Plant Breeding Reviews

By Jules Janick

Plant Breeding Reviews presents state-of-the-art reviews on plant genetics and the breeding of all types of crops by both traditional means and molecular methods. Many of the crops widely grown today stem from a very narrow genetic base; understanding and preserving crop genetic resources is vital to the security of food systems worldwide. The emphasis of the series is on methodology, a fundamental understanding of crop genetics, and applications to major crops. It is a serial title that appears in the form of one or two volumes per year.

• Language: English
• Publisher: Wiley
• Release date: Aug 24, 2015
• ISBN: 9781119107729

Book preview

CONTENTS

Cover

Series Page

Title Page

Copyright

Contributors

Chapter 1: Charles W. Stuber: Maize Geneticist and Pioneer of Marker-Assisted Selection

I. Biographical Sketch

II. Scientific Achievements

III. Leadership Before and After Retirement

IV. Awards and Honors

V. Impact on Breeding Paradigms in the Private Sector

VI. Impact on Students and Postdocs

Literature Cited

Chapter 2: Plant Mutation Breeding: Current Progress and Future Assessment

Abbreviations

I. Introduction

II. Causes and Effects of Mutations

III. Types of Mutation

IV. Mutation Nomenclature

V. Mutation Induction

VI. Mutant Population Development and Handling of Mutagenic Populations

VII. Screening Mutagenic Populations for Desired Traits

VIII. Induced Mutation in Breeding Programs

IX. Enabling Biotechnologies

X. Intellectual Property Issues

XI. Limitations and Achievements

Acknowledgments

Literature Cited

Chapter 3: Recent Advances in Sorghum Biofortification Research

I. Sorghum Biofortification and its Importance

II. Grain Structure

III. Base Levels of Fe and Zn, Breeding Targets, and Phenotyping Techniques

IV. Enhancing Fe and Zn by Nutrient Management

V. Genetics and Breeding

VI. Product Development Pipeline

VII. The Way Forward

Literature Cited

Chapter 4: Breeding Tropical Vegetable Corns

Abbreviations

I. Tropical Versus Temperate Vegetable Corns

II. Genetics of Vegetable Corns

III. Breeding Populations and Hybrids

IV. Breeding Objectives

V. Production and Products

VI. Conclusions

Acknowledgments

Literature Cited

Chapter 5: Maize Breeding in the United States: Views from Within Monsanto

Abrreviations and Acronyms

I. Introduction

II. Breeding Objectives and the Genetic Gain Equation

III. People and Careers

IV. Safety, Rules, and Protocols

V. Intellectual Property

VI. Germplasm

VII. Diseases

VIII. Marker Technologies

IX. Traits

X. Doubled Haploids

XI. Automation

XII. Year-Round Nurseries

XIII. Yield Trials and Field Operations

XIV. Genotype by Environment by Management Interactions

XV. Information Technology and Predictive Modeling

XVI. Running a Modern Breeding Program

XVII. Final Considerations

Disclosure Statement

Acknowledgments

Literature Cited

Chapter 6: The History, Development, and Importance of the New Mexican Pod-Type Chile Pepper to the United States and World Food Industry

Abbreviations

I. Introduction

II. Origin of The New Mexican Pod Type

III. Uses of The New Mexican Pod Type

IV. Red Chile and Paprika

V. Capsaicinoids (Heat)

VI. Breeding for Machine Innovations

VII. Breeding For Diseases & Pests in New Mexico

VIII. Biotechnology

IX. Future Directions

Literature Cited

Chapter 7: Fruit Domestication in the Near East

I. Introduction

II. Botany, Ecology, and Reproductive Biology

III. Geographic Origin, Agro-Ecological Adaptation, And Evolution Under Domestication

IV. Adoption of Domestication

V. Evolutionary Patterns Under Domestication

VI. The Role of Conscious and Unconscious Selection and Subsequent Evolution Under Domestication

VII. Fruit Trees as Part of the Socioeconomic System

VIII. Concluding Remarks

Acknowledgments

Literature Cited

Chapter 8: The Geneva Apple Rootstock Breeding Program

I. History of Apple Rootstocks

II. Traits Relevant for the Selection of Improved Apple Rootstocks

III. General Approaches and Research Procedures for Breeding New Apple Rootstocks

IV. Future of Apple Rootstock Breeding

V. Conclusions

Literature Cited

Subject Index

Cumulative Subject Index

Cumulative Contributor Index

End User License Agreement

List of Tables

Table 2.1

Table 2.2

Table 2.3

Table 2.4

Table 2.5

Table 2.6

Table 3.1

Table 3.2

Table 3.3

Table 3.4

Table 3.5

Table 3.6

Table 3.7

Table 3.8

Table 4.1

Table 4.2

Table 4.3

Table 4.4

Table 5.1

Table 5.2

Table 6.1

List of Illustrations

Fig. 2.1

Fig. 2.2

Fig. 2.3

Fig. 2.4

Fig. 2.5

Fig. 2.6

Fig. 3.1

Fig. 3.2

Plate 4.1

Fig. 4.1

Fig. 4.2

Plate 5.1

Plate 5.2

Plate 5.3

Plate 5.4

Plate 5.5

Plate 5.6

Fig. 5.1

Fig. 5.2

Plate 5.7

Plate 5.8

Plate 6.1

Plate 6.2

Fig. 6.1

Fig. 6.2

Fig. 8.1

Fig. 8.2

Fig. 8.3

Fig. 8.4

Fig. 8.5

Fig. 8.6

Fig. 8.7

Plant Breeding Reviews is sponsored by:

American Society for Horticultural Science

International Society for Horticultural Science

Society of American Foresters

National Council of Commercial Plant Breeders

Editorial Board, Volume 39

I. L. Goldman

C. H. Michler

Rodomiro Ortiz

Plant Breeding Reviews

Volume 39

edited by

Jules Janick

Purdue University

Wiley Logo

Cover design: John Wiley & Sons, Inc.

