المؤلفون: Sandeep Sharma, Tarun Kumar, M. John Foulkes, Simon Orford, Anju Mahendru Singh, Luzie U. Wingen, Venkatesh Karnam, Lekshmy S. Nair, Pranab Kumar Mandal, Simon Griffiths, Malcolm J. Hawkesford, Peter R. Shewry, Alison R. Bentley, Renu Pandey

المصدر: CABI Agriculture and Bioscience, Vol 4, Iss 1, Pp 1-20 (2023)

مصطلحات موضوعية: Biomass partitioning, Grain protein concentration, Grain protein deviation, Low soil nitrogen, Nitrogen remobilization efficiency, Triticum aestivum, Agriculture (General), S1-972

الوصف: Abstract Background In wheat, nitrogen (N) remobilization from vegetative tissues to developing grains largely depends on genetic and environmental factors. The evaluation of genetic potential of crops under limited resource inputs such as limited N supply would provide an opportunity to identify N-efficient lines with improved N utilisation efficiency and yield potential. We assessed the genetic variation in wheat recombinant inbred lines (RILs) for uptake, partitioning, and remobilization of N towards grain, its association with grain protein concentration (GPC) and grain yield. Methods We used the nested association mapping (NAM) population (195 lines) derived by crossing Paragon (P) with CIMMYT core germplasm (P × Cim), Baj (P × Baj), Watkins (P × Wat), and Wyalkatchem (P × Wya). These lines were evaluated in the field for two seasons under limited N supply. The plant sampling was done at anthesis and physiological maturity stages. Various physiological traits were recorded and total N uptake and other N related indices were calculated. The grain protein deviation (GPD) was calculated from the regression of grain yield on GPC. These lines were grouped into different clusters by hierarchical cluster analysis based on grain yield and N-remobilization efficiency (NRE). Results The genetic variation in accumulation of biomass at both pre- and post-anthesis stages were correlated with grain-yield. The NRE significantly correlated with aboveground N uptake at anthesis (AGNa) and grain yield but negatively associated with AGN at post-anthesis (AGNpa) suggesting higher N uptake till anthesis favours high N remobilization during grain filling. Hierarchical cluster analysis of these RILs based on NRE and yield resulted in four clusters, efficient (31), moderately efficient (59), moderately inefficient (58), and inefficient (47). In the N-efficient lines, AGNa contributed to 77% of total N accumulated in grains, while it was 63% in N-inefficient lines. Several N-efficient lines also exhibited positive grain protein deviation (GPD), combining high grain yield and GPC. Among crosses, the P × Cim were superior and N-efficient, while P × Wya responded poorly to low N input. Conclusions We propose that traits favouring pre- or post-anthesis biomass accumulation and pre-anthesis N uptake may be targeted for breeding to improve grain-yield under limited N. The lines with positive GPD, a first report of genotype-dependent GPD associated with both AGNpa and AGNa in wheat, may be used as varieties or genetic resources to improve grain yield with high GPC for sustainable development under limited N conditions.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2662-4044Test

الوصول الحر: https://doaj.org/article/1a4ec08c7ef642b0b4c57685adf170f4Test

المؤلفون: Reda Amezrou, Colette Audéon, Jérôme Compain, Sandrine Gélisse, Aurélie Ducasse, Cyrille Saintenac, Nicolas Lapalu, Clémentine Louet, Simon Orford, Daniel Croll, Joëlle Amselem, Sabine Fillinger, Thierry C Marcel

المصدر: PLoS Pathogens, Vol 19, Iss 5, p e1011376 (2023)

مصطلحات موضوعية: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5

الوصف: Zymoseptoria tritici is the fungal pathogen responsible for Septoria tritici blotch on wheat. Disease outcome in this pathosystem is partly determined by isolate-specific resistance, where wheat resistance genes recognize specific fungal factors triggering an immune response. Despite the large number of known wheat resistance genes, fungal molecular determinants involved in such cultivar-specific resistance remain largely unknown. We identified the avirulence factor AvrStb9 using association mapping and functional validation approaches. Pathotyping AvrStb9 transgenic strains on Stb9 cultivars, near isogenic lines and wheat mapping populations, showed that AvrStb9 interacts with Stb9 resistance gene, triggering an immune response. AvrStb9 encodes an unusually large avirulence gene with a predicted secretion signal and a protease domain. It belongs to a S41 protease family conserved across different filamentous fungi in the Ascomycota class and may constitute a core effector. AvrStb9 is also conserved among a global Z. tritici population and carries multiple amino acid substitutions caused by strong positive diversifying selection. These results demonstrate the contribution of an 'atypical' conserved effector protein to fungal avirulence and the role of sequence diversification in the escape of host recognition, adding to our understanding of host-pathogen interactions and the evolutionary processes underlying pathogen adaptation.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/1553-7366Test; https://doaj.org/toc/1553-7374Test

