detecting paratuberculosis because infected animals progress in the disease process and most tests are more effective in the later stages of the disease. These factors generally cause the prevalence of paratuberculosis to be underestimated at both herd or flock and regional level. Greater understanding of the epidemiology and pathogenesis of M a paratuberculosis infection is critical in order to design improved diagnostic strategies, assess the feasibility of eradication and develop control options, particularly in small ruminants.

The major aim of crop variety evaluation is to predict the future performance of varieties. This paper presents the routine statistical analysis of data from late‐stage testing of crop varieties in Australia. It uses a two‐stage approach for analysis. The data from individual trials from the current year are analysed using spatial techniques. The resultant table of variety‐by‐trial means is combined with tables from previous years to form the data for an overall mixed model analysis. Weights allow for the data being estimates with varying accuracy. In view of the predictive aim of the analysis, variety effects and interactions are regarded as random effects. Appropriate inferential tools have been developed to assist with interpretation of the results. Analyses must be conducted in a timely manner so that variety predictions can be published and disseminated to growers immediately after harvest each year. Factors which facilitate this include easy access to historic data and the use of specialist mixed model software.

Definitive diagnosis of Johne's disease in ruminants depends on confirming the presence of the causative bacterium, Mycobacterium avium subsp. paratuberculosis, in tissues of the host. This is readily achieved in most ruminant species by culture. However, culture of clinical specimens from sheep in many countries has been unrewarding. Such a culture from sheep was achieved recently in Australia by using a radiometric culture medium. The aims of the present study were to evaluate the culture of M. avium subsp. paratuberculosis from sheep by using modified BACTEC 12B radiometric medium, to determine the sensitivity of culture in relation to histopathology, and to evaluate a range of solid media. Culture of M. avium subsp. paratuberculosis from sheep with Johne's disease is a sensitive method of diagnosis: intestinal tissues from all 43 animals with multibacillary disease and all 22 animals with paucibacillary disease were culture positive, while 98% of feces from 53 animals with multibacillary disease and 48% of feces from 31 animals with paucibacillary disease were culture positive. Of sheep without histological evidence of Johne's disease from infected flocks, intestinal tissue from 32% of 41 were culture positive, while feces from 17% of 41 were culture positive. Consequently, culture is recommended as the "gold standard" test for detection of ovine Johne's disease. Of the wide range of solid media that were evaluated, only modified Middlebrook 7H10 and 7H11 agars, which were very similar in composition to modified BACTEC 12B medium, yielded growth of ovine strains of M. avium subsp. paratuberculosis. The sensitivity of detection of M. avium subsp. paratuberculosis on solid media was slightly lower than that in modified BACTEC 12B radiometric medium. Both egg yolk and mycobactin J were essential additives for growth of ovine strains of M. avium subsp. paratuberculosis in both liquid and solid media.

Summary When bright red beef and discoloured beef are sold together, shopper discrimination against the discoloured meat increases with increase in metmyoglobin content. The relationship between the level of discolouration in terms of metmyoglobin content and the proportion of total sales of discoloured meat is linear over the range tested, 5–33% metmyoglobin. The ratio of sales of discoloured beef to bright red beef is approximately 1: 2 when 20% metmyoglobin is present in the discoloured batch. There is clearly discrimination against discoloured beef, which is appreciable even at low levels of metmyoglobin. The value of using an ‘in‐store’ consumer‐study technique to evaluate a particular quality attribute of meat is established, thus providing a useful tool for similar studies on other meat characteristics. The close association established between the subjective evaluation of colour and an instrumental measurement provides a significant practical basis for using reflectance spectrophotometry in meat colour work.

The high molecular weight glutenin protein subunits (those with apparent molecular weight in the range 80000 to 140000) of 98 wheat cultivars have been examined using a discontinuous gel-electrophoresis system. The number of bands present in each cultivar ranged from three to five and at least 34 different band patterns were observed. Examination of these patterns revealed that some bands, or band combinations, are mutually exclusive and that they can be assigned to three groups. In one group, two pairs of bands occur as alternatives and these bands are controlled by genes on chromosome 1D of wheat. In the second group, three possibilities occur with cultivars possessing either one of two single bands or neither band. These patterns are controlled by a gene or genes on chromosome 1A. In the third group nine patterns occur, four consisting of single bands and five consisting of a pair of bands. Four of these nine patterns have been shown to be controlled by genes on chromosome 1B. The variation detected in the glutenin subunits is useful for cultivar identification, has a bearing on our understanding of wheat evolution, and raises questions concerning the nature of this variation.

In March 2010, an outbreak of low pathogenicity avian influenza A (H10N7) occurred on a chicken farm in Australia. After processing clinically normal birds from the farm, 7 abattoir workers reported conjunctivitis and minor upper respiratory tract symptoms. Influenza virus A subtype H10 infection was detected in 2 workers.

The exact relationship between polyamine, abscisic acid and proline metabolisms is still poorly understood. In the present study, the effects of putrescine and abscisic acid treatments alone or in combination with polyethylene glycol-induced osmotic stress were investigated in young wheat plants. It was observed that abscisic acid plays a role in the coordinated regulation of the proline and polyamine biosynthetic pathways, which compounds are related to each other through a common precursor. Abscisic acid pre-treatment induced similar alteration of polyamine contents as the osmotic stress, namely increased the putrescine, but decreased the spermidine contents in the leaves. These changes were mainly related to the polyamine cycle, as both the synthesis and peroxisomal oxidation of polyamines have been induced at gene expression level. Although abscisic acid and osmotic stress influenced the proline metabolism differently, the highest proline accumulation was observed in the case of abscisic acid treatments. The proline metabolism was partly regulated independently and not in an antagonistic manner from polyamine synthesis. Results suggest that the connection, which exists between polyamine metabolism and abscisic acid signalling leads to the controlled regulation and maintenance of polyamine and proline levels under osmotic stress conditions in wheat seedlings.

The global dissemination of the multiply-antibiotic-resistant Salmonella enterica serovar Typhimurium DT104 clone with the resistance genes located in a class 1 integron, here designated In104, within genomic island SGI1 is a significant public health issue. Here, we have shown that SGI1 and variants of it carrying different combinations of resistance genes are found in several Salmonella enterica serovars. These are serovars Cerro, Derby, Dusseldorf, Infantis, Kiambu, and Paratyphi B dT(+) isolated from human infections and serovar Emek from sewage effluent. Two new variants, SGI1-I and SGI1-J, both of which include the dfrA1-orfC cassette array, were identified.