The Role of Bioinformatics in Agriculture

483 Pages·2014·3.57 MB·English

by  Santosh Kumar

THE ROLE OF
BIOINFORMATICS IN
AGRICULTURE
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THE ROLE OF
BIOINFORMATICS IN
AGRICULTURE
Edited by
Santosh Kumar, PhD
Apple Academic Press
TORONTO NEW JERSEY
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ABOUT THE EDITOR
Santosh Kumar, PhD
Research Associate in Plant Science, University of Manitoba, Canada
Dr. Santosh Kumar obtained his BSc Agriculture degree in plant breed-
ing from Punjab Agricultural University, Ludhiana, India. He obtained his
MSc working on wheat phytosiderophores from the Indian Agricultural
Research Institute, New Delhi, India, and PhD working on control of flow-
ering and germination in barley from University of Manitoba, Canada. At
present, Dr. Kumar is stationed at the Cereal Research Centre, Manitoba,
Canada, working for the University of Manitoba. Dr. Kumar has studied
various disciplines in plant sciences and received many awards through-
out his academic career. His current interests include crop genomics and
bioinformatics. Dr. Kumar is member of various plant science societies
in Canada and the US. Dr. Kumar has publications that include research
articles, a review paper, and a book chapter in areas of plant physiology,
genetics, and bioinformatics.
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CONTENTS
Acknowledgment and How to Cite ..................................................xi
List of Contributors .........................................................................xi
Introduction ....................................................................................xix
Part I: Genome Data Mining Through Modern Sequencing
Technologies
1. Comparison of Next-Generation Sequencing Systems ............................1
Lin Liu, Yinhu Li, Siliang Li, Ni Hu, Yimin He, Ray Pong, Danni Lin,
Lihua Lu, and Maggie Law
2. Why Assembling Plant Genome Sequences Is So Challenging ............27
Manuel Gonzalo Claros, Rocío Bautista,
Darío Guerrero-Fernández, Hicham Benzerki, Pedro Seoane,
and Noé Fernández-Pozo
3. Genome Walking by Next Generation Sequencing Approaches ..........55
Mariateresa Volpicella, Claudia Leoni, Alessandra Costanza,
Immacolata Fanizza, Antonio Placido, and Luigi R. Ceci
4. Molecular Tools for Exploring Polyploid Genomes in Plants ...............73
Riccardo Aversano, Maria Raffaella Ercolano, Immacolata Caruso, Carlo Fasano,
Daniele Rosellini, and Domenico Carputo
5. Wheat Genomics: Present Status and Future Prospects ................99
P. K. Gupta, R. R. Mir, A. Mohan, and J. Kumar
6. Development in Rice Genome Research Based on Accurate
Genome Sequence ...................................................................................167
Takashi Matsumoto, Jianzhong Wu, Baltazar A. Antonio, and Takuji Sasaki
7. Genomic Databases for Crop Improvement ........................................189
Kaitao Lai, Michał T. Lorenc, and David Edwards
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viii Contents
Part II: Going Beyond DNA Variations to Understand
Environmental Adaptations
8. Uncovering the Complexity of Transcriptomes with RNA-Seq ........ 207
Valerio Costa, Claudia Angelini, Italia De Feis, and Alfredo Ciccodicola
9. Effi cient Experimental Design and Analysis Strategies for the
Detection of Differential Expression Using RNA-Sequencing ........... 249
José A. Robles, Sumaira E. Qureshi, Stuart J. Stephen,
Susan R. Wilson, Conrad J. Burden, and Jennifer M. Taylor
10. Analyzing the microRNA Transcriptome in Plants Using Deep
Sequencing Data .....................................................................................281
Xiaozeng Yang and Lei Li
11. Maize (Zea mays L.) Genome Diversity as Revealed by
RNA-Sequencing .....................................................................................299
Candice N. Hansey, Brieanne Vaillancourt, Rajandeep S. Sekhon, Natalia de Leon,
Shawn M. Kaeppler, and C. Robin Buell
12. Molecular Mechanisms of Epigenetic Variation in Plants ..................327
Ryo Fujimoto, Taku Sasaki, Ryo Ishikawa, Kenji Osabe, Takahiro Kawanabe,
and Elizabeth S. Dennis
13. Metagenomics: A Guide from Sampling to Data Analysis ..................357
Torsten Thomas, Jack Gilbert, and Folker Meyer
Part III: Single Nucleotide Polymorphism Is the Ideal Marker
14. SNP Markers and Their Impact on Plant Breeding ............................387
Jafar Mammadov, Rajat Aggarwal, Ramesh Buyyarapu, and Siva Kumpatla
15. Genotyping-by-Sequencing in Plants ....................................................415
Stéphane Deschamps , Victor Llaca, and Gregory D. May
Author Notes ...........................................................................................447
Index ........................................................................................................453
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ACKNOWLEDGMENT
AND HOW TO CITE
The chapters in this book were previously published in various places and in
various formats. By bringing them together here in one place, we offer the
reader a comprehensive perspective on recent investigations into the role of
bioinformatics in agriculture. Each chapter is added to and enriched by being
placed within the context of the larger investigative landscape. Specifically:
• Chapter 1 provides a description of hands-on experience with function-
ing, accuracy, and cost of sequencing from second generation sequencers.
The authors also discuss the applications of data generated through high
throughput second generation sequencers.
• Chapter 2 focuses on the typical challenges of plant genomes that explains
why plant genomics is less developed than animal genomics. It provides a
discussion on factors hindering accurate plant genome assembly.
• Chapter 3 sheds light on the development of several protocols for the ap-
plication of next generation sequencing technologies to genome walking.
• Chapter 4 focuses on technologies and strategies that may allow an in-depth
analysis of polyploid genomes. Origin and genetics of polyploids as well
as the main tools available for genome and gene expression analysis are
discussed. The implications of next generation sequencing in study of poly-
ploids is also discussed.
• Chapter 5 discusses the advances in wheat genomics and also describes the
available resources which can be used for future genomics research; this
review is important because wheat has a large genome and is a relatively
difficult for genomics research.
• Chapter 6 focuses on producing accurate genome sequences of rice and
studying its functional and evolutionary implications for comparative ge-
nomics
• Chapter 7 is a concise list of plant genome databases, resources for indi-
vidual crop improvement and potential course of action for future improve-
ment of genome databases.
• Chapter 8 surveys the RNA-Seq methods and the bioinformatics challenges
that follow in analyzing the sequence data.
• Chapter 9 provides insights into power and accuracy of differential gene
estimation based on different experimental designs.
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