الوصول الحر: https://doaj.org/article/ebbf29ffb49c4df8adf7c1d88fb71ef1Test

المؤلفون: Jemima Brinton, Ricardo H. Ramirez-Gonzalez, James Simmonds, Luzie Wingen, Simon Orford, Simon Griffiths, Wheat Genome Project, Georg Haberer, Manuel Spannagl, Sean Walkowiak, Curtis Pozniak, Cristobal Uauy

المصدر: Communications Biology, Vol 3, Iss 1, Pp 1-11 (2020)

مصطلحات موضوعية: Biology (General), QH301-705.5

الوصف: Brinton, Uauy and colleagues utilize genomic data from the 10+ Wheat Genome Project to develop a useful tool for studying and generating new wheat cultivars. This framework uses advanced exploitation of wheat haplotypes to bring newfound precision and efficiency to wheat breeding.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2399-3642Test

الوصول الحر: https://doaj.org/article/616bdb9138f44300a374cdd45d90d5e6Test

المؤلفون: Elizabeth A. Chapman, Simon Orford, Jacob Lage, Simon Griffiths

المصدر: Frontiers in Plant Science, Vol 12 (2021)

مصطلحات موضوعية: senescence, phenotyping, selection, staygreen, grain development, peduncle, Plant culture, SB1-1110

الوصف: Senescence is a highly quantitative trait, but in wheat the genetics underpinning senescence regulation remain relatively unknown. To select senescence variation and ultimately identify novel genetic regulators, accurate characterization of senescence phenotypes is essential. When investigating senescence, phenotyping efforts often focus on, or are limited to, the visual assessment of flag leaves. However, senescence is a whole-plant process, involving remobilization and translocation of resources into the developing grain. Furthermore, the temporal progression of senescence poses challenges regarding trait quantification and description, whereupon the different models and approaches applied result in varying definitions of apparently similar metrics. To gain a holistic understanding of senescence, we phenotyped flag leaf and peduncle senescence progression, alongside grain maturation. Reviewing the literature, we identified techniques commonly applied in quantification of senescence variation and developed simple methods to calculate descriptive and discriminatory metrics. To capture senescence dynamism, we developed the idea of calculating thermal time to different flag leaf senescence scores, for which between-year Spearman’s rank correlations of r ≥ 0.59, P < 4.7 × 10–5 (TT70), identify as an accurate phenotyping method. Following our experience of senescence trait genetic mapping, we recognized the need for singular metrics capable of discriminating senescence variation, identifying thermal time to flag leaf senescence score of 70 (TT70) and mean peduncle senescence (MeanPed) scores as most informative. Moreover, grain maturity assessments confirmed a previous association between our staygreen traits and grain fill extension, illustrating trait functionality. Here we review different senescence phenotyping approaches and share our experiences of phenotyping two independent recombinant inbred line (RIL) populations segregating for staygreen traits. Together, we direct readers toward senescence phenotyping methods we found most effective, encouraging their use when investigating and discriminating senescence variation of differing genetic bases, and aid trait selection and weighting in breeding and research programs alike.

وصف الملف: electronic resource

العلاقة: https://www.frontiersin.org/articles/10.3389/fpls.2021.638738/fullTest; https://doaj.org/toc/1664-462XTest

الوصول الحر: https://doaj.org/article/17f9aa0cc19445ff816682eef06044b5Test

المؤلفون: Alison Lovegrove, Luzie U Wingen, Amy Plummer, Abigail Wood, Diana Passmore, Ondrej Kosik, Jackie Freeman, Rowan A C Mitchell, Kirsty Hassall, Mehmet Ulker, Karolina Tremmel-Bede, Marianna Rakszegi, Zoltán Bedő, Marie-Reine Perretant, Gilles Charmet, Caroline Pont, Jerome Salse, Michelle Leverington Waite, Simon Orford, Amanda Burridge, Till K Pellny, Peter R Shewry, Simon Griffiths

