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"Clifton‐Brown, John"
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Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grass Miscanthus sinensis
2014
Increasing demands for food and energy require a step change in the effectiveness, speed and flexibility of crop breeding. Therefore, the aim of this study was to assess the potential of genome-wide association studies (GWASs) and genomic selection (i.e. phenotype prediction from a genome-wide set of markers) to guide fundamental plant science and to accelerate breeding in the energy grass Miscanthus.
We generated over 100 000 single-nucleotide variants (SNVs) by sequencing restriction site-associated DNA (RAD) tags in 138 Micanthus sinensis genotypes, and related SNVs to phenotypic data for 17 traits measured in a field trial.
Confounding by population structure and relatedness was severe in naïve GWAS analyses, but mixed-linear models robustly controlled for these effects and allowed us to detect multiple associations that reached genome-wide significance. Genome-wide prediction accuracies tended to be moderate to high (average of 0.57), but varied dramatically across traits. As expected, predictive abilities increased linearly with the size of the mapping population, but reached a plateau when the number of markers used for prediction exceeded 10 000–20 000, and tended to decline, but remain significant, when cross-validations were performed across subpopulations.
Our results suggest that the immediate implementation of genomic selection in Miscanthus breeding programs may be feasible.
Journal Article
Modeled spatial assessment of biomass productivity and technical potential of Miscanthus × giganteus, Panicum virgatum L., and Jatropha on marginal land in China
by
Faaij, André P. C.
,
Clifton‐Brown, John C.
,
Hastings, Astley
in
Agricultural production
,
Alternative energy sources
,
Biodiesel fuels
2020
This article identifies marginal land technically available for the production of energy crops in China, compares three models of yield prediction for Miscanthus × giganteus, Panicum virgatum L. (switchgrass), and Jatropha, and estimates their spatially specific yields and technical potential for 2017. Geographic Information System (GIS) analysis of land use maps estimated that 185 Mha of marginal land was technically available for energy crops in China without using areas currently used for food production. Modeled yields were projected for Miscanthus × giganteus, a GIS‐based Environmental Policy Integrated Climate model for switchgrass and Global Agro‐Ecological Zone model for Jatropha. GIS analysis and MiscanFor estimated more than 120 Mha marginal land was technically available for Miscanthus with a total potential of 1,761 dry weight metric million tonne (DW Mt)/year. A total of 284 DW Mt/year of switchgrass could be obtained from 30 Mha marginal land, with an average yield of 9.5 DW t ha−1 year−1. More than 35 Mha marginal land was technically available for Jatropha, delivering 9.7 Mt/year of Jatropha seed. The total technical potential from available marginal land was calculated as 31.7 EJ/year for Miscanthus, 5.1 EJ/year for switchgrass, and 0.13 EJ/year for Jatropha. A total technical bioenergy potential of 34.4 EJ/year was calculated by identifying best suited crop for each 1 km2 grid cell based on the highest energy value among the three crops. The results indicate that the technical potential per hectare of Jatropha is unable to compete with that of the other two crops in each grid cell. This modeling study provides planners with spatial overviews that demonstrate the potential of these crops and where biomass production could be potentially distributed in China which needs field trials to test model assumptions and build experience necessary to translate into practicality. As China urgently need to proceed energy transition from fossil energy to renewable energy, studies regarding assessments on the yields of energy crops on marginal land should be conducted to explore the technical potential of bioenergy from energy crops. This study was done by using GIS analysis combined with yield estimation models. Policymakers and bioenergy industries are provided with overviews of the spatial distributions of the yields and technical potential from Miscanthus, switchgrass, and Jatropha that can be obtained from marginal land in China. This study helps them initially exclude and screen some regions with low potential of energy crops.