Cover illustration: Courtesy of the Series Editor

Copyright © 2015 by Wiley-Blackwell. All rights reserved

Published by John Wiley & Sons, Inc., Hoboken, New Jersey

Published simultaneously in Canada

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Library of Congress Cataloging-in-Publication Data:

ISBN 978-1-110-10771-2 (cloth)

ISSN 0730-2207

Contributors

Shahal Abbo, The Levi Eshkol School of Agriculture, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel

Herb S. Aldwinckle, Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY, USA

Abdelbagi M. Ali, Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria

Kotla Anuradha, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India

Souleymane Bado, Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria

Fufa H. Birru, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Marv L. Boerboom, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Paul W. Bosland, Department of Plant and Environmental Sciences, Chile Pepper Institute, New Mexico State University, Las Cruces, NM, USA

James L. Brewbaker, Department of Tropical Plant and Soil Science, University of Hawaii, Honolulu, HI, USA

David V. Butruille, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Edward J. Cargill, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Duane A. Davis, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Prabhakar Dhungana, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Gerald M. Dill Jr., Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Fenggao Dong, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Gennaro Fazio, USDA-ARS Plant Genetics Resources Unit, Geneva, NY, USA

Agustin E. Fonseca, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Brian P. Forster, Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria

H. Frederick, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Bamako, Mali, Africa

Brian W. Gardunia, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Avi Gopher, The Sonia and Marco Nadler Institute of Archaeology, Tel Aviv University, Ramat Aviv, Israel

Geoffrey I. Graham, Dupont Pioneer, Johnston, IA, USA

Stefania Grando, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India

Gregory J. Holland, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

James B. Holland, USDA-ARS Plant Science Research Unit, Department of Crop Science, North Carolina State University, Raleigh, NC, USA

Nan Hong, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Are Ashok Kumar, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India

Pierre J.L. Lagoda, Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria

Margit Laimer, Plant Biotechnology Unit, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria

Simcha Lev-Yadun, Department of Biology & Environment, Faculty of Natural Sciences, University of Haifa at Oranim, Tivon, Israel

Paul Linnen, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Ian Martin, Queensland Department of Primary Industry, Kairi Research Station, Kairi, Queensland, Australia

J. Paul Murphy, Department of Crop Science, North Carolina State University, Raleigh, NC, USA

Thomas E. Nickson, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Stephan Nielen, Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria

Jerald K. Pataky, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Wolfgang H. Pfeiffer, HarvestPlus, International Center for Tropical Agriculture (CIAT), Cali, Colombia

Nalini Polavarapu, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Jon Popi, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Bhavanasi Ramaiah, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India

W. Rattunde, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Bamako, Mali, Africa

Terence L. Robinson, Department of Horticulture, Cornell University, Geneva, NY, USA

M. Lynn Senior, Syngenta Seeds, Inc., NC, USA

Steve B. Stark, Global Corn Breeding, Monsanto Company, St. Louis, MO, USA

Bradley J. Till, Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria

Parminder Virk, HarvestPlus, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India

Charles W. Stuber

1

Charles W. Stuber: Maize Geneticist and Pioneer of Marker-Assisted Selection

James B. Holland

USDA-ARS Plant Science Research Unit Department of Crop Science North Carolina State University Raleigh, NC, USA

Geoffrey I. Graham

Dupont Pioneer Johnston, IA, USA

J. Paul Murphy

Department of Crop Science North Carolina State University Raleigh, NC, USA

M. Lynn Senior

Syngenta Seeds, Inc. NC, USA

I. Biographical Sketch

II. Scientific Achievements

III. Leadership Before and After Retirement

IV. Awards and Honors

V. Impact on Breeding Paradigms in the Private Sector

VI. Impact on Students and Postdocs

Literature Cited

Charles W. Stuber is considered a pioneer of quantitative genetic mapping and marker-assisted selection in maize. The achievements of his four-decade career in research include the development of genetic marker systems used in maize and adapted in many other crops, the first methods and studies to identify quantitative trait loci (QTL), and creation of new breeding methods that integrated molecular markers into applied breeding. His work was instrumental in creating the foundation for modern plant breeding that relies heavily on combining genetic marker information with field evaluations of quantitative traits. He also trained several generations of students and postdoctoral researchers who have had influential careers in their own right. Finally, Charlie Stuber has provided leadership at many levels throughout his career and continues to lead the North Carolina State University Center for Plant Breeding and Applied Genomics as its director today, more than a decade after his retirement from research.

As colleagues and former students of Charlie, we dedicate this chapter to his amazing career in science, his foresight and persistence in bringing his ideas to fruition, and his leadership as a mentor to students. He influenced many outstanding students as a graduate advisor, and he continues to mentor and help students today as the director of the NCSU Center for Plant Breeding and Applied Genomics. We congratulate Charlie on his accomplishments and thank him for his positive influence on the students and colleagues he interacted with over the years.

