Plant Sciences and the Bioeconomy

TitlePlant Sciences and the Bioeconomy
TypeScience Department
InstituteRothamsted Research
HeadFreddie Theodoulou
Executive AssistantSue Steele

Outputs

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Haplotype-resolved and near-T2T genome assembly of the African catfish (Clarias gariepinus)

A - Papers appearing in refereed journals
Nguinkal, J.A., Zoclanclounon, A., Brunner, R.M., Chen, Y. and Goldammer, T. 2024. Haplotype-resolved and near-T2T genome assembly of the African catfish (Clarias gariepinus). Scientific Data. 11, p. 1095. https://doi.org/10.1038/s41597-024-03906-9

An inducible whole-cell biosensor for detection of formate ions

A - Papers appearing in refereed journals
Cherenkova, A. A., Yuzbashev, T. and Melkina, O. E. 2024. An inducible whole-cell biosensor for detection of formate ions. Applied Biochemistry and Microbiology. 60 (5), pp. 950-957. https://doi.org/10.1134/S0003683824605183

Data from: A conserved fungal Knr4/Smi1 protein is vital for maintaining cell wall integrity and host plant pathogenesis

N - Datasets
Kroll, E., Bayon, C., Rudd, J. J., Armer, V., Magaji-Umashankar, A., Ames, R., Urban, M., Brown, N. A. and Hammond-Kosack, K. E. 2024. Data from: A conserved fungal Knr4/Smi1 protein is vital for maintaining cell wall integrity and host plant pathogenesis. Rothamsted Research. https://doi.org/10.23637/rothamsted.99163

The lowdown on breakdown: Open questions in plant proteolysis

A - Papers appearing in refereed journals
Eckardt, N. A., Wittenberg, T. A., Bassham, D. C., Chen, P., Chen, Q., Fang, J., Genschik, P., Ghifari, A. S., Guercio, A. M., Gibbs, D. J., Heese, M., Jarvis, R. P., Michaeli, S., Murcha, M. W., Mursalimov, S., Noir, S., Palayam, M., Peixoto, B., Rodriguez, P. L., Schaller, A., Schnittger, A., Serino, G., Shabek, N., Stintzi, A., Theodoulou, F. L., Üstün, S., van Wijk, K. J., Wei, N., Xie, Q., Yu, F. and Zhang, H. 2024. The lowdown on breakdown: Open questions in plant proteolysis. The Plant Cell. p. koae193. https://doi.org/10.1093/plcell/koae193

Genome-wide screening and characterization of phospholipase A (PLA)-like genes in sorghum (Sorghum bicolor L.).

A - Papers appearing in refereed journals
Sapara, V. J., Shankhapal, A. and Reddy, A. R. 2024. Genome-wide screening and characterization of phospholipase A (PLA)-like genes in sorghum (Sorghum bicolor L.). Planta. 260, p. 35. https://doi.org/10.1007/s00425-024-04467-2

Assessment of the pathogen genomics landscape highlights disparities and challenges for effective AMR Surveillance and outbreak response in the East African community

A - Papers appearing in refereed journals
Nguinkal, J. A., Zoclanclounon, A., Molina, A., Roba, A., Nyakio, N. M., Lokamar, P. N., Nzoyikorera, N., Ihorimbere, T., Nyandwi, J., Aguer, M. A., Maror, J. A., Lokore, M. L., Francis, M. F., Mapunda, L. A., Beyanga, M., Muyigi, T., Pimundu, G., Nabadda, S. N., Kabalisa, E., Umuringa, J. D., Tare, I. M., Lagu, H. I., Achol, E., May, J., Affara, M. and Gehre, F. 2024. Assessment of the pathogen genomics landscape highlights disparities and challenges for effective AMR Surveillance and outbreak response in the East African community. BMC Public Health. 24, p. 1500. https://doi.org/10.1186/s12889-024-18990-0

Detecting the genetic variants associated with key culinary traits in Dioscorea alata

