Jim Dunwell

University of Reading, School of Agriculture, Policy and Development, Faculty Member

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Papers by Jim Dunwell

Stable Isotope Analyses Reveal Impact of Fe and Zn on Cd Uptake and Translocation by Theobroma cacao

Plants, Feb 17, 2024

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Study on the differences of gene expression between pear and apple wild cultivation materials based on RNA-seq technique

BMC Plant Biology, Jun 4, 2021

Background: Pears and apples are both perennial deciduous trees of the Rosaceae family, and both ... more Background: Pears and apples are both perennial deciduous trees of the Rosaceae family, and both are important economic fruit trees worldwide. The emergence of many varieties in the market has been mostly domesticated from wild to cultivated and regulated by the differential expression of genes. However, the molecular process and pathways underlying this phenomenon remain unclear. Four typical wild and cultivar pear and apple trees at three developmental stages were used in our study to investigate the molecular process at the transcriptome level. Result: Physiological observations indicated the obvious differences of size, weight, sugar acid content and peel color in wild and cultivar fruit among each developmental stage. Using next-generation sequencing based RNA-seq expression profiling technology, we produced a transcriptome in procession of a large fraction of annotated pear and apple genes, and provided a molecular basis underlying the phenomenon of wild and cultivar fruit tree differences. 5921 and 5744 differential expression genes were identified in pear and apple at three developmental stages respectively. We performed temporal and spatial differential gene expression profiling in developing fruits. Several key pathways such as signal transduction, photosynthesis, translation and many metabolisms were identified as involved in the differentiation of wild and cultivar fruits. Conclusion: In this study, we reported on the next-generation sequencing study of the temporal and spatial mRNA expression profiling of pear and apple fruit trees. Also, we demonstrated that the integrated analysis of pear and apple transcriptome, which strongly revealed the consistent process of domestication in Rosaceae fruit trees. The results will be great influence to the improvement of cultivar species and the utilization of wild resources.

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Genomic Investigation of the Strawberry Pathogen Phytophthora fragariae Indicates Pathogenicity Is Associated With Transcriptional Variation in Three Key Races

Frontiers in Microbiology, Apr 15, 2020

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Genome-wide identification and comparative evolutionary analysis of sorbitol metabolism pathway genes in four Rosaceae species and three model plants

BMC Plant Biology, Jul 15, 2022

In contrast to most land plant species, sorbitol, instead of sucrose, is the major photosynthetic... more In contrast to most land plant species, sorbitol, instead of sucrose, is the major photosynthetic product in many Rosaceae species. It has been well illustrated that three key functional genes encoding sorbitol-6-phosphate dehydrogenase (S6PDH), sorbitol dehydrogenase (SDH), and sorbitol transporter (SOT), are mainly responsible for the synthesis, degradation and transportation of sorbitol. In this study, the genome-wide identification of S6PDH, SDH and SOT genes was conducted in four Rosaceae species, peach, mei, apple and pear, and showed the sorbitol bio-pathway to be dominant (named sorbitol present group, SPG); another three related species, including tomato, poplar and Arabidopsis, showed a non-sorbitol bio-pathway (named sorbitol absent group, SAG). To understand the evolutionary differences of the three important gene families between SAG and SPG, their corresponding gene duplication, evolutionary rate, codon bias and positive selection patterns have been analyzed and compared. The sorbitol pathway genes in SPG were found to be expanded through dispersed and tandem gene duplications. Branch-specific model analyses revealed SDH and S6PDH clade A were under stronger purifying selection in SPG. A higher frequency of optimal codons was found in S6PDH and SDH than that of SOT in SPG, confirming the purifying selection effect on them. In addition, branch-site model analyses revealed SOT genes were under positive selection in SPG. Expression analyses showed diverse expression patterns of sorbitol-related genes. Overall, these findings provide new insights in the evolutionary characteristics for the three key sorbitol metabolism-related gene families in Rosaceae and other non-sorbitol dominant pathway species.

