Table Of ContentMethods in
Molecular Biology 1892
Nese Sreenivasulu Editor
Rice Grain
Quality
Methods and Protocols
M M B
ethods in olecular iology
Series Editor:
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, United Kingdom
For further volumes:
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Rice Grain Quality
Methods and Protocols
Editors
Nese Sreenivasulu
Grain Quality and Nutrition Center, International Rice Research Institute, Manila, Philippines
Editor
Nese Sreenivasulu
Grain Quality and Nutrition Center
International Rice Research Institute
Manila, Philippines
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-8912-6 ISBN 978-1-4939-8914-0 (eBook)
https://doi.org/10.1007/978-1-4939-8914-0
Library of Congress Control Number: 2018960445
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Dedication
I dedicate this book to Dr. Bienvenido O. Juliano (August 15, 1936–February 21, 2018),
who immensely contributed significant knowledge in the area of cereal chemistry research.
Dr. Juliano pioneered the research of grain quality at the International Rice Research Institute
(IRRI) in 1961; he went on to spend more than 32 years at IRRI, who made significant
research contributions in the area of cooking, eating, and nutritional qualities of rice grain.
He also helped to build the grain-quality research capability of PhilRice, where he continued to
pursue his rice research as a senior consultant/expert.
v
Preface
Acceptance of new rice genotypes requires their ability to satisfy consumer preferences for
premium grain quality, besides being high yielding. As rice consumers become increasingly
particular about the quality of the rice, we need to ensure that modern varieties were less
susceptible to breaking during milling and assure premium cooking quality with optimum
texture, flavor, and aroma. Translating human health benefits by enhancing nutritional
properties includes enriching micronutrients, ensuring food safety, and introducing slower
digestibility factors. Recent advances made in introducing various high-throughput pheno-
typing methods to screen milling quality, cooking quality, and nutritional quality in the
pool of breeding material are discussed in depth. This volume presents the relevant meth-
ods and detailed protocols with appropriate instructions outlined by experts to facilitate
grain quality and nutritional screening in the germplasm. Detailed protocols to define seed
development stages, panicle architectural traits to understand yield components, and mea-
sure physical traits such as grain dimensions using imaging techniques and chalk and head
rice yield have been discussed in Chapters 1, 3, 4, 5, and 6. We need to link initial indicators
of cooking quality (amylose, gel consistency, and gelatinization temperature) with texture
and viscoelastic properties to capture distinct cooking quality classes. Also covered are bio-
chemical methods that measure properties related to cooking such as starch structure and
protein properties in Chapters 2, 7, 8, 9, and 10. Holistic understanding of grain quality
traits by exploring metabolomics platforms to screen primary metabolites and volatiles has
been described in Chapter 11. In addition, health and nutritional aspects need to be fac-
tored into rice breeding programs to contribute to the overall wellness of rice consumers.
Therefore, we need to take into account breeding healthier target traits by capturing the
diversity for low glycemic index and high-resistant starch and enriching nonstructural poly-
saccharides and micronutrients with acceptable cooking quality, texture, and palatability.
Methods related to micronutrient profiling, screening heavy metals, and identifying rice
cultivars with lower glycemic index have been addressed in Chapters 13–15.
We need to establish the genetic basis of the variation of cooking and eating quality
traits through genome-wide association studies by studying both diverse set of lines and
pre-breeding core collection. Genome-wide -omics analyses have provided efficient
approaches to identify key genomic regions that control grain quality traits. Knowledge of
these genes and the influence of specific alleles present in both domesticated and wild rice
gene pools provide a robust platform for marker-assisted selection in breeding to introgress
premium grain quality traits in high-yielding backgrounds. Emphasis has been given to
utilizing resequencing resources for the gene discovery programs via structural genomics,
exploring transcriptome, epigenetics, and genome editing technologies to unravel grain
quality, and nutritional traits have been discussed in Chapters 12 and 16–18. In summary,
overall emphasis has been given to holistic understanding of grain quality traits covering
various phenomics technologies and links it through to gene discovery via QTL cloning
and structural-functional genomics strategies.
