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Cover
Title Page
Contributors
1 Hari Deo Upadhyaya
1. ABBREVIATIONS
2. I. INTRODUCTION
3. II. BIOGRAPHICAL SKETCH
4. III. CONTRIBUTIONS
5. IV. UPADHYAYA, THE MAN
6. V. PUBLICATIONS
7. VI. PRODUCTS
8. REFERENCES CITED AND FURTHER READING
2 Crop Improvement Using Genome Editing
1. ABBREVIATIONS
2. I. INTRODUCTION
3. II. CONCEPTUAL FRAMEWORK FOR GENOME EDITING
4. III. PLANT TRANSFORMATION STRATEGIES
5. IV. HARNESSING BREAKS FOR TARGETED MUTAGENESIS
6. V. PRECISION GENE EDITING VIA HOMOLOGOUS RECOMBINATION
7. VI. GENOME EDITING AT THE GENOME LEVEL
8. VII. FUTURE PERSPECTIVES
9. ACKNOWLEDGEMENTS
10. LITERATURE CITED
3 Development and Commercialization of CMS Pigeonpea Hybrids
1. ABBREVIATIONS
2. I. INTRODUCTION
3. II. REPRODUCTIVE CYCLE AND MORPHOLOGY OF PIGEONPEA
4. III. CROP PRODUCTION
5. IV. EXTENT AND NATURE OF HETEROSIS IN PIGEONPEA
6. V. GENETIC MALE STERILITY‐BASED HYBRID TECHNOLOGY
7. VI. TEMPERATURE‐SENSITIVE MALE STERILITY
8. VII. CYTOPLASMIC‐NUCLEAR MALE STERILITY‐BASED HYBRID TECHNOLOGY
9. VIII. BREEDING NEW HYBRID PARENTS
10. IX. APPLICATION OF GENOMICS IN BREEDING HYBRIDS
11. X. COMMERCIALIZATION OF HYBRID PIGEONPEA TECHNOLOGY
12. XI. OUTLOOK
13. ACKNOWLEDGEMENTS
14. LITERATURE CITED
4 The Evolution of Potato Breeding
1. ABBREVIATIONS
2. I. INTRODUCTION
3. II. CLASSIFICATION OF CULTIVATED POTATO
4. III. ORIGIN OF THE CULTIVATED POTATO
5. IV. DYNAMICS OF POTATO LANDRACE EVOLUTION
6. V. ORIGIN OF THE EUROPEAN POTATO
7. VI. NINETEENTH CENTURY POTATO BREEDING
8. VII. EARLY TWENTIETH CENTURY POTATO BREEDING
9. VIII. CONVENTIONAL POTATO BREEDING
10. IX. LATE TWENTIETH CENTURY POTATO BREEDING
11. X. TWENTY‐FIRST CENTURY POTATO BREEDING
12. XI. CONCLUSIONS
13. LITERATURE CITED
5 Flavour Evaluation for Plant Breeders
1. ABBREVIATIONS
2. I. INTRODUCTION
3. II. TYPES OF RAPID SENSORY ANALYSIS METHODS
4. III. DATA ANALYSIS FOR RAPID SENSORY METHODS
5. IV. EXAMPLE OF USING SENSORY ANALYSIS FOR BREEDING
6. V. OUTLOOK
7. ACKNOWLEDGEMENTS
8. LITERATURE CITED
6 The Genetic Improvement of Black Walnut for Timber Production
1. ABBREVIATIONS
2. I. INTRODUCTION
3. II. BIOLOGY OF BLACK WALNUT
4. III. BREEDING
5. IV. EVALUATION OF HERITABLE TRAITS
6. V. HOST PLANT RESISTANCE TO PATHOGENS AND INSECT PESTS
7. VI. PROPAGATION
8. VII. PLOT MANAGEMENT
9. VIII. FUTURE DIRECTIONS
10. LITERATURE CITED
7 A Life in Horticulture and Plant Breeding
1. ABBREVIATIONS
2. I. INTRODUCTION
3. II. HONORS AND COMMENDATIONS
4. III. STUDENTS AND TEACHING
5. IV. EDITORIAL WORK
6. V. BOOKS AND PROCEEDINGS
7. VI. RESEARCH
8. VII. PUBLIC ADDRESSES, INVITED SEMINARS AND SPEECHES
9. VIII. SERVICE CONTRIBUTIONS
10. IX. EPILOGUE
11. LITERATURE CITED
Auhtor Index
Subject Index
Cumulative Subject Index
Cumulative Contributor Index
End User License Agreement