A - Papers appearing in refereed journals
Dossa, K., Houngbo, M. E., Lechaudel, M., Malédon, E., Zoclanclounon, A., Irep, J.-L., Nazir, M. F., Chair, H. and Cornet, D. 2024. Detecting the genetic variants associated with key culinary traits in Dioscorea alata. LWT. 202 (15 June), p. 116301. https://doi.org/10.1016/j.lwt.2024.116301

A fungal endophyte induces local cell-wall mediated resistance in wheat roots against take-all disease

A - Papers appearing in refereed journals
Chancellor, T., Smith, D. P., Chen, W., Clark, S. J., Venter, E., Halsey, K., Carrera, E., Mcmillan, V. E., Canning, G., Armer, V., Hammond-Kosack, K. E. and Palma-Guerrero, J. 2024. A fungal endophyte induces local cell-wall mediated resistance in wheat roots against take-all disease. Frontiers in Plant Science. 15, p. 1444271. https://doi.org/10.3389/fpls.2024.1444271

Global wild rice germplasm resources conservation alliance: World Wild-Rice Wiring

A - Papers appearing in refereed journals
Zheng, X., Ratnasekera, D., Fan, J., Henry, R. J., Song, B., Olsen, K. M., Joshi, B. K., Banaticla-Hilario, M. C. N., Pusadee, T., Melaku, A. G., Loko, Y. L. E., Vilayheuang, K., Oppong, G., Poku, S. A., Wambugu, P. W., Ge, S., Junior, A. M., Aung, O. M., Venuprasad, R., Kohli, A., Zhou, W. and Qian, Q. 2024. Global wild rice germplasm resources conservation alliance: World Wild-Rice Wiring. Molecular Plant. 17 (4), pp. 516-518. https://doi.org/10.1016/j.molp.2024.03.001

BIG enhances Arg/N-degron pathway-mediated protein degradation to regulate Arabidopsis hypoxia responses and suberin deposition

A - Papers appearing in refereed journals
Zhang, H., Rundle, C., Winter, N., Miricescu, A., Mooney B. C., Bachmair, A., Graciet, E. and Theodoulou, F. L. 2024. BIG enhances Arg/N-degron pathway-mediated protein degradation to regulate Arabidopsis hypoxia responses and suberin deposition. The Plant Cell. p. koae117. https://doi.org/10.1093/plcell/koae117

Feeling the Heat: Investigating the dual assault of Zymoseptoria tritici and Heat Stress on Wheat (Triticum aestivum)

Conference poster
Blyth, H. R., Zarsav, A., Smith, D., Kanyuka, K., Hassall, K. L., Michaelson, L. V., Rudd, J. J. and Haslam, R. P. 2024. Feeling the Heat: Investigating the dual assault of Zymoseptoria tritici and Heat Stress on Wheat (Triticum aestivum) . 32nd Fungal Genetics Conference. Asilomar Conference Grounds, Pacific Grove, CA 12 Mar 2024

Characterisation of fatty acyl reductases of sunflower (Helianthus annuus L.) seed

A - Papers appearing in refereed journals
DeAndres-Gil, C., Moreno-Perez, A. J., Villoslada-Valbuena, M., Halsey, K., Martinez-Force, E., Garces, R., Kurup, S., Beaudoin, F., Salas, J. J. and Venegas-Caleron, M. 2024. Characterisation of fatty acyl reductases of sunflower (Helianthus annuus L.) seed. Plant Science. 341, p. 111992. https://doi.org/10.1016/j.plantsci.2024.111992

The First Comprehensive Chemical Profiling of Vachellia gummifera (Willd.) Kyal. & Boatwr., a Plant with Medicinal Value

A - Papers appearing in refereed journals
Kisiriko, M., Noleto-Dias, C., Bitchagno-Mbahbou, G., Naboulsi, I., Anastasiadi, M., Terry, L.A., Sobeh, M., Beale, M. H. and Ward, J. L. 2024. The First Comprehensive Chemical Profiling of Vachellia gummifera (Willd.) Kyal. & Boatwr., a Plant with Medicinal Value. Chemistry & Biodiversity. p. e202400396. https://doi.org/10.1002/cbdv.202400396

