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Mechanised non-contact, non-destructive imaging methodologies have revolutionised plant phenotyping, increasing throughput well beyond what was possible using traditional manual methods. Quantifying the variation in post-harvest material such as seeds and fruits, usually the economically important part of the crop, can be critical for commercial quality assessment as well as breeding and research. Therefore, reliable methods that gather metrics of interest, quickly and efficiently, are of widespread interest across sectors. This study focuses on evaluating the phenotyping capabilities of the Cgrain Value™, a novel grain imaging machine designed for quality and purity assessment and used primarily in commercial cereal production and processing. The performance of the Cgrain Value™ in its generation of high-throughput quantitative phenotypic data is compared with a well-established machine, MARVIN, assessing repeatability and reproducibility across a range of metrics. The findings highlight the potential of the Cgrain Value™, and some shortcomings, to provide detailed three-dimensional size, shape, and colour information rapidly, offering insights into oat grain morphology that could enhance genome-wide association studies and inform the breeding efforts in oat improvement programmes. [ABSTRACT FROM AUTHOR]

Genomic prediction has mostly been used in single environment contexts, largely ignoring genotype x environment interaction, which greatly affects the performance of plants. However, in the last decade, prediction models including marker x environment (MxE) interaction have been developed. We evaluated the potential of genomic prediction in red clover (Trifolium pratense L.) using field trial data from five European locations, obtained in the Horizon 2020 EUCLEG project. Three models were compared: (1) single environment (SingleEnv), (2) across environment (AcrossEnv), (3) marker x environment interaction (MxE). Annual dry matter yield (DMY) gave the highest predictive ability (PA). Joint analyses of DMY from years 1 and 2 from each location varied from 0.87 in Britain and Switzerland in year 1, to 0.40 in Serbia in year 2. Overall, crude protein (CP) was predicted poorly. PAs for date of flowering (DOF), however ranged from 0.87 to 0.67 for Britain and Switzerland, respectively. Across the three traits, the MxE model performed best and the AcrossEnv worst, demonstrating that including marker x environment effects can improve genomic prediction in red clover. Leaving out accessions from specific regions or from specific breeders' material in the cross validation tended to reduce PA, but the magnitude of reduction depended on trait, region and breeders' material, indicating that population structure contributed to the high PAs observed for DMY and DOF. Testing the genomic estimated breeding values on new phenotypic data from Sweden showed that DMY training data from Britain gave high PAs in both years (0.43-0.76), while DMY training data from Switzerland gave high PAs only for year 1 (0.70-0.87). The genomic predictions we report here underline the potential benefits of incorporating MxE interaction in multi-environment trials and could have perspectives for identifying markers with effects that are stable across environments, and markers with environment-specific effects. [ABSTRACT FROM AUTHOR]

Abstract Background Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT). Results Approximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' × 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure. Conclusion These markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity.

A soluble acid invertase was extracted by mechanical disruption of mycelium of the psychrophile Monographella nivalis grown on sucrose in submerged culture. The crude preparation was stable to incubation at pH 6.2 for 1 h at temperatures up to 47 °C and was stable to handling at room temperature. Half of the initial activity was lost after 1 h at 52 °C and all activity was lost after 1 h at 57 °C. A single isoform with activity against sucrose was detected on both native PAGE and IEF activity gels, exhibiting an isoelectric point of pH 3.6. The activity bound tightly to Concanavalin A-sepharose and was not displaced by 500 mM α-methyl mannopyranosidase indicating the enzyme to be a mannose-containing glycoprotein. By gel filtration, the apparent Mr was determined at 195 kDa. The invertase was purified 106-fold by salt precipitation. The partially purified enzyme exhibited maximal activity at pH 4.2 and apparent Michaelis constants for sucrose of 1.2, 2.0 and 2.6 mM at 3, 9 and 15 °C. The activity increased exponentially with temperature in the range 7-55 °C. Q10 fell with increased temperature giving values of 1.96 between 5 and 15 °C and 1.60 between 40 and 50°C. Maximal activity was recorded at 55 °C. Arrhenius analysis of temperature data in the range 7-52 °C produced a continuous linear relationship. The activation energy for sucrose hydrolysis was 38.8 kJ mol-1. The thermal stability and thermal kinetic properties of the invertase were similar to those of invertases from mesophilic organisms. The invertase catalysed fructosyl transfer at 13% of the molar activity against sucrose when assayed under conditions analogous to those in culture. The major fructan products were neokestose, isokestose, kestose and an unidentified tetrasaccharide. Traces of larger fructans were also detected. The transient accumulation of fructan in cultures of M. nivalis can be explained as a side reaction of invertase activity. The enzymological and physiological data do not suggest a cryoprotective function for fructan during the growth of the fungus. [ABSTRACT FROM AUTHOR]

An asporogenous strain of the pink snow mould fungus, Monographella nivalis (Schaffnit) E. Müller, anamorph Gerlachia nivalis Ces. ex Sac.) W. Gams & E. Müller (Syn. Fusarium nivale Ces. ex Sacc.), grew at 5 °C on a defined salts medium plus vitamins and utilized a variety of simple and polymeric carbohydrates as the sole carbon and energy source. Mycelium was grown at temperatures between 3 and 15 °C in aerated submerged fermentation culture in chemically defined mediam plus sucrose. Optimum growth rates of 0.035-0.033 h-1 occurred between 9 and 12 °C. Growth in a simple medium showed that all biochemical and physiological processes necessary for growth were functional at 3 °C. The growth performance of the organism at low temperatures was no better than would be expected from extrapolation of mesophilic growth responses to temperature. The optimum growth temperature of 9-12 °C showed that some biochemical or physiological process was impaired above 12 °C. Uptake and incorporation of 35S-methionine by mycelium at different temperatures showed that general protein synthesis increased up to 25 °C, and hence was not responsible per se for the sensitivity to temperatures above 12 °C. Heat shock proteins were synthesized at the relatively low temperature of 25 °C, consistent with the low temperature optimum for growth. When grown with sucrose as the sole carbon source, the mycelium catalyzed the extracellular hydrolysis of sucrose, releasing glucose and fructose together with a small amount of fructan trisaccharides and a trace of tetra- and penta-saccharides. Fructan accumulation was transient, corresponding with maximal rates of sucrose hydrolysis. Most biomass formation occurred in the absence of fructan in the culture, hence fructan was not necessary for growth at low temperature and did not appear to function as a cryoprotectant. Invertase activity was mostly (60-70%) bound to mycelium; the remainder was free in the culture supernatant. The regulation of invertase expression appeared to be by sucrose-induction, rather than by end-product repression. Rates of sucrose hydrolysis in culture were temperature-sensitive and were markedly depressed above 12c, indicating inhibition of invertase formation. [ABSTRACT FROM AUTHOR]