Journal Article
Projections of global and UK bioenergy potential from Miscanthus × giganteus—Feedstock yield, carbon cycling and electricity generation in the 21st century
by
Clifton‐Brown, John
,
Hastings, Astley
,
Shepherd, Anita
in
Agricultural production
,
bioenergy
,
Biomass
2020
In this article, we modify bioenergy model MiscanFor investigating global and UK potentials for Miscanthus × giganteus as a bioenergy resource for carbon capture in the 21st century under the RCP 2.6 climate scenario using SSP2 land use projections. UK bioenergy land projections begin in the 2040s, 60 year average is 0.47 Mega ha rising to 1.9 Mega ha (2090s). Our projections estimate UK energy generation of 0.09 EJ/year (60 year average) and 0.37 EJ/year (2090s), under stable miscanthus yields of 12 t ha−1 year−1. We estimate aggregated UK soil carbon (C) increases of 0.09 Mt C/year (60 year average) and 0.14 Mt C/year (2090s) with C capture plus sequestration rate of 2.8 Mt C/year (60 year average) and 10.49 Mt C/year (2090s). Global bioenergy land use begins in 2010, 90 year average is 0.13 Gha rising to 0.19 Gha by the 2090s, miscanthus projections give a 90 year average energy generation of 16 EJ/year, rising to 26.7 EJ/year by the 2090s. The largest national capabilities for yield, energy and C increase are projected to be Brazil and China. Ninety year average global miscanthus yield of 1 Gt/year will be 1.7 Gt/year by the 2090s. Global soil C sequestration increases less with time, from a century average of 73.6 Mt C/year to 42.9 Mt C/year by the 2090s with C capture plus sequestration rate of 0.54 Gt C/year (60 year average) and 0.81 Gt C/year (2090s). M. giganteus could provide just over 5% of the bioenergy requirement by the 2090s to satisfy the RCP 2.6 SSP2 climate scenario. The choice of global land use data introduces a potential source of error. In reality, multiple bioenergy sources will be used, best suited to local conditions, but results highlight global requirements for development in bioenergy crops, infrastructure and support. We investigate the global contribution Miscanthus × giganteus bioenergy feedstock can make towards the requirements of the RCP 2.6 climate projections which assume considerable bioenergy use. These are achieved by enhancement and use of the MiscanFor bioenergy model. Projections estimate M × giganteus can provide 5% of global bioenergy requirements for RCP 2.6 by the end of century, 1.72 Gt/year crop yield generating 26.7 EJ/year bioenergy, with 42.9 Mt/year soil carbon increase and 3 Gt CO2 equiv. y‐1 capture. The United Kingdom can provide 0.37 EJ/year but the majority of bioenergy would come from tropical climates. Attaining 2° warming limits are at risk without further investment, development and support in bioenergy.
Journal Article
Valorisation of marginal agricultural land in the bioeconomy
by
Clifton‐Brown, John
,
Lewandowski, Iris
,
Kiesel, Andreas
in
Abandoned land
,
Agricultural land
,
Agricultural production
2023
[...]the aggregated ‘lessons learnt’ in the last decade of perennial biomass crop research are translated into recommendations to shape EU policy for the support of perennial cropping systems. The results of this study show that radar-based analysis is a relatively simple method to detect land abandonment at an early stage and allow monitoring and rapid policy response. While drought conditions have a particularly negative effect on the productivity of hemp, it was identified as an added-value crop for income diversification in mountain environments less susceptible to drought. While a sharp decline in Normalized Difference Vegetation Index (NDVI) was observed for the drought-sensitive hybrids compared to the control, the drought-resilient hybrids showed a stay-green strategy resulting in only a slight NDVI decline and a lower phenotypic plasticity.
