Improvement of Crop Plants for Industrial End Uses

531 Pages·2007·8.687 MB·English

by  Paolo Pesaresi (auth.), P. RANALLI (eds.)

IMPROVEMENTOF CROPPLANTS
FOR INDUSTRIALEND USES
Improvement of Crop Plants
for Industrial End Uses
Edited by
P. RANALLI
C.R.A. -ISCI, Bologna, Italy
AC.I.P. Catalogue record for this book is available from the Library of Congress.
ISBN-10 1-4020-5485-8 (HB)
ISBN-13 978-1-4020-5485-3 (HB)
ISBN-10 1-4020-5486-6 (e-book)
ISBN-13 978-1-4020-5486-0 (e-book)
Published by Springer,
P.O. Box 17, 3300 AADordrecht, The Netherlands.
www.springer.com
Printed on acid-free paper
All Rights Reserved
© 2007 Springer
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TABLE OF CONTENTS
Preface.................................................................................................vii
1. The use of functional genomics to understand components
of plant metabolism and the regulation occurring
at molecular, cellular and whole plant levels
Paolo Pesaresi……..……………………………….…………………..1
2. Improving photosynthesis and yield potential
Jeffrey S. Amthor……..………………………….…………………..27
3. Marker assisted selection and genomics of industrial plants
Giuseppe Mandolino………………………………………...……….59
4. Improved agronomy and management of crop plants
for industrial end uses
Lorenzo Barbanti, Andrea Monti and Gianpietro Venturi...…………83
5. Lignin manipulation for fibre improvement
Jennifer Stephens and Claire Halpin……………...………………...129
6. Improvement of fibre and composites for new markets
Marcel Toonen, Michel Ebskamp and Robert Kohler……...…...….155
7. In planta novel starch synthesis
Ravindra N. Chibbar, Seedhabadee Ganeshan and Monica Båga......181
8. Bioethanol: role and production technologies
David Chiaramonti………………...………………………………..209
9. Complex lipid biosynthesis and its manipulation in plants
Irina A. Guschina and John L. Harwood………………………...….253
10. Biodiesel production
Jon Van Gerpen..................................................................................281
11. Bioelectricity and cogeneration
Giuliano Grassi and Alexander Allan…………………..…….……..291
12. Genetic improvement of crops for energy generation:
comparison of different provision chains with respect
to biomass and biofuel production
Paolo Ranalli and Mario Di Candilo………...…………………..….307
v
vi Table of Contents
13. Anaerobic digestion: a multi-faceted process for energy,
environmental management and rural development
Rudolf Braun………………………………………………………..335
14. Molecular farming for antigen (vaccine) production in plants
Chiara Lico, Selene Baschieri, Carla Marusic
and Eugenio Benvenuto………………………………………...…..417
15. Molecular farming of antibodies in plants
RichardM.Twyman,StefanSchillberg and Rainer Fischer ….…... 435
16. Molecular tailoring and boosting of bioactive secondary
metabolites in medicinal plants
Antonella Leone , Stefania Grillo, Luigi Monti
and Teodoro Cardi …………………………………………….…....471
17. Potential market for bio-based products in the context
of European greenhouse gas reduction strategies
Bengt Hillring and Matti Parikka…………………………………...509
Index...................................................................................................523
Preface
New uses are already being found for existing crops (e.g. bioethanol
and biodiesel from oil crops) and “new” crops are being developed
(e.g. willow/poplar for biomass production, and primrose for
pharmaceutical uses). Advanced biotechnologies will enable
breeders to produce a whole generation of new crops for specialist
needs (“designer crops”), including raw materials for the energy,
chemical and pharmaceutical industries.
In this book, the advances gained in different fields of research are
reviewed. In particular, research carried out on the application of
biotechnology in order to: i) produce new compounds by expressing
foreign heterologous genes in specific parts of a plant, ii) or modify
pathways to influence quality and/or yield of existing indigenous
target molecules, iii) or bioprocess plant or organic waste stream
into value-added products. The gained know how is basical to
identify bottlenecks in the major production chains and to propose
actions for moving these issues forward.
This book gives an overview of recent research and technological
development in biotechnology and biobased products and addresses
the following thematic priorities: Metabolic engineering. Work on
gene sequencing (genomics) and cataloguing the proteins that genes
express (proteomics) has reached relevant advances in recent years.
Unfortunately, research on plant metabolic pathways attracted,
during the 1990s, much lower levels of funding than genomics.
Consequently, a paucity of knowledge in the area of plant metabolic
processes is identified as the main scientific constraint to the rational
development of bio-based products using biotechnology. Plant
breeding tools. Conventional breeding can dramatically increase
yields and improve biomaterial qualities. Moreover, genetic markers
can now assist plant breeders by identifying lines with genes linked
vii
viii Preface
to particular traits. However, genetic manipulation offers the greatest
potential for producing raw materials in a volume and of a quality
attractive to industry. It is also a tool for producing novel
biomaterials which are unobtainable in plants by any other means.
Renewable biomass for energy generation. Comparison of different
provision chains with respect to bioethanol and biodiesel fuel
production has been investigated. Cogeneration of biomass-based
products as substitutes of fossils in the frame of greenhouse gas
reduction strategies was explored. Vegetable oil-based solvents and
lubrificants are already used in many industrial niche markets, but
industry may soon be looking for a much greater range of plant-
derived oils as alternatives to fossil-based oils. Biotechnology will
play a key role in raising oil yields, fine-tuning metabolic processes
