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Phenomics: Approaches and Application in Crop Improvement Current Journal of Applied Science and Technology 33(3): 1-10, 2019; Article no.CJAST.46420 ISSN: 2457-1024 (Past name: British Journal of Applied Science & Technology, Past ISSN: 2231-0843, NLM ID: 101664541) Phenomics: Approaches and Application in Crop Improvement P. Roshni1* and K. A. Prajwala2 1Department of Vegetable Science, College of Horticulture, Dr. Y.S.R. HU, Venkataramannagudem, A.P., India. 2Department of Fruit Science, College of Horticulture, Dr. Y.S.R. HU, Venkataramannagudem, A.P., India. Authors’ contributions This work was carried out in collaboration between both authors. Both authors read and approved the final manuscript. Article Information DOI: 10.9734/CJAST/2019/v33i330080 Editor(s): (1) Dr. Tushar Ranjan, Assistant Professor-cum-Scientist (PG), Dept. of Molecular Biology & Genetic Engineering, Bihar Agricultural University, Sabour, Bhagalpur-813210 (Bihar), India. Reviewers: (1) Ana Maria Arambarri, Universidad Nacional De La Plata, La Plata, Argentina. (2) Dennis, Amaechi, Biochemistry,Veritas University, Nigeria. (3) Zeynel Dalkiliç, Aydın Adnan Menderes, Turkey. Complete Peer review History: http://www.sdiarticle3.com/review-history/46420 Received 21 December 2018 Accepted 09 January 2019 Review Article Published 05 March 2019 ABSTRACT Phenotype is the combination of genotype and environment where the plant grows. Phenomics is a way of speeding up phenotyping with the help of high-tech imaging systems and computing power. It has been a practice in plant breeding for selecting the best genotype after studying phenotypic expression in different environmental conditions and also using them in hybridization programs, to develop new improved genotypes. Phenomics share the advantages of faster evaluation, facilitating a more dynamic whole-of-lifecycle measurement with improved precision, being less dependent on periodic destructive assays and with reduced need for replication in the field. Phenomics aids to obtain high-dimensional phenotypic data on an organism at large scale with the various tools involved. Phenomics, however is more than just data collection paired with data mining. It is a comprehensive approach that combines systems biology and statistical correlation. Data mining techniques and big data approaches have the power to create knowledge that cannot be created otherwise with accurate precision manually. _____________________________________________________________________________________________________ *Corresponding author: E-mail: [email protected]; Note: This paper was presented in National Conference on Biotechnological Initiatives for Crop Improvement (BICI 2018), December 08-09, 2018, Organized by Bihar Agricultural University, Sabour, Bhagalpur - 813210 (Bihar), India. Conference organizing committee and Guest Editorial Board completed peer-review of this manuscript. Roshni and Prajwala; CJAST, 33(3): 1-10, 2019; Article no.CJAST.46420 Keywords: Fluorescence imaging; hyperspectral imaging; magnetic resonance imaging; phenomics, phenotyping; spectral reflectance. 1. INTRODUCTION 2. IMPORTANCE OF PLANT PHENOMICS Plant phenotyping has been a part of crop and By 2050, it is estimated that 9.1 billion people will variety selection since the time of human populate the planet earth. And the need of high civilization when humans selected the best yielding varieties would give sustainable yields individuals of a crop species for domestication even under adverse and changing environmental [1]. A plant’s genotype is the genetic constitution conditions. Therefore, phenomics can act as a of an organisms and a plant’s phenotype is how powerful tool to overcome one of humanity’s it looks and performs. Plant’s phenotype is a greatest challenges: Hunger. combination of its genotype and the environment it grows in (Vp = Vg + Ve). Plants with the same Biofuels are fuels such as ethanol and biodiesel genotype can have different phenotypes that are produced from plant matter, depending on the environmental conditions they and are called ‘feedstocks’. Such crops could not are grown in [2-4]. It has been a practice in plant only be eaten by people instead can be turned breeding for selecting the best genotype after into fuel. These crops could compete with food studying phenotypic expression in different crops for the best agricultural land. Hence, environmental conditions and also using them in researchers are in need to make trials for hybridization programs, to develop new improved alternative plant species as feedstock that can genotypes [5]. Phenomics share the advantages grow on less productive lands. But, then these of faster evaluation, facilitating a more dynamic crops will need to tolerate a wide range of whole-of-lifecycle measurement with