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Mycorrhizal symbiosis induces divergent patterns of transport and partitioning of Cd and Zn in Populus trichocarpa

Environmental and Experimental Botany, Mar 1, 2020

This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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Differentially expression analyses in fruit of cultivated and wild species of grape and peach

Scientific Reports, Feb 3, 2023

Through agronomic traits and sequencing data, the cultivated and wild varieties of grapes and pea... more Through agronomic traits and sequencing data, the cultivated and wild varieties of grapes and peaches were analyzed and compared in terms of fruit size, fruit flavor, fruit resistance, and fruit color. Cultivated grapes and peaches have advantages in fruit size, soluble sugar content, sugar and acid ratio, etc. Wild grapes and peaches have utility value in resistance. The results showed that there were 878 and 301 differentially expressed genes in cultivated and wild grapes and peaches in the three growth stages, respectively based on the next-generation sequencing study. Ten and twelve genes related to the differences between cultivated and wild grapes and peaches were found respectively. Among them, three genes, namely chalcone synthase (CHS), glutathione S-transferase (GST) and malate dehydrogenase (MDH1) were present in both cultivated and wild grapes and peaches. Grapes (Vitis vinifera L.) are woody vines of the Vitaceae family (Vitis L.) 1. There are currently approximately 70 different grape types grown throughout the world, with the majority found in temperate or subtropical regions of East Asia and North America 2. In 2021, the world's grape production exceeded 82 million tons (2021, FAOSTAT). The peach tree (Prunus persica L.) is a perennial tree in the rose family 3. In 2020, China's peach cultivation area and output both ranked first in the world, with an output exceeding 77,600 tons. Through the improvement of fruit tree varieties and the continuous optimization of cultivation methods, from 2000 to 2021, the production of grapes and peaches in China increased exceeding fourfold (2021, FAOSTAT). Artificial selection and natural selection have resulted in cultivated and wild grapes and peaches having great differences in fruit traits such as quality, peel color, and flavor. The present study was designed to reveal the associated differences between cultivated and wild grape and peach fruit traits, and to conduct transcriptome analysis to identify differences in gene expression 4. Such sequencing technology can accurately quantify the expression level of specific genes, and their alleles; this is helpful for in-depth analysis of biological problems 5. Much research has been conducted on transcriptome sequencing of grapes and peaches 6-11. For example, QTL analysis revealed candidate genes (Ppa004358m、Ppa010376m、Ppa018828m and Ppb018041m) related to fruit swelling, and discussed the significance of fruit swelling speed and during fruit growth and development and the potential gene regulatory network related to peach fruit. Ye 12 selected the peel of peach variety 'Jinxiu' at three time points (105, 120 and 135 days after flowering) as samples, performed transcriptome sequencing and annotated 25,694 unigenes, 31 genes were found significantly related to anthocyanin content, including 8 enzyme genes (CHS、CHI、F3H、DFR、UFGT、4CL、FLS and F3'H). This study providesd an important reference for further understanding of peach skin color formation mechanism. Most previous transcriptome studies have focused on the differences under different treatment conditions and there are few studies conducted on the differences between cultivated and wild fruit trees. The regulatory mechanism of domestication research is required because many great genes in wild germplasm resources can be exploited for the domestication and cultivation of cultivated kinds. In this study, cultivated grapes 'Pinot Noir' (Vitis vinifera L.) and wild grapes 'Changbai No. 9' (Vitis amurensis Rur.), cultivated peaches 'Okubo' (Prunus persica L.) and wild peach 'Lianyungang Maotao' (Amygdalus persica L.) were selected as the experimental material to study the difference in the fruit traits:-single fruit weight, horizontal diameter, vertical diameter, soluble sugar content and organic acid content. Gene expression of grapes and peaches from typical cultivated and wild fruit trees, and their influence on fruit quality during domestication were investigated. The differences in fruit traits such as size, resistance and peel color were discussed. These

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Sugar beet guard cell protoplasts demonstrate a remarkable capacity for cell division enabling applications in stomatal physiology and molecular breeding

Journal of Experimental Botany, 1997

A highly-efficient protocol for the large-scale isolation of guard cell protoplasts from sugar be... more A highly-efficient protocol for the large-scale isolation of guard cell protoplasts from sugar beet (Beta vulgaris L.) has been developed. Optimization of conditions for culturing these protoplasts resulted in extensive cell division and colony formation, at frequencies exceeding 50%. Plants can subsequently be regenerated from these guard cell-derived colonies. This provides definitive confirmation that, in sugar beet leaf protoplast populations, only guard cells are the source of totipotent protoplasts. These findings are the outcome of a directed, non-empirical approach to overcoming plant cell recalcitrance which was initiated by exploiting computer-assisted microscopy to couple in vitro response to cell origin. The results reaffirm the conclusion that, in plants, extreme degrees of cytodifferentiation need not entail terminal specialization. The responsive nature of this system can be ascribed to the unique use of cultures essentially comprising a single in vivo cell type. A uniform model system has thus been created with potential for widespread application. Their distinct morphological (and mechanical) features make guard cells a valuable choice for studying various fundamental aspects, not only of stomatal physiology, but also of plant cell (de)differentiation, differential gene expression etc. Furthermore, an applied value for such a system can also be envisaged. Results indicate that these cells are highly amenable to genetic manipulation techniques. The importance of these observations to our understanding of plant cell function and behaviour is discussed.