Journal Article
Commercial experience with miscanthus crops: Establishment, yields and environmental observations
by
Clifton‐Brown, John
,
Kam, Jason
,
Hastings, Astley
in
Agricultural production
,
Biodiversity
,
bioenergy
2020
This study investigates the condition of commercial miscanthus fields, growers’ concerns and reasons for growing the crop and also the modelling of a realistic commercial yield. Juvenile and mature Miscanthus × giganteus crops of varying age are surveyed in growers’ fields across mid‐England. We record in‐field plant density counts and the morphology of crops of different ages. Mature crops thrive on both clay and sandy soils. Plants surveyed appear robust to drought, weeds and disease, the only vulnerability is rhizome condition when planting. Mature miscanthus planted pre‐2014 continues to develop, spreading into planting gaps and growing more tillers. In stands planted post‐2014, improved planting techniques reduce planting gaps and create a reasonably consistent planting density of 12,500 plants/ha. The main reason for growers' investment in miscanthus is not financial return, but relates to its low requirement for field operations, low maintenance cost and regeneration. This offers practical solutions for difficult field access and social acceptability near public places (related to spray operations and crop vandalism). Wildlife is abundant in these fields, largely undisturbed except for harvest. This contributes to the greening of agriculture; fields are also used for gamebird cover and educational tours. This crop is solving practical problems for growers while improving the environment. Observed yield data indicate gradual yield increase with crop age, a yield plateau but no yield decrease since 2006. In stands with low planting densities, yields plateau after 9 years. Surveyed yield data are used to parameterize the MiscanFor bioenergy model. This produces options to simulate either juvenile yields or a yield for a landscape containing different aged crops. For mature English crop yields of 12 t ha−1 year−1, second‐ and third‐year juvenile harvests average 7 t ha−1 year−1 and a surrounding 10 km by 10 km area of distributed crop age would average 9 t ha−1 year−1. Not many miscanthus grower surveys are available, with reasons for their investment and experience of grower issues, yet bioenergy is developing apace due to decarbonization requirements. We discover that miscanthus is a solution to urban boundary and inaccessibility problems, that there is a mature plant expansion despite a yield plateau, that the litter layer attracts insects and is wildlife‐rich. The crop has vulnerable rhizomes at planting and there is a subtle drought influence on yield. Modelling bioenergy capacity assumes mature crops, and most data are from research plots, we investigate how commercial yield develops and create a landscape distributed‐age yield.
Journal Article
Influence of cutting height on biomass yield and quality of miscanthus genotypes
by
Clifton‐Brown, John
,
Lewandowski, Iris
,
Kiesel, Andreas
in
Agricultural production
,
Alternative energy sources
,
Biomass
2021
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. Cutting height is one of the key factors influencing the ‘commercial yield gap’. This term refers to the phenomena that commercial miscanthus yields are lower than those determined in scientific trials. This study quantifies the impacts of cutting height on biomass yield and quality of miscanthus genotypes with contrasting weather conditions before and during harvest in Germany. The results indicate a yield decrease of 270 kg ha−1 with each 1 cm increase in cutting height, but only limited influence on nutrient and moisture content. Therefore, we recommend that cutting is performed as low as is practically possible to maximize biomass yield.