improved environmental stresses, such as low water precision, being less dependent on periodic availability, salinity or low nutrient supplies, to be destructive assays and with reduced need for able to grow successfully in such replication in the field. Phenomics aids to obtain ‘marginal’ lands. It was estimated that half of the high-dimensional phenotypic data on an increase in yield of the main agricultural crops organism at large scale. has come through plant breeding processes [9,10]. Johannsen coined the terms ‘genotype’ and ‘phenotype’. He demonstrated, variation in Phenotyping can be a laborious process, taking quantitative traits in genetically-identical material, many days, weeks or even months. The high- thus proved that variation in a given observed tech automated plant analysis systems of plant traits is not controlled entirely by genetics. It led phenomics have speeded up traditional, time to origin of the word – “pheno”. After 1950, consuming methods of plant analysis. ‘phenotyping’ as a noun, ‘to phenotype’ as a verb Phenomics is focused on coming up with and ‘phenome’ as the collective noun were practical solutions to problems that will affect us introduced, which have been accepted and our future. This technology can be used for scientifically and are being utilized commonly in study plants from the small scale to studying literature. The word ‘phenome’ refers to the individual cells or leaves to up to the large scale phenotype as whole [6] i.e., expression of of an entire ecosystem. genome for a trait in a given environment. Ecologists used phenotyping to study phenotypic Phenomics technology allows plants, which are plasticity of genotypes and suggested the role of only one month old, move through a series of the genotype and environmental conditions in the chambers, each one automatically expression of plant phenotypes under which it taking different images and measurements. develops [7]. While phenomics refers to Within a few hours, the high-tech imaging and the high-dimensional phenotypic data on an computing systems automatically measure the organism at large scale is obtained, plants and the necessary data are given. The phenomics is used as an analogy to genomics. In young plants with the characteristics the genomics, complete characterization of a researcher looking for can be selected and genome is possible while in phenomics, grown on to mature for seed; thereby, the rest complete characterization of phenome is difficult can be discarded. due to the change in the phenotypic expression of traits over the environmental The scientific accuracy of molecular breeding is conditions [8]. strongly related to phenomics and therefore 2 Roshni and Prajwala; CJAST, 33(3): 1-10, 2019; Article no.CJAST.46420 phenotyping [11]. The main aim of phenomics is 2.1 Types of Phenomics to connect between genetic, plant function, and agricultural characteristics [12]. Performing of 2.1.1 Forward phenomics sensor technologies and algorithmic applications for automatic phenotyping are being handled to Forward phenomics is a way of finding the plant overcome the defect of the manual techniques varieties that are the ‘best of the best’. It speeds [13]. Agro-morphological traits should be up plant breeding by screening large number of universal. If not, different and inconsistent plants at the seedling stage using automated characterization might lead to misunderstanding imaging technology. This makes it faster to for breeding studies. Hence, it states the identify interesting traits, as the plants do not importance of phenotyping for the identification have to be grown to an adult stage in the field. and utilisation of better cultivars. 2.1.2 Reverse phenomics The science of genomics which is the study of Reverse phenomics is pulling the ‘best’ varieties genes has produced masses of information. But, apart to discover why they are the best. The a ‘bottleneck’ has developed in which phenotype or desired trait such as “drought developments based on genomic information are tolerance” is already known. Researchers then unable to keep pace with the huge amount of try to work out the mechanisms that control the data that genomics produces daily. Phenomics trait and the gene or genes that are responsible can translate this information into useful for it. applications. Phenomics links the resulting data to gene sequence information. In this way, gene Plant phenotyping technology involves two discovery can be put to good use by the faster insights, i.e., looking inward and looking outward. development of useful crop varieties. The Looking inward involves the study of leaves and plant phenomic developments are actually roots with hi-tech imaging systems and Looking helping to make simply plant physiology in ‘new outward involves the study of plant
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