Skip to main content

The Use of Big Data in the Modern Biology: The Case of Agriculture

  • Chapter
  • First Online:
Intelligent and Complex Systems in Economics and Business

Abstract

There is a data revolution in the agriculture that involves the analysis of this data, the development of new models and the application of these models in a practical and simple way. All new technologies allow to process big volumes of data with new mathematical algorithms, checking the information in real time, creating new value standards and changing the conception of agriculture. The aim of this chapter is to show some alternatives for the improvement of the crops using the big data, produced with the new technologies for massive sequencing in two specific examples: microbial massive analysis and molecular breeding.

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

Access this chapter

eBook
USD 16.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Acharya, A., Poudel, A., Sah, A. K., Maharjan, D., Tibrewal, S., Mandal, P. K., & Maharjan, D. (2016). Isolation and identification of bacteria from meat processing units of Kathmandu Valley. International Journal of Microbiology and Allied Sciences, 2(3), 33–37.

    Google Scholar 

  • Bashir, Y., Pradeep-Singh, S., & Kumar-Konwar, B. (2014). Metagenomics: An application based perspective. Chinese Journal of Biology, 2014, 1–7.

    Article  Google Scholar 

  • Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7(5), 335.

    Article  Google Scholar 

  • Chen, K., & Pachter, L. (2005). Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Computational Biology, 1(2), e24.

    Article  Google Scholar 

  • Delmont, T. O., Robe, P., Cecillon, S., Clark, I. M., Constancias, F., Simonet, P., et al. (2011). Accessing the soil metagenome for studies of microbial diversity. Applied and Environmental Microbiology, 77(4), 1314–1324.

    Article  Google Scholar 

  • Ekblom, R., & Galindo, J. (2011). Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity, 107, 1–15.

    Article  Google Scholar 

  • Escobar-Zepeda, A., de León, A. V. P., & Sanchez-Flores, A. (2015). The road to metagenomics: From microbiology to DNA sequencing technologies and bioinformatics. Frontiers in Genetics, 6, 1–15.

    Article  Google Scholar 

  • Garsmeur, O., Droc, G., Antonise, R., Grimwood, J., Potier, B., Aitken, K., Jenkins, J., Martin, G., Charron, C., Hervouet, C., Costet, L., Yahiaoui, N., Healey, A., Sims, D., Cherukuri, Y., Sreedasyam, A., Kilian, A., Chan, A., Van Sluys, M.-A., Swaminathan, K., Town, C., Bergès, H., Simmons, B., Glaszmann, J. C., van der Vossen, E., Henry, R., Schmutz, J., & D’Hont, A. (2018). A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nature Communications, 9, 2638. https://doi.org/10.1038/s41467-018-05051-5

  • George, I. Stenuit, B., & Agathos, S. (2010). Application of metagenomics to bioremediation. Metagenomics: Theory, methods and applications (1st ed., pp. 119–140). Norfolk: Caister Academic Press

    Google Scholar 

  • Glick, B. R. (2014). Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiological Research, 169(1), 30–39.

    Article  Google Scholar 

  • Huson, D. H., Mitra, S., Weber, N., Ruscheweyh, H. J., & Schuster, S. C. (2011). Integrative analysis of environmental sequences using MEGAN 4. Genome Research, 21(9), 1552–1560.

    Article  Google Scholar 

  • Iorizzo, M., Ellison, S., Senalik, D., Zeng, P., Satapoomin, P., Huang, J., et al. (2016). A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nature Genetics., 48, 657–666. https://doi.org/10.1038/ng.3565

    Article  Google Scholar 

  • Kwong, W. K., Engel, P., Koch, H., & Moran, N. A. (2014). Genomics and host specilization of honey bee and bumble bee gut symbionts. Proceedings of the National Academy of Sciences, 111(31), 11509–11514.

    Article  Google Scholar 

  • Lewin, H. A., Robinson, G. E., Kress, W. J, Baker, W. J., Coddington, J., Crandall, K. A, Durbin, R, Edwards, S. V, Forest, F., Gilbert, M. T. P., Goldstein, M. M, Grigoriev, I. V., Hackett, K. J., Haussler, D., Jarvis, E. D., Johnson, W. E., Patrinos, A., Richards, S., Castilla-Rubio, J. C., van Sluys, M. A., Soltis, P. S., Xu, X., Yang, H., Zhang, G. (2018). Earth biogenome project. Sequencing life for the future of life. In Procedings of the National Academy of Sciences USA, 115(17), 4325–4333

    Google Scholar 

  • Menzel, P., Ng, K. L., & Krogh, A. (2016). Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nature Communications, 7, 11257.

