Plant Breeding: Mendelian to Molecular Approaches

812 Pages·2004·32.78 MB·English

by  H. K. Jain (auth.)

PLANT BREEDING
Mendelian to Molecular Approaches
PLANT BREEDING
Mendelian to Molecular Approaches
Editors
HKJain
MCKharkwal
Springer-Science+Business Media, B.V.
A C./.P. catalogue recordfor the book is availablefrom the Library ofCongress
ISBN 978-94-010-3773-0 ISBN 978-94-007-1040-5 (eBook)
DOI 10.1007/978-94-007-1040-5
In India, Bangladesh, Nepal, Pakistan and Sri Lanka by Narosa Publishing House
22 Daryaganj, Delhi Medical Association Road, New Delhi 110 002, India
Copyright © 2004 Springer Science+Business Media Dordrecht
Originally published by Kluwer Academic Publishers in 2004
Softcover reprint of the hardcover 1s t edition 2004
AII rights reserved. No part ofthis publication may be reproduced,
stored in a retrieval system or transmitted in any form or by any means,
electronic, mechanical, photocopying, recording or otherwise,
without prior written permission ofthe publishers.
FOREWORD
The Indian Society ofGenetics and Plant Breeding was established in 1941 in recognition of the
growingcontributionofimproved cropvarietiestothecountry'sagriculture.Scientificplantbreeding
hadstarted inIndiasoon aftertherediscoveryofMendel'slawsofheredity.The Indian Agricultural
Research Institute set up in 1905 and a number ofAgricultural Colleges in different parts of the
countrycarried outsomeoftheearliest workmostly intheformofpure-line selections. Insubsequent
years, hybridization programmes incrops like wheat, rice,oilseeds, grain legumes,sugarcane and
cotton yieldedalarge numberof improvedcultivars with significantly higher yields.
Aturning point cameinthe 1960swiththedevelopmentofhybrids inseveral crops including
inter-specific hybrids incotton.And when new germplasm with dwarfing genes became available
inwheatandricefromCIMMYTandIRRI,respectively,Indian plantbreeders quickly incorporated
thesegenes intothegenetic backgroundofthecountry'swidelygrown varieties withexcellentgrain
quality and otherdesirabletraits.This was to mark the beginning ofmodem agriculture inIndia as
more and more varieties were developed, characterized by a high harvest index and response to
modem farm inputs like the inorganic fertilizers.India's green revolution which has led to major
surpluses offood grains andothercommoditieslikesugar andcotton hasbeen made possiblebythe
work ofone of the largestgroups of plant breeders working inacoordinatednetwork.
The Indian Society of Genetics and Plant Breeding with a membership of over 2000 is a
representative body of this large community of agricultural scientists in the country.The Society
hasbeenfostering close interactionsbetween itsmembers located indifferentparts ofIndia aswell
as all over the world. As a part of this effort,theSociety organizesperiodic symposia on topics of
current interest. The present book "Plant Breeding: Mendelian to Molecular Approaches" is the
outcome ofan international symposium entitled "Hundred Yearsof Post-Mendelian Genetics and
Plant Breeding - Retrospect and Prospects". The symposium marked the Diamond Jubilee
Celebrations of the Society and coincided with the Centenary of rediscovery ofMendel's laws of
biological inheritance. The focus of the symposium was on hundred years of plant breeding as a
tribute to GregorJohann Mendel.
As the world isalready celebrating the Golden Jubileeofthe discoveryofstructureof DNA
inthe year 2003,Ihope that documentation ofplant breeding researches inthe past century in this
book willdemonstrate the immenseeconomic impact ofthe science ofgenetics and itsapplication
in agriculture.
Iwould like toplace on record our sincerethanks tothe previous Executive Council,which
wasinstrumentalinorganizingthesymposium.OnbehalfofthepresentExecutiveCouncil,Iliketo
expressmydeep appreciationespeciallytoDr.MangalaRai,pastPresidentandDr.M.C.Kharkwal,
OrganizingSecretary oftheInternational DiamondJubileeSymposium, who worked hard to make
theevent successful.Weoweour thanks totheEditors fortheiruntiringefforts inthepreparationof
this book. I am sure the book will be of value to students, teachers and practitioners of plant
breeding.