Journal Article
Expanding the Miscanthus market in the UK: Growers in profile and experience, benefits and drawbacks of the bioenergy crop
by
Kam, Jason
,
Clifton‐Brown, John
,
Rowe, Rebecca
in
Agricultural economics
,
Agricultural land
,
Agricultural practices
2022
To achieve net zero greenhouse gas emission by 2050 as set out by the 2019 amendment to the 2008 UK Climate Change Act, a major shift towards renewable energy is needed. This includes the development of new methods along with improving and upscaling existing technologies. One example of new methods in bioenergy is developing new Miscanthus cultivars for electricity generation via thermal power station furnaces. Miscanthus is still relatively new compared with other agriculture practices, so market assessments and improvements are needed to reduce the barriers to entry for prospective growers. This publication provides a profile of UK Miscanthus growers and their businesses, their experiences of benefits and drawbacks of the crop, and what they see as potential barriers to entry for prospective farmers. A survey of current Miscanthus growers in England and Wales was conducted and indicated that most farmers were content with the crop and that its environmental and economic benefits were noted. However, it was evident that with a geographically limited UK market, growers wanted to see a better distribution of biomass processing stations to reduce the ongoing costs of transport. With growing demand for renewables, including bio‐energy sources, it was determined important to provide information and support for stable farming operations and to incentivise the adoption of Miscanthus. Such incentives include ongoing development of new cultivars, focussing on traits such as production potential and stressor resilience, and growers indicated preference for an annual planting grant. These developments are predicted to further improve the crop's profit margin, making it a more cost‐effective crop for farmers. Sensitively managed Miscanthus also has the potential to contribute to carbon sequestration, soil health, and aspects of farmland biodiversity. Incentivising such management in government land–based environmental schemes would offer additional income streams and help to promote environmental positive crop planting. This paper outlines the profile and experience of Miscanthus growers and development needs to upscale the UKs Miscanthus crop area in accordance with the industry requirements, to achieve the country’s net zero target by 2050. We found that current growers are satisfied with the crop, but long‐term stability is required to incentivise prospective growers. Moreover, the network of processing facilities needs to improve to reduce transport costs, and recognition of the crop’s role in reaching the UK CCC targets is needed, as well as information on the other ecological benefits it provides.
Journal Article
Yield development and nutrient offtake in contrasting miscanthus hybrids under green and brown harvest regimes
by
Lewin, Eva
,
Clifton Brown, John
,
Lewandowski, Iris
in
Agricultural production
,
agronomy
,
Alternative energy sources
2024
Harvest time is an important variable that determines the yield of miscanthus biomass, its possible end uses, and the nutrient offtake from the field. Green harvests result in a higher yield and greater nutrient removal from the field. Brown miscanthus harvests, carried out in late winter or early spring, result in lower yields and a lower nutrient offtake, whereby the harvested biomass is better suited to use in combustion. To look at the long‐term impact of green harvests on miscanthus, this experiment followed the yield development of two miscanthus hybrids subjected to green and brown harvests over a period of seven years at one site in Southern Germany. The standard commercial hybrid Miscanthus × giganteus (Mxg) was compared with a novel late‐ripening Miscanthus sinensis hybrid: Syn55. Average yields of Mxg were 19.9 t ha−1 for green harvests and 13.2 t ha−1 for brown harvests compared to 13.9 and 12.9 t ha−1 for green and brown harvested Syn55, respectively. Yields of Mxg were very different for green and brown harvests; green harvested Mxg had very high nutrient offtake, while brown harvested Mxg had the lowest nutrient offtakes of all treatments. Syn55 showed a less marked difference between green and brown harvests likely due to its tendency to retain its leaves over winter. Syn55 was however not tolerant of a green harvest, with yields of brown harvested stands surpassing the yield of green harvested stands in several years. Although Mxg demonstrated consistently high yields when harvested in October, some signs of yield decline were detected in both hybrids when harvested green, which was due to insufficient carbohydrate relocation. Alternating green and brown harvests are recommended to allow stands to replenish carbohydrate stores and to form a litter layer. This paper looks at the response of two miscanthus varieties subjected to two different harvest regime. Over 7 years, Syn55 and Mxg were harvested in either October or March. These hybrids responded differently to each harvest regime, due to differences in the way they undergo senescence over winter.
