John N. Ferguson
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View article: KineticGP: a computational framework for genomic prediction of leaf photosynthesis traits
KineticGP: a computational framework for genomic prediction of leaf photosynthesis traits Open
Crop traits are the integrated outcome of genetic factors, environment effects, and their complex interactions, rendering accurate prediction from genetic markers alone a challenging problem. Here we present KineticGP, a computational fram…
View article: Kinetic parameter prediction using neural networks identifies limitations to C<sub>4</sub> photosynthesis
Kinetic parameter prediction using neural networks identifies limitations to C<sub>4</sub> photosynthesis Open
Large-scale kinetic models of photosynthesis enable time-resolved predictions of traits related to this key process, and provide the means to identify factors limiting photosynthesis. However, their use is currently limited by the lack of …
View article: Generalizability of machine learning models for plant traits using hyperspectral reflectance data: The case of maize
Generalizability of machine learning models for plant traits using hyperspectral reflectance data: The case of maize Open
Hyperspectral reflectance provides rapid and precise phenotyping of plants in a non-destructive manner both in field and well-controlled settings. The resulting data have been used to devise machine learning (ML) models for paired measurem…
View article: Improving Multi-Trait Genomic Prediction Efficiency Through The Incorporation Of Synthetic Traits Selected Based on Co-heritability
Improving Multi-Trait Genomic Prediction Efficiency Through The Incorporation Of Synthetic Traits Selected Based on Co-heritability Open
Genomic prediction (GP) is an essential tool in the field of plant breeding to accelerate the cultivar development pipeline by predicting the performance of unphenotyped lines. The precision of prediction is constrained by the heritability…
View article: Generalizability of machine learning models for plant traits using hyperspectral reflectance data: The case of maize
Generalizability of machine learning models for plant traits using hyperspectral reflectance data: The case of maize Open
View article: CSR Calculator: An R package and Shiny application for assigning plant ecological strategies using trait data
CSR Calculator: An R package and Shiny application for assigning plant ecological strategies using trait data Open
1. The competitor, stress-tolerator, ruderal (CSR) theory, first proposed by John Philip Grime, is a useful framework for understanding plant ecological strategies and predicting responses to environmental changes and pressures. However, c…
View article: High throughput screen of NPQ in sorghum shows highly polygenic architecture of photoprotection
High throughput screen of NPQ in sorghum shows highly polygenic architecture of photoprotection Open
Summary Natural genetic variation in photosynthesis and photoprotection within crop germplasm represents an untapped resource for crop improvement. Sorghum bicolor (sorghum) is one of the world’s most widely grown crops, yet the genetic ba…
View article: Extensive photophysiological variation in wild barley is linked to environmental origin
Extensive photophysiological variation in wild barley is linked to environmental origin Open
Summary Intraspecific variation between crop wild relatives (CWRs) represents a source of untapped genetic diversity for crop improvement. At the same time, improving photosynthesis in crops has the potential to enhance yield. Thus, explor…
View article: A deficient CP24 allele defines variation for dynamic nonphotochemical quenching and photosystem II efficiency in maize
A deficient CP24 allele defines variation for dynamic nonphotochemical quenching and photosystem II efficiency in maize Open
Maize (Zea mays L.) is a global crop species in which CO2 assimilation occurs via the C4 pathway. C4 photosynthesis is typically more efficient than C3 photosynthesis under warm and dry conditions; however, despite this inherent advantage,…
View article: MYB59 is linked to natural variation of water use associated with warmer temperatures in <i>Arabidopsis thaliana</i>
MYB59 is linked to natural variation of water use associated with warmer temperatures in <i>Arabidopsis thaliana</i> Open
Water-use contributes significantly to plant growth and productivity, yet the extent to which variation in water-use is a function of adaptive differentiation is unknown. Here, we studied natural variation of water use in Arabidopsis thali…
View article: Unraveling a hidden effective signal in leaf hyperspectral reflectance data
Unraveling a hidden effective signal in leaf hyperspectral reflectance data Open
View article: Unraveling a Hidden Effective Signal in Leaf Hyperspectral Reflectance Data
Unraveling a Hidden Effective Signal in Leaf Hyperspectral Reflectance Data Open
View article: Reducing stomatal density by expression of a synthetic epidermal patterning factor increases leaf intrinsic water use efficiency and reduces plant water use in a C4 crop
Reducing stomatal density by expression of a synthetic epidermal patterning factor increases leaf intrinsic water use efficiency and reduces plant water use in a C4 crop Open
Enhancing crop water use efficiency (WUE) is a key target trait for climatic resilience and expanding cultivation on marginal lands. Engineering lower stomatal density to reduce stomatal conductance (gs) has improved WUE in multiple C3 cro…
View article: A guide to photosynthetic gas exchange measurements: Fundamental principles, best practice and potential pitfalls
A guide to photosynthetic gas exchange measurements: Fundamental principles, best practice and potential pitfalls Open
Gas exchange measurements enable mechanistic insights into the processes that underpin carbon and water fluxes in plant leaves which in turn inform understanding of related processes at a range of scales from individual cells to entire eco…
View article: Reducing stomatal density by expression of a synthetic EPF increases leaf intrinsic water use efficiency and reduces plant water use in a C<sub>4</sub>crop
Reducing stomatal density by expression of a synthetic EPF increases leaf intrinsic water use efficiency and reduces plant water use in a C<sub>4</sub>crop Open
Enhancing crop water use efficiency (WUE) is a key target trait for climatic resilience and expanding cultivation on marginal lands. Reducing stomatal conductance ( g s ) through manipulating stomatal density has been observed to translate…