List of Tables

Chapter 01
1. Table 1.1. Core collections formed by Hari Deo Upadhyaya in chickpea, groundnut, pearl millet, pigeonpea, and small millets.
2. Table 1.2. Mini‐core collections formed by Hari Deo Upadhyaya in chickpea, groundnut, pearl millet, pigeonpea, sorghum, and small millet.
3. Table 1.3. Composite collections and reference sets formed by Hari Deo Upadhyaya in chickpea, groundnut, pearl millet, pigeonpea, sorghum, finger millet, and foxtail millet.
4. Table 1.4. Some of the awards and honours received by Hari Deo Upadhyaya from 2002 to 2017.
5. Table 1.5. List of 27 groundnut cultivars and their local names released in 18 countries in Africa and Asia.
Chapter 02
1. Table 2.1. Applications of genome editing.
2. Table 2.2. Sequence‐specific nucleases used for genome editing.
3. Table 2.3. Plant transformation systems used for genome editing.
Chapter 03
1. Table 3.1. Area, production, and grain yield of the main pigeonpea growing countries.
2. Table 3.2. Pigeonpea maturity groups based on days to flowering and maturity of genotypes planted by mid‐June at ICRISAT in Patancheru, India (17°N 30’, 78°16’E, 545 m.a.s.l.) Table based on Vales et al. (Vales et al., 2012) and Green et al. (Green et al., 1979). Expanded to show divisions based on days to 75% maturity.
3. Table 3.3. Distinctive characteristics of genetic male sterility (GMS) systems reported over time in pigeonpea.
4. Table 3.4. Summary of standard heterosis^z (%) reported in genetic male sterile‐based experimental hybrids produced at ICRISAT in the early phases.
5. Table 3.5. Standard heterosis of genetic male sterile pigeonpea hybrids belonging to early and medium maturity, released across India in the 1990s.
6. Table 3.6. Number of sterile/fertile plants recorded in temperature‐sensitive male sterile (TSMS) selections planted under an insect‐proof net at ICRISAT, Patancheru (17°N), India. The plants were male‐sterile at temperatures above 25°C (could be used to produce hybrids). The same plants became fully fertile at temperatures below 24°C (produced self‐pollinated seed of the maternal line).
7. Table 3.7. Cytoplasmic male sterility (CMS) systems reported in pigeonpea, based on various cytoplasm donors.
8. Table 3.8. Phenotypic variation observed for important traits among pigeonpea fertility restorers (R lines) and maintainers (B lines) used to produce cytoplasmic male sterile (CMS) hybrids.
9. Table 3.9. Performance of medium maturity pigeonpea hybrids involving A‐lines with obcordate leaf shape.
10. Table 3.10. Distribution of CMS A lines and restorer lines in different heterotic groups based on diversity using SSR markers.
11. Table 3.11. Yield and standard heterosis of CMS pigeonpea hybrids, representing three major maturity groups, recorded in multi‐location trials across India.
12. Table 3.12. Yield and standard heterosis of the cytoplasmic male sterile medium maturity pigeonpea hybrid ICPH 2671 in comparison with cultivar Maruti, planted across India in multi‐location trials from 2005–2008.
13. Table 3.13. Yield of medium maturity cytoplasmic male sterile pigeonpea hybrid ICPH 2671 and popular cultivar Maruti recorded from on‐farm trials spread over four states in India in 2008 and 2009.
14. Table 3.14. Yield and standard heterosis of medium maturity cytoplasmic male sterile pigeonpea hybrid ICPH 3762 and popular cultivar Asha obtained from on‐farm trials conducted in four districts of Odisha, India, in 2013.
15. Table 3.15. Yield and standard heterosis of medium maturity cytoplasmic male sterile pigeonpea hybrid ICPH 2740 and popular cultivar Asha obtained from on‐farm trials conducted in four states in India from 2009 to 2011.
16. Table 3.16. Main areas in India suited for cytoplasmic male sterile pigeonpea hybrid seed production (A × R) based on accomplished yields in farmers’ fields, 2008–09.
17. Table 3.17. Better parent heterosis for yield, male sterility systems, and out‐crossing rates recorded in several food legumes.
Chapter 04
1. Table 4.1. Typical schedule for a conventional potato breeding programme.
Chapter 05
1. Table 5.1. Production and culinary traits of interest to farmers for the 12 species included in the 2014 and 2015 variety trials.
2. Table 5.2. ANOVA of crew flavour evaluation on tomatoes in 2016 using intensity scaling.
Chapter 07
1. Table 7.1. Honours and Commendations of Professor Jules Janick.
2. Table 7.2. Postdoctoral associates, graduate students, and theses supervision.
3. Table 7.3. Journal volumes and reviews where Jules Janick has served as editor.
4. Table 7.4. Books and proceedings written and edited by Jules Janick.
5. Table 7.5. Patents, plant patents, and plant variety protection certificates of Jules Janick.