المصدر: PLoS ONE, Vol 15, Iss 2, p e0227826 (2020)

مصطلحات موضوعية: Medicine, Science

الوصف: Dietary fibre (DF) has multiple health benefits and wheat grains are major sources of DF for human health. However, DF is depleted in white wheat flour which is more widely consumed than wholegrain. The major DF component in white flour is the cell wall polysaccharide arabinoxylan (AX). We have identified the Chinese wheat cultivar Yumai 34 as having unusually high contents of AX in both water-soluble and insoluble forms. We have therefore used populations generated from crosses between Yumai 34 and four other wheat cultivars, three with average contents of AX (Ukrainka, Altigo and Claire) and one also having unusually high AX (Valoris), in order to map QTLs for soluble AX (determined as relative viscosity of aqueous extracts of wholemeal flours) and total AX (determined by enzyme fingerprinting of white flour). A number of QTL were mapped, but most were only detected in one or two crosses. However, all four crosses showed strong QTLs for high RV/total AX on chromosome 1B, with Yumai 34 being the increasing parent, and a KASP marker for the Yumai 34 high AX allele was validated by analysis of high AX lines derived from Yumai 34 but selected by biochemical analysis. A QTL for RV was also mapped on chromosome 6B in Yumai 34 x Valoris, with Valoris being the increasing allele, which is consistent with the observation of transgressive segregation for this population. Association studies in an independent germplasm panel identified marker trait associations for relative viscosity in these same locations while direct selection for fibre content in breeding resulted in high levels of enrichment for the Yumai 34 1B allele. The data therefore indicate that marker-assisted breeding can be used to develop wheat with high AX fibre in white flour.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/1932-6203Test

الوصول الحر: https://doaj.org/article/28ccb3210c1344c69c7fffc103ce20f7Test

المؤلفون: Ji Zhou, Christopher Applegate, Albor Dobon Alonso, Daniel Reynolds, Simon Orford, Michal Mackiewicz, Simon Griffiths, Steven Penfield, Nick Pullen

المصدر: Plant Methods, Vol 13, Iss 1, Pp 1-17 (2017)

مصطلحات موضوعية: Growth phenotypes, Automated trait analysis, Feature extraction, Computer vision, Software engineering, Arabidopsis, Plant culture, SB1-1110, Biology (General), QH301-705.5

الوصف: Abstract Background Plants demonstrate dynamic growth phenotypes that are determined by genetic and environmental factors. Phenotypic analysis of growth features over time is a key approach to understand how plants interact with environmental change as well as respond to different treatments. Although the importance of measuring dynamic growth traits is widely recognised, available open software tools are limited in terms of batch image processing, multiple traits analyses, software usability and cross-referencing results between experiments, making automated phenotypic analysis problematic. Results Here, we present Leaf-GP (Growth Phenotypes), an easy-to-use and open software application that can be executed on different computing platforms. To facilitate diverse scientific communities, we provide three software versions, including a graphic user interface (GUI) for personal computer (PC) users, a command-line interface for high-performance computer (HPC) users, and a well-commented interactive Jupyter Notebook (also known as the iPython Notebook) for computational biologists and computer scientists. The software is capable of extracting multiple growth traits automatically from large image datasets. We have utilised it in Arabidopsis thaliana and wheat (Triticum aestivum) growth studies at the Norwich Research Park (NRP, UK). By quantifying a number of growth phenotypes over time, we have identified diverse plant growth patterns between different genotypes under several experimental conditions. As Leaf-GP has been evaluated with noisy image series acquired by different imaging devices (e.g. smartphones and digital cameras) and still produced reliable biological outputs, we therefore believe that our automated analysis workflow and customised computer vision based feature extraction software implementation can facilitate a broader plant research community for their growth and development studies. Furthermore, because we implemented Leaf-GP based on open Python-based computer vision, image analysis and machine learning libraries, we believe that our software not only can contribute to biological research, but also demonstrates how to utilise existing open numeric and scientific libraries (e.g. Scikit-image, OpenCV, SciPy and Scikit-learn) to build sound plant phenomics analytic solutions, in a efficient and effective way. Conclusions Leaf-GP is a sophisticated software application that provides three approaches to quantify growth phenotypes from large image series. We demonstrate its usefulness and high accuracy based on two biological applications: (1) the quantification of growth traits for Arabidopsis genotypes under two temperature conditions; and (2) measuring wheat growth in the glasshouse over time. The software is easy-to-use and cross-platform, which can be executed on Mac OS, Windows and HPC, with open Python-based scientific libraries preinstalled. Our work presents the advancement of how to integrate computer vision, image analysis, machine learning and software engineering in plant phenomics software implementation. To serve the plant research community, our modulated source code, detailed comments, executables (.exe for Windows; .app for Mac), and experimental results are freely available at https://github.com/Crop-Phenomics-Group/Leaf-GP/releasesTest .