Breeding for novel chemistry in willow: new hetero Diels-Alder cyclodimers based on arbusculoidin and salicortin suggest parallel biosynthetic pathways

A - Papers appearing in refereed journals
Noleto-Dias, C., Lomax, C., Bellisai, A., Ruvo, G., Harflett, C., Macalpine, W. J., Hanley, S. J., Beale, M. H. and Ward, J. L. 2024. Breeding for novel chemistry in willow: new hetero Diels-Alder cyclodimers based on arbusculoidin and salicortin suggest parallel biosynthetic pathways. Plants - Basel. 13 (12), p. 1609. https://doi.org/10.3390/plants13121609

Concerted Transport and Phosphorylation of Diacylglycerol at ER-PM Contacts Sites Regulates Phospholipid Dynamics During Stress

A - Papers appearing in refereed journals
Garcia-Hernandez, S., Haslam, R. P., Moya-Cuevas, J., Catala, R., Michaelson, L. V., Amorim-Silva, V., Markovic, V., Salinas, J., Napier, J. A., Jaillais, Y., Ruiz-Lopez, N. and Botella, M. A. 2024. Concerted Transport and Phosphorylation of Diacylglycerol at ER-PM Contacts Sites Regulates Phospholipid Dynamics During Stress. bioRxiv. https://doi.org/10.1101/2024.01.16.575708

Plant U-box E3 ligases PUB20 and PUB21 negatively regulate pattern-triggered immunity in Arabidopsis

A - Papers appearing in refereed journals
Yi, S.Y., Nekrasov, V., Ichimura, K., Kang, S.Y. and Shirasu, K. 2024. Plant U-box E3 ligases PUB20 and PUB21 negatively regulate pattern-triggered immunity in Arabidopsis. Plant Molecular Biology. 114 (7), pp. 1-14. https://doi.org/10.1007/s11103-023-01409-6

The mechanisms behind the contrasting responses to waterlogging in black-grass (Alopecurus myosuroides) and wheat (Triticum aestivum)

A - Papers appearing in refereed journals
Harrison, C., Noleto-Dias, C., Ruvo, G., Hughes, D. J., Smith, D., Mead, A., Ward, J. L., Heuer, S. and Macgregor, D. 2024. The mechanisms behind the contrasting responses to waterlogging in black-grass (Alopecurus myosuroides) and wheat (Triticum aestivum). Functional Plant Biology. 51, p. FP23193. https://doi.org/10.1071/FP23193

Ketocarotenoid production in tomato triggers metabolic reprogramming and cellular adaptation: The quest for homeostasis

A - Papers appearing in refereed journals
Nogueira, M., Enfissi, E. M. A., Price, E. J., Menard, G. N., Venter, E., Eastmond, P. J., Bar, E., Lewinsohn, E. and Fraser, P. D. 2023. Ketocarotenoid production in tomato triggers metabolic reprogramming and cellular adaptation: The quest for homeostasis. Plant Biotechnology Journal. 22 (2), pp. 427-444. https://doi.org/10.1111/pbi.14196

A study on L-threonine and L-serine uptake in Escherichia coli K-12

A - Papers appearing in refereed journals
Khozov, A. A., Bubnov, D. M., Plisov, E. D., Vybornaya, T. V., Yuzbashev, T., Agrimi, G., Messina, E., Stepanova, A. A., Kudina, M. D., Alekseeva, N. V., Netrusov, A. I. and Sineoky, S. P. 2023. A study on L-threonine and L-serine uptake in Escherichia coli K-12. Frontiers in Microbiology. 14, p. 1151716. https://doi.org/10.3389/fmicb.2023.1151716