List of Illustrations

Chapter 01
1. Figure 1.1. Cajanus albicans, a wild species from a secondary genepool with many desirable characteristics, and a potential source for gene introgression in cultivated pigeonpea.
2. Figure 1.2. Cryptic genetic variation captured in groundnut by Hari Deo Upadhyaya that originated from a cross between TMV 2 (a leading groundnut variety in southern India) and amphidiploid (TxAG 6).
3. Figure 1.3. ICGV 91114, an improved groundnut variety that was developed by Hari Deo Upadhyaya and shows early maturity (90 days), drought tolerance and resistance to rust and late leaf spot, which is now popularly grown in India.
Chapter 02
1. Figure 2.1. Sequence‐specific nuclease (SSN) platforms and variations used for genome editing. Homing endonucleases (meganucleases) are natural endonucleases with multifunctional domains, capable of binding double‐strand DNA targets and making double‐stranded breaks (DSBs; paired scissors). Zinc finger nucleases (ZFNs) are synthetic nucleases composed of assembled zinc finger DNA binding domains (black hexagons) and the FokI nuclease domain (grey trapezoids). Transcription activator‐like effector nucleases (TALENs) are synthetic nucleases composed of assembled TAL effector DNA binding domains (black boxes) and the FokI nuclease. Clustered regularly interspaced short palindromic repeats/CRISPR‐associated system (CRISPR/Cas) is a RNA‐guided endonuclease system employing the Cas9 nuclease (grey circle), with RuvC and HNH nuclease domains and a single‐guide RNA to guide Cas9 to DNA targets. Modification of Cas9 where RuvC or HNH nuclease domain activity is eliminated results in creation of D10A and H840A CRISPR/Cas nickases, respectively capable of producing single‐strand breaks (SSBs; single scissors). Replacement of the TALEN FokI nuclease domain with the I‐Tev nuclease domain results a compact TALEN (cTALEN) nickase capable of creating SSBs. Target DNA recognition lengths are in base pairs (bp).
2. Figure 2.2. DNA damage and DNA repair pathways used for genome editing. DNA damage, in the form of double‐strand breaks (DSBs) and single‐strand breaks (SSBs or ‘nicks’), underlie most applications of genome editing. DNA damage can originate both from natural (ionizing radiation, chemical, cellular processes, and oxidative damage) and synthetic (sequence‐specific nucleases and ‘nickases’) sources, and typically results in random or directed DNA damage, respectively. DSBs are a severe form of DNA damage, which induce a strong DNA repair response, primarily of the non‐homologous end‐joining (NHEJ) pathway (thick arrow). SSBs, or ‘nicks’, are a less severe form of DNA damage, but can stimulate the homologous recombination (HR) pathway (thin arrow), or can be directed to an adjacent region to induce DSBs and NHEJ. NHEJ follows two sub‐pathways, called canonically NHEJ (cNHEJ) or alternative NHEJ (aNHEJ), for low‐fidelity repair and loss or gain of sequence at the break site and frame‐shift mutations (Targeted mutagenesis). A sub‐pathway of HR, called single‐strand annealing (SSA), can also result in loss of sequence and frame‐shift mutations in the form of targeted mutagenesis. An alternative HR sub‐pathway, called synthesis‐dependent strand annealing (SDSA), uses a DNA repair template (Repair template) to repair both SSBs and DSBs, and is capable of introducing new sequence at the break site with high fidelity (grey stars), resulting in so‐called gene targeting. Gene targeting is the most useful form of genome editing but is least preferred in most plant cells, compared with other sub‐pathways of DNA repair.
3. Figure 2.3. Possible modes of inheritance for SSNs and targeted modifications. In this example, a selfing crop species (line ‘Inbred A’) is stably transformed with a CRISPR/Cas9 transgene that targets a specific mutation, and the desired genotype is a homozygous mutated line with no transgene. The transgene and the target locus are unlinked, permitting independent segregation of the two loci. The subscript accompanying each letter represents the number of generations, since the introduction of the transgene (‘T’) or induction of a mutation (‘M’). Solid lines represent direct descent from the previous generation, while dashed lines represent multiple generations. Individuals with fixed states (no longer segregating) are shown in rectangles (undesired genotypes) or circles (desired genotypes). Individuals not within rectangles or circles are heterozygous for at least one locus, or still capable of generating new mutations (i.e. carrying the transgene in the heterozygous or homozygous state). The diagram does not show all possible outcomes, but instead represents several possible scenarios that illustrate the complexity of tracking the two segregating loci and recovering the desired plant.
Chapter 03
1. Figure 3.1. Short duration non‐determinate pigeonpea CMS hybrid ICPH 2433 at the flowering stage. ICRISAT, Telangana, India.
2. Figure 3.2. Medium duration non‐determinate pigeonpea CMS hybrid ICPH 2740 at podding stage. Jalgaon, Maharashtra, India.
Chapter 05
1. Figure 5.1. Results of the PCA on LS Mean values from crew flavour evaluation: a shows the factor loadings of the different flavour components on the first two principal components and b shows the placement of varieties. The first two principal components capture 85.81% of the total variation.
2. Figure 5.2. Correlation between perceived flavour intensity least squared means and overall flavour appreciation least squared means for the crew flavour evaluation. Error bars shown are standard error of the mean.
3. Figure 5.3. Consensus plot from MFA of chef 2015 evaluation of tomato varieties. Axes were labelled by chefs in advance of the tasting.
4. Figure 5.4. Consensus plot from MFA of chef 2016 evaluation of tomato varieties. Axes were labelled based on the results of the crew PCA flavour component factor loadings.
5. Figure 5.5. Correlation between perceived flavour intensity and overall flavour appreciation for the chef flavour evaluation. Each point corresponds to one chef’s rating of one sample.
Chapter 07
1. Figure 7.1. Professor Jules Janick.
2. Figure 7.2. Jules Janick in 1945 at Victory Farm Corps, obtaining agricultural training to enter Cornell University.
3. Figure 7.3. Jules Janick with ‘GoldRush’ apple.

This edition first published 2018
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Library of Congress Cataloging‐in‐Publication Data

Library of Congress Catalog Control Number: 83‐641963

PLANT BREEDING REVIEWS

Volume 41

Contributors