Next-generation sequencing and bioinformatics for plant science

204 Pages·2017·2.246 MB·English

by  Bhadauria V (ed.)

Next-generation Sequencing
and Bioinformatics for Plant
Science
Edited by
Vijai Bhadauria
Caister Academic Press
Next-generation Sequencing and
Bioinformatics for Plant Science
https://doi.org/10.21775/9781910190654
Edited by
Vijai Bhadauria
Crop Development Centre and Department of Plant Sciences
University of Saskatchewan
Saskatoon, SK
Canada
Caister Academic Press
Copyright © 2017
Caister Academic Press
Norfolk, UK
www.caister.com
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A catalogue record for this book is available from the British Library
ISBN: 978-1-910190-65-4 (paperback)
ISBN: 978-1-910190-66-1 (ebook)
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Cover design adapted from an image provided by Dr Xifeng Chen and Dr Bojun Ma.
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Contents
Editorial vii
1 Status and Prospects of Next-generation Sequencing Technologies in Crop Plants 1
Tilak R. Sharma, Basavantraya N. Devanna, Kanti Kiran, Pankaj K. Singh,
Kirti Arora, Priyanka Jain, Ila M. Tiwari, Himanshu Dubey, Banita K. Saklani,
Mandeep Kumari, Jyoti Singh, Rajdeep Jaswal, Ritu Kapoor, Deepak V. Pawar,
Shruti Sinha, Deepak S. Bisht, Amolkumar U. Solanke and Tapan K. Mondal
2 Next-generation Sequencing Promoted the Release of Reference
Genomes and Discovered Genome Evolution in Cereal Crops 37
Yong Huang, Haiyang Liu and Yongzhong Xing
3 Advanced Applications of Next-generation Sequencing Technologies
to Orchid Biology 51
Chuan-Ming Yeh, Zhong-Jian Liu and Wen-Chieh Tsai
4 Bioinformatics Resources for Plant Genomics: Opportunities and
Bottlenecks in the -omics Era 71
Luca Ambrosino, Chiara Colantuono, Francesco Monticolo and
Maria Luisa Chiusano
5 Applications of Bioinformatics to Plant Biotechnology 89
Diego F. Gomez-Casati, María V. Busi, Julieta Barchiesi, Diego A. Peralta,
Nicolás Hedin and Vijai Bhadauria
6 Quantitative Genetics of Disease Resistance in Wheat 105
Vijai Bhadauria and Lucia Popescu
7 A Rice Genetic Improvement Boom by Next-generation Sequencing 109
Xiangchun Zhou, Xufeng Bai and Yongzhong Xing
8 Dual RNA-seq to Elucidate the Plant–Pathogen Duel 127
Sanushka Naidoo, Erik Andrei Visser, Lizahn Zwart, Yves du Toit, Vijai Bhadauria
and Louise Simone Shuey
9 Next-generation Sequencing Sheds New Light on Small RNAs in
Plant Reproductive Development 143
Xiaobai Li
iv | Contents
10 ChIP-seq: A Powerful Tool for Studying Protein–DNA Interactions in Plants 171
Xifeng Chen, Vijai Bhadauria and Bojun Ma
11 Cataloguing Plant Genome Structural Variations 181
Xingtan Zhang, Xuequn Chen, Pingping Liang and Haibao Tang
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Full details at www.caister.com