Large-scale bioproduction of natural astaxanthin in Yarrowia lipolytica

A - Papers appearing in refereed journals
Yuzbasheva, E. Y., Taratynova, M. O., Fedyaeva, I. M., Dementev, D. A., Korobov, V. S., Fedorov, A. S., Vidal, L. S., Yuzbashev, T., Sineoky, S. P. and Mikheev, M. 2023. Large-scale bioproduction of natural astaxanthin in Yarrowia lipolytica. Bioresource Technology. 21, p. 101289. https://doi.org/10.1016/j.biteb.2022.101289

A multiplex approach of MS, 1D-, and 2D-NMR metabolomicsin plant ontogeny A case study on Clusia minor L. organs (leaf, flower, fruit, and seed)

A - Papers appearing in refereed journals
Noleto-Dias, C., Farag, M. A., Porzel, A., Tavares, J. F. and Wessjohann, L. A. 2023. A multiplex approach of MS, 1D-, and 2D-NMR metabolomicsin plant ontogeny A case study on Clusia minor L. organs (leaf, flower, fruit, and seed). Phytochemical Analysis. https://doi.org/10.1002/pca.3300

Genomics of predictive radiation mutagenesis in oilseed rape: modifying seed oil composition.

A - Papers appearing in refereed journals
Havlickova, L., He, Z., Berger, M., Wang, L., Sandmann, G., Chew, Y. P., Yoshikawa, G. V., Lu, G., Hu, Q., Banga, S. S., Beaudoin, F. and Bancroft, I. 2023. Genomics of predictive radiation mutagenesis in oilseed rape: modifying seed oil composition. Plant Biotechnology Journal. 22 (3), pp. 738-750. https://doi.org/10.1111/pbi.14220

Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement for Successful Crop Establishment in Deep Sown Direct-Seeded Rice

A - Papers appearing in refereed journals
Sandhu, N., Ankush, A. P., Singh, J., Raigar, O. P., Bains, S., Jindal, T., Singh, M. P., Sethi, M., Pruthi, G., Augustine, G., Verma, V. K., Goyal, S., Kumar, A., Panwar, H., Sihag, M. K., Kaur, R., Kurup, S. and Kumar, A. 2023. Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement for Successful Crop Establishment in Deep Sown Direct-Seeded Rice. Rice. 16, p. 46. https://doi.org/10.1186/s12284-023-00665-w

A causal inference and Bayesian optimisation framework for modelling multi-trait relationships—Proof-of-concept using Brassica napus seed yield under controlled conditions

A - Papers appearing in refereed journals
Calderwood, A., Siles-Suarez, L., Eastmond, P. J., Kurup, S. and Morris, R. 2023. A causal inference and Bayesian optimisation framework for modelling multi-trait relationships—Proof-of-concept using Brassica napus seed yield under controlled conditions. PLOS ONE. 18 (9), p. 0290429. https://doi.org/10.1371/journal.pone.0290429

A semiochemical view of the ecology of the seed beetle Acanthoscelides obtectus Say (Coleoptera: Chrysomelidae, Bruchinae)

A - Papers appearing in refereed journals
Vuts, J., Powers, S. J., Venter, E. and Szentesi, A. 2023. A semiochemical view of the ecology of the seed beetle Acanthoscelides obtectus Say (Coleoptera: Chrysomelidae, Bruchinae). Annals of Applied Biology - AAB. 184 (1), pp. 19-36. https://doi.org/10.1111/aab.12862

A DNA assembly toolkit to unlock the CRISPR/Cas9 potential for metabolic engineering

A - Papers appearing in refereed journals
Yuzbashev, T., Yuzbasheva, E. Y., Melkina, O. E., Patel, D., Bubnov, D., Dietz, H. and Ledesma-Amaro, R. 2023. A DNA assembly toolkit to unlock the CRISPR/Cas9 potential for metabolic engineering. Communications Biology. 6, p. 858. https://doi.org/10.1038/s42003-023-05202-5

