Skip to main content

Bioinformatics in Agriculture: Translating Alphabets for Transformation in the Field

  • Chapter
  • First Online:
Plant Bioinformatics

Abstract

Essentiality of bioinformatics was perceived from a long time for the advancement of science and innovation. Bioinformatics finds direct application in the crop improvement programs. It helps out researchers in connecting genetic makeup with commercial traits. Availability of complete genomes of numerous economically important crops and advancement in facilities and experimentation for high-throughput studies open new avenues for crop improvement. Different approaches like plant genome comparisons, genetic mapping strategies, evolutionary analyses, etc. involved in crop development programs are nowadays possible through bioinformatics data analysis. For a few of the scientists, the new genes, novel proteins, and their functions, unique metabolites, quantitative profile, metabolic pathways, etc. seemed to have yielded fewer than what have been earlier expected in terms of new targets or strategies for development of crop plants in agricultural science. Though, recent work on this subject has helped us further realistically and still optimistically deal with such issues in a socially responsible academic exercise. Thus, while some “microarray” or “bioinformatics” scientists may have been criticized as doing “cataloging research,” mass of researchers consider that they are genuinely exploring novel scientific and technological systems and techniques to help human health, human food and animal feed production, overall agricultural productivity, and environmental protection. Indeed, the complexity, extent, and measure of cross talks in biological systems are huge, but simultaneously we need to become more knowledgeable and able to start addressing honestly and skillfully the significant issues regarding global agriculture and the environment.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Institutional subscriptions

References

  • Agarwal G, Jhanwar S, Priya P, Singh VK, Saxena MS, Parida SK et al (2012) Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers. PLoS One 7(12):e52443

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aghaei K, Komatsu S (2013) Crop and medicinal plants proteomics in response to salt stress. Front Plant Sci 8: 1–9

    Google Scholar 

  • Altaf-Ul-Amin M, Afendi FM, Kiboi SK, Kanaya S (2014) Systems biology in the context of big data and networks. Biomed Res Int 2014

    Google Scholar 

  • Atkinson NJ, Urwin PE (2012) The interaction of plant biotic and abiotic stresses: from genes to the field. J Exp Bot 63(10):3523

    Article  CAS  PubMed  Google Scholar 

  • Balbuena TS, Dias LLC, Martins MLB, Chiquieri TB, Santa-Catarina C, Floh EIS, Silveira V (2011) Challenges in proteome analyses of tropical plants. Braz J Plant Physiol 23(2):91–104

    Google Scholar 

  • Bansal AK (2005) Bioinformatics in microbial biotechnology – a mini review. Microb Cell Factories 4:19

    Article  CAS  Google Scholar 

  • Beddington J (2010) Food security: contributions from science to a new and greener revolution. Philos Trans R Soc B 365:61–71

    Article  Google Scholar 

  • Beyer A, Bandyopadhyay S, Ideker T (2007) Integrating physical and genetic maps: from genomes to interaction networks. Nat Rev Genet 8(9):699–710

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bhattacharya S, Mariani TJ (2013) Systems biology approaches to identify developmental bases for lung diseases. Pediatr Res 73(402):514–522

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Birthal PS (2013) Application of frontier technologies for agricultural development. Ind Jn Agri Econ 68(1):20–38

    Google Scholar 

  • Bita CE, Gerats T (2013) Plant tolerance to high temperature in a changing environment: scientific fundamentals and production of heat stress-tolerant crops. Front Plant Sci 4:273

    Article  PubMed  PubMed Central  Google Scholar 

  • Booth SC, Weljie AM, Turner RJ (2013) Computational tools for the secondary analysis of metabolomics experiments. Comput Struct Biotechnol J 4:e201301003

    Article  PubMed  PubMed Central  Google Scholar 

  • Brown ME, Funk CC (2008) Food security under climate change. Science 319:580–581

    Article  CAS  PubMed  Google Scholar 

  • Chen J, Agrawal V, Rattray M, West MAL, Clair DAS, Michelmore RW et al (2007) A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis. BMC Genomics 8:414

    Article  PubMed  PubMed Central  Google Scholar 

  • Chilana P, Sharma A, Rai A (2012) Insect genomic resources: status, availability and future. Curr Sci 102(4):571–580