to improve oil quality, and engineering novel oils for specific
applications. Fibres and composites. Modified plants with improved
fibre qualities could exploit new markets for biodegradable
composites, textiles and fabrics. Biotechnology is also helping to
improve the efficiency of wood and pulp processing by reducing the
content of lignin and other polymers in woody plant tissue. Fibres
from novel crops are replacing petroleum-based composite materials
used by industry. Biopharmaceuticals. The plants have great
potential for economical, large-scale biopharmaceutical production
and they have been explored to produce vaccine components, such
as antigens and/or adjuvants; in this field, plants can be used merely
as “biofactories” for the massive production of the product of
interest or, in addition, as a tool for vaccine delivery. The different
plant-based production systems used to synthesize recombinant
antibodies are discussed and the merits of plants compared with
other platforms evaluated.
Conclusively, the new book provides concerns useful to promote
an increase of the productivity of crops by using functional
genomics (to understand the regulation of plant metabolism at
molecular, cellular and whole plants) and the improvement of
photosynthetic efficiency (to design new plants with enhanced raw
materials percent and recovery).
Preface ix
The Chapters of this book have been written by experts
from all around the world. Consequently, the book is expected to be
of great interest for scientists, researchers, farmers, processors and
retailers, but also for students, technocrats and planners interested in
the progress made with the development of new industrial crops.
Paolo Ranalli
1
The use of functional genomics to understand
components of plant metabolism and the
regulation occurring at molecular, cellular and
whole plant levels
Paolo Pesaresi1,2
1Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900,
Lodi, Italy
2Dipartimento di Produzione Vegetale, Università Statale di Milano,
Via Celoria 2, 20133 Milano, Italy (e-mail: [email protected])
1. Introduction
The completion of the genome sequence of the small weed plant Arabi-
dopsis thaliana (The Arabidopsis genome initiative 2000), and more re-
cently ofrice (Goff et al. 2002; Yu et al. 2002, 2005), has greatly changed
the face of plant biology. Knowing the exact sequence and location of all
the genes of a given organism is the first step towards understanding how
all parts of a biological system work together. Information about the hy-
pothesized function of an unknown gene may be deduced from its se-
quence homology to other genes of known function. However, genome se-
quencing projects have revealed the existence of a tremendous amount of
biological diversity, with large proportion of genes sharing no homology to
genes with known or hypothesized functions. In this respect functional ge-
nomics is the key approach to transforming quantity into quality (Borevitz
and Ecker 2004; Holtfort et al. 2002). Functional genomics is a general
approach toward understanding how the genes of an organism work
1
P. Ranalli (ed.), Improvement of Crop Plants for Industrial End Uses, 1–26 .
© 2007 Springer.
2 Paolo Pesaresi
together by assigning new functions to unknown genes. For efficient gene
function analysis, researchers can choose from a multitude of different
methods, most of them derived from genomic research performed on
model organisms such as yeast, nematodes, flies and mice, not forgetting
the technological spin-offs that were inspired by the human genome pro-
ject. Arabidopsis populations, mutagenized by random insertion of T-DNA
or transposon elements, have been generated with the aim to perform high-
throughput reverse genetics studies and comprehensive forward genetics
studies of the entire gene compendium (Alonso et al. 2003). Additionally,
information about the spatial and temporal expression pattern of a gene can
be gained from analysis of qualitative and quantitative changes of messen-
ger RNAs, proteins, and metabolites. These techniques, able to simultane-
ously analyze large numbers of transcripts, proteins and chemical constitu-
ents, have led to the creation of new research fields within functional
genomics, named transcriptomics, proteomics, and metabolomics. Each
method has its inherent limitations and none of them alone is sufficient to
assign a function to a gene of interest. However, the organization of the
vast amount of data from the various approaches into central databases al-
lows easy extraction and comparison of meaningful information.
This chapter has the aim to highlight the major approaches that makes
up modern plant functional genomics and to describe how they add a new
dimension to the comprehension of plant biology with particular emphasis
to the model plant, Arabidopsis thaliana.
2. Plant genome sequences
The public effort to sequence the genome of the model flowering plant,
Arabidopsis thaliana, was completed in December 2000 (The Arabidopsis
genome initiative 2000), and it was the third complete genome of a higher
eukaryote, after Drosophila melanogaster, and Caenorhabditis elegans.
This tiny mustard plant, a common weed of the Brassicaceae family, had
been chosen as the first reference plant to be sequenced, because it has
several advantages over other species. Its nuclear genome is very small
with 115 million base pairs (Mb) of euchromatin out of the estimated 125
Mb total, its generation time is very short, and it is genetically very well
characterized. The total number of Arabidopsis genes revealed by the five
chromosome sequences was initially estimated at 25,490 and later revised
to 30,700 (version 5 annotation), resulting in 11,000-15,000 gene families,
with about one quarter of genes believed to be plant specific. The entire
Arabidopsis genome dataset has been stored and can be retrieved from