Charlie was presented with a special issue of the journal Maydica (volume 45, 2000) dedicated to him that included a very comprehensive laudation paper covering his research career in detail (Eberhart et al. 2000). We hope readers will seek out that paper. Here, we recapitulate highlights of his research career, discuss his leadership following retirement, provide some perspectives from his former students and postdocs, and include some insights that we gleaned from Charlie himself during a seminar he presented to the NCSU plant breeding group in 2013 (http://cals6.online.ncsu.edu/online/Play/9be7a7893703416c8186f347fedeb9341d). Direct quotations in this chapter were taken from that seminar.

I. Biographical Sketch

Charles W. Stuber was born in 1931 and raised on a farm near Ravenna, Nebraska. He attended the University of Nebraska at Lincoln and received his B.S. with distinction in Technical Science in Agriculture in 1952. After graduation from college, Charlie served as an officer in the U.S. Navy until 1956. During his time in the Navy, Charlie married Marilyn Cook, and after finishing his Navy service, he and Marilyn farmed for 3 years near Shelton, Nebraska. During this time, he also served as a vocational agricultural instructor at Broken Bow High School.

In 1959, Charlie enrolled again at the University of Nebraska in Lincoln to study for an M.S. in plant breeding in the Department of Agronomy. His advisor was Dr. John Schmidt and he worked in wheat breeding, completing a thesis in 1961 on "Intraplant and interplant variation of grain protein content in a cross of Triticum aestivum L. He then enrolled at North Carolina State College (now University) to pursue a Ph.D. in genetics under the direction of Dr. Warren Hanson, a statistical geneticist. He obtained his Ph.D. in 1965 in genetics and experimental statistics with a thesis on Characterization and estimation of genetic parameters in the interpopulation formed by crossing two populations of maize."

Charlie began his career in research in 1962 with the U.S. Department of Agriculture—Agricultural Research Service. He was hired to conduct statistical genetics experiments in corn with the long-term goal of improving breeding methods for quantitative traits. Clearly, Charlie was something of a prodigy, as his potential for excellence in research was obvious to Dr. G.F. Sprague, who was the investigation leader for corn and sorghum research for USDA-ARS at that time and who hired Charlie as a half-time research geneticist to lead statistical genetics work in maize in Raleigh before he had even completed his Ph.D.

Charlie started his full-time employment with USDA-ARS in 1965 following completion of his Ph.D. and remained with USDA-ARS in Raleigh, NC for his entire career until his retirement in 1998. He served as Supervisory Research Geneticist and Research Leader, Plant Science Research Group, USDA-ARS, Raleigh, NC, 1975–1998, and Location Coordinator, Raleigh, NC, 1991–1995. He was also a faculty member in the Department of Genetics at NC State University in 1965 and was promoted to Professor in 1975, an appointment he held until his retirement in 1998. He is presently a professor emeritus at NC State University, and since 2006 he has been the Director of the Center for Plant Breeding and Applied Genomics at NC State.

Charlie celebrated 60 years of marriage to Marilyn in 2013. Marilyn also received a Ph.D. (in Occupational Education at NC State) and had a 30-year career as a Professor and Department Chair in Home Economics at Meredith College in Raleigh. They have one son, Charles Jr., who served as an FBI agent for almost 30 years, and who worked on numerous high-profile political corruption cases in North Carolina.

II. Scientific Achievements

For much of his career, Charlie was part of a strong maize quantitative and genetics breeding group at NC State, including Bob Moll in the Department of Genetics, and later, Major Goodman in the Department of Statistics. When choosing the direction for his initial research, Charlie's supervisor, Dr. Sprague, gave him free reign to choose his research objectives, with only one stipulation—that the work involve corn. I felt with the training I had, I had a couple of options, said Charlie later, one of which was to develop new theory or advance existing statistical genetic theory. But I soon realized, I did not really enjoy doing that…and I was not smart enough to compete with people like Clark Cockerham and Bruce Weir. Therefore, Charlie started his research career by testing theory with appropriate experiments. I was much happier doing empirical investigations, he said in 2013. In those years, much emphasis was placed on obtaining experimental estimates of additive and dominance genetic variation, particularly at North Carolina State where the mating designs I, II, and III were developed (Comstock and Robinson 1948; Comstock and Robinson 1952), so Charlie decided to pursue experiments to estimate epistatic genetic variances and gene action, a substantially more difficult goal (Stuber and Moll 1969, 1971; Stuber et al. 1973).

Charlie had some success with these approaches, but ultimately felt frustrated by the nature of field experiments and the inherent random experimental error variation that accompanies them. Thus, in the late 1960s, during a time when there was considerable interest in using molecular variation (mostly protein isozyme variation) to study genetic variance in natural populations and evolution (Shaw 1965; Marshall and Allard 1970; Brown 1971; Lewontin 1974), Charlie envisioned using biochemical or molecular traits that could be evaluated precisely under laboratory conditions but also might be correlated with field traits, as a way to study inheritance of field traits and also possibly enhance selection response. Charlie reports that Dr. Sprague was open to his pursuing this line of research but that Dr. Sprague also advised him, do not throw away your pollinating apron. Thus, Charlie began a two-pronged research effort to develop isozyme assays in the laboratory while also maintaining a field research program.