    Google Scholar 

  • Cook CE, Bergman MT, Finn RD, Cochrane G, Birney E, Apweiler R (2016) The European bioinformatics institute in 2016: data growth and integration. Nucleic Acids Res 44(D1):D20–D26

    Article  CAS  PubMed  Google Scholar 

  • Dare AP, Schaffer RJ, Lin-Wang K, Allan AC, Hellens RP (2008) Identification of a cis-regulatory element by transient analysis of co-ordinately regulated genes. Plant Methods 4:17

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Draghici S, Khatri P, Tarca AL, Amin K, Done A, Voichita C, Georgescu C, Romero R (2007) A systems biology approach for pathway level analysis. Genome Res 17(10):1537–1545

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eckardt NA (2000) Sequencing the rice genome. Plant Cell 12:2011–2017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Edwards D. Bioinformatics tools to assist breeding for climate change. Kole C. Genomics and breeding for climate-resilient crops. Springer Berlin Heidelberg; 2013, pp. 391–414

    Google Scholar 

  • Edwards D, Batley J (2004) Plant bioinformatics: from genome to phenome. Trends Biotechnol 22(5):232–237

    Google Scholar 

  • Emon JMV (2016) The omics revolution in agricultural research. J Agric Food Chem 64(1):36–44

    Article  PubMed  CAS  Google Scholar 

  • Esposito A, Colantuono C, Ruggieri V, Chiusano ML (2016) Bioinformatics for agriculture in the next-generation sequencing era. Chem Biol Technol Agric 3:9

    Article  CAS  Google Scholar 

  • Faccioli P, Stanca AM, Morcia C, Terzi V (2009) From DNA sequence to plant phenotype: bioinformatics meets crop science. Curr Bioinforma 4(3):173–176

    Article  CAS  Google Scholar 

  • Fedoroff NV (2015) Food in a future of 10 billion. Agric Food Secur 4:11

    Article  Google Scholar 

  • Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH (2004) An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res 14(9):1812–1819

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Field D, Feil EJ, Wilson GA (2005) Databases and software for the comparison of prokaryotic genomes. Microbiology 151:2125–2132

    Article  CAS  PubMed  Google Scholar 

  • Fita A, Rodríguez-Burruezo A, Boscaiu M, Prohens J, Vicente O (2015) Breeding and domesticating crops adapted to drought and salinity: a new paradigm for increasing food production. Front Plant Sci 6:978

    Article  PubMed  PubMed Central  Google Scholar 

  • Fletcher J, Bender C, Budowle B, Cobb WT, Gold SE, Ishimaru CA et al (2006) Plant pathogen forensics: capabilities, needs, and recommendations. Microbiol Mol Biol Rev 70(2):450–471

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Flint J, Mott R (2001) Finding the molecular basis of quantitative traits: successes and pitfalls. Nat Rev Genet 2:437–445

    Article  CAS  PubMed  Google Scholar 

  • Fridman E, Zamir D (2012) Next-generation education in crop genetics. Curr Opin Plant Biol 2:218–223

    Article  Google Scholar 

  • Fryer RM, Randall J, Yoshida T, Hsiao L, Blumenstock J, Jensen KE et al (2002) Global analysis of gene expression: methods, interpretation, and pitfalls. Exp Nephrol 10:64–74

    Article  CAS  PubMed  Google Scholar 

  • Gomez-Casati DF, Zanor MI, Busi MV (2013) Metabolomics in plants and humans: applications in the prevention and diagnosis of diseases. Biomed Res Int 2013:792527

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Govindaraj M, Vetriventhan M, Srinivasan M (2015) Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genet Res Int 2015

    Google Scholar 

  • Green ED, Guyer MS, National Human Genome Research Institute (2011) Charting a course for genomic medicine from base pairs to bedside. Nature 470:204–213

    Article  CAS  PubMed  Google Scholar 

  • Greene AC, Giffin KA, Greene CS, Moore JH (2015) Adapting bioinformatics curricula for big data. Brief Bioinform 17(1):43–50

    Article  PubMed  PubMed Central  Google Scholar 

  • Guillouzo A (2001) Applications of biotechnology to pharmacology and toxicology. Cell Mol Biol (Noisy-le-Grand) 47(8):1301–1308

    CAS  Google Scholar 

  • Guo P, Baum M, Grando S, Ceccarelli S, Bai G, Li R et al (2009) Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage. J Exp Bot 60(12):3531–3544