Manila, Philippines Nese Sreenivasulu
vii
Contents
Preface ................................................................. vii
Contributors ............................................................ xi
1 Improving Head Rice Yield and Milling Quality: State-of- the-Art
and Future Prospects ........................................... 1
Vito M. Butardo Jr. and Nese Sreenivasulu
2 Improving Rice Grain Quality: State-of-the-Art and Future Prospects. . . . . . . 19
Vito M. Butardo Jr., Nese Sreenivasulu, and Bienvenido O. Juliano
3 Morphology of Rice Seed Development and Its Influence
on Grain Quality .............................................. 57
Paul A. Counce and Karen A. K. Moldenhauer
4 Novel Imaging Techniques to Analyze Panicle Architecture .............. 75
Erstelle Pasion, Roinand Aguila, Nese Sreenivasulu, and Roslen Anacleto
5 Measuring Head Rice Recovery in Rice ............................. 89
Jennine Rose Lapis, Rosa Paula O. Cuevas, Nese Sreenivasulu,
and Lilia Molina
6 Measurement of Rice Grain Dimensions and Chalkiness,
and Rice Grain Elongation Using Image Analysis ...................... 99
Marnol V. Santos, Rosa Paula O. Cuevas, Nese Sreenivasulu,
and Lilia Molina
7 Method Development of Near-Infrared Spectroscopy Approaches
for Nondestructive and Rapid Estimation of Total Protein in Brown
Rice Flour ................................................... 109
Rosario Jimenez, Lilia Molina, Iman Zarei, Jennine Rose Lapis,
Ruben Chavez, Rosa Paula O. Cuevas, and Nese Sreenivasulu
8 Multi-Dimensional Cooking Quality Classification Using Routine
Quality Evaluation Methods ...................................... 137
Lilia Molina, Rosario Jimenez, Nese Sreenivasulu, and Rosa Paula O. Cuevas
9 Characterization of Mechanical Texture Attributes of Cooked Milled
Rice by Texture Profile Analyses and Unraveling Viscoelasticity
Properties Through Rheometry ................................... 151
Rosa Paula O. Cuevas, Pawan S. Takhar, and Nese Sreenivasulu
10 Characterizing Starch Molecular Structure of Rice ..................... 169
Cheng Li, Hongyan Li, and Robert G. Gilbert
11 Rice Grain Quality Benchmarking Through Profiling of Volatiles
and Metabolites in Grains Using Gas Chromatography Mass Spectrometry ... 187
Cindy Llorente, Rosario Jimenez, Jackie, Yariv Brotman, Alisdair R. Fernie,
and Nese Sreenivasulu
12 Re-sequencing Resources to Improve Starch and Grain Quality in Rice ..... 201
Gopala Krishnan Subbaiyan, Ardashir K. Masouleh, Agnelo Furtado,
Daniel L. E. Waters, and Robert J. Henry
ix
x Contents
13 Quantifying Grain Digestibility of Starch Fractions in Milled Rice ......... 241
Crisline Mae Alhambra, Sushil Dhital, Nese Sreenivasulu,
and Vito M. Butardo Jr.
14 Determination of Macronutrient and Micronutrient Content
in Rice Grains Using Inductively Coupled Plasma-Optical Emission
Spectrometry (ICP-OES) ........................................ 253
Lilia Molina, Jennine Rose Lapis, Nese Sreenivasulu,
and Rosa Paula O. Cuevas
15 Determination of Cadmium Concentration in Milled and Brown
Rice Grains Using Graphite Furnace Atomic Absorption Spectrometry ...... 265
Lilia Molina, Jennine Rose Lapis, Nese Sreenivasulu,
and Rosa Paula O. Cuevas
16 Analysis of Developing Rice Grain Transcriptome Using the Agilent
Microarray Platform ............................................ 277
Mandy Püffeld, Christiane Seiler, Markus Kuhlmann, Nese Sreenivasulu,
and Vito M. Butardo Jr.