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$Research paper thumbnail of An investigation of zinc isotope fractionation in cacao (Theobroma cacao L.) and comparison of zinc and cadmium isotope compositions in hydroponic plant systems under high cadmium stress$

An investigation of zinc isotope fractionation in cacao (Theobroma cacao L.) and comparison of zinc and cadmium isotope compositions in hydroponic plant systems under high cadmium stress

Scientific Reports

This study aims to establish whether zinc (Zn) and cadmium (Cd) share similar physiological mecha... more This study aims to establish whether zinc (Zn) and cadmium (Cd) share similar physiological mechanisms for uptake and translocation in cacao plants (Theobroma cacao L.). Multiple-collector ICP-MS was used to determine the Zn stable isotope compositions in the roots, stems and leaves of 19 diverse cacao genotypes grown in hydroponics with 20 µmol L−1 CdCl2. Additional plants of one genotype were grown in hydroponic solutions containing lower Cd concentrations (0 and 5 µmol L−1 added CdCl2). Regardless of the Cd concentration used in the exposures, the Zn stable isotope compositions show the same systematic patterns in plant organs, with δ66Znroot > δ66Znstem > δ66Znleaf (δ66Zn denotes relative differences in 66Zn/64Zn ratios in parts per thousand). The mean Zn stable isotope fractionation between the plants and the hydroponic solutions was ε66Znuptake = –1.15 ± 0.36‰ (2SD), indicating preferential uptake of isotopically light Zn by plants from the hydroponic solution. The mean ...

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Barley anther culture: Pretreatment on mannitol stimulates production of microspore-derived embryos

Plant Cell Tissue and Organ Culture (PCTOC)

A period of four days preincubation at 25 °C on a medium containing mannitol was found to be supe... more A period of four days preincubation at 25 °C on a medium containing mannitol was found to be superior to those pretreatments requiring incubation at 4 °C. In addition, the yield of green plants was improved by orienting anthers 'flat' on the medium during mannitol preincubation, and reducing the number of anthers cultured per dish.

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CGIAR research program on grain legumes

EXECUTIVE SUMMARY Background and context The Grain Legumes CRP was established to bring all resea... more EXECUTIVE SUMMARY Background and context The Grain Legumes CRP was established to bring all research and development work on grain legumes within the CGIAR system under one umbrella. It was set up to provide public goods outcomes to serve the needs of the sustainable production and consumption of grain legumes in the developing world, capitalising upon their properties that enhance the natural resource base upon which production so unequivocally depends. The choice of species and research foci were finalised following extensive consultation with all stakeholders (though perhaps fewer end users), and cover all disciplines that contribute to long-lasting solutions to the issues of developing country production and consumption. ICRISAT leads Grain Legumes and is partnered by the CGIAR centers ICARDA, IITA and CIAT and a number of other important partners, both public and private, and of course farmers in the developed and developing world. Originally in mid-2012 Grain Legumes was structured around eight Product Lines (PL) (i.e. technological innovations) intersecting five Strategic Components (SC) (i.e. arranged as components along the value chain). However, in 2015, it was restructured along a more R4D output model leading to Intermediate Development Outcomes (IDOs). Thus five Flagship Projects (FP) more closely reflecting a systematic pipeline of progression from fundamental science, implementation of interventions and the development of capacity and partnerships to promote and adopt impactful outcomes: FP1) Managing Productivity through crop interactions with biotic and abiotic constraints; FP2) Determination of traits that address production constraints and opportunities; FP3) Trait Deployment of those traits through breeding; FP4) Seed Systems, post-harvest processing and nutrition; FP5) Capacity-Building and Partnerships. Another three cross-cutting FPs analyse the broader environment surrounding the adoption of outputs, the capitalising of investments in genomics research, and a focus on the Management and Governance of Grain Legumes: FP6) Knowledge, impacts, priorities and gender organisation; FP7) Tools and platforms for high throughput genotyping and bioinformatics; and FP8) Management and Governance. Five FPs focus on R4D; FPs 5 and 6 are considered cross-cutting; FP 7 has a technical focus and FP 8 has an overarching objective. Over the three year period since its inception in July 1012, Grain Legumes has had a total budget of $140 million, with $62M originally to come from W1/W2 and the remaining $78M to come from W3/bilateral. In actuality only $45M came from W1/W2 but $106M from W3/bilateral corresponding to 106% of expectation. Purpose, scope and objectives of the external evaluation Principally, the evaluation of Grain Legumes is to ensure that the program is progressing in an effective manner towards addressing the system-level outcomes of the CGIAR as they relate to grain legumes. In essence, the evaluation aims to provide essential evaluative information for decision-making by Program Management and its funders on issues such as extension, expansion and structuring of the program and adjustments in relevant parts of the program. Subsequent to the formal signing of the agreed terms of reference, the evaluation team was also invited to comment upon the mooted options for merging and/or disaggregating of Grain Legumes. The audiences are therefore manifold, from the CGIAR Fund Council and Consortium, the Boards of Trustees of the four component CGIAR centres, the Grain Legumes Steering, Management and Independent Advisory Committees, to the researchers and others involved in the delivery of R4D outcomes and their partner organisations. The evaluation was not only summative in measuring results from Grain Legumes at arm’s length; it was also formative in promoting learning and improvements, and developmental in nurturing adaption to transformational change with time. The evaluation report was written in a manner that allows for engagement of key partners and funders in a dialogue as to how to increase ownership and a common understanding of how the goals are to be achieved. We reviewed research undertaken before the CRPs but leading to impacts during Grain Legumes, and research commenced over the past 2.5 years. For related activities pre- and post-commencement of Grain Legumes, we reviewed the relevance of activities and their relation to CGIAR and the Grain Legumes goals, whether they were likely to lead to the outcomes and impacts as documented in the Grain Legumes proposal, and the quality of the science underpinning the likelihood to deliver outcomes. Throughout, we were cognisant of the extent of the reach of CGIAR centres’ activities, and those of stakeholders upon which the impact of CGIAR R4D depends. Within our remit we evaluated the original and modified management and governance structures, and all the processes/responsibilities managed within those structures. Besides the…