View article: The genetic basis of dynamic non-photochemical quenching and photosystem II efficiency in fluctuating light reveals novel molecular targets for maize (<i>Zea mays</i>) improvement
The genetic basis of dynamic non-photochemical quenching and photosystem II efficiency in fluctuating light reveals novel molecular targets for maize (<i>Zea mays</i>) improvement Open
Maize ( Zea mays L.) is a major global crop species which uses C4 photosynthesis. Although C4 is typically considered to be more efficient than C3 photosynthesis, especially under warmer and drier conditions, there is substantial evidence …
View article: Excised leaves show limited and species-specific effects on photosynthetic parameters across crop functional types
Excised leaves show limited and species-specific effects on photosynthetic parameters across crop functional types Open
Photosynthesis is increasingly becoming a recognized target for crop improvement. Phenotyping photosynthesis-related traits on field-grown material is a key bottleneck to progress here due to logistical barriers and short measurement days.…
View article: Chlorophyll fluorescence-based high-throughput phenotyping facilitates the genetic dissection of photosynthetic heat tolerance in African (<i>Oryza glaberrima</i>) and Asian (<i>Oryza sativa</i>) rice
Chlorophyll fluorescence-based high-throughput phenotyping facilitates the genetic dissection of photosynthetic heat tolerance in African (<i>Oryza glaberrima</i>) and Asian (<i>Oryza sativa</i>) rice Open
Rising temperatures and extreme heat events threaten rice production. Half of the global population relies on rice for basic nutrition, and therefore developing heat-tolerant rice is essential. During vegetative development, reduced photos…
View article: Leaf excision has minimal impact on photosynthetic parameters across crop functional types
Leaf excision has minimal impact on photosynthetic parameters across crop functional types Open
Photosynthesis is increasingly becoming a recognised target for crop improvement. Phenotyping photosynthesis-related traits on field-grown material is a key bottleneck to progress here due to logistical barriers and short measurement days.…
View article: The leaf economics spectrum of triploid and tetraploid C<sub>4</sub> grass <i>Miscanthus <b>x</b> giganteus</i>
The leaf economics spectrum of triploid and tetraploid C<sub>4</sub> grass <i>Miscanthus <b>x</b> giganteus</i> Open
The leaf economics spectrum (LES) describes multivariate correlations in leaf structural, physiological and chemical traits, originally based on diverse C 3 species grown under natural ecosystems. However, the specific contribution of C 4 …
View article: Approaches and determinants to sustainably improve crop production
Approaches and determinants to sustainably improve crop production Open
Plant scientists and farmers are facing major challenges in providing food and nutritional security for a growing population, while preserving natural resources and biodiversity. Moreover, this should be done while adapting agriculture to …
View article: The barley immune receptor Mla recognizes multiple pathogens and contributes to host range dynamics
The barley immune receptor Mla recognizes multiple pathogens and contributes to host range dynamics Open
View article: Out of Africa: characterizing the natural variation in dynamic photosynthetic traits in a diverse population of African rice (<i>Oryza glaberrima</i>)
Out of Africa: characterizing the natural variation in dynamic photosynthetic traits in a diverse population of African rice (<i>Oryza glaberrima</i>) Open
African rice (Oryza glaberrima) has adapted to challenging environments and is a promising source of genetic variation. We analysed dynamics of photosynthesis and morphology in a reference set of 155 O. glaberrima accessions. Plants were g…
View article: Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions
Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions Open
Sorghum (Sorghum bicolor) is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is studied as a feedstock for biofuel and forage. Mechanistic modeling suggests that reducing stomatal c…
View article: WEST Diversity Panel GBS information (Ferguson et al., 2020)
WEST Diversity Panel GBS information (Ferguson et al., 2020) Open
Genotyping by sequencing information (5,512,653 SNPs on 850 individuals [842 unique]) used in the manuscript "Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions" (Ferguson et al., 202…
View article: WEST Diversity Panel GBS information (Ferguson et al., 2020)
WEST Diversity Panel GBS information (Ferguson et al., 2020) Open
Genotyping by sequencing information (5,512,653 SNPs on 850 individuals [842 unique]) used in the manuscript "Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions" (Ferguson et al., 202…
View article: The potential of resilient carbon dynamics for stabilizing crop reproductive development and productivity during heat stress
The potential of resilient carbon dynamics for stabilizing crop reproductive development and productivity during heat stress Open
Impaired carbon metabolism and reproductive development constrain crop productivity during heat stress. Reproductive development is energy intensive, and its requirement for respiratory substrates rises as associated metabolism increases w…
View article: Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions
Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions Open
Sorghum is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is also studied as a feedstock for biofuel and forage. Mechanistic modelling suggests that reducing stomatal conductance (…
View article: Rapid temperature responses of photosystem II efficiency forecast genotypic variation in rice vegetative heat tolerance
Rapid temperature responses of photosystem II efficiency forecast genotypic variation in rice vegetative heat tolerance Open
SUMMARY A key target for the improvement of Oryza sativa (rice) is the development of heat‐tolerant varieties. This necessitates the development of high‐throughput methodologies for the screening of heat tolerance. Progress has been made t…
View article: Accelerated flowering time reduces lifetime water use without penalizing reproductive performance in Arabidopsis
Accelerated flowering time reduces lifetime water use without penalizing reproductive performance in Arabidopsis Open
Natural selection driven by water availability has resulted in considerable variation for traits associated with drought tolerance and leaf‐level water‐use efficiency ( WUE ). In Arabidopsis, little is known about the variation of whole‐pl…