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Exploring Genomics: Tools and Traits in Biotechnology

delve into genomics tools, DNA sequencing impact, microarray analysis, input/output traits, and gene discovery strategies in biotechnology for agribusiness. Discuss innovative input traits for enhancing production and the quest for bacterial herbicide resistance genes.

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Exploring Genomics: Tools and Traits in Biotechnology

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  1. Lecture 12 Chapter 8 Genomics and Genes and traits of interest I Neal Stewart

  2. Discussion questions • What is genomics (and “omics” in general)? What are the tools for finding genes that might be useful in biotechnology. • What is next-generation DNA sequencing? What is the impact or potential impact? • Why is microarray analysis useful? What omics would it be applied to? 4. What are the differences between “input” and “output” traits? Considering the environmental and biological factors that limit production in a farmer’s field, what are some new input traits that might be good candidates for improvement using biotechnology? 5. Consider the possibility that you are employed by an agricultural biotechnology company, and they ask you to find a bacterial gene for resistance to a specific herbicide. The herbicide has been manufactured by the company for many years. Using a strategy similar to that used to find glyphosate resistance, where might you start to look for a bacterium resistant to that herbicide?

  3. Finding genes: functional genomics • Biochemistry • Functional screens • Hunting for specific genes– cDNAs • Searching databases for similar genes • Omics: e.g., • Genomic sequencing projects • Microarrays for finding upregulated genes • “Extremophiles” unusual genes from unusual organisms

  4. How plant genome sizes compare with other organisms http://fig.cox.miami.edu/~cmallery/150/gene/genome2.jpg

  5. Creating cDNAscomplementary DNA from mRNA

  6. Next-generation DNA sequencing technology Finding more genes than you’d ever imagined 454 sequencing: http://www.youtube.com/watch?v=bFNjxKHP8Jc Illumina sequencing: http://www.youtube.com/watch?v=l99aKKHcxC4

  7. Microarrays

  8. Sample preparation Test material Reference material Source: Murali Rao Total RNA isolation mRNA purification

  9. Image Collection Sample Array Data

  10. Progression of GM plants • 1st Generation: Input traits (herbicide tolerance, insect resistance, etc.) • 2nd Generation: Output traits: (pharmaceuticals, enhanced nutrition, etc.) • 3rd Generation: Non-traditional– (pharmaceuticals, phytoremediation, phytosensors, next-generation biofuels)

  11. First generation Input traits

  12. Herbicide-resistant crops

  13. Figure 8.1

  14. Finding a glyphosate resistance gene • Discovery of glyphosate—kills most plants • Knowledge of shikimate pathway • Targeting enyzme (gene) for resistance • Functional screen for resistance • Clone resistance gene • Overexpress gene in plants

  15. Figure 8.2

  16. Discussion question Consider the possibility that you are employed by an agricultural biotechnology company, and they ask you to find a bacterial gene for resistance to a specific herbicide. The herbicide has been manufactured by the company for many years. Using a strategy similar to that used to find glyphosate resistance, where might you start to look for a bacterium resistant to that herbicide?

  17. Transgenic disease resistance • Viruses (yes) • Bacteria (no) • Fungi (no) • Nematodes (no)

  18. Photo by Dennis Gonsalves. Stewart, 2004. Genetically Modified Planet 2004

  19. Biotechnologist of the dayDennis Gonsalves • From Hawaii • At USDA-ARS in Hilo, Hawaii • Humbolt Prize 2002 • Virus resistant papaya credited for saving papaya industry in Hawaii

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