Nt-acetylation-independent turnover of SQUALENE EPOXIDASE 1 by Arabidopsis DOA10-like E3 ligases

A - Papers appearing in refereed journals
Etherington, R. D., Bailey, M., Boyer, J-B., Armbruster, L., Cao, X., Coates, J. C., Meinnel, T., Wirtz, M., Giglione, C. and Gibbs, D. J. 2023. Nt-acetylation-independent turnover of SQUALENE EPOXIDASE 1 by Arabidopsis DOA10-like E3 ligases. Plant Physiology. 193 (3), p. 2086–2104. https://doi.org/10.1093/plphys/kiad406

Boosting Geranyl Diphosphate Synthesis for Linalool Production in Engineered Yarrowia lipolytica

A - Papers appearing in refereed journals
Taratynova, M. O., Tikhonova, E. E., Fedyaeva, I. M., Dementev, D. A., Yuzbashev, T., Solovyev, A. I., Sineoky, S. P. and Yuzbasheva, E. Y. 2023. Boosting Geranyl Diphosphate Synthesis for Linalool Production in Engineered Yarrowia lipolytica. Applied Biochemistry and Biotechnology. https://doi.org/10.1007/s12010-023-04581-z

Chemical profiling of Artemisia herba-alba, Cuminum cyminum, Cinnamomum camphora, and Salvia rosmarinus essential oils and assessment of their insecticidal potential to control the wild cochineal Dactylopius opuntiae (Cockerell)

A - Papers appearing in refereed journals
Naboulsi, I., El Fakhouri, K., Annaz, H., Lamzira, R., Ramdani, C., Bitchagno-Mbahbou, G., Boulamtat, R., Ben Bakrim, W., Mahdi, I., Aboulmouhajir, A., Yasri, A., El Bouhssini, M., Ward, J. L. and Sobeh, M. 2023. Chemical profiling of Artemisia herba-alba, Cuminum cyminum, Cinnamomum camphora, and Salvia rosmarinus essential oils and assessment of their insecticidal potential to control the wild cochineal Dactylopius opuntiae (Cockerell). Crop Protection. 171, p. 106286. https://doi.org/10.1016/j.cropro.2023.106286

The potential of integrative phenomics to harness underutilized crops for improving stress resilience

A - Papers appearing in refereed journals
Grosskinsky, D. K., Faure, J-D., Gibon, Y., Haslam, R. P., Usabel, B., Zanetti, F. and Jonak, C. 2023. The potential of integrative phenomics to harness underutilized crops for improving stress resilience. Frontiers in Plant Science. 2023 (14), p. 1216337. https://doi.org/10.3389/Fpls.2023.1216337

Chapter 11: The Properties, Distribution and Functionality of Cereal Lipids

B - Book chapters etc edited externally
Haslam, R. P. and Melis, S. 2023. Chapter 11: The Properties, Distribution and Functionality of Cereal Lipids. in: Shewry, P. R., Koshe, H. and Taylor, J. R. N (ed.) ICC Handbook of 21st Century Cereal Science and Technology Elsevier. pp. 103-110

Comparative compositions of grain of tritordeum, durum wheat and bread wheat grown in multi-environment trials

A - Papers appearing in refereed journals
Shewry, P. R., Brouns, F., Dunn, J., Hood, J., Burridge, A. J., America, A. H. P., Gilissen, L., Proos-Huijsmans, Z. A. M., Van Straaten, J. P., Jonkers, D., Lazzeri, P. A., Ward, J. L. and Lovegrove, A. 2023. Comparative compositions of grain of tritordeum, durum wheat and bread wheat grown in multi-environment trials. Food Chemistry. 423 (15 Oct), p. 136312. https://doi.org/10.1016/j.foodchem.2023.136312

Metabolomics characterizes early metabolic changes and markers of tolerant Eucalyptus ssp. clones against drought stress

A - Papers appearing in refereed journals
Noleto-Dias, C., De T. Picoli E. A., Porzel, A., Wessjohann L. A., Tavares Josean F. and Farag, M. A. 2023. Metabolomics characterizes early metabolic changes and markers of tolerant Eucalyptus ssp. clones against drought stress. Phytochemistry. 212, p. 113715. https://doi.org/10.1016/j.phytochem.2023.113715

The post-registration monitoring of glyphosate-treated plants using anecic earthworms

A - Papers appearing in refereed journals
Halsey, K. and Stroud, J. L. 2023. The post-registration monitoring of glyphosate-treated plants using anecic earthworms. Annals of Applied Biology - AAB. 183 (2), pp. 141-147. https://doi.org/10.1111/aab.12838

High temperature tolerance in a novel, high-quality Phaseolus vulgaris breeding line is due to maintenance of pollen viability and successful germination on the stigma

A - Papers appearing in refereed journals
Rose, T., Lowe, C., Miret, J. A., Walpole, H., Halsey, K., Venter, E., Urban, M. O., Buendia, H. F., Kurup, S., O’Sullivan, D., Beebe, S. and Heuer, S. 2023. High temperature tolerance in a novel, high-quality Phaseolus vulgaris breeding line is due to maintenance of pollen viability and successful germination on the stigma. Plants - Basel. 12 (13), p. 2491. https://doi.org/10.3390/plants12132491

A modified Agrobacterium-mediated transformation for two oomycete pathogens

A - Papers appearing in refereed journals
Wang, L., Zhao, F., Liu, H., Chen, H., Zhang, F., Li, S., Sun, T., Nekrasov, V., Huang, S. and Dong, S. 2023. A modified Agrobacterium-mediated transformation for two oomycete pathogens. PLOS Pathogens. 19 (4), p. e1011346. https://doi.org/10.1371/journal.ppat.1011346

Targeted and untargeted metabolomics for the evaluation of plant metabolites in response to the environment - editorial

A - Papers appearing in refereed journals
Han, W., Ward, J. L., Kong, Y. and Li, X. 2023. Targeted and untargeted metabolomics for the evaluation of plant metabolites in response to the environment - editorial. Frontiers in Plant Science. 14, p. 1167513. https://doi.org/10.3389/fpls.2023.1167513

Fungal plant pathogen "mutagenomics" reveals tagged and untagged mutations in Zymoseptoria tritici and identifies SSK2 as key morphogenesis and stress-responsive virulence factor

A - Papers appearing in refereed journals
Blyth, H., Smith, D., King, R., Bayon, C., Ashfield, T., Walpole, H., Venter, E., Kanyuka, K. and Rudd, J. J. 2023. Fungal plant pathogen "mutagenomics" reveals tagged and untagged mutations in Zymoseptoria tritici and identifies SSK2 as key morphogenesis and stress-responsive virulence factor. Frontiers in Plant Science. 14, p. 1140824. https://doi.org/10.3389/fpls.2023.1140824

A high soluble-fibre allele in wheat encodes a defective cell wall peroxidase responsible for dimerization of ferulate moieties on arabinoxylan

A - Papers appearing in refereed journals
Mitchell, R. A. C., Oszvald, M., Pellny, T. K., Freeman, J., Halsey, K., Sparks, C. A., Huttly, A. K., Specel, S., Leverington-Waite, M., Griffiths, S., Shewry, P. R. and Lovegrove, A. 2023. A high soluble-fibre allele in wheat encodes a defective cell wall peroxidase responsible for dimerization of ferulate moieties on arabinoxylan. bioRxiv. https://doi.org/10.1101/2023.03.08.531735

Automated extraction of pod phenotype data from micro-computed tomograph

A - Papers appearing in refereed journals
Corcoran, E., Siles-Suarez, L., Kurup, S. and Ahnert, S. 2023. Automated extraction of pod phenotype data from micro-computed tomograph. Frontiers in Plant Science. 14, p. 1120182. https://doi.org/10.3389/fpls.2023.1120182

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