Collaborating with Dr. Major Goodman, then an Assistant Professor in the Department of Statistics at North Carolina State University, Charlie Stuber first developed the laboratory protocols to efficiently assay multiple isozyme systems in maize. Together, Stuber and Goodman then worked out the inheritance of these markers (Stuber et al. 1977; Goodman et al. 1980a,b; Goodman et al. 1981; Stuber and Goodman 1984; Wendel et al. 1989). Inheritance of isozyme patterns was in some cases quite complicated, due to more than one locus coding for the same enzyme and dimerization of some isozyme proteins. Malate dehydrogenase is a good (or perhaps bad) example of this, as it is encoded by three cytoplasmic and two nuclear loci, with more than two alleles at each locus (Goodman et al. 1980).

Having a model system for molecular genetics worked out for maize, Dr. Goodman used these markers primarily to study the diversity and classification/relationships in diverse maize germplasm. Charlie Stuber focused instead on identifying markers related to phenotypic variation (what we would call in today's fashion association analysis). However, as Charlie said We worked together on all of this, certainly. Particularly in the lab; Major and I checked every gel that was done in the lab, it was truly a collaborative operation.

The earliest studies by Dr. Stuber on the use of isozymes for plant breeding were to establish changes in isozyme allele frequencies associated with response to selection for higher yield in several long-term selection studies (Stuber and Moll 1972; Stuber et al. 1980). Stuber commented on these studies, All along during my research, I was not interested in just doing these analyses and publishing papers on QTL, and so forth. I wanted to see whether or not something useful could be made with this data, so the next thing I tried then was to see whether or not we could improve one of these corn populations just by selecting on isozyme loci. To do this, Dr. Stuber and colleagues went back to one of the base populations and recreated a population with allele frequencies similar to a population resulting from 10 cycles of family selection simply by selecting on isozymes. Field evaluations of this population demonstrated that they obtained a response almost equal to two cycles of direct phenotypic family selection simply by manipulating allele frequencies at seven isozyme loci (Stuber et al. 1982). This was probably the first empirical demonstration of marker-assisted breeding in plants and was followed by additional studies (Frei et al. 1986b).

Another research goal was the prediction of single-cross hybrid performance based on the genetic divergence of parental inbreds at molecular marker loci. Drs. Stuber and Goodman had surveyed isozyme variation in 406 public inbred lines (Stuber and Goodman 1983), and using those available data, were able to choose pairs of inbred lines that represented a range of genetic differentiation at the isozyme markers as well as pedigree differentiation. Field evaluation of these hybrids demonstrated a general, but far from perfect, association between allozyme diversity and yield. Importantly, they showed that the prediction of hybrid yield based on allozymes depended on the pedigree similarity of the parental lines (Frei et al. 1986a).

These initial marker-assisted selection studies provided results sufficiently encouraging to prompt further experiments, but Charlie also recognized their limitations. The number of marker loci was relatively small, with less than 20 loci segregating in any one study, meaning that large portions of the genome were not being tracked by markers. In addition, most of the studies involved random-mated populations with limited linkage disequilibrium, further reducing the relationship between isozyme markers and nearby genes that affected yield. Finally, hybrid prediction based on markers could be improved by having an idea of the relative effects of each genome region on heterosis and yield, but such information was lacking. This prompted the next phase of Charlie's research—the search for genetic factors, later to be described as quantitative trait loci, affecting yield by linkage analysis with molecular markers.

Using the isozyme data surveyed on 406 inbred lines, Dr. Stuber chose several pairs of lines with allelic differences at large numbers of isozyme loci and also high levels of agronomic trait differentiation. These pairs were crossed to generate F2 generations with high levels of linkage disequilibrium to improve the chances of having strong linkage disequilibrium between isozyme loci and the genetic factors controlling agronomic traits. In terms of population sampling, these initial genetic factor (QTL) mapping studies were exemplary, as Charlie's research team evaluated a total of 3,706 individual F2 plants from two crosses both genetically and phenotypically. Each plant was first germinated from seed in the laboratory and coleoptile tissue was sampled for isozyme analysis, then each seedling was transplanted to the experimental field for phenotypic evaluation of 82 traits (Edwards et al. 1987; Stuber et al. 1987). The large sample sizes used were based on theoretical work by Soller et al. (1976) demonstrating that large sample sizes (∼1,000–2,000) were necessary to have good power to detect genes controlling a small proportion of trait genetic variation. The populations were segregating for 15–18 isozyme marker loci each, providing reasonable tagging of about 40–45% of the maize genome.

As Charlie later said, When people heard that we were going to be doing this kind of analysis on single F2 plants, they said ‘that will never work’! We had skeptics all over the place. However, Charlie suggested that the transplanting procedure itself helped to reduce random environmental variation, because the plants were germinated under uniform conditions and transplanted at equivalent developmental stages with well-developed roots. We had a beautiful uniform study, much better than seed-planted, Charlie said. We were also lucky that year, we had a very good [growing] season. Indeed, the papers resulting from this study remain classics of the QTL mapping literature (Edwards et al. 1987; Stuber et al. 1987). Although genome coverage was not complete, it was sufficiently dense for the first time, inferences could be made to the number and effect sizes of genetic factors controlling quantitative traits in plants. For most traits, QTL were distributed throughout the genome, with varying effect sizes; a few QTL with larger effects (up to 17% of trait variation) were observed. Furthermore, Charlie and his postdoc, Dr. Marlin Edwards, used the estimated QTL effects to conduct marker-assisted selection for one cycle, observing a 20% increase in yield using only 15 markers in one of the populations (Stuber and Edwards 1986).

