Using k-NN to analyse images of diverse germination phenotypes and detect single seed germination in Miscanthus sinensis

Background: Miscanthus is a leading second generation bio-energy crop, which is currently planted using rhizomes; however, increasingly the use of seed is being explored to improve efficiency of propagation. Miscanthus seed are small, germination is often poor and without sterilisation so germination detection must be sufficiently adaptable for example to the presence or absence of mould. Results: Machine learning using k-NN improved the scoring of different seed phenotypes encountered in scoring germination for Miscanthus. The k-NN-based algorithm was effective in scoring the germination of seed images when compared with human scores of the same images. The trueness of the k-NN result was 0.69 to 0.7, as measured using the area under a ROC curve. When the k-NN classifier was tested on an optimised image subset of seed an area under the ROC curve of 0.89 was achieved. Conclusions: With non-ideal seed images that included mould and broken seed the k-NN classifier was less consistent with human assessments. The most accurate assessment of germination with which to train classifiers is difficult to determine but the k-NN classifier provided an impartial consistent measurement of this important trait. It was more reproducible than the existing human scoring methods and was demonstrated to give a high degree of trueness to the human score.publishersversionPeer reviewe

Influence of cutting height on biomass yield and quality of miscanthus genotypes

Abstract Commercially achieved biomass yields are often lower than those obtained in scientific plot trials and estimated by crop models. This phenomenon is commonly referred to as the ‘commercial yield gap’. It needs to be understood and managed to achieve the yield expectations that underpin business models. Cutting height at harvest is one of the key factors determining biomass yield and quality. This study quantifies the impacts of cutting heights of diverse genotypes with different morphologies and in years with contrasting weather conditions before and during harvest. Harvests were made in March 2015 and March 2018 of six diverse miscanthus genotypes planted as part of the ‘OPTIMISC project’ in 2013 near Stuttgart, Germany. Biomass yield, dry matter content and nutrient concentrations were analysed in four 10 cm fractions working upwards from the ground level and a fifth fraction with the shoot biomass higher than 40 cm. As stems are slightly tapered (i.e. diameter decreases slightly with increasing cutting height), it was hypothesized that low cutting may lead to yield gains, but that these may be associated with lower quality biomass with higher moisture and higher nutrient offtakes. We calculated average yield losses of 270 kg ha−1 (0.83%) with each 1 cm increase in cutting height up to 40 cm. Although whole shoot mineral concentrations were significantly influenced by both genotype and year interactions, total nitrogen (1.89 mg g−1), phosphorus (0.51 mg g−1), potassium (3.72 mg g−1) and calcium (0.89 mg g−1) concentrations did not differ significantly from the concentrations in the lower basal sections. Overall, cutting height had a limited influence on nutrient and moisture content. Therefore, we recommend that cutting is performed as low as is practically possible with the available machinery and local ground surface conditions to maximize biomass yield

An interyear comparison of CO2 flux and carbon budget at a commercial-scale land-use transition from semi-improved grassland to Miscanthus x giganteus

A 6‐ha field at Aberystwyth, UK, was converted in 2012 from semi‐improved grassland to Miscanthus x giganteus for biomass production; results from transition to the end of the first 3 years are presented here. An eddy covariance sensor mast was established from year one with a second mast added from year two, improving coverage and providing replicated measurements of CO2 exchange between the ecosystem and atmosphere. Using a simple mass balance approach, above‐ground and below‐ground biomass production are combined with partitioned CO2 fluxes to estimate short‐term carbon deltas across individual years. Years one and two both ended with the site as a net source of carbon following cultivation disturbances, cumulative NEE by the end of year two was 138.57 ± 16.91 g C m−2. The site became a cumulative net sink for carbon by the end of June in the third growing season and remained so for the rest of that year; NEE by the end of year three was −616.52 ± 39.39 g C m−2. Carbon gains were primarily found in biomass pools, and SOC losses were limited to years one (−1.43 Mg C ha−1 yr−1) and two (−3.75 Mg C ha−1 yr−1). Year three saw recoupment of soil carbon at 0.74 Mg C ha−1 yr−1 with a further estimate of 0.78 Mg C ha−1 incorporated through litter inputs over the 3 years, suggesting a net loss of SOC at 3.7 Mg ha−1 from a 0‐ to 30‐cm baseline of 78.61 ± 3.28 Mg ha−1, down 4.7%. Assuming this sequestration rate as a minimum would suggest replacement of cultivation losses of SOC by year 8 of a potential 15‐ to 20‐year crop. Potential coal replacement per hectare of harvest over the three‐year study would offset 6–8 Mg of carbon emission, more than double the SOC losses

Non-structural carbohydrate profiles and ratios between soluble sugars and starch serve as indicators of productivity for a bioenergy grass

There is a pressing need to find a sustainable alternative to fossil fuels that will not compromise food security or require extensive use of agrochemicals. Miscanthus is a perennial energy grass predominantly used for combustion but with the current advancement of ligno-cellulosic fermentation technologies there is an interest in using Miscanthus for bioethanol production. Currently, the only commercially grown genotype of Miscanthus is M.× giganteus; a high yielding, interspecific hybrid of M. sacchariflorus and M. sinensis. As M.× giganteus is a sterile triploid, it cannot be used as a parent so Miscanthus breeding effort is focused on producing new interspecific varieties that out-perform M.× giganteus. The carbohydrate profiles of four genotypes of Miscanthus, including M. sacchariflorus (Sac-5), M.× giganteus (Gig-311), M. sinensis (Sin-11) and M. sinensis (Goliath), were characterized at replicated field sites in Aberystwyth, West Wales and Harpenden, south-east England. Our hypothesis was that a distinctive carbohydrate profile underlies enhanced biomass accumulation. Biomass accumulation is greatest when day-lengths and solar intensity are highest; so, observations were made in the middle of UK summer (July) for 2 years. Gig-311 had a greater abundance of fructose in its stems at both sites, and both Gig-311 and Sac-5 had low abundance of starch. At both sites, the highest yielding genotype was Gig-311 and Sac-5 was also high yielding at Harpenden, but performed comparatively poorly at Aberystwyth. At both sites Gig-311 had a distinctly high concentration of fructose, low starch and a high ratio of soluble sugars: starch, and at Harpenden, Sac-5 was similar. We conclude that the abundance of starch and fructose and a greater partitioning of soluble sugars, relative to starch, are candidate biomarkers of productivity in Miscanthus