385 D. Barh et al. (eds.), PlantOmics: The Omics of Plant Science, DOI 10.1007/978-81-322-2172-2_13, © Springer India 2015 Contents Introduction ............................................................ 386 Phenotype: Interaction Between Genotype and Environment ...................................................... 387 Phenomics ............................................................... 387 Forward Phenomics vs Reverse Phenomics ............. 388 Techniques Used in Plant Phenomics ...................... 388 Visible Light (Monochromatic or Color) Imaging ................................................................ 388 Infrared and Hyperspectral Imaging .................... 391 Fluorescence Imaging .......................................... 391 3D (Three-Dimensional) Imaging........................ 392 Magnetic Resonance Imaging (MRI)................... 392 Positron Emission Tomography (PET) ................ 392 Field-Based Plant Phenomics .................................. 393 Field-Based Phenotyping Using Static Sensor or Movable Vehicle .................................. 393 Application of Phenomics in Agricultural Research ................................................................... 394 Screening for Abiotic Stress Tolerance- Related Traits ....................................................... 394 Measuring Levels of Salinity Tolerance............... 395 Measuring Drought Tolerance-Related Traits ...... 395 Biotic Stress Tolerance......................................... 397 Measuring Yield and Quality-Related Traits........ 397 Role of Bioinformatics in Phenomics ...................... 398 Data Handling and Management ......................... 398 Image Analysis Software and Platforms .................. 401 Limitations and Future Perspectives ........................ 402 References ............................................................... 404 Abstract To meet the challenges of global food security in the changing climatic scenario, it would be most imperative to enhance crop productivity under resource competence. It is estimated that approximately 70 % of reduction in crop yield is due to the direct impact of abiotic stresses such as drought, salinity, and extreme tempera- tures. In the present context, one of the major challenges is large-scale screening of crop per- formance as a consequence of its genetic makeup. The development of advanced bio- technological and next-generation sequencing tools has lead to the accumulation of enormous data on genomics; nevertheless, data on pheno- type and functions is yet to be fully annotated. To exploit the wealth of large-scale genomic data sets, it is necessary to characterize the crop performance quantitatively and link it to the genomic data. High-throughput phenomics studies offer strategies to screen large-scale population (s) for a particular phenotype employing advanced robotics, high-tech sen- sors, imaging systems, and computing power. Advanced bioinformatics tools further facilitate the analysis of large-scale multi-dimensional, H. Rahman, Ph.D. (*) • V. Ramanathan, Ph.D. N. Jagadeeshselvam, Ph.D. • S. Ramasamy, Ph.D. S. Rajendran, Ph.D. • M. Ramachandran, Ph.D. S. Natesan, Ph.D. • R. Muthurajan, Ph.D. Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, India e-mail: rahman.biotech@gmail.com P.D.V.N. Sudheer, Ph.D. • S. Chauhan, Ph.D. Department of Chemical and Biochemical Engineering, Dongguk University, Seoul 100-715, South Korea Phenomics: Technologies and Applications in Plant and Agriculture Hifzur Rahman, Valarmathi Ramanathan, N. Jagadeeshselvam, Sasikala Ramasamy, Sathishraj Rajendran, Mahendran Ramachandran, Pamidimarri D.V.N. Sudheer, Sushma Chauhan, Senthil Natesan, and Raveendran Muthurajan