    Article  Google Scholar 

  • Morgan, X. C., & Huttenhower, C. (2012). Human microbiome analysis. PLoS Computational Biology, 8(12), e1002808.

    Article  Google Scholar 

  • Nakamura, S., Maeda, N., Miron, I. M., Yoh, M., Izutsu, K., Kataoka, C., et al. (2008). Metagenomic diagnosis of bacterial infections. Emerging Infectious Diseases, 14(11), 1784–1786.

    Article  Google Scholar 

  • Parker, J., & Chen, J. (2017). Application of next generation sequencing for the detection of human viral pathogens in clinical specimens. Journal of Clinical Virology, 86, 20–26.

    Article  Google Scholar 

  • Potato Genome Consortium. (2011). Genome sequence and analysis of the tuber crop potato. Nature, 475, 189–197. https://doi.org/10.1038/nature10158

    Article  Google Scholar 

  • Schäfer, M. O., Genersch, E., Fünfhaus, A., Poppinga, L., Formella, N., Bettin, B., & Karger, A. (2014). Rapid identification of differentially virulent genotypes of Paenibacillus larvae, the causative organism of American foulbrood of honey bees, by whole cell MALDI-TOF mass spectrometry. Veterinary Microbiology, 170(3), 291–297.

    Article  Google Scholar 

  • Schmieder, R., & Edwards, R. (2011). Quality control and preprocessing of metagenomic datasets. Bioinformatics, 27(6), 863–864.

    Article  Google Scholar 

  • Schüürmann, J., Quehl, P., Festel, G., & Jose, J. (2014). Bacterial whole-cell biocatalysts by surface display of enzymes: Toward industrial application. Applied Microbiology and Biotechnology, 98(19), 8031–8046.

    Article  Google Scholar 

  • Tamaki, H., Wright, C. L., Li, X., Lin, Q., Hwang, C., Wang, S., & Liu, W. T. (2011). Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform. PLoS ONE, 6(9), 1–6.

    Article  Google Scholar 

  • Thomas, T., Gilbert, J., & Meyer, F. (2012). Metagenomics-a guide from sampling to data analysis. Microbial Informatics and Experimentation, 2(1), 3.

    Article  Google Scholar 

  • Tieman, D., Guangtao, Z., Resende Jr. Marcio F. R., Tao, L., Cuong, N., Dawn, B., Luis, R. J., Stephanie, O. B. K., Taylor, M., Bo, Z., Hiroki, I., Zhongyuan, L., Josef, F., Itay, Z., Antonio, M., Dani, Z., Antonio, G., Matias, K., Sanwen, H., & Klee, H. (2017). A chemical genetic roadmap to improved tomato flavor. Science, 355(6323), 391–394. https://doi.org/10.1126/science.aal1556

  • Tomato Genome Consortium. (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485, 635–641. https://doi.org/10.1038/nature11119

    Article  Google Scholar 

  • Velsko, I. M., Frantz, L. A., Herbig, A., Larson, G., & Warinner, C. G. (2018). Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research. Msystems, 3, 1–28.

    Article  Google Scholar 

  • Whiteley, A. S., Jenkins, S., Waite, I., Kresoje, N., Payne, H., Mullan, B., et al. (2012). Microbial 16S rRNA Ion Tag and community metagenome sequencing using the ion torrent (PGM) platform. Journal of Microbiological Methods, 91(1), 80–88.

    Article  Google Scholar 

  • Wilke, A., Bischof, J., Gerlach, W., Glass, E., Harrison, T., Keegan, K. P., & Chaterji, S. (2015). The MG-RAST metagenomics database and portal in 2015. Nucleic Acids Research, 44(1), 590–594.

    Google Scholar 

Download references

Acknowledgements

Thanks to Universidad De la Salle Bajío Campus Campestre and Universidad Autónoma de Querétaro for financial support.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Andrés Cruz-Hernández .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Campos-Guillén, J. et al. (2021). The Use of Big Data in the Modern Biology: The Case of Agriculture. In: León-Castro, E., Blanco-Mesa, F., Gil-Lafuente, A.M., Merigó, J.M., Kacprzyk, J. (eds) Intelligent and Complex Systems in Economics and Business. Advances in Intelligent Systems and Computing, vol 1249. Springer, Cham. https://doi.org/10.1007/978-3-030-59191-5_10

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-59191-5_10

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-59190-8

  • Online ISBN: 978-3-030-59191-5

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics