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Constitutive basis of root system architecture:uncovering a promising trait for breeding nutrient-and drought-resilient crops

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aBIOTECH 2023年第4期4卷 315-331页

作者： Zhigang Liu Tongfei Qin Michaella Atienza Yang Zhao Hanh Nguyen Huajin Sheng Toluwase Olukayode Hao Song Karim Panjvani Jurandir Magalhaes William J.Lucas leon v.kochian Global Institute for Food Security University of SaskatchewanSaskatoonSK S7N 4L8Canada Department of Computer Science University of SaskatchewanSaskatoonSK S7N 5C9Canada Embrapa Maize and Sorghum Brazilian Agricultural Research CorporationSete LagoasMG 35701-970Brazil Department of Plant Biology College of Biological SciencesUniversity of CaliforniaDavisCA 95616USA

Root system architecture(RSA)plays a pivotal role in efficient uptake of essential nutrients,such as phosphorous(P),nitrogen(N),and water In soils with heterogeneous nutrient distribution,root plasticity can optimize acquisition and plant growth.Here,we present evidence that a constitutive RSA can confer benefits for sorghum grown under both sufficient and limiting growth conditions.Our studies,using P efficient SC103 and inefficient BTx635 sorghum cultivars,identified significant differences in root traits,with SC103 developing a larger root system with more and longer lateral roots,and enhanced shoot biomass,under both nutrient sufficient and deficient conditions.In addition to this constitutive attribute,under P deficiency,both cultivars exhibited an initial increase in lateral root development;however,SC103 still maintained the larger root biomass.Although N deficiency and drought stress inhibited both root and shoot growth,for both sorghum cultivars,SC103 again maintained the better performance.These findings reveal that SC103,a P efficient sorghum cultivar,also exhibited enhanced growth performance under N deficiency and drought.Our results provide evidence that this constitutive nature of RSA can provide an avenue for breeding nutrient-and drought-resilient crops.

关键词： Constitutive root system architecture Abiotic stress Nutrient efficiency Drought resilience Plant breeding

The role of aluminum sensing and signaling in plant aluminum resistance

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Journal of Integrative Plant Biology 2014年第3期56卷 221-230页

作者： Jiping Liu Miguel A.Piros leon v.kochian USDA‐ARS Robert W.Holley Center for Agriculture and Health Tower Road Cornell University

As researchers have gained a better understanding in recent years into the physiological, molecular, and genetic basis of how plants deal with aluminum （AI） toxicity in acid soils prevalent in the tropics and sub-tropics, it has become clear that an important component of these responses is the triggering and regulation of cellular pathways and processes by AI. In this review of plant AI signaling, we begin by summarizing the understanding of physiological mechanisms of AI resistance, which first led researchers to realize that AI stress induces gene expression and modifies protein function during the activation of AI resistance responses. Subsequently, an overview of AI resistance genes and their function provides verification that AI induction of gene expression plays a major role in AI resistance in many plant species. More recent research into the mechanistic basis for Al-induced transcrip- tional activation of resistance genes has led to the identifica- tion of several transcription factors as well as cis-elements in the promoters of AI resistance genes that play a role in greater Al-induced gene expression as well as higher constitutive expression of resistance genes in some plant species. Finally, the post-transcriptional and translational regulation of AI resistance proteins is addressed, where recent research has shown that AI can both directly bind to and alter activity of certain organic acid transporters, and also influence AI resistance proteins indirectly, via protein phosphorylation.

关键词： ALMT aluminum resistance aluminum signaling aluminumtoxicity MATE

Application of an Improved 2-Dimensional High-Throughput Soybean Root Phenotyping Platform to Identify Novel Genetic variants Regulating Root Architecture Traits

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Plant Phenomics 2023年第4期5卷 728-745页

作者： Rahul Chandnani Tongfei Qin Heng Ye Haifei Hu Karim Panjvani Mutsutomo Tokizawa Javier Mora Macias Alma Armenta Medina Karine C.Bernardino Pierre-Luc Pradier Pankaj Banik Ashlyn Mooney Jurandir v.Magalhaes Henry T.Nguyen leon v.kochian Global Institute for Food Security University of SaskatchewanSaskatoonSKCanada NRGene Canada 110 Research Dr Suite 101SaskatoonSKCanada Division of Plant Sciences and Technology University of MissouriColumbiaM065211USA School of Biological Sciences The University of Western AustraliaCrawleyWA 6009Australia Rice Research Institute Guangdong Academy of Agricultural Sciences&Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China(Co-construction by Ministry and Province)Ministry of Agriculture and Rural Affairs&Guangdong Key Laboratory of New Technology in Rice Breeding&Guangdong Rice Engineering LaboratoryGuangdongChina Embrapa Maize and Sorghum Sete LagoasBrazil

Nutrient-efficient root system architecture(RSA)is becoming an important breeding objective for generating crop varieties with improved nutrient and water acquisition efficiency.Genetic variants shaping soybean RSA is key in improving nutrient and water acquisition.Here,we report on the use of an improved 2-dimensional high-throughput root phenotyping platform that minimizes background noise by imaging pouch-grown root systems submerged in water.We also developed a background image cleaning Python pipeline that computationally removes images of small pieces of debris and filter paper fibers,which can be erroneously quantified as root tips.This platform was used to phenotype root traits in 286 soybean lines genotyped with 5.4 million single-nucleotide polymorphisms.There was a substantially higher correlation in manually counted number of root tips with computationally quantified root tips(95%correlation),when the background was cleaned of nonroot materials compared to root images without the background corrected(79%).Improvements in our RSA phenotyping pipeline significantly reduced overestimation of the root traits influenced by the number of root tips.Genome-wide association studies conducted on the root phenotypic data and quantitative gene expression analysis of candidate genes resulted in the identification of 3 putative positive regulators of root system depth,total root length and surface area,and root system volume and surface area of thicker roots(DOF1-like zinc finger transcription factor,protein of unknown function,and C2H2 zinc finger protein).We also identified a putative negative regulator(gibberellin 20 oxidase 3)of the total number of lateral roots.

关键词： Python Root submerged

Identification of a novel pathway involving a GATA transcription factor in yeast and possibly in plant Zn uptake and homeostasis

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Journal of Integrative Plant Biology 2014年第3期56卷 271-280页

作者： Matthew J.Milner Nicole S.Pence Jiping Liu leon v.kochian Robert W.Holley Center for Agriculture and Health USDA‐ARS Cornell University Department of Plant Biology Cornell University

To gain a better understanding of the regulation of Zn homeostasis in plants and the degree of conservation of Zn homeostasis between plants and yeast, a cDNA library from the Zn/Cd hyperaccumulating plant species, Noccaea caerulescens, was screened for its ability to restore growth under Zn limiting conditions in the yeast mutant zaplA. ZAP1 is a transcription factor that activates the Zn dependent transcription of yeast genes involved in Zn uptake, including ZRT1, the yeast high affinity Zn transporter. From this screen two members of the E2F family of transcription factors were found to activate ZRT1 expression in a Zn independent manner. The activation of ZRTI by the plant E2F proteins involves E2F- mediated activation of a yeast GATA transcription factor which in turn activates ZRT1 expression. A ZRT1 promoter region necessary for activation by E2F and GATA proteins is upstream of two zinc responsive elements previously shown to bind ZAP1 in ZRT1. This activation may not involve direct binding of E2F to the ZRT1 promoter. The expression of E2F genes in yeast does not replace function of ZAP1; instead it appears to activate a novel GATA regulatory pathway involved in Zn uptake and homeostasis that is not Zn responsive.

关键词： E2F transcription factor GATA transcription factor ZRT1 Znhomeostasis

Plant mineral nutrient sensing and signaling

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Journal of Integrative Plant Biology 2014年第3期56卷 190-191页

作者： leon v.kochian William J.Lucas Robert W.Holley Center for Agriculture and Health USDA‐ARS Cornell University Department of Plant Biology College of Biological Sciences University of California

As terrestrial plants are sessile organisms and therefore must directly deal with an often complex and changing environment, they have had to develop complex and elegant strategies to survive and thrive in the face of environmental stress. This is particularly true for plant adaptation to the soil environment, where essential mineral nutrients often are found at sub- optimal levels and their concentrations can vary significantly, both spatially and temporally. Furthermore, plants also at times have to respond to excessively high and potentially toxic levels of essential nutrients, as well as toxic levels of non- essential metals and metalloids in the soil. Although plant mineral nutrition as a bona ~ide research discipline has a history of over 15o years, beginning with the pioneering work of Justus von Liebieg and others in the mid-1800＇s, it is only very recently that researchers have begun to truly appreciate how sophisticated plants are with regards to the sensing of their mineral status and the maintaining of mineral homeostasis in the plant.

关键词： Plant mineral nutrient sensing and signaling root

Developmental and genomic architecture of plant embryogenesis: from model plant to crops

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Plant Communications 2021年第1期2卷 1-12页

作者： Alma Armenta-Medina C.Stewart Gillmor Peng Gao Javier Mora-Macias leon v.kochian Daoquan Xiang Raju Datla Global Institute for Food Security University of SaskatchewanSaskatoonSK S7N 4J8Canada Laboratorio Nacional de Genòmica para la Biodiversidad(Langebio) Unidad de Genòmica AvanzadaCentro de Investigaciòny Estudios Avanzados del IPN(CINVESTAV-IPN)IrapuatoGuanajuatoMéxico National Research Council Canada 110 Gymnasium PlaceSaskatoonSK S7N 0W9Canada

Embryonic development represents an important reproductive phase of sexually reproducing plant species.The fusion of egg and sperm produces the plant zygote,a totipotent cell that,through cell division and cell identity specification in early embryogenesis,establishes the major cell lineages and tissues of the adult plant.The subsequent morphogenesis phase produces the full-sized embryo,while the late embryogenesis maturation process prepares the seed for dormancy and subsequent germination,ensuring continuation of the plant life cycle.In this review on embryogenesis,we compare the model eudicot Arabidopsis thaliana with monocot crops,focusing on genome activation,paternal and maternal regulation of early zygote development,and key organizers of patterning,such as auxin and WOX transcription factors.While the early stages of embryo development are apparently conserved among plant species,embryo maturation programs have diversified between eudicots and monocots.This diversification in crop species reflects the likely effects of domestication on seed quality traits that are determined during embryo maturation,and also assures seed germination in different environmental conditions.This review describes the most important features of embryonic development in plants,and the scope and applications of genomics in plant embryo studies.

关键词： embryogenesis embryo patterning zygote genome activation transcription factors genomics transcriptomics

An Arabidopsis ABC Transporter Mediates Phosphate Deficiency-Induced Remodeling of Root Architecture by Modulating Iron Homeostasis in Roots

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Molecular Plant 2017年第2期10卷 244-259页

作者： Jinsong Dong Miguel A. PiSeros Xiaoxuan Li Haibing Yang Yu Liu Angus S. Murphy leon v. kochian Dong Liu Ministry of Education Key Laboratory of Bioinformatics Center for Plant Biology School of Life Sciences Tsinghua University Beijing 100084 China USDA-ARS Robert Holley Center for Agriculture and Health Cornell University ithaca NY 14580 USA Department of Horticulture Purdue University West Lafayette IN 47907-2010 USA State Key Laboratory of Plant Physiology and Biochemistry College of Life Science Zhejiang University Hangzhou 310058 China Department of Plant Science and Landscape Architecture University of Maryland College Park MD 20742 USA GIobal Institute for Food Security University of Saskatchewan Saskatoon S7N 4J8 Canada

The remodeling of root architecture is a major developmental response of plants to phosphate （Pi） deficiency and is thought to enhance a plant＇s ability to forage for the available Pi in topsoil. The underlying mechanism controlling this response, however, is poorly understood. In this study, we identified an Arabidopsis mutant, hps 10 （hypersensitive to Pi starvation 10）, which is morphologically normal under Pi sufficient condition but shows increased inhibition of primary root growth and enhanced production of lateral roots under Pi defi- ciency, hpslO is a previously identified allele （als3-3） of the ALUMINUM SENSITIvE3 （ALS3） gene, which is involved in plant tolerance to aluminum toxicity. Our results show that ALS3 and its interacting protein AtSTAR1 form an ABC transporter complex in the tonoplast. This protein complex mediates a highly electro- genic transport in Xenopus oocytes. Under Pi deficiency, als3 accumulates higher levels of Fe3＋ in its roots than the wild type does. In Arabidopsis, LPR1 （LOW PHOSPHATE ROOT1） and LPR2 encode ferroxidases, which when mutated, reduce Fe3＋ accumulation in roots and cause root growth to be insensitive to Pi defi- ciency. Here, we provide compelling evidence showing that ALS3 cooperates with LPR1/2 to regulate Pi deficiency-induced remodeling of root architecture by modulating Fe homeostasis in roots.

关键词： phosphate deficiency root architecture iron homeostasis ABC transporter ALUMINUM SENSI-TIvE3 AtS TAR1

Evolving technologies for growing,imaging and analyzing 3D root system architecture of crop plants

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Journal of Integrative Plant Biology 2016年第3期58卷 230-241页

作者： Miguel A.Pieros Brandon G.Larson Jon E.Shaff David J.Schneider Alexandre Xavier Falcao Lixing Yuan Randy T.Clark Eric J.Craft Tyler W.Davis Pierre-Luc Pradier Nathanael M.Shaw Ithipong Assaranurak Susan R.Mc Couch Craig Sturrock Malcolm Bennett leon v.kochian USDA-ARS Robert Holley Center for Agriculture and Health538 Tower RoadIthacaNY 14580USA Department of Information Systems Institute of ComputingUniversity of CampinasAv.Albert Einstein1251CEP 13083-852CampinasSPBrazil Department of Plant Nutrition China Agricultural UniversityBeijing 100193China Department of Plant Breeding and Genetics Cornell UniversityIthacaNY 14853USA Centre for Plant Integrative Biology School of BiosciencesUniversity of NottinghamSutton BoningtonLE12 5RDUK College of Science King Saud UniversityRiyadh 11451Kingdom of Saudi Arabia

A plant＇s ability to maintain or improve its yield under limiting conditions,such as nutrient de ficiency or drought,can be strongly in fluenced by root system architecture（RSA）,the three-dimensional distribution of the different root types in the soil. The ability to image,track and quantify these root system attributes in a dynamic fashion is a useful tool in assessing desirable genetic and physiological root traits. Recent advances in imaging technology and phenotyping software have resulted in substantive progress in describing and quantifying RSA. We have designed a hydroponic growth system which retains the three-dimensional RSA of the plant root system,while allowing for aeration,solution replenishment and the imposition of nutrient treatments,as well as high-quality imaging of the root system. The simplicity and flexibility of the system allows for modi fications tailored to the RSA of different crop species and improved throughput. This paper details the recent improvements and innovations in our root growth and imaging system which allows for greater image sensitivity（detection of fine roots and other root details）,higher ef ficiency,and a broad array of growing conditions for plants that more closely mimic those found under field conditions.

关键词： Abiotic stress digital root phenotyping mineral nutrition root system architecture

Aluminium is essential for root growth and development of tea plants(Camellia sinensis)^∞

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Journal of Integrative Plant Biology 2020年第7期62卷 984-997页

作者： Lili Sun Mengshi Zhang Xiaomei Liu Qianzhuo Mao Chen Shi leon vkochian Hong Liao Root Biology Center College of Resources and EnvironmentFujian Agriculture and Forestry UniversityFuzhou 350002China vector-Borne virus Research Center Fujian Agriculture and Forestry UniversityFuzhou 350002China Global Institute for Food Security University of SaskatchewanSaskatoon S7N 4J8Canada

On acid soils,the trivalent aluminium ion(Al3+)predominates and is very rhizotoxic to most plant species.For some native plant species adapted to acid soils including tea(Camellia sinensis),Al3+has been regarded as a beneficial mineral element.In this study,we discovered that Al3+is actually essential for tea root growth and development in all the tested varieties.Aluminum ion promoted new root growth in five representative tea varieties with dose-dependent responses to Al3+availability.In the absence of Al3+,the tea plants failed to generate new roots,and the root tips were damaged within 1 d of Al deprivation.Struc-tural analysis of root tips demonstrated that Al was required for root meristem development and activity.In situ morin@staining of Al3+in roots revealed that Al mainly localized to nuclei in root meristem cells,but then gradually moved to the cytosol when Al3+was subsequently withdrawn.This movement of Al3+from nuclei to cytosols was accompanied by exacerbated DNA damage,which suggests that the nuclear-targeted Al primarily acts to maintain DNA integrity.Taken together,these results provide novel evidence that Al3+is essential for root growth in tea plants through maintenance of DNA integrity in meristematic cells.

关键词： sinensis roots Camellia