Weighted Gene Correlation Network Analysis (WGCNA) Reveals Novel Transcription Factors Associated With Bisphenol A Dose-Response

Frontiers in Genetics, 2018

Despite Bisphenol-A (BPA) being subject to extensive study, a thorough understanding of molecular... more Despite Bisphenol-A (BPA) being subject to extensive study, a thorough understanding of molecular mechanism remains elusive. Here we show that using weighted gene correlation network analysis (WGCNA), which takes advantage of a graph theoretical approach to understanding correlations amongst genes and grouping genes into modules that typically have coordinated biological functions and regulatory mechanisms, that despite some commonality in altered genes, there is minimal overlap between BPA and estrogen in terms of network topology. We confirmed previous findings that ZNF217 and TFAP2C are involved in the estrogen pathway, and are implicated in BPA as well, although for BPA they appear to be active in the absence of canonical estrogen-receptor driven gene expression. Furthermore, our study suggested that PADI4 and RACK7/ZMYNDB8 may be involved in the overlap in gene expression between estradiol and BPA. Lastly, we demonstrated that even at low doses there are unique transcription factors that appear to be driving the biology of BPA, such as SREBF1. Overall, our data is consistent with other reports that BPA leads to subtle gene changes rather than profound aberrations of a conserved estrogen signaling (or other) pathways.

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Changes in the sugar content of barley anthers during culture on different carbohydrates

Plant Cell, Tissue and Organ Culture, 1990

The quantity of glucose liberated by an anther homogenate from nine different carbon substrates, ... more The quantity of glucose liberated by an anther homogenate from nine different carbon substrates, was examined to elucidate the rate of carbohydrate breakdown by anther tissues in culture. The possible relationship between these results and development in culture was examined by extraction, and HPLC analysis of the soluble sugars from anthers cultured on medium containing one of four of the previously tested carbon substrates. Similarly, sugars from anthers subjected to one of three different inductive pretreatments, were analysed and compared with extracts from fresh anthers. The most successful carbon source in culture, when measured by fresh, and dry weight gain of the developing anthers, were the diglucoses maltose and cellobiose. Glucose was probably liberated from these diglucose substrates at a similar rate to that at which it could be utilized during the development of microspore derived structures. Pretreatments were shown to increase the glucose content of anthers, providing a pulse of the sugar at the start of culture. This effect was particularly pronounced when anthers were preincubated on a medium containing mannitol, and this type of pretreatment was found to be the most successful in promoting the development of microspore derived structures (measured by gain in fresh and dry weight) when subsequently cultured on medium containing maltose.