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guttman DS, McHardy AC, Schulze-Lefert P (2014) Microbial genome-enabled insights into plant–microorganism interactions. Nat Rev Genet 15:797–813

    Article  CAS  PubMed  Google Scholar 

  • Hagel JM, Facchini PJ (2008) Plant metabolomics: analytical platforms and integration with functional genomics. Phytochem Rev 7(3):479–497

    Article  CAS  Google Scholar 

  • Hardigan MA, Crisovan E, Hamilton JP, Kim J, Laimbeer P, Leisner CP et al (2016) Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum. Plant Cell 28(2):388–405

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • He G, Elling AA, Deng XW (2011) The epigenome and plant development. Annu Rev Plant Biol 62:411–435

    Article  CAS  PubMed  Google Scholar 

  • Hefferon KL (2015) Nutritionally enhanced food crops; progress and perspectives. Int J Mol Sci 16(2):3895–3914

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hernandez-Garcia CM, Finer JJ (2014) Identification and validation of promoters and cis-acting regulatory elements. Plant Sci 217–218:109–119

    Article  PubMed  CAS  Google Scholar 

  • Hogeweg P (2011) The roots of bioinformatics in theoretical biology. PLoS Comput Biol 7:e1002021–e1002021

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hori K, Takehara S, Nankaku N, Sato K, Sasakuma T, Takeda K (2007) Barley EST markers enhance map saturation and QTL mapping in diploid wheat. Breed Sci 57:39–45

    Article  CAS  Google Scholar 

  • Hu B, Xie G, Lo CC, Starkenburg SR, Chain PS (2011) Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics. Brief Funct Genom 6:322–333

    Article  CAS  Google Scholar 

  • Hu J, Rampitsch C, Bykova NV (2015) Advances in plant proteomics toward improvement of crop productivity and stress resistance. Front Plant Sci 6:209

    PubMed  PubMed Central  Google Scholar 

  • Jewell MC, Campbell BC, Godwin ID (2010) Transgenic plants for abiotic stress resistance. In: Kole C et al (eds) Transgenic crop plants. Springer-Verlag, Berlin

    Google Scholar 

  • Joyce AR, Palsson BØ (2006) The model organism as a system: integrating ‘omics’ data sets. Nat Rev Mol Cell 7:198–210

    Article  CAS  Google Scholar 

  • Kang J (2012) Principles and applications of LC-MS/MS for the quantitative bioanalysis of analytes in various biological samples. In: Prasain J (ed) Tandem mass spectrometry – applications and principles. InTech, ISBN: 978–953–51-0141-3

    Google Scholar 

  • Kind T, Fiehn O (2010) Advances in structure elucidation of small molecules using mass spectrometry. Bioanal Rev 2(1–4):23–60

    Article  PubMed  PubMed Central  Google Scholar 

  • Koia JH, Moyle RL, Botella JR (2012) Microarray analysis of gene expression profiles in ripening pineapple fruits. BMC Plant Biol 12:240

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Komatsu S, Hiraga S, Yanagawa Y (2012) Proteomics techniques for the development of flood tolerant crops. J Proteome Res 11:68–78

    Article  CAS  PubMed  Google Scholar 

  • Kuenne C, Grosse I, Matthies I, Scholz U, Sretenovic-Rajicic T, Stein N et al (2007) Using data warehouse technology in crop plant bioinformatics. J Integr Bioinform 4(1):88

    Article  Google Scholar 

  • Kumari D, Kumar R (2014) Impact of biological big data in bioinformatics. Int J Comput Appl 101(11):22–24

    Google Scholar 

  • Kuravadi NA, Yenagi V, Rangiah K, Mahesh HB, Rajamani A, Shirke MD et al (2015) Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree. Peer J 3:e1066

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lai K, Lorenc MT, Edwards D (2012) Genomic databases for crop improvement. Agronomy 2:62–73

    Article  Google Scholar 

  • Liang Y, Zhang F, Wang J, Joshi T, Wang Y, Xu D (2011) Prediction of drought-resistant genes in Arabidopsis thaliana using SVM-RFE. PLoS One 6:e21750

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Luscombe NM, Greenbaum D, Gerstein M (2001) What is bioinformatics? An introduction and overview. Yearbook of medical informatics. 1: 83–99.