وصف الملف: electronic resource

العلاقة: http://link.springer.com/article/10.1186/s13007-017-0266-3Test; https://doaj.org/toc/1746-4811Test

الوصول الحر: https://doaj.org/article/3cd99371e76e4567a64380dfb1f59ad0Test

المؤلفون: Reda Amezrou, Colette Audéon, Jérôme compain, Sandrine Gélisse, Aurélie Ducasse, Cyrille Saintenac, Nicolas Lapalu, Clémentine Louet, Simon Orford, Daniel Croll, Joëlle Amselem, Sabine Fillinger, Thierry C Marcel

الوصف: Zymoseptoria triticiis the fungal pathogen responsible for Septoria tritici blotch on wheat. Disease outcome in this pathosystem is partly determined by isolate-specific resistance, where wheat resistance genes recognize specific fungal factors triggering an immune response. Despite the large number of known wheat resistance genes, fungal molecular determinants involved in such cultivar-specific resistance remain largely unknown. We identified the avirulence factorAvrStb9using association mapping and functional validation approaches. PathotypingAvrStb9transgenic strains onStb9cultivars, near isogenic lines and wheat mapping populations, showed thatAvrStb9interacts withStb9resistance gene, triggering an immune response.AvrStb9encodes an unusually large avirulence gene with a predicted secretion signal and a protease domain. It belongs to a S41 protease family conserved across different filamentous fungi in the Ascomycota class and may constitute a core effector.AvrStb9is also conserved among a globalZ. triticipopulation and carries multiple amino acid substitutions caused by strong positive diversifying selection. These results demonstrate the contribution of an ‘atypical’ conserved effector protein to fungal avirulence and the role of sequence diversification in the escape of host recognition, adding to our understanding of host-pathogen interactions and the evolutionary processes underlying pathogen adaptation.Author SummaryFungal avirulence (Avr) genes are involved in gene-for-gene relationships with host resistance genes.Avrgenes may at the same time target host defenses to allow infection and be recognized by a host resistance gene triggering a defense response. The fungusZymoseptoria triticicauses Septoria tritici blotch, a major disease of wheat worldwide.Z. triticipopulations rapidly adapt to selection pressures such as host resistance, leading to resistance breakdown. We report the identification of the avirulence geneAvrStb9based on genetic mapping, sequence polymorphisms and allele swapping.AvrStb9is involved in the interaction withStb9resistance gene following the gene-for-gene model, and its recognition hinders disease symptoms in hosts carrying the corresponding resistance gene. Unlike other knownZ. tritici Avreffectors,AvrStb9encodes for an unusually large Avr protein with a predicted protease S41 domain conserved among diverse ascomycete lineages. We also highlight several gene mutations likely involved in escapingStb9-mediated recognition.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::de7da4dee30063d9e6103570b4d9d54eTest
https://doi.org/10.1101/2022.10.31.514577Test

المؤلفون: Jacob Lage, Simon Orford, Elizabeth A Chapman, Simon Griffiths

المصدر: Journal of Experimental Botany

مصطلحات موضوعية: Senescence, senescence, Physiology, Quantitative Trait Loci, Mutant, exome capture, Plant Science, Biology, Bulk segregant analysis, wheat, mutant, Allele, Gene, Alleles, Triticum, Genetic association, Genetics, AcademicSubjects/SCI01210, food and beverages, Research Papers, Phenotype, Forward genetics, forward genetics, staygreen, remobilization, Crop Molecular Genetics, NAM, grain fill, Edible Grain, Genetic screen