M.Mahadevappa
President, ISGPB
PREFACE
The ideaofpreparingthis book grew outofasymposiumwhich the Indian Society ofGeneticsand
Plant Breeding had organized to mark the rediscovery of Mendel's laws of biological inheritance.
Mendel's work has had its greatest economic impact in the rapid development of the science of
plantbreeding.Improvedvarietiesofcropplants currentlyhelptofeed ahuman populationofmore
than six million people. One hundred years later following major advances in molecular genetics,
plant breeding, with the availability of new tools of modem biotechnology, is again expected to
make major contributionsto world agriculture.
Theparticipantsinthesymposiumwereaskedtowritecriticalreviews onanumberofselected
topicsingenetics,biotechnologyandplantbreeding.Theconceptsandmethodology ofplantbreeding
supportedbyadvances inclassicalandmoleculargeneticsreceivedspecialattentioninthepreparation
of the book. The purpose has been to document the development of the science of plant breeding
beginning with some of the landmarkdiscoveries.
Plant breeding in the 21st century will be characterized by an increasing integration of the
tried and tested classical methods with the newer techniques of modem biotechnology.The book
points tothekind of integrationwhich willbetaking place. Firstandforemost, plant breedersofthe
future willbemuch betterplaced inthefield ofanalysis ofgenetic diversity whichthey willseekfor
their hybrdization programmes.Microsatellites and many other loci known for their polymorphic
DNA sequences have led to the development of elegant techniques for the assessment of genetic
diversity available in different plant populations. Marker assisted selection should offer new
opportunities to pick up traits of interest in segregating populations. Already, plant breeders are
interested in the marking and manipulation of quantitative trait loci (QTLs) of value for higher
yields and durable resistance to biotic and abiotic stresses. Transgenic crop varieties are being
released with increasing frequency despite some of the controversy surrounding them.The safety
concernsmust obviouslyreceiveserious attention consideringthatsomeofthegenes ofinterest and
the proteins they code for diverged from the ancestoral populations of humans millions of years
ago. However, the newly found ability to transfer genes across taxonomic barriers of all kinds
provides such a powerful recombinant DNA technology that it is bound to increase the range of
genetic variability available to plant breeders.
Ourhigh-yieldagriculturehascomealongwaysincethedomesticationofthewildprogenitors
of the presentday crop plants.Mendel's work paved the wayfor their scientific improvement. The
identificationand incorporationofplant-typegenes inthe 1960sledtothegenetic reconstructionof
traditional cultivarstofitthemintoamoremodemagriculture. Thehighyielding varieties ofvarious
crops now availablewould befurther improvedwith theemergenceofmoreefficienttechniquesof
plant breeding.
Weare grateful to the contributors of the various chapters for their positive response and to
the members of the Programme Committeefor their assistance in determining the contents of this
book. The support received from many colleagues in the preperation of the final manuscript is
thankfully acknowledged.
H.K.JAIN
M.e. KHARKWAL
CONTENTS
Foreword ... v
Preface vii
Abbreviations Xl
1. Hundred Years of Genetics: Revisiting Some of the Landmarks
H.K Jain ... 1
2. A Century of Advances in Plant Breeding Methodologies
M.C. Kharkwa1 and Darbeshwar Roy ... 17
3. Plant Breeding Science and Practice in the Twentieth Century: Some Landmarks
N.G.P. Rao ... 49
4. Chromosome Manipulations for Crop Improvement
D.S. Brar and H.S. Dhaliwal 65
5. Advances in Molecular Cytogenetics: Potential for Crop Improvement
P.K Gupta and M.K Dhar 97
6. Transposable Elements and Epigenetic Mechanisms:Significance and Implications
KC. Upadhyaya and B.M. Prasanna 115
7. Genetics of Host-Pathogen Interaction and Breeding for Durable Resistance
Ravi P. Singh, S. Rajaram, R.G. Saini, 1. Huerta-Espino and M. William 145
8. Genetic Improvement for Abiotic Stress Responses
Ani! Grover, Avnish Kapoor, D. Kumar, H.E. Shashidhar and S. Hittalmani 167
9. In-vitro Approaches to Crop Improvement
P.S. Ahuja and P.B. Kirti 195
10. Molecular Markers in Improvement of Wheat and Brassica
M. Lakshrnikumaran, T. Mohapatra, V.S. Gupta and P.K Ranjekar 229
11. Genome Mapping and Map Based Cloning
C. Kole and P.K Gupta 257
12. Genome-Wide Molecular Approaches in Plants: From Structure to Function
Akhilesh K Tyagi, 1.P. Khurana, P. Khurana, A Mohanty and AK Bharti 301
13. Application of Biotechnology to Maize and Wheat Improvement
David Hoisington 317
14. Transgenics in Crop Improvement
Swapan K Datta, Niranjan Baisakh, Vai Ramanathan and KK Narayanan 333
15. Selection for Simple and Complex Traits
v.P. Gupta, G.S. Nanda and Darbeshwar Roy 373
x
16. Population Improvement Strategies for Crop Improvement
S.K Vasal, N.N. Singh, B.S. Dhillon and SJ. PatH ... 391
17. Classical and Molecular Concepts of Heterosis
S.S. Virmani, MP. Pandey, I.S. Singh and Wei Jun Xu ... 407
18. Advances in Hybrid Breeding Methodology
B.S. Dhillon, AK Singh, B.P.S. Lather and G. Srinivasan ... 419
19. Heterosis in Crop Improvement
EA Siddiq, O.P. Govila and S.S. Banga ... 451
20. Cytoplasmic-Nuclear Male Sterility: Origin, Evaluation and Utilization
B.V.S. Reddy, KN. Rai, N.P. Sharma, Ish Kumar and KB. Saxena ... 473
21. Quantitative Trait Improvement: Classical and Molecular Concepts
V. Arunachalam, KV. Prabhu and V. Sujata ... 501
22. Mating Designs and Their Implications for Plant Breeding
R.K Singh, H.S. Pooni, Mahender Singh and A Bandyopadhyaya 523
23. Genotype-by-Environment Interaction in Crop Improvement
MS. Kang, V.T, Prabhakaran and R.B. Mehra 535
24. Breeding for Wider Adaptability
Darbeshwar Roy and M.C. Kharkwa1 ... 573
25. Plant Ideotype: The Concept and Application
J.P. Tandon and H.K Jain 585
26. Mutation Breeding for Crop Improvement
MC. Kharkwal, R.N. Pandey and S.E. Pawar 601
27. Induced Mutations and Selection Techniques for Quantitative Traits
B. Sharma and S.K Sharma ... 647
28. Collection, Conservation and Utilization of Plant Genetic Resources
P.L. Gautam, B.B. Singh, Sanjeev Saxena and Rajiv K Sharma ... 657
29. Intellectual Property Rights Related Issues in Plant Breeding
Mangala Rai and S. Mauria 691
30. Breeding Legumes for Improved Nitrogen Fixation
O.P. Rupela and D.L.N. Rao 719
31. Rising Atmospheric Carbon Dioxide and Crop Responses
D.C. Uprety, AP. Mitra, S.c. Garg, B. Kimball and D. Lawlor 749
The Contributors 759
Author Index 763
Subject Index 797
ABBREVIATIONS
ADP-Adenosine diphosphate DUS-Distinctness,uniformityandstability
AFLP-Amplifiedfragment length polymorphism ECFs -Extendedchromatinfibers
AFP-Antifreeze protein ECR-Extended chromosomalregion
AGI-TheArabidopsisgenomeinitiative EDFs -Extended DNA fibers
AIDS-Acquiredimmunedeficiencysyndrome EDV-Essentially derived varieties
AMMI -Additivemaineffects andmultiplicative ELC-Expression-linkedcopy
interaction ELISA -Enzyme-linkedimmunosorbentassay
AP-PCR-Arbitrary primerPCR EMS-Ethylmethane sulphonate
APR-Adult plant resistance ESAG-Expression site-associatedgene
ARS-Autonomouslyreplicatingsequences EST-Expressed sequencetags
AS-PCR-AllelespecificPCR FACS-Fluorescenceactivatedcellsorter
ATP-Adenosinetriphosphate FDR· Firstdivision restitution
BAC-Bacterial artificial chromosome FISH-Fluorescence in-situhybridization
BCTV -Beetcurly topvirus GAIT-General AgreementonTarrifandTrade
BGMV -Bean golden mosaic virus GEl -Genotype byenvironmentinteraction
BIPs-Biparentalprogenies GISH•Genomic in-situ hybridization
BLB•Bacterialleafblight GLC-Gas-liquidchromatography
BLUP-Bestlinearunbiasedprediction GMO-Geneticallymodifiedorganisms
BMV-Brome mosaic virus GPC-Grainprotein content
BSA-Bulked segregantanalysis GRU -Geneticresources unit
Bt-Bacillusthuringiensis GUS-P-glucuronidasegene
BYDV-Barley yellow dwarfvirus HI-Harvestindex
CAP -Cataboliteactivatorprotein HPLC-Highpressureliquidchromatography
CAPS-Cleavedamplified polymorphicsequences HSPs-Heatshock proteins
CBD-Conventiononbiologicaldiversity HVR-Hypervariable repeats
CBF -C-repeatbindingfactors HUGE-Humangenome project
CCA-Clone-by-cloneapproach IDA-International depositoryauthority
CCD-Chargedcoupleddevice IEDC-Inducedembryonicdeterminedcells
CCMV -Cowpeachloroticmottle virus lPR -Intellectual property rights
cDNA •ComplementaryDNA IRAP-Interretrotransposonamplified
CEPH -Centreforstudies onhuman polymorphism polymorphism
CGRFA·Commissionongenetic resources forfood IRGSP•International ricegenome sequencing
andagriculture project
CHA -Chemicalhybridizingagents ISSR- Intersimple sequencerepeats
CHlAS-Chromosomeimageanalyzingsystem ITMI-International triticeae mappinginitiative
ClM -Compositeinterval mapping kb-kilobase orkilobasepairs
CMS •Cytoplasmicmalesterility LAI-Leafareaindex
CRP-Cyclic AMP receptorprotein LINEs· Longinterspersednuclearelements
DAF-DNA amplificationfingerprinting LRR-Leucine richrepeats
DGGE -Denaturinggradientgelelectrophoresis LTR•Longterminal repeats
DH-Doubledhaploid MAALs -Monosomicalienaddition lines
DNA -Deoxyribonucleicacid MAB-Molecularmarker assistedbreeding
dNTP-Deoxy-nucleotidetri-phosphate MARs -Matrixattachmentregions
DRE-Droughtresponsiveelement MAS -Molecularmarker assisted selection
dsRNA -Doublestranded RNA MBC-Mapbasedcloning
xii
McFISH -MulticolourFISH RWC -Relative watercontent
MITEs -Miniature inverted repeattransposable SAMPL-Selective amplificationofmicrosatellite
elements polymorphicloci
MME-Mixed modelequation SAGE -Serialanalysis ofgene expression
MRD-ModifiedRoger's distance SAR-Scaffold attachmentregion
mRNA -MessengerRNA SCARs -Sequence characterizedamplified regions
MS-MurashigeandSkoog medium SDR-Seconddivision restitution
MTAs-Material transfer agreements SDRF -Singledose restriction fragment
NHP-Non-histoneprotein SIM-Simpleinterval mapping
NILs-Nearisogenic lines SINEs -Shortinterspersednuclearelements
NMR-Nuclearmagneticresonance SITL-Simplyinherited traitloci
ORF-Open reading frame SITM.Simplyinherited traitmarkers
PAC-Plant arfiticial chromosome SMA-Singlemarker approach
PAGE-Polyacrylamidegelelectrophoresis SNPs-Singlenucleotidepolymorphisms
PAP-Protein amountpolymorphism SRAP-Sequence-relatedamplified polymorphism
PBRs-Plantbreedersrights SSAP -Sequence specific amplified polymorphism
PCR-Polymerasechain reaction SSCP-Singlestrand conformationalpolymorphism
PEDC-Pre-embryonicdeterminedcells SSLP-Simplesequencelength polymorphism
PEG-Polyethyleneglycol SSRs-Simplesequencerepeats
PFGE -Pulse-fieldgelelectrophoresis STMs -Sequencetagged microsatellites
PGFRA -Plantgenetic resources forfoodand STS-Sequencetaggedsites
agriculture T-DNA -DNAofTi plasmid transferred toplant
PGR-Plantgeneticresources TGMS .Temperaturesensitivegenetic malesterility
PIC-Prior informed consent TGMV -Tomato golden mosaic virus
PTGS-Post-transcriptionalgene silencing TGS -Transcriptionalgenesilencing
PVPA-Plant variety protectionact Ti•Tumorinducing plasmid ofAgrobacterium
QPM-Quality protein maize tumefaciens
RAP-RNA amountpolymorphism TIR -Terminal invertedrepeats
RAGE -Reversionanalysis ofgene expression TLC•Thin layer chromatography
RAMP -Random amplified microsatellite TLP-Thaumatin-likeprotein
polymorphism TMV -Tobacco mosaic virus
RAPD -Random amplifiedpolymorphicDNA TNV -Tobacconecrosis virus
RBIP-Retrotransposonbased insertional tRNA-TransferRNA
polymorphism TRIPs -Trade related (aspects 00intellectual
RCS-Ricecentromericsequence property
rDNA-Ribosomal DNA TIC-Tripple testcross
REMAP -Retrotransposonmicrosatelliteamplified UPOV-UnionIeprotection deobtentionvegetale
polymorphism (International UnionforProtectionofNew
REML •Restricted maximum likelihood VarietiesofPlants)
RFLP-Restrictionfragment length polymorphism UTR-Untranslated region
RGA -Resistancegeneanalogue VAM-Vesiculararbuscularmycorriza
RGP-Ricegenomeproject VNTR-Variable numberoftandom repeats
RILs-Recombinantinbred lines WGSA -Wholegenome shotgun approach
RNA- Ribonucleicacid WIPO-Worldintellectualproperty organization
RNAi-InterferingRNA WTO·World tradeorganization
RNase -Ribonuclease WUE-Wateruseefficiency
RUE-Radiationuseefficiency YAC-Yeastartificialchromosome
1
PlantBreeding·Mendelian toMolecularApproaches
H.K.JainandM.C.Kharkwal (eds.)
Copyright©2004NarosaPublishingHouse,NewDelhi,India
Hundred Years of Genetics: Revisiting some of the Landmarks
H.K. Jain!
Abstract
The human genome sequencereportpublished in the year 2000followed the
rediscovery of Mendel's laws of biological inheritance ahundred years earlier.
The intervening period has been marked by majordiscoveries which have
becomelandmarksinthe history ofgenetics.The present paper recounts some of
these landmarkdiscoveries.The treatmentisnotexhaustive;ratheranattempt
has been made to show how one importantfinding followed another in rapid
succession, asimportantquestions were asked ateach stage. This only indicates
the intense interestof a large numberofscientistsfrom differentdisciplines as
the young science started to unfold its potential as an integrating force in
biology.
Introduction
Aremarkablefeature of genetics isthat within arelatively short span of ahundred years,
one can see its beginning, and, one might say, itsend, with the completion of the Human
GenomeProject. The latter part of this statement, however, isnot true because many new
discoveries remain to be made particularly in the field ofgene expression and
development. There are whole new fields which remain to be fully explored such as
neurogenetics. At the same time, it would probably be true to say that some of the most
important questions which arose from Mendel's (1866) discovery have already been
answered and the focus is now shiftingto new applications in the field of medicine and
agriculture.
Mendel's Lasting Legacy
Mendel's own work in some ways accounts for this rapid advancement. Mendel's
discovery ofgenes which he called 'factors' showed them to be robust and discreet
entities that could be traced through generations ofsexual reproduction without
contamination and loss of structure or function.Thesefindings gave rise to the conceptof
particulatenature of genetic material very differentfrom the idea of blending inheritance
that had prevailed inearlier years. Today, itis possible to isolate individual genes and to
clone, sequence and patentthem, and put them inthe market place for sale. All this bears
testimony to the essence ofMendel'sfindings.
Mendel's discovery raised many questions and answers and these have become
milestones in the developmentof genetics in the last hundred years.Ipropose to recount
ICentre for Science Writing, 40 Surya Niketan, New Delhi 110 092, India