    Google Scholar 

  • Ly A, Buck A, Balluff B, Sun N, Gorzolka K, Feuchtinger A et al (2016) High-mass-resolution MALDI mass spectrometry imaging of metabolites from formalin-fixed paraffin-embedded tissue. Nat Protoc 11:1428–1443

    Article  PubMed  Google Scholar 

  • Ma Y, Qin F, Tran LP (2012) Contribution of genomics to gene discovery in plant abiotic stress responses. Mol Plant 5(6):1176–1178

    Article  CAS  PubMed  Google Scholar 

  • Mackay TFC, Stone EA, Ayroles JF (2009) The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 10:565–577

    Article  CAS  PubMed  Google Scholar 

  • Mahalakshmi V, Ortiz R (2001) Plant genomics and agriculture: from model organisms to crops, the role of data mining for gene discovery. EJB Electron J Biotechnol 4(2):169

    Google Scholar 

  • Mantione KJ, Kream RM, Kuzelova H, Ptacek R, Raboch J, Samuel JM, Stefano GB (2014) Comparing bioinformatic gene expression profiling methods: microarray and RNA-Seq. Med Sci Monit Basic Res 20:138–141

    Article  PubMed  PubMed Central  Google Scholar 

  • Marx V (2013) Biology: the big challenges of big data. Nature 498:255–260

    Article  CAS  PubMed  Google Scholar 

  • Mauser W, Klepper G, Rice M, Schmalzbauer BS, Hackmann H, Leemans R, Moore H (2013) Transdisciplinary global change research: the co-creation of knowledge for sustainability. Curr Opin Environ Sustain 5(3–4):420–431

    Article  Google Scholar 

  • Mehmood MA, Sehar U, Ahmad N (2014) Use of bioinformatics tools in different spheres of life sciences. J Data Min Genom Proteomics 5:158

    Google Scholar 

  • Mochida K, Shinozaki K (2010) Genomics and bioinformatics resources for crop improvement. Plant Cell Physiol 51(4):497–523

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mochida K, Shinozaki K (2011) Advances in omics and bioinformatics tools for systems analyses of plant functions. Plant Cell Physiol 52(12):2017–2038

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mochida K, Saisho D, Yoshida T, Sakurai T, Shinozaki K (2008) TriMEDB: a database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae. BMC Plant Biol 8:72

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92(5):255–264

    Article  CAS  PubMed  Google Scholar 

  • Morrell PL, Buckler ES, Ross-Ibarra J (2011) Crop genomics: advances and applications. Nat Rev Genet 13:85–96

    Article  PubMed  CAS  Google Scholar 

  • Nakano M, Nobuta K, Vemaraju K, Tej SS, Skogen JW, Meyers BC (2006) Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res 34(Database issue):D731–D735

    Article  CAS  PubMed  Google Scholar 

  • Narayanan P (2005) Bioinformatics: a primer. New Age International. pp 2. ISBN : 978–81–224-1610-7

    Google Scholar 

  • Ni J, Pujar A, Youens-Clark K, Yap I, Jaiswal P, Tecle I et al (2009) Gramene QTL database: development, content and applications. Database (Oxford) 2009:bap005

    Article  CAS  Google Scholar 

  • O'Brien MA, Costin BN, Miles MF (2012) Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from rna integrity to network topology. Int Rev Neurobiol 104:91–133

    Article  PubMed  PubMed Central  Google Scholar 

  • Oellrich A, Walls RL, Cannon EKS, Cannon SB, Cooper L, Gardiner J et al (2015) An ontology approach to comparative phenomics in plants. Plant Methods 11:10

    Article  PubMed  PubMed Central  Google Scholar 

  • Ogbe RJ, Ochalefu DO, Olaniru OB (2016) Bioinformatics advances in genomics – a review. Int J Curr Res Rev 8(10):05–11

    Google Scholar 

  • Pandey A, Mann M (2000) Proteomics to study genes and genomes. Nature 405:837–846

    Article  CAS  PubMed  Google Scholar 

  • Parween S, Nawaz K, Roy R, Pole AK, Suresh BV, Misra G et al (2015) An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.) Sci Rep 5:12806

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pattin KA, Greene AC, Altman RB, Hunter LE, Ross DA, Foster JA, Moore JH (2014) Building the next generation of quantitative biologists. Pac Symp Biocomput:417–421

