Library Science

Erich Grotewold has assembled a team of leading plant scientists to describe in detail the most commonly used methods for investigating plant gene function in a wide variety of plants, during plant pathogen interactions, and even in algae. These readily reproducible protocols include computational, molecular, and genetic methodologies designed for both general and specific problems. Here the reader will learn about powerful computational and statistical tools to help predict gene function either on the basis of comparative genomics, or from the analysis of complex genome sequences. Numerous loss-of-function and gain-of-function techniques for discovering gene function are presented in step-by-step detail.

Authors: Grotewold, Erich

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Table of Contents

1. An Improved Method for Plant BAC Library Construction (pp. 3-20)
   Luo, Meizhong; Wing, Rod A.
2. Constructing Gene-Enriched Plant Genomic Libraries Using Methylation Filtration Technology (pp. 21-36)
   Rabinowicz, Pablo D.
3. RescueMu Protocols for Maize Functional Genomics (pp. 37-58)
   Raizada, Manish N.
4. Precious Cells Contain Precious Information: Strategies and Pitfalls in Expression Analysis from a Few Cells (pp. 59-78)
   Henry, Isabelle M.; Mandoli, Dina F.
5. Combined ESTs from Plant–Microbe Interactions: Using GC Counting to Determine the Species of Origin (pp. 79-84)
   Huitema, Edgar; Torto, Trudy A.; Styer, Allison; Kamoun, Sophien
6. Computer Software to Find Genes in Plant Genomic DNA (pp. 87-108)
   Davuluri, Ramana V.; Zhang, Michael Q.
7. Genomic Colinearity as a Tool for Plant Gene Isolation (pp. 109-122)
   Ramakrishna, Wusirika; Bennetzen, Jeffrey L.
8. Using Natural Allelic Diversity to Evaluate Gene Function (pp. 123-140)
   Whitt, Sherry R.; Buckler, Edward S.
9. Quantitative Trait Locus Analysis as a Gene Discovery Tool (pp. 141-154)
   McMullen, Michael D.
10. Transposon Tagging Using Activator (Ac) in Maize (pp. 157-176)
    Brutnell, Thomas P.; Conrad, Liza J.
11. T-DNA Mutagenesis in Arabidopsis (pp. 177-188)
    Alonso, Jose M.; Stepanova, Anna N.
12. Physical and Chemical Mutagenesis (pp. 189-204)
    Kodym, Andrea; Afza, Rownak
13. High-Throughput TILLING for Functional Genomics (pp. 205-220)
    Till, Bradley J.; Colbert, Trenton; Tompa, Rachel; Enns, Linda C.; Codomo, Christine A.; Johnson, Jessica E.; Reynolds, Steven H.; Henikoff, Jorja G.; Greene, Elizabeth A.; Steine, Michael N.; Comai, Luca; Henikoff, Steven
14. Gene and Enhancer Traps for Gene Discovery (pp. 221-240)
    Rojas-Pierce, Marcela; Springer, Patricia S.
15. High-Throughput TAIL-PCR as a Tool to Identify DNA Flanking Insertions (pp. 241-272)
    Singer, Tatjana; Burke, Ellen
16. Custom Knock-Outs with Hairpin RNA-Mediated Gene Silencing (pp. 273-286)
    Wesley, Susan Varsha; Liu, Qing; Wielopolska, Anna; Ellacott, Geoff; Smith, Neil; Singh, Surinder; Helliwell, Chris
17. Virus-Induced Gene Silencing (pp. 287-294)
    Dinesh-Kumar, S. P.; Anandalakshmi, Radhamani; Marathe, Rajendra; Schiff, Michael; Liu, Yule
18. Exploring the Potential of Plant RNase P as a Functional Genomics Tool (pp. 295-310)
    Pulukkunat, Dileep K.; Raj, M. L. Stephen; Pattanayak, Debasis; Lai, Lien B.; Gopalan, Venkat
19. Maintaining Collections of Mutants for Plant Functional Genomics (pp. 311-326)
    Scholl, Randy; Sachs, Martin M.; Ware, Doreen
20. Vector Construction for Gene Overexpression as a Tool to Elucidate Gene Function (pp. 329-344)
    Lloyd, Alan
21. T-DNA Activation Tagging (pp. 345-362)
    Memelink, Johan
22. Expression Profiling Using cDNA Microarrays (pp. 365-380)
    Zhao, Suling; Bruce, Wesley B.
23. Open Architecture Expression Profiling of Plant Transcriptomes and Gene Discovery Using GeneCalling® Technology (pp. 381-394)
    Crasta, Oswald R.; Folkerts, Otto
24. Proteomics as a Functional Genomics Tool (pp. 395-414)
    Mathesius, Ulrike; Imin, Nijat; Natera, Siria H. A.; Rolfe, Barry G.
25. Metabolite Profiling as a Functional Genomics Tool (pp. 415-426)
    Dias, Anusha P.; Brown, Johnny; Bonello, Pierluigi; Grotewold, Erich
26. Growth Stage-Based Phenotypic Profiling of Plants (pp. 427-442)
    Kjemtrup, Susanne; Boyes, Douglas C.; Christensen, Cory; McCaskill, Amy J.; Hylton, Michelle; Davis, Keith

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