Journal Article
Developing Miscanthus seed plug establishment protocols with mulch film for commercial upscaling
by
Kam, Jason
,
Clifton‐Brown, John
,
Ashman, Chris
in
Agricultural production
,
agronomics
,
biodegradable mulch film
2023
High‐yielding crops with C4 photosynthesis arising in tropical climates are being bred for, and increasingly grown in, temperate climates. Miscanthus, a C4 from Eastern Asia is a leading perennial biomass crop, but commercial deployment is limited by low temperatures in Northern Europe, low clonal multiplication rates and slow establishment rates requiring up to 4 years to reach mature yields. While new seeded hybrids have multiplication rates >2000, direct field sown seed has proven impractical. Protocols for safe establishment of seeded hybrids require that seedlings are raised in the glasshouse in compost filled modules (also known as ‘plugs’) which are transplanted into the field in springtime. To protect seedlings from damage from late frosts, drought and grazing and to increase temperature stimulating growth rates, plug plants were covered with oxo‐degradable plastic mulch film designed for maize. At two sites in the UK, this mulch film significantly reduced plant losses at transplanting and overwintering, increased stem heights and shoot counts, and reduced the time to mature yield from 4 to 3 years (p < 0.01). However, the breakdown products of oxo‐degradable mulch films contribute to microplastics in the soil. Therefore, further mulch film experiments were conducted with bio‐derived plastics which are bio‐degradable in soil at extruded thicknesses of 10, 18 and 30 microns. The 10 micron film combined sufficient strength for machine laying and worked as well as oxo‐degradable film on de‐risking establishment. Halving the mulch film widths covering 1 row rather than 2 reduced the amount of plastic by 25%. Commercial plug‐to‐field protocols are built on results from the plot experiments and field‐scale plantings over multiple years and locations and are ready for future upscaling of biomass production from seed‐based Miscanthus hybrids. From seed to plug to field. Seed‐based Miscanthus hybrids offer much higher multiplication rates than rhizome‐based establishment methods but require seedlings to be raised in the glasshouse in compost filled modules which are transplanted into the field in springtime. Commercial plug‐to‐field protocols utilizing plant‐based biodegradable mulch films are built on results from the plot experiments and field‐scale plantings over multiple years and locations and are ready for future upscaling of biomass production from seed‐based Miscanthus hybrids.
Journal Article
Moisture content estimation and senescence phenotyping of novel Miscanthus hybrids combining UAV‐based remote sensing and machine learning
by
Kam, Jason
,
Clifton‐Brown, John
,
Martani, Enrico
in
Agricultural production
,
Algorithms
,
Biomass
2022
Miscanthus is a leading perennial biomass crop that can produce high yields on marginal lands. Moisture content is a highly relevant biomass quality trait with multiple impacts on efficiencies of harvest, transport, and storage. The dynamics of moisture content during senescence and overwinter ripening are determined by genotype × environment interactions. In this paper, unmanned aerial vehicle (UAV)‐based remote sensing was used for high‐throughput plant phenotyping (HTPP) of the moisture content dynamics during autumn and winter senescence of 14 contrasting hybrid types (progeny of M. sinensis x M. sinensis [M. sin x M. sin, eight types] and M. sinensis x M. sacchariflorus [M. sin x M. sac, six types]). The time series of moisture content was estimated using machine learning (ML) models and a range of vegetation indices (VIs) derived from UAV‐based remote sensing. The most important VIs for moisture content estimation were selected by the recursive feature elimination (RFE) algorithm and were BNDVI, GDVI, and PSRI. The ML model transferability was high only when the moisture content was above 30%. The best ML model accuracy was achieved by combining VIs and categorical variables (5.6% of RMSE). This model was used for phenotyping senescence dynamics and identifying the stay‐green (SG) trait of Miscanthus hybrids using the generalized additive model (GAM). Combining ML and GAM modeling, applied to time series of moisture content values estimated from VIs derived from multiple UAV flights, proved to be a powerful tool for HTPP. This study estimated the moisture content of 14 contrasting Miscanthus hybrids combining unmanned aerial vehicle (UAV) remote sensing and machine learning. The random forest (RF) model was trained with moisture content values measured directly from each plot trial, UAV multispectral data (the vegetation indices) and categorical variables of Miscanthus hybrids (material, hybrid code, and genotype). The time series of the moisture content values estimated by RF model from VIs derived from multiple UAV flights were used for phenotyping senescence dynamics and identifying the stay‐green (SG) trait of Miscanthus hybrids using the generalized additive model.
Journal Article