    Google Scholar 

  • Pérez-de-Castro AM, Vilanova S, Cañizares J, Pascual L, Blanca JM, Díez MJ, Prohens J, Picó B (2012) Application of genomic tools in plant breeding. Curr Genomics 13(3):179–195

    Article  PubMed  PubMed Central  Google Scholar 

  • Pierson III LS, Ishimaru CA (2000) Genomics of plant-associated bacteria: a glimpse of the future that has become reality. APSnet Features

    Google Scholar 

  • Piquerez SJM, Harvey SE, Beynon JL, Ntoukakis V (2014) Improving crop disease resistance: lessons from research on Arabidopsis and tomato. Front Plant Sci 5:671

    Article  PubMed  PubMed Central  Google Scholar 

  • Potato Genome Sequencing Consortium, Xu X, Pan S, Cheng S, Zhang B, Mu D et al (2011) Genome sequence and analysis of the tuber crop potato. Nature 475(7355):189–195

    Article  CAS  Google Scholar 

  • Rahaman MM, Chen D, Gillani Z, Klukas C, Chen M (2015) Advanced phenotyping and phenotype data analysis for the study of plant growth and development. Front Plant Sci 6:619

    Article  PubMed  PubMed Central  Google Scholar 

  • Mehboob-ur-Rahman, Shaheen T, Mahmood-ur-Rahman, Iqbal MA, Zafar Y (2016). Bioinformatics: a way forward to explore “plant omics”. In: Abdurakhmonov IY (ed) Bioinformatics – updated features and applications. InTech, DOI: 10.5772/64043

    Google Scholar 

  • Raza K (2010) Application of data mining in bioinformatics. Indian J Comput Sci Eng 1(2):114–118

    Google Scholar 

  • Rhee SY, Dickerson J, Xu D (2006) Bioinformatics and its applications in plant biology. Annu Rev Plant Biol 57:335–360

    Article  CAS  PubMed  Google Scholar 

  • Robinson GE, Banks JA, Padilla DK, Burggren WW, Cohen CS, Delwiche CF, Funk V, Hoekstra HE, Jarvis ED, Johnson L, Martindale MQ, Martinez del Rio C, Medina M, Salt DE, Sinha S, Specht C, Strange K, Strassmann JE, Swalla BJ, Tomanek L (2010) Empowering 21st century biology. Bioscience 60(11):923–930

    Article  Google Scholar 

  • Rohrmann J, Tohge T, Alba R, Osorio S, Caldana C, McQuinn R et al (2011) Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development. Plant J 68:999–1013

    Article  CAS  PubMed  Google Scholar 

  • Rudd S, Schoof H, Mayer K (2005) PlantMarkers – a database of predicted molecular markers from plants. Nucleic Acids Res 33(Database issue):D628–D632

    Article  CAS  PubMed  Google Scholar 

  • Rung J, Brazma A (2013) Reuse of public genome-wide gene expression data. Nat Rev Genet 14:89–99

    Article  CAS  PubMed  Google Scholar 

  • Sasaki T, Burr B (2000) International rice genome sequencing project: the effort to completely sequence the rice genome. Curr Opin Plant Biol 3:138–141

    Article  CAS  PubMed  Google Scholar 

  • Siepel AC, Tolopko AN, Farmer AD, Steadman PA, Schilkey FD, Perry BD, Beavis WD (2001) An integration platform for heterogeneous bioinformatics software components. IBM Syst J 40(2):570–591

    Article  Google Scholar 

  • Silva DJC (2015) Plant breeding for harmony between modern agriculture production and the environment. Agric Sci 6:87–116

    Google Scholar 

  • Simpson JC, Pepperkok R (2003) Localizing the proteome. Genome Biol 4(12):240

    Article  PubMed  PubMed Central  Google Scholar 

  • Singh VK, Singh AK, Chand R, Kushwaha C (2011) Role of bioinformatics in agriculture and sustainable development. Int J Bioinforma Res 3(2):221–226

    Article  Google Scholar 

  • Singh DP, Prabha R, Rai A, Arora DK (2012) Bioinformatics-assisted microbiological research: tasks, developments and upcoming challenges. Am J Bioinforma 1(1):10–19

    Google Scholar 

  • Sircar S, Parekh N (2015) Functional characterization of drought-responsive modules and genes in Oryza sativa: a network-based approach. Front Genet 6:256

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Skuse GR, Du C (2008) Bioinformatics tools for plant genomics. Intl J Plant Genomics 2008

    Google Scholar 

  • Strange RN, Scott PR (2005) Plant disease: a threat to global food security. Annu Rev Phytopathol 43:83–116

    Article  CAS  PubMed  Google Scholar 

  • Takeda S, Matsuoka M (2008) Genetic approaches to crop improvement: responding to environmental and population changes. Nat Rev Genet 9:444–457

    Article  CAS  PubMed  Google Scholar 

  • Tecle IY, Menda N, Buels RM, van der Knaap E, Mueller LA (2010) solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database. BMC Bioinforma 11:525

    Article  Google Scholar 

  • Thampi SM (2009). Introduction to bioinformatics

    Google Scholar 

  • Thao NP, Tran VL (2016) Enhancement of plant productivity in the post-genomics era. Curr Genomics 17(4):295–296

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tomato Genome Consortium, Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K, Isobe S et al (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485(7400):635–641

    Article  CAS  Google Scholar 

  • Tremblay A, Hosseini P, Alkharouf NW, Li S, Matthews BF (2011) Gene expression in leaves of susceptible Glycine max during infection with Phakopsora pachyrhizi using next generation sequencing. Sequencing 2011

    Google Scholar 

  • Tripathi KK (2000) Bioinformatics: the foundation of present and future biotechnology. Curr Sci 79(5):570

    CAS  Google Scholar 

  • Turner WR, Oppenheimer M, Wilcove DS (2009) A force to fight global warming. Nature 462:278–279

    Article  CAS  PubMed  Google Scholar 

  • Tyagi AK, Khurana JP, Khurana P, Raghuvanshi S, Gaur A, Kapur A, Gupta V, Kumar D, Ravi V, Vij S, Khurana P, Sharma S (2004) Structural and functional analysis of rice genome. J Genet 83(1):79

    Article  CAS  PubMed  Google Scholar 

  • Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA et al (2012) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30:83–89

    Article  CAS  Google Scholar 

  • Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG et al (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 31:240–246

    Article  CAS  PubMed  Google Scholar 

  • Vassilev D, Leunissen J, Atanassov A, Nenov A, Dimov G (2005) Application of bioinformatics in plant breeding. Biotechnol Biotechnol Eq 19

    Google Scholar 

  • Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270(5235):484–487

    Article  CAS  PubMed  Google Scholar 

  • Wally O, Punja ZK (2010) Genetic engineering for increasing fungal and bacterial disease resistance in crop plants. GM Crops 1(4):199–206

    Article  PubMed  Google Scholar 

  • Watanabe K (2015) Potato genetics, genomics, and applications. Breed Sci 65(1):53–68

    Article  PubMed  PubMed Central  Google Scholar 

  • Wishart DS (2007) Current progress in computational metabolomics. Brief Bioinform 8(5):279–293

    Article  CAS  PubMed  Google Scholar 

  • Xu J, Yuan Y, Xu Y, Zhang G, Guo X, Wu F et al (2014) Identification of candidate genes for drought tolerance by whole-genome resequencing in maize. BMC Plant Biol 14:83

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yang N. (2011) Systems and computational biology – bioinformatics and computational modeling. InTech

    Google Scholar 

  • Yip KY, Cheng C, Gerstein M (2013) Machine learning and genome annotation: a match meant to be? Genome Biol 14:205

    Article  PubMed  PubMed Central  Google Scholar 

  • Zamir D (2001) Improving plant breeding with exotic genetic libraries. Nat Rev Genet 2:983–989

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

Financial support from the Indian Council of Agricultural Research, India, in the form of Centre for Agricultural Bioinformatics (CABin) is gratefully acknowledged. Ratna Prabha is thankful for the financial support in the form of SERB-National Post Doctoral Fellowship (File no.PDF/2016/000714).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to D. P. Singh .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Prabha, R., Verma, M.K., Singh, D.P. (2017). Bioinformatics in Agriculture: Translating Alphabets for Transformation in the Field. In: Hakeem, K., Malik, A., Vardar-Sukan, F., Ozturk, M. (eds) Plant Bioinformatics. Springer, Cham. https://doi.org/10.1007/978-3-319-67156-7_7

Download citation

Publish with us

Policies and ethics