الوصف: Senescence is a complex trait under genetic and environmental control, in which resources are remobilized from vegetative tissue into grain. Delayed senescence, or ‘staygreen’ traits, can confer stress tolerance, with extended photosynthetic activity hypothetically sustaining grain filling. The genetics of senescence regulation are largely unknown, with senescence variation often correlated with phenological traits. Here, we confirm staygreen phenotypes of two Triticum aestivum cv. Paragon ethyl methane sulfonate mutants previously identified during a forward genetic screen and selected for their agronomic performance, similar phenology, and differential senescence phenotypes. Grain filling experiments confirmed a positive relationship between onset of senescence and grain fill duration, reporting an associated ~14% increase in final dry grain weight for one mutant (P
Two staygreen mutants were identified for which grain fill duration and grain weight were enhanced. Independent amino acid substitutions within NAC subdomain IV of NAM-1 homoeologues are proposed as causative.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::676a0fdb9e72c321e8bd1bcc7e2b8902Test
https://doi.org/10.1093/jxb/erab368Test

المؤلفون: Laura E, Dixon, Marianna, Pasquariello, Roshani, Badgami, Kara A, Levin, Gernot, Poschet, Pei Qin, Ng, Simon, Orford, Noam, Chayut, Nikolai M, Adamski, Jemima, Brinton, James, Simmonds, Burkhard, Steuernagel, Iain R, Searle, Cristobal, Uauy, Scott A, Boden

المصدر: Science advances. 8(19)

مصطلحات موضوعية: MicroRNAs, Gene Expression Regulation, Plant, Genes, Homeobox, Grain Proteins, Inflorescence, Edible Grain, Alleles, Triticum, Plant Proteins

الوصف: Plant and inflorescence architecture determine the yield potential of crops. Breeders have harnessed natural diversity for inflorescence architecture to improve yields, and induced genetic variation could provide further gains. Wheat is a vital source of protein and calories; however, little is known about the genes that regulate the development of its inflorescence. Here, we report the identification of semidominant alleles for a class III homeodomain-leucine zipper transcription factor

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=pmid________::33a959a2d42435862e055e37af4ca6daTest
https://pubmed.ncbi.nlm.nih.gov/35544571Test

المؤلفون: Saule Abugalieva, M. Chhetry, Yerlan Turuspekov, A Amalova, Michelle Leverington-Waite, Simon Orford, K. Yermekbayev, Simon Griffiths

المصدر: Russian Journal of Genetics. 56:1090-1098

مصطلحات موضوعية: 0106 biological sciences, Genetics, 0303 health sciences, education.field_of_study, Genetic diversity, Population, Biology, 01 natural sciences, Genome, SNP genotyping, 03 medical and health sciences, Genetic marker, Genotype, Plant breeding, Allele, education, 030304 developmental biology, 010606 plant biology & botany

الوصف: The main purposes of the study were (i) to develop a mapping population, (ii) to construct its genetic map for further identification of genes associated with important agronomic traits. To the best of our knowledge this is the first segregating population and genetic map developed for Kazakh bread wheat. The work is an example of how plant breeding programs in Kazakhstan have started successfully using next generation plant breeding methods to carry out systematic plant breeding to enhance final grain harvest. The KASP technology and SNP DNA-markers have been exploited to genotype and build a genetic map. The total length of the map was 1376 cM. A total 157, which spanned A, B and D subgenomes, out of the initial 178 SNP markers used formed 26 linkage groups leaving 1 duplicated and 20 unassigned markers. As threshold distance between markers was set ≤30 cM, two linkage groups were obtained for chromosomes such as 2А, 2В, 2D, 3A, 5A, 6B and 7A. Kosambi mapping function was employed to calculate recombination units. RILs were developed through SSD method up to F4 generation. Almost 97% of identified alleles were useful in evaluating the population’s genetic diversity; the remaining 3% showed no outcome. As a result, 77 DNA markers were mapped for A, 74 for B and 27 for D genomes. The mapping population will be genotyped using a high marker density array platform such as Illumina iSelect to obtain a genetic map with a relatively high coverage. Then, the population and high-resolution genetic map will be used to identify genes influencing wheat adaptation in Kazakhstan.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::a218e436c48b67107c1fc000a12a6ca3Test
https://doi.org/10.1134/s102279542009015xTest