17 Quantification of DNA Methylation as Biomarker for Grain Quality ........ 301
Christiane Seiler and Markus Kuhlmann
18 CRISPR-Cas9-Mediated Genome Editing of Rice Towards Better
Grain Quality ................................................. 311
Anindya Bandyopadhyay, Xiaojia Yin, Akshaya Biswal, Robert Coe,
and William Paul Quick
Index ............................................................... 337
Contributors
Roinand aguila • International Rice Research Institute, Los Baños, Laguna, Philippines
CRisline Mae alhaMbRa • International Rice Research Institute, Los Baños, Laguna,
Philippines
Roslen anaCleto • International Rice Research Institute, Los Baños, Laguna,
Philippines
anindya bandyopadhyay • International Rice Research Institute, Los Baños, Laguna,
Philippines; Syngenta Beijing Innovation Center, Changping District, Beijing, China
akshaya biswal • International Rice Research Institute, Los Baños, Laguna, Philippines
yaRiv bRotMan • Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm,
Germany; Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba,
Israel
vito M. butaRdo JR. • International Rice Research Institute, Los Baños, Laguna,
Philippines; Department of Chemistry and Biotechnology, Faculty of Science, Engineering
and Technology, Swinburne University of Technology, Hawthorn, VIC, Australia; Faculty
of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn,
VIC, Australia
Ruben Chavez • International Rice Research Institute, Los Baños, Laguna, Philippines
RobeRt Coe • International Rice Research Institute, Los Baños, Laguna, Philippines
paul a. CounCe • University of Arkansas, Rice Research and Extension Center,
Stuttgart, AR, USA
Rosa paula o. Cuevas • International Rice Research Institute, Los Baños, Laguna,
Philippines
sushil dhital • ARC Centre of Excellence in Plant Cell Walls, Centre for Nutrition and
Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University
of Queensland, St Lucia, QLD, Australia
alisdaiR R. FeRnie • Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm,
Germany; Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
agnelo FuRtado • Queensland Alliance for Agriculture and Food Innovation, University
of Queensland, Brisbane, QLD, Australia
RobeRt g. gilbeRt • Joint International Research Laboratory of Agriculture and Agri-
Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou,
China; Centre for Nutrition & Food Sciences, QAAFI, University of Queensland,
Brisbane, Australia
gopala kRishnan subbaiyan • Division of Genetics, ICAR-Indian Agricultural Research
Institute, New Delhi, India
RobeRt J. henRy • Queensland Alliance for Agriculture and Food Innovation, University
of Queensland, Brisbane, QLD, Australia
JaCkie • Shimadzu (Asia Pacific) Pte. Ltd., Singapore, Singapore
RosaRio JiMenez • International Rice Research Institute, Los Baños, Laguna, Philippines
bienvenido o. Juliano • Philippine Rice Research Institute, Los Baños, Laguna,
Philippines
xi
xii Contributors
MaRkus kuhlMann • Leibniz Institute of Plant Genetics and Crop Plant Research,
Gatersleben, Germany
Jennine Rose lapis • International Rice Research Institute, Los Baños, Laguna,
Philippines
Cheng li • Joint International Research Laboratory of Agriculture and Agri-Product
Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
hongyan li • School of Food and Chemical Engineering, Beijing Technology and Business
University, Beijing, China
Cindy lloRente • International Rice Research Institute, Los Baños, Laguna, Philippines
aRdashiR k. Masouleh • Queensland Alliance for Agriculture and Food Innovation,
University of Queensland, Brisbane, QLD, Australia
kaRen a. k. MoldenhaueR • University of Arkansas, Rice Research and Extension
Center, Stuttgart, AR, USA
lilia Molina • International Rice Research Institute, Los Baños, Laguna, Philippines
eRstelle pasion • International Rice Research Institute, Los Baños, Laguna, Philippines
Mandy püFFeld • Leibniz Institute of Plant Genetics and Crop Plant Research,
Gatersleben, Germany
williaM paul QuiCk • International Rice Research Institute, Los Baños, Laguna,
Philippines
MaRnol v. santos • International Rice Research Institute, Los Baños, Laguna,
Philippines
ChRistiane seileR • Leibniz Institute of Plant Genetics and Crop Plant Research,
Gatersleben, Germany
nese sReenivasulu • International Rice Research Institute, Los Baños, Laguna,
Philippines
pawan s. takhaR • Department of Food Science and Human Nutrition, University of
Illinois at Urbana-Champaign, Urbana, IL, USA
daniel l. e. wateRs • Southern Cross Plant Science, Southern Cross University, Lismore,
NSW, Australia; ARC ITTC for Functional Grains, Charles Sturt University, Wagga,
NSW, Australia
XiaoJia yin • International Rice Research Institute, Los Baños, Laguna, Philippines
Iman ZareI • International Rice Research Institute, Los Baños, Laguna, Philippines