Prompted by the success of the initial QTL mapping study in F2 populations, Charlie then turned his attention to attempting to identify and characterize genetic factors influencing heterosis. He focused on the commercially important hybrid made from the cross of inbreds B73 and Mo17. Charlie employed a clever mating design that involved generating 264 F3 lines from the F2 generation of the cross and backcrossing each line to both parents. The lines were genotyped with 76 molecular markers, now including restriction fragment length polymorphisms (RFLPs) in addition to the isozyme markers, enabling complete, if not dense, coverage of the genome. The crosses were evaluated in multiple environments. Results of the study again showed that QTL were distributed throughout the genome. Estimation of additive and dominant gene action for each QTL indicated that dominance effects were important and a number of loci had dominance effects estimated to be greater than the additive effects, which Charlie interpreted as resulting from pseudo-overdominance due to repulsion-phase linkages between dominant favorable alleles (Stuber et al. 1992).

One QTL, on chromosome 5, was associated with 21% of the grain yield variation, a huge effect. Therefore, Charlie's next experiment was to fine-map the QTL to more precisely localize the gene(s) conferring the effect. Charlie and his student Geoff Graham showed that upon higher resolution analysis, the one very large effect QTL could be fractionated by recombination into at least two smaller effect QTL (Graham et al. 1997). In accordance with the original prediction, they found that the two QTL have dominant gene action, with the favorable dominant alleles at the two QTL contributed by different parents. This repulsion-phase linkage generated the apparent overdominance of the QTL in the original study. Another follow-up study was to try to identify QTL responsible for genotype-by-environment interactions associated with abiotic stresses. In this study, recombinant inbred lines from the B73 × Mo17 cross were backcrossed to each parent, and the crosses were evaluated in a factorial combination of low and high nitrogen, low and high soil moisture, and low and high population density in four environments. Surprisingly, despite a 10-fold difference in yield between stress treatments, little genotype-by-environment or QTL-by-environment interaction was detected (LeDeaux et al. 2006), perhaps in part because heterosis is very important in this widely adapted cross, overshadowing the environmental interaction effects.

Having identified QTL contributing to heterosis in B73 × Mo17, Charlie then turned his attention to improving the yield of this F1 hybrid: Again, I was interested in how we might use these QTL as a plant breeding tool. Thus, he began a large experiment to enhance the B73 × Mo17 hybrid by introgressing QTL alleles from donor lines Tx303 and Oh43 into the recurrent parents B73 and Mo17, respectively. The basic idea was to generate a series of near-isogenic lines (NILs) that contained most of the recurrent parent line genome but contained a few introgressed regions from the donor parents. By crossing the NILs to the opposite parental line, they could be screened to identify those introgressions that improved the yield of the cross. The experiment required screening many hundreds of segregating progenies in each of several backcross and selfing generations with isozyme and RFLP markers, a daunting undertaking given the state of genotyping technology available. This was followed by extensive field evaluation of crosses among the resulting enhanced lines; the results of which showed that substantial increases in yield could be achieved by identifying optimal combinations of enhanced NILs (Stuber 1994a,b; Stuber 1998).

Charlie then proposed a modification to the idea of enhancing elite lines by first mapping QTL into F2- or BC1-derived generations, then introgressing genomic segments found to carry favorable QTL alleles into an elite genetic background. The newer approach would be to develop a set of NILs, each carrying a small number of introgressions, but collectively representing introgressions of most of the donor parent genome. Then, the whole set of unselected NILs would be tested for hybrid yield, leading to simultaneous testing of the effects of different introgressions and identification of NILs carrying favorable genome introgressions. The advantage of this method is that the NILs with favorable QTL introgressions and better yields than the recurrent were immediately available as fixed homozygous hybrid parents or as breeding parents; no additional marker-assisted breeding steps would be required to transfer the favorable alleles into the elite parent genetic background. This method combined the genetics and breeding work into an upfront investment into germplasm development with the idea that the payoff would be the ability to more rapidly deploy improved (or ‘enhanced’) inbred lines for cultivar development (Stuber et al. 1999; Szalma et al. 2007). Charlie and his student, Scott Furbeck, demonstrated that this method could be effectively applied to the problem of introgression exotic maize germplasm into elite lines (Furbeck 1993). Importantly, they found that one important favorable introgression block from the exotic donor was adjacent to an exotic donor block that decreased yield. The combined effect of these two segments from the exotic donor was about nil (so to speak), but by identifying NILs resulting from recombination that unlinked the favorable and unfavorable yield alleles, they demonstrated the power of combining introgression breeding work with marker analysis.

In addition to Charlie's landmark work in QTL mapping and marker-assisted breeding, he supported the development of new and more efficient molecular marker systems for maize. Recognizing that isozymes were limited in number and that RFLPs were more abundant, but required significant time and labor to obtain reliable genotype information, Lynn Senior, a technician and graduate student in Charlie's laboratory, created the first set of publicly available simple sequence repeat (SSR) markers for maize (Senior et al. 1996). SSRs were abundant in the genome and much cheaper and faster to assay than RFLPs, because they relied on polymerase chain reaction technologies instead of Southern blotting. SSRs were quickly put to use in Charlie's laboratory to improve fingerprinting techniques for maize (Senior et al. 1998) and creating linkage maps (Mickelson et al. 2002). At the time of Charlie's retirement in 1998, SSRs were the state-of-the-art genotyping system for maize, widely used in both public and private laboratories.

III. Leadership Before and After Retirement

During his research career, Charlie served as graduate advisor to 12 M.S. and Ph.D. graduate students in genetics at NC State and served on the advisory committees of more than 45 other graduate students. He also supervised 10 postdoctoral researchers. In addition, Charlie was the Research Leader of the USDA-ARS Plant Science Research Unit at Raleigh from 1975 to 1998. After his retirement, Charlie remained active in agricultural research. First, he chaired a committee sponsored by the American Seed Trade Association to develop guidelines for determining essentially derived varieties using rapidly increasing DNA marker technologies (Stuber 2002). Several years later, he was asked by the Chancellor of NC State University to return to NC State and serve as the first director of the Center for Plant Breeding and Applied Genomics beginning in 2006. He continues to serve as the Center director today.

Charlie approached this part-time directorship with the enthusiasm and zeal of a faculty member one-half his age. No request, no enquiry, and no opportunity to mentor or support were too trivial to receive his full attention. His dedication to make the Center a success served as an inspiration to faculty and graduate students alike. During his time as director of the Center for Plant Breeding and Applied Genomics, Charlie had been very successful at securing graduate student funding from the seed industry to support students obtaining advanced degrees in plant breeding. We estimate that Charlie was primarily responsible for obtaining funding to support 25 graduate students during this time. Students frequently commented on how they always knew Charlie was looking out for their best interests and held him in the highest regard and affection. After observing Charlie working with students as Center director, one faculty member suggested that if Charlie's career in academia had taken a different tack, he could have become one of those iconic undergraduate coordinators often found in Land Grant Institutions who guide generations of students with encouragement and understanding. One additional task Charlie attended to was managing the Charles Stuber Graduate Student Travel Fund supported by an endowment that he setup upon his retirement from USDA-ARS.

IV. Awards and Honors

Charlie has received numerous awards for his pioneering work in maize genetics and breeding. He was inducted into the USDA-ARS Science Hall of Fame in 1990. Among the criteria for election to the Science Hall of Fame are that the honoree has produced a major impact on agricultural research—by solving a significant agricultural problem through research or providing outstanding leadership that significantly advanced agricultural research, and has made accomplishments that continue to be recognized by the agricultural research community (http://www.ars.usda.gov/careers/hof/). His laudation reads as follows: Charles W. Stuber was inducted into the Hall of Fame for pioneering the use of molecular markers in identifying, mapping, and manipulating quantitative trait genes. His research stimulated interest in DNA-based marker technology for improving crop traits, led industry giants to revolutionize many of their crop breeding procedures, and influenced animal breeding technology, (http://www.ars.usda.gov/careers/hof/).

Charlie has received many other awards during his distinguished career, we will not list them all, but they include the Crop Science Research Award, the Presidential Award, and the DEKALB Genetics Crop Science Distinguished Career Award, all from the Crop Science Society of America. He was also presented with the Public Sector Award from the Nation Council of Commercial Plant Breeders, and the Lifetime Achievement Award from National Association of Plant Breeders. Charlie was named the USDA-ARS Outstanding Scientist of the Year Award in 1989 and an Outstanding Alumnus of NC State University. He was also presented an Award of Merit from the University of Nebraska, College of Agricultural Science and Natural Resources Alumni Association. The Quantitative Genetics Team in Raleigh, NC, including Charlie, received the USDA Superior Service Award.

V. Impact on Breeding Paradigms in the Private Sector

The work by Charlie and Major Goodman on isozymes had a tremendous impact on seed industry beyond its utility in academic studies. Isozymes were the first molecular system used to ensure purity and quality control in the hybrid seed industry. The technical bulletin developed by Stuber and Goodman and their postdocs (Stuber et al. 1988) was widely used as the manual for isozyme techniques, even in other crop species. Isozymes were also used as evidence in a landmark legal case between two commercial seed companies of wrongful appropriation of a proprietary maize inbred line. The isozyme evidence introduced by the plaintiffs in this case appears to have been critical in establishing the infringement upon their proprietary property: The Court concludes that isozymes electrophoresis alone can and did provide competent evidence relating to derivation (United States District Court 1987). Dr. Stuber himself was an expert witness in this case, and the decision goes on to say, As Dr. Stuber testified, isozyme electrophoresis can accurately predict parents and progeny (United States District Court 1987). This case alone resulted in a finding for tens of millions of dollars to the plaintiffs.

The concept of creating NIL libraries to identify and rapidly deploy favorable QTL from donor lines into elite lines has also been exploited in private industry. Lynn Senior brought this concept with her to Syngenta. Along with another former North Carolina State graduate, Randy Holley, Lynn worked to develop the Maize Allelic Diversity Platform. This platform contains over 60,000 NILs developed by crossing both public and proprietary inbreds with a wide range of diverse donor lines. In 2008, Syngenta donated approximately 7,500 of these genetic stocks for public research. This platform can enable researchers to make concrete use of knowledge of the corn genome to improve delivery of complex corn traits.

More generally, Charlie's conviction that practical plant breeding could be improved by joining molecular biology, field breeding, and statistical techniques has probably been his greatest scientific legacy. As he said, when he started this line of work in the 1960s, the idea that molecular markers could ever be useful for applied breeding was ridiculed by some. By persistence, careful experimentation, hard work, and championing the ideas over decades, Charlie's idea has come to full fruition in modern commercial plant breeding, where marker-assisted selection is undertaken at a massive, global, and industrial scale, and taken for granted. In private industry today, the application of genetic information systems to cultivar and hybrid development is as much a part of the breeding process as planters and combines. In the late 1980s and continuing into the 1990s, the mechanization of plant breeding was probably responsible for the single biggest increase in the number of genetic entities a breeder could test. With new genetic information systems pioneered in the last two decades, a commercial breeder can now screen 5–10 times more genetic samples than previously possible, significantly increasing the size of breeding programs.

VI. Impact on Students and Postdocs

Perhaps Charlie's biggest impact has been his influence on the graduate students and postdocs he mentored and advised. This went well beyond scientific training, showing students the value of excellence at each step of the research process, the value of hard work, and the importance of bringing different disciplines together to solve a common problem. While he was always present if needed, Charlie's style encouraged independent thinking among his students, positioning them well for future careers in academia and industry. He also made each student feel welcome and part of the NCSU scientific community, opening doors to opportunities that students probably would not have had otherwise. At the end of each student's career at NCSU, Charlie would write a custom poem outlining all the trials, tribulations, and fun of their time spent in Raleigh, NC.

Charlie's impact on the development of young scientists was captured in comments from some of his former students and postdocs. Charlie influenced me to think more deeply about marker–phenotype correlations, as we worked together on what I think was the first maize QTL paper, said Jonathan Wendel, Professor and Chair, Department of Ecology, Evolution, and Organismal Biology, Iowa State University. Geoff Graham, Vice President of Research, Maize Product Development, DuPont Pioneer also added, I think the biggest impact Charlie had on me was he showed me the value of quality data. The fact that he was out in the field collecting it with me only reinforced this notion. I really appreciated the way that Charlie allowed his students the freedom to develop their own way forward, providing his support as needed. This form of mentoring has been instrumental in my success in industry and I cannot express enough gratitude, sums up Lynn Senior, Corn Breeding Technology Business Change Manager, Syngenta.

Paul Williams, Research Leader and Supervisory Research Geneticist with the USDA-ARS Corn Host Plant Resistance Research Unit in Starkville, MS commented that: One thing I learned from Charlie was the importance of productive collaborations with colleagues. Although I was Charlie's first graduate student, and he was just beginning what became a remarkable professional career at the time, he had already established effective, long-term collaborations with several colleagues at North Carolina State University including Bob Moll, Sam Levings, and Major Goodman. He also led a regional genetic vulnerability of maize project that included USDA-ARS scientists at several locations in the Southeast. Charlie also possessed a quest for knowledge. At the time I was his student, Charlie was studying biochemistry in addition to conducting research and handling the other responsibilities of his position. The knowledge he gained from those studies, together with his extensive knowledge of quantitative genetics, undoubtedly made his pioneering work on mapping of quantitative trait loci possible.

According to Marlin Edwards, Chief Technology Officer for Monsanto Vegetable Seeds and a former postdoc with Charlie, It was a great experience working in Charlie's lab. His was one of the most cooperative of the programs in NCSU genetics, allowing exposure to Goodman, Moll and the interesting staff in those programs. Charlie's program was both well focused, with clear and continuous commitment to some key issues, and it was diversified, ranging from characterization of maize diversity to practical insights into the nature of quantitative genetic variation. Charlie was great about providing support and oversight but also providing the freedom to put all your heart and passion into work that you felt you owned. Working with Charlie was a great time in my life and one that I reflect upon many years later with fondness. His strong Midwestern work ethic and commitment to making meaningful contributions in his area of Science were reflected in the many ways he has and continues to dedicate himself to causes beyond his own program, ranging from journal editorship to student mentoring.

Charlie was well liked and respected not only for his scientific leadership but also for the fairness and generosity with which he treated students and staff. According to Wayne Dillard, who worked as Charlie's field technician from 1968 to 1996, Charlie was very good to everyone who worked for him. As an example, Charlie requested an USDA grade promotion for Wayne that was denied. Charlie could have very easily said, ‘I'm sorry, I tried’ and left it at that, but Charlie would not take no for an answer. He dropped everything he was doing and re-wrote the promotion and resubmitted it until it was approved. He was top notch to work for, remembered Wayne.

In his role as the Director of the Center for Plant Breeding and Applied Genomics at NC State, Charlie has been a champion, fund raiser, and mentor to numerous grad students. His scientific credibility and personal connections with public and private partners have made a significant impact in a short amount of time. This has resulted in new funding sources for the department and integration of new disciplines into traditional plant breeding education pathways. Often in plant breeding, we talk about the realized breeding value of a parental line when we observe a significant number of outstanding offspring in the subsequent generation. While Charlie's scientific contributions are spectacular in their own right, his realized breeding value as an advisor, mentor, and friend will surpass even his scientific leadership.

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Frei, O.M., C.W. Stuber, and M.M. Goodman. 1986b. Yield manipulation from selection on allozyme genotypes in a composite of elite corn lines. Crop Sci. 26:917–921.

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Senior, M.L., E.C.L. Chin, M. Lee, J.S.C. Smith, and C.W. Stuber. 1996. Simple sequence repeat markers developed from maize sequences found in the GENBANK database: map construction. Crop Sci. 36:1676–1683.

Senior, M.L., J.P. Murphy, M.M. Goodman, and C.W. Stuber. 1998. Utility of SSRs for determining genetic similarities and relationships in maize using an agarose gel system. Crop Sci. 38:1088–1098.

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Stuber, C.W. 1998. Case history in crop improvement: yield heterosis in maize. p. 197–206. In: A. H. Paterson (ed.), Molecular dissection of complex traits. CRC Press, Boca Raton, FL.

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Stuber, C.W., and M.M. Goodman. 1984. Inheritance, intracellular localization, and genetic variation of 6-phosphogluconate dehydrogenase isozymes in maize. Maydica 29:453–471.

Stuber, C.W., M.M. Goodman, and F.M. Johnson. 1977. Genetic control of racial variation of b-glucosidase isozymes in maize. Biochem. Genet. 15:383–394.

Stuber, C.W., M.M. Goodman, and R.H. Moll. 1982. Improvement of yield and ear number resulting from selection at allozyme loci in a maize population. Crop Sci. 22:737–740.

Stuber, C.W., S.E. Lincoln, D.W. Wolff, T. Helentjaris, and E.S. Lander. 1992. Identification of genetic factors contributing to heterosis in a hybrid from two elite maize inbred lines using molecular markers. Genetics 132:823–839.

Stuber, C.W., and R.H. Moll. 1969. Epistasis in maize (Zea mays L.). I. F1 hybrids and their S1 progeny. Crop Sci. 9:124–127.

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Stuber, C.W., and R.H. Moll. 1972. Frequency changes of isozyme alleles in a selection experiment for grain yield in maize (Zea mays L.). Crop Sci. 12:337–340.

Stuber, C.W., R.H. Moll, M.M. Goodman, H.E. Schaffer, and B.S. Weir. 1980. Allozyme frequency changes associated with selection for increased grain yield in maize (Zea mays L.). Genetics 95:225–236.

Stuber, C.W., M. Polacco, and M.L. Senior. 1999. Synergy of empirical breeding, marker-assisted selection, genomics, and genetic engineering to increase crop yield potential. Crop Sci. 39:1571–1583.

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Papers of Charles W. Stuber

Abler, B.S., M.D. Edwards, and C.W. Stuber. 1991. Isoenzymatic identification of quantitative trait loci in crosses of elite maize inbreds. Crop Sci. 31:267–274.

Bretting, P.K., M.M. Goodman, and C.W. Stuber. 1987. Karyological and isozyme variation in West Indian and allied American mainland races of maize. Am. J. Bot. 74:1601–1613.

Bretting, P.K., M.M. Goodman, and C.W. Stuber. 1990. Isozymatic variation in Guatemalan races of maize. Am. J. Bot. 77:211–225.

Brim, C.A., and C.W. Stuber. 1973. Application of genetic male sterility to recurrent selection schemes in soybean. Crop Sci. 13:528–530.

Burr, B., F.A. Burr, K.H. Thompson, M.C. Albertson. and C.W. Stuber. 1988. Gene mapping with recombinant inbreds of maize. Genetics 118:519–526.

Burton, J.W., C.W. Stuber, and R.H. Moll. 1978. Variability of response to low levels of inbreeding in a population of maize. Crop Sci. 18:65–68.

Cardy, B.J., C.W. Stuber, and M.M. Goodman. 1980. Techniques for starch gel electrophoresis of enzymes from maize (Zea mays L.). Dep. of Statistics Mimeo Series 1317 North Carolina State Univ., Raleigh.

Carson, M., C. Stuber, and M. Senior. 2004. Identification and mapping of quantitative trait loci conditioning resistance to southern leaf blight of maize caused by Cochliobolus heterostrophus race O. Phytopathology 94:862–867.

Carson, M., C. Stuber, and M. Senior. 2005. Quantitative trait loci conditioning resistance to phaeosphaeria leaf spot of maize caused by Phaeosphaeria maydis. Plant Dis. 89:571–574.

Doebley, J.F., M.M. Goodman, and C.W. Stuber. 1983. Isozyme variation in maize from the southwestern United States: taxonomic and anthropological implications. Maydica 28:97–120.

Doebley, J.F., M.M. Goodman, and C.W. Stuber. 1984. Isoenzymatic variation in Zea (gramineae). Syst. Bot. 9:204–218.

Doebley, J.F., M.M. Goodman, and C.W. Stuber. 1985. Isozyme variation in the races of maize from Mexico. Am. J. Bot. 72:629–639.

Doebley, J.F., M.M. Goodman, and C.W. Stuber. 1986. Exceptional genetic divergence of Northern Flint corn. Am. J. Bot. 73:64–69.

Doebley, J., M.M. Goodman, and C.W. Stuber. 1987. Patterns of isozyme variation between maize and Mexican annual teosinte. Econ. Bot. 41:234–246.

Doebley, J., J.D. Wendel, J.S.C. Smith, C.W. Stuber, and M.M. Goodman. 1988. The origin of Cornbelt maize: the isozyme evidence. Econ. Bot. 42:120–131.

Edwards, M.D., T. Helentjaris, S. Wright, and C.W. Stuber. 1992. Molecular-marker-facilitated investigations of quantitative trait loci in maize. 4. Analysis based on genome saturation with isozyme and restriction fragment length polