High-Throughput and Computational Study of Leaf Senescence through a Phenomic Approach

Leaf senescence is influenced by its life history, comprising a series of developmental and physiological experiences. Exploration of the biological principles underlying leaf lifespan and senescence requires a schema to trace leaf phenotypes, based on the interaction of genetic and environmental factors. We developed a new approach and concept that will facilitate systemic biological understanding of leaf lifespan and senescence, utilizing the phenome high-throughput investigator (PHI) with a single-leaf-basis phenotyping platform. Our pilot tests showed empirical evidence for the feasibility of PHI for quantitative measurement of leaf senescence responses and improved performance in order to dissect the progression of senescence triggered by different senescence-inducing factors as well as genetic mutations. Such an establishment enables new perspectives to be proposed, which will be challenged for enhancing our fundamental understanding on the complex process of leaf senescence. We further envision that integration of phenomic data with other multi-omics data obtained from transcriptomic, proteomic, and metabolic studies will enable us to address the underlying principles of senescence, passing through different layers of information from molecule to organism.

[1]  Hong Gil Nam,et al.  Toward Systems Understanding of Leaf Senescence: An Integrated Multi-Omics Perspective on Leaf Senescence Research. , 2016, Molecular plant.

[2]  B. Mueller‐Roeber,et al.  Comprehensive Dissection of Spatiotemporal Metabolic Shifts in Primary, Secondary, and Lipid Metabolism during Developmental Senescence in Arabidopsis1[W] , 2013, Plant Physiology.

[3]  A high-throughput pipeline for detecting locus-specific polymorphism in hexaploid wheat (Triticum aestivum L.) , 2015, Plant Methods.

[4]  H. Nam,et al.  Leaf senescence. , 2007, Annual review of plant biology.

[5]  I. C. Lee,et al.  Cytokinin-mediated control of leaf longevity by AHK3 through phosphorylation of ARR2 in Arabidopsis. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Jin Ok Yang,et al.  Programming of Plant Leaf Senescence with Temporal and Inter-Organellar Coordination of Transcriptome in Arabidopsis1[OPEN] , 2016, Plant Physiology.

[7]  L. Xiong,et al.  Plant phenomics and high-throughput phenotyping: accelerating rice functional genomics using multidisciplinary technologies. , 2013, Current opinion in plant biology.

[8]  C. Klukas,et al.  Dissecting the Phenotypic Components of Crop Plant Growth and Drought Responses Based on High-Throughput Image Analysis[W][OPEN] , 2014, Plant Cell.

[9]  C. Fournier,et al.  High-throughput estimation of incident light, light interception and radiation-use efficiency of thousands of plants in a phenotyping platform. , 2015, The New phytologist.

[10]  J. Selbig,et al.  More effort - more results: recent advances in integrative 'omics' data analysis. , 2016, Current opinion in plant biology.

[11]  Yunbi Xu,et al.  Envirotyping for deciphering environmental impacts on crop plants , 2016, Theoretical and Applied Genetics.

[12]  C. Granier,et al.  Phenotyping and beyond: modelling the relationships between traits. , 2014, Current opinion in plant biology.

[13]  D. Roby,et al.  Investigation of the geographical scale of adaptive phenological variation and its underlying genetics in Arabidopsis thaliana , 2013, Molecular ecology.

[14]  Yuequan Shen,et al.  CaM/BAG5/Hsc70 signaling complex dynamically regulates leaf senescence , 2016, Scientific Reports.

[15]  I. C. Lee,et al.  NORE1/SAUL1 integrates temperature-dependent defense programs involving SGT1b and PAD4 pathways and leaf senescence in Arabidopsis. , 2016, Physiologia plantarum.

[16]  H. Thomas Senescence, ageing and death of the whole plant. , 2013, The New phytologist.

[17]  O. Keech,et al.  Dark-induced leaf senescence: new insights into a complex light-dependent regulatory pathway. , 2016, The New phytologist.

[18]  C. Wagstaff,et al.  Living to Die and Dying to Live: The Survival Strategy behind Leaf Senescence1 , 2015, Plant Physiology.

[19]  M. Tester,et al.  Phenomics--technologies to relieve the phenotyping bottleneck. , 2011, Trends in plant science.

[20]  Detlef Weigel,et al.  Natural allelic variation underlying a major fitness tradeoff in Arabidopsis thaliana , 2010, Nature.

[21]  J. Jobst,et al.  Senescence-related gene expression profiles of rosette leaves of Arabidopsis thaliana: leaf age versus plant age. , 2004, Plant biology.

[22]  Jos H. M. Schippers Transcriptional networks in leaf senescence. , 2015, Current opinion in plant biology.

[23]  T. Shiina,et al.  A Scalable Open-Source Pipeline for Large-Scale Root Phenotyping of Arabidopsis[W][OPEN] , 2014, Plant Cell.

[24]  Christopher A. Penfold,et al.  High-Resolution Temporal Profiling of Transcripts during Arabidopsis Leaf Senescence Reveals a Distinct Chronology of Processes and Regulation[C][W][OA] , 2011, Plant Cell.

[25]  Jan F. Humplík,et al.  Automated phenotyping of plant shoots using imaging methods for analysis of plant stress responses – a review , 2015, Plant Methods.

[26]  Paul R Zurek,et al.  3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture , 2013, Proceedings of the National Academy of Sciences.

[27]  R. Sekhon,et al.  Transcriptional and Metabolic Analysis of Senescence Induced by Preventing Pollination in Maize1[W][OA] , 2012, Plant Physiology.

[28]  C. Klukas,et al.  Advanced phenotyping and phenotype data analysis for the study of plant growth and development , 2015, Front. Plant Sci..

[29]  A. Greenberg,et al.  High-Resolution Inflorescence Phenotyping Using a Novel Image-Analysis Pipeline, PANorama1[W][OPEN] , 2014, Plant Physiology.

[30]  K. Shinozaki,et al.  Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions , 2011, Plant & cell physiology.

[31]  Yongfeng Guo Towards systems biological understanding of leaf senescence , 2012, Plant Molecular Biology.

[32]  Joy Bergelson,et al.  Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana , 2010, Proceedings of the National Academy of Sciences.

[33]  Vicky Buchanan-Wollaston,et al.  Comparative transcriptome analysis reveals significant differences in gene expression and signalling pathways between developmental and dark/starvation-induced senescence in Arabidopsis. , 2005, The Plant journal : for cell and molecular biology.

[34]  H. Nam,et al.  Identification of three genetic loci controlling leaf senescence in Arabidopsis thaliana. , 1997, The Plant journal : for cell and molecular biology.

[35]  L. Xiong,et al.  Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice , 2014, Nature Communications.