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Successful Agricultural Innovation in Emerging Economies: New Genetic Technologies for Global Food Production

Crop Science, 2014

Haploids and doubled haploids: a new powerful tool for genomics and genetics research in palms

Identification and Expression Analysis of Fragaria Vesca MLO Genes Involved in Interaction with Powdery Mildew (Podosphaera Aphanis)

Journal of advances in plant biology, Nov 22, 2017

Strawberry powdery mildew, caused by Podosphaera aphanis is a major fungal disease that affects s... more Strawberry powdery mildew, caused by Podosphaera aphanis is a major fungal disease that affects strawberry yield and quality. In the model plant species Arabidopsis and the crop plants barley, tomato and pea, the Mildew resistance locus O (MLO) proteins have been found to be required for powdery mildew susceptibility. The present study, based on the sequence of a wild plum (Prunus americana) MLO protein, identified 16 MLO genes within the genome of woodland strawberry, Fragaria vesca and examined their expression pattern in response to powdery mildew infection in three diploid strawberry cultivars. Phylogenetic analysis showed that the FvMLO genes can be classified into six clades. Four FvMLO genes were grouped into clade III, which comprises MLO genes from Arabidopsis, tomato and grapevine that mediate powdery mildew susceptibility. A RNA-seq analysis of two diploid strawberry cultivars, F. vesca ssp. vesca accession Hawaii 4 (HW) and F. vesca f. semperflorens line "Yellow Wonder 5AF7" (YW) at 1 d (1 DAI) and 8 d (8 DAI) after infection showed the expression of 12 out of the 16 FvMLO genes. The comparison of Fragments Per Kilobase of transcript per Million mapped reads (FPKM values) detected by RNA-seq and expression values of qRT-PCR for FvMLO genes showed substantial agreement. The FvMLO3 gene, which was grouped in clade III and orthologous to the Arabidopsis, tomato and grapevine genes, was highly expressed in YW compared to other FvMLO genes across varieties. The results showed that FvMLO genes can be used as potential candidates to engineer powdery mildew resistance in strawberry based on MLO suppression or genome editing.

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Mergers and acquisitions in global ag-biotech

Biotechnology of major cereals

Comprehensive analysis of Arabidopsis thaliana DNA polymerase epsilon catalytic subunit A and B mutants – an insight into differentially expressed genes and protein-protein interactions

One of the main replicative enzymes in most eukaryotes, DNA polymerase ε (POLE), is composed of f... more One of the main replicative enzymes in most eukaryotes, DNA polymerase ε (POLE), is composed of four subunits, namely a single catalytic and three regulatory subunits. In Arabidopsis, the catalytic subunit of POLE is encoded by two genes: Arabidopsis thaliana DNA POLYMERASE EPSILON CATALYTIC SUBUNIT A (AtPOL2A) and B (AtPOL2B). Although studies have shown AtPOL2A to be involved in various biological processes, the role of AtPOL2B is unclear. Here, we investigated the transcriptomes of both atpol2a and atpol2b mutants, and the promoter sequences to provide a better insight into the targets of AtPOL2s at the molecular level. In the present study, leaf cDNA libraries of four AtPOL2 mutants (atpol2a-1 and atpol2b-1, -2 and - 3) were sequenced using the Illumina platform. Analysis of gene expression profiles identified a total of 198, 76, 141 and 67 differentially expressed genes in atpol2a-1, atpol2b-1, atpol2b-2 and atpol2b-3, respectively; the majority of pericentromeric transposable ...

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Should we get over GM food

Transgenic Crops: The Current and Next Generations

Transgenic Plants

This chapter describes the present status and future prospects for transgenic (genetically modifi... more This chapter describes the present status and future prospects for transgenic (genetically modified) crops. It concentrates on the most recent data obtained from patent databases and field trial applications, as well as the usual scientific literature. By these means, it is possible to obtain a useful perspective into future commercial products and international trends. The various research areas are subdivided on the basis of those associated with input (agronomic) traits and those concerned with output (e.g., food quality) characteristics. Among the former group are new methods of improving stress resistance, and among the latter are many examples of producing pharmaceutical compounds in plants.

Transgenic Wheat, Barley and Oats: Future Prospects

Methods in Molecular Biology™, 2008

Following the success of transgenic maize and rice, methods have now been developed for the effic... more Following the success of transgenic maize and rice, methods have now been developed for the efficient introduction of genes into wheat, barley and oats. This review summarizes the present position in relation to these three species, and also uses information from field trial databases and the patent literature to assess the future trends in the exploitation of transgenic material. This analysis includes agronomic traits and also discusses opportunities in expanding areas such as biofuels and biopharming.

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