Editorial
With the advent of high-throughput sequencing rice, maize and sorghum (Chapter 2) and orchids
platforms, such as Illumina’s Genome Analyzer, (Chapter 3) shed light on the challenges in the
HiSeq, MiSeq and NextSeq, Roche/454’s Genome post-NGS era, such as genome assembly and anno-
Sequencer FLX, Thermo-Fisher Scientific’s SOLiD, tation. Gomez-Casati and colleagues, in Chapter 5,
Ion Torrent and Ion Proton, PacBio’s Real-Time describe the application of omics (gene expression
Sequencer and more recently Oxford Nanopore’s and regulation as well as quantitative proteomics
MinION, it has become feasible to sequence entire approaches, such as iTRAQ) in fruit development
genomes and transcriptomes at an exponential and ripening, and plant disease resistance. Bioinfor-
pace. This has huge implications in plant breeding matics resources for plant genomics are detailed and
and genetics. The reviews presented in this volume discussed in two reviews (Chapters 4 and 5). The
summarize recent developments in next-generation NGS-based genotyping-by-sequencing approaches
sequencing (NGS) and bioinformatics tools and are useful to map polymorphism in experimental
their application in understanding and improving populations and germplasm, which then can be
agronomic traits. used to track genomic regions controlling quantita-
tive traits, such as fusarium head blight and stripe
Next-generation sequencing (NGS) coupled with rust resistance in wheat (Chapater 6) and rice
high-performance computing have revolutionized (Chapter 7). Sequencing of the transcriptome from
the field of plant breeding and genetics (Bhadauria infected plant tissues (dual RNA-seq) can provide
and Banniza, 2014; Bhadauria et al., 2016). This molecular insight into host defence and pathogen
volume compiles recent advances in the NGS as virulence during incompatible and compatible
well as the application of NGS in understanding interactions, thereby facilitating in designing crops
and improving agronomics traits such as yield, with improved resistance (Chapter 8). In addition
drought tolerance and disease resistance. to genome and transcriptome sequencing, the
In this volume, the review by Sharma et al. NGS can also be used in sequencing of small RNA
(Chapter 1) outlines the evolution of DNA (20–24 nucleotides; Chapter 9) and transcription
sequencing techniques and platforms, including factor binding sites (ChIP-seq; Chapter 10) in
the first generation (Sanger’s chain-termination genomes. Structural variations, such as abnormal
method and Maxam–Gilbert’s chemical cleav- chromosome number, chromosomal rearrange-
age method), second-generation (Illumina’s GA, ment, copy number variation, presence or absence
HiSeq and MiSeq as well as Roche/454’s GS variation, mobile element insertion and deletion
FLX), third-generation single molecule real-time and homologous exchange play key role in pheno-
sequencing (PacBio’s SMRT RS) and the more typic diversity of agronomic traits, such as biotic
recent fourth-generation sequencing platform and abiotic stress tolerance. Zhang and colleagues
Oxford Nanopore’s MinIon. The application of looked into the application of NGS in mapping
NGS in the genome sequencing and evolution of such structural variations.
viii | Editorial
References Bhadauria, V., Wong, M.M., Bett, K.E., and Banniza, S.
(2016). Wild help for enhancing genetic resistance in
Bhadauria, V., and Banniza, S. (2014). What lies ahead
lentil against fungal diseases. Curr. Issues Mol. Biol. 19,
in post-genomics era: a perspective on genetic
3–6.
improvement of crops for fungal disease resistance?
Plant Signal Behav. 9, e28503.
Vijai Bhadauria
Crop Development Centre and Department of Plant Sciences,
University of Saskatchewan, Saskatoon, SK,
Canada
Lucia Popescu
Department of Soil Science,
University of Saskatchewan, Saskatoon, SK,
Canada
https://doi.org/10.21775/9781910190654.01
Status and Prospects of
1
Next-generation Sequencing
Technologies in Crop Plants
Tilak R. Sharma*, Basavantraya N. Devanna, Kanti Kiran,
Pankaj K. Singh, Kirti Arora, Priyanka Jain, Ila M. Tiwari,
Himanshu Dubey, Banita K. Saklani, Mandeep Kumari, Jyoti Singh,
Rajdeep Jaswal, Ritu Kapoor, Deepak V. Pawar, Shruti Sinha,
Deepak S. Bisht, Amolkumar U. Solanke and Tapan K. Mondal
ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
*Correspondence: [e-mail] and [e-mail]
https://doi.org/10.21775/9781910190654.02
Abstract Introduction
The history of DNA sequencing dates back to The overall growth, development and behavioural
1970s. During this period, the two first-generation characteristics of every living creature are largely
nucleotide sequencing techniques were devel- determined by its genetic constitution. Subse-
oped. Subsequently, Sanger’s dideoxy method of quent to the famous double-helix model of DNA,
sequencing gained popularity over Maxam and Gil- proposed by Watson and Crick (1953), scientists
bert’s chemical method of sequencing. However, began to find the ways and means to determine the
in the last decade, we have observed revolutionary nucleotide sequence of DNA. The first significant
changes in DNA sequencing technologies leading breakthrough in this area was achieved in late 1970s
to the emergence of next-generation sequenc- when two groups working independently reported
ing (NGS) techniques. NGS technologies have two different approaches for DNA sequencing
enhanced the throughput and speed of sequencing (Maxam and Gilbert, 1977; Sanger et al., 1977).
combined with bringing down the overall cost of Though Maxam and Gilbert’s approach for DNA
the process over a time. The major applications of sequencing was preferred initially, it was Sanger’s
NGS technologies being genome sequencing and sequencing technology which subsequently got
resequencing, transcriptomics, metagenomics in popularized among the scientific community. The
relation to plant–microbe interactions, exon and classical genome sequencing projects such as the
genome capturing, development of molecular Human Genome Project (HGP), the Arabidopsis
markers and evolutionary studies. In this review, Genome Initiative and the International Rice
we present a broader picture of evolution of Genome Sequencing Project were successfully
NGS tools, its various applications in crop plants, completed using Sanger’s sequencing approach.
and future prospects of the technology for crop Subsequently, many plant genomes were sequenced
improvement. using this sequencing technology. Though Sanger’s
dideoxy sequencing method is considered as gold
standard with respect to genome sequencing, there