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Phylogenomic discovery of deleterious mutants completes the potato breeding revolution

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Molecular Plant 2023年第7期16卷 1103-1105页

作者： Alisdair R.Fernie Saleh Alseekh Max-Planck-lnstitute of Molecular Plant Physiology Am Muhlenberg 114476 Potsdam-GolmGermany Center for Plant Systems Biology and Biotechnology 4000 PlovdivBulgaria

After many decades of attempts,recent years have finally witnessed the reinvention of potato from a clonally propagated autotetraploid to a seed-propagated inbred line-based diploid hybrid(Zhang et al.,2021).This can be anticipated to accelerate potato breeding from a cumbersome,non-accumulative mode to a rapid iterative one(Wu et al.,2023).That said,a major hurdle in achieving this is the fact that the clonally propagated potato has amassed a huge number of deleterious mutations(Zhang et al.,2019).These mutations are at least partially masked in the heterozygous state,but their detrimental effects are exposed during the process of developing inbred lines,rendering this a considerable challenge.While Zhang et al.(2021)previously developed two inbred lines,the first generation of highly homozygous inbred lines,these contained mutations that collectively resulted in negative fitness manifesting in frail growth,reduced fertility,and low yield.In a recent study,Wu et al.(2023)utilized genomic evolutionary rate profiling(GErP)analysis to identify and quantify deleterious mutations at the genome-wide scale.

关键词： breeding fertility collective

Plant gene co-expression defines the biosynthetic pathway of neuroactive alkaloids

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Molecular Plant 2024年第3期17卷 372-374页

作者： Fang Liu' Alisdair R.Fernie Youjun Zhang Key Laboratory of Seed Innovation Institute of Genetics and Developmental BiologyChinese Academy of Sciences100101 BeijingChina Max Planck Institute of Molecular Plant Physiology Am Muhlenberg 114476 Potsdam-GolmGermany Center for Plant Systems Biology and Biotechnology 4000 PlovdivBulgaria University of Chinese Academy of Sciences 100049 BeijingChina

Transcriptomes comprise gene co-expression clustersor modules,showcasing distinct patterns of coordinated expression among groups of genes across independent biological samples(Serin et al.,2016).The"guilt-by-association"hypothesis suggests the functional importance of these clusters;for example,co-expressed genes associated with metabolism typically contain genes encoding several enzymes associated with the same pathways.

关键词： metabolism alkaloids

Targeting Key Genes to Tailor Old and New Crops for a Greener Agriculture

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Molecular Plant 2020年第3期13卷 354-356页

作者： Alisdair R.Fernie Jianbing Yan Department of Molecular Physiology Max-Planck-lnstitute of Molecular Plant PhysiologyAm Muhlenberg 114476 PotsdamGermany National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China

Growing crops closer to the consumer is one of many approaches proposed to lessen the environmental footprint associated with food production(Banerjee and Adenauer,2014).This is complicated by an increasingly urban population,the lack of available land in cities and the consequent need for rapid crop cycling.Given these constraints,to date only lettuce and related leafy greens are currently cultivated at scale in urban farms(Touliatos et al.,2016).In recent years,there are increasing interests in the urban agriculture of fruits and berries,since controlled automated vertical farming systems offer the twin advantages of optimizing land use and the ease with which they can be designed to be more environmentally friendly and sustainable than traditional agriculture.However,a considerable challenge is that commercial crop varieties were historically,and still are,bred to be high yielding under typical field and greenhouse parameters.Moreover,given the perishable nature of fruits and berries,a reduced distance from farm to fork renders the shelf-life trait(and its associated detrimental effects on fruit quality)less imperative.Thus,the possibility to improve fruit and berry quality traits is a particularly attractive aspect of urban agriculture.In addition,the environmental benefit for these species is perhaps even greater than for other crops,since they are more often transported by air.A recent study uses multi-site CrISPr/Cas9-mediated genome editing to restructure vine line tomato plants into compact early-yielding plants suitable for urban agriculture(Figure 1),while demonstrating that a single gene editing strategy can produce a compact stature in the related plant groundcherry(Kwon et al.,2019).

关键词： crops yielding Figure

Understanding source-sink interactions: Progress in model plants and translational research to crops

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Molecular Plant 2023年第1期16卷 96-121页

作者： Laise rosado-Souza ryo Yokoyama Uwe Sonnewald Alisdair R.Fernie Max-Planck-Institute of Molecular Plant Physiology Am Mühlenberg 114476 Potsdam-GolmGermany Department of Biochemistry University of Erlangen-NurembergStaudtstrasse 591058 ErlangenGermany

Agriculture is facing a massive increase in demand per hectare as a result of an ever-expanding population and environmental deterioration.While we have learned much about how environmental conditions and diseases impact crop yield,until recently considerably less was known concerning endogenous factors,including within-plant nutrient allocation.In this review,we discuss studies of source-sink interactions covering both fundamental research in model systems under controlled growth conditions and how the findings are being translated to crop plants in the field.In this respect we detail efforts aimed at improving and/or combining C3,C4,and CAM modes of photosynthesis,altering the chloroplastic electron transport chain,modulating photorespiration,adopting bacterial/algal carbon-concentrating mechanisms,and enhancing nitrogen-and water-use efficiencies.Moreover,we discuss how modulating TCA cycle activities and primary metabolism can result in increased rates of photosynthesis and outline the opportunities that evaluating natural variation in photosynthesis may afford.Although source,transport,and sink functions are all covered in this review,we focus on discussing source functions because the majority of research has been conducted in this field.Nevertheless,considerable recent evidence,alongside the evidence from classical studies,demonstrates that both transport and sink functions are also incredibly important determinants of yield.We thus describe recent evidence supporting this notion and suggest that future strategies for yield improvement should focus on combining improvements in each of these steps to approach yield optimization.

关键词： photosynthesis assimilate transport nitrogen-use efficiency water-use efficiency source-sink natural variance transgenic intervention

Integrating multiomics data accelerates elucidation of plant primary and secondary metabolic pathways

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aBIOTECH 2023年第1期4卷 47-56页

作者： Feng Zhu Weiwei Wen Yunjiang Cheng Saleh Alseekh Alisdair R.Fernie National r&D Center for Citrus Preservation Hubei Hongshan LaboratoryNational Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural CropsKey Laboratory of Horticultural Plant BiologyMinistry of EducationHuazhong Agricultural UniversityWuhan 430070China Max Planck Institute of Molecular Plant Physiology Am Mühlenberg 1Potsdam-Golm 14476Germany Center of Plant Systems Biology and Biotechnology Plovdiv 4000Bulgaria

Plants are the most important sources of food for humans,as well as supplying many ingredients that are of great importance for human health.Developing an understanding of the functional components of plant metabolism has attracted considerable attention.The rapid development of liquid chromatography and gas chromatography,coupled with mass spectrometry,has allowed the detection and characterization of many thousands of metabolites of plant origin.Nowadays,elucidating the detailed biosynthesis and degradation pathways of these metabolites represents a major bottleneck in our understanding.recently,the decreased cost of genome and transcriptome sequencing rendered it possible to identify the genes involving in metabolic pathways.Here,we review the recent research which integrates metabolomic with different omics methods,to comprehensively identify structural and regulatory genes of the primary and secondary metabolic pathways.Finally,we discuss other novel methods that can accelerate the process of identification of metabolic pathways and,ultimately,identify metabolite function(s).

关键词： Metabolome Transcriptome Genome Crop improvement

De Novo Domestication:An Alternative route toward New Crops for the Future

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Molecular Plant 2019年第5期12卷 615-631页

作者： Alisdair R.Fernie Jianbing Yan Department of Molecular Physiology Max-Planck-lnstitute of Molecular Plant PhysiologyAm Muhlenberg 114476 Potsdam-GolmGermany National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China

Current global agricultural production must feed over 7 billion people.However,productivity varies greatly across the globe and is under threat from both increased competitions for land and climate change and associated environmental deterioration.Moreover,the increase in human population size and dietary changes are putting an ever greater burden on agriculture.The majority of this burden is met by the cultivation of a very small number of species,largely in locations that differ from their origin of domestication.recent technological advances have raised the possibility of de novo domestication of wild plants as a viable solution for designing ideal crops while maintaining food security and a more sustainable lowinput agriculture.Here we discuss how the discovery of multiple key domestication genes alongside the development of technologies for accurate manipulation of several target genes simultaneously renders de novo domestication a route toward crops for the future.

关键词： De Novo Domestication redomestication New Crops Genome Editing Food Security Sustainable Agriculture

The genomes of Taxus species unveil novel candidates in the biosynthesis of taxoids

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Molecular Plant 2021年第11期14卷 1773-1775页

作者： Youjun Zhang Federico Scossa Alisdair R.Fernie Center of Plant Systems Biology and Biotechnology 4000 PlovdivBulgaria Max-Planck-lnstitut fur Molekulare Pflanzenphysiologie Am Muhlenberg 114476 Potsdam-GolmGermany research Center for Genomics and Bioinformatics(CrEA-GB) Via Ardeatina 54600178 RomeItaly

Taxaceae is the yew family of conifers and includes evergreen trees and small shrubs mainly distributed in Eurasia and North America.The genus of Taxus has attracted considerable attention since Monroe E.Wall and Mansukh C.Wani firstly isolated and characterized an unusual cyclic diterpenoid from the bark of the Pacific yew tree(Wani et al.,1971).This compound,subsequently called paclitaxel,was shown to promote tubulin assembly into microtubules,preventing their disassembly.Subsequently,paclitaxel was approved for medical use against ovarian cancer in 1992(Fischer and Ganellin,2010).

关键词： unusual Monro compound

Metabolomics-centered mining of plant metabolic diversity and function:Past decade and future perspectives

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Molecular Plant 2023年第1期16卷 43-63页

作者： Shuangqian Shen Chuansong Zhan Chenkun Yang Alisdair R.Fernie Jie Luo Sanya Nanfan research Institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China College of Tropical Crops Hainan UniversityHaikou 570228China Max Planck Institute of Molecular Plant Physiology Potsdam-Golm 14476Germany

Plants are natural experts in organic synthesis,being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival challenges.Metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry,statistics,and biochemistry.Its ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites.Metabolomics is usually performed by targeting either a specific cell,a specific tissue,or the entire organism.Considerable advances in science and technology over the last three decades have propelled us into the era of multi-omics,in which metabolomics,despite at an earlier developmental stage than genomics,transcriptomics,and proteomics,offers the distinct advantage of studying the cellular entities that have the greatest influence on end phenotype.Here,we summarize the state of the art of metabolite detection and identification,and illustrate these techniques with four case study applications:(i)comparing metabolite composition within and between species,(ii)assessing spatio-temporal metabolic changes during plant development,(iii)mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses,and(iv)assessing the performance of metabolomics as a means of functional gene identification,metabolic pathway elucidation,and metabolomics-assisted breeding through analyzing plant populations with diverse genetic variations.In addition,we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets,including those from genomics,transcriptomics,proteomics,epigenomics,phenomics,microbiomes,and ion-omics studies.Finally,we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.

关键词： metabolomics multi-omics high-throughput metabolic profiling bioactive markers

On the role of the tricarboxylic acid cycle in plant productivity

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Journal of Integrative Plant Biology 2018年第12期60卷 1199-1216页

作者： Youjun Zhang Alisdair R.Fernie Max-Planck-lnstitute of Molecular Plant Physiology Am Muhlenberg 114476 Potsdam-GolmGermany Center of Plant System Biology and Biotechnology 4000 PlovdivBulgaria

The tricarboxylic acid(TCA) cycle is one of the canonical energy pathways of living systems, as well as being an example of a pathway in which dynamic enzyme assemblies, or metabolons, are well characterized. The role of the enzymes have been the subject of saturated transgenesis approaches, whereby the expression of the constituent enzymes were reduced or knocked out in order to ascertain their in vivo function.Some of the resultant plants exhibited improved photosynthesis and plant growth, under controlled greenhouse conditions. In addition, overexpression of the endogenous genes, or heterologous forms of a number of the enzymes, has been carried out in tomato fruit and the roots of a range of species, and in some instances improvement in fruit yield and postharvest properties and plant performance, under nutrient limitation, have been reported, respectively. Given a number of variants, in nature, we discuss possible synthetic approaches involving introducing these variants, or at least a subset of them, into plants. We additionally discuss the likely consequences of introducing synthetic metabolons, wherein certain pairs of reactions are artificially permanently assembled into plants, and speculate as to future strategies to further improve plant productivity by manipulation of the core metabolic pathway.

关键词： On the role of the tricarboxylic acid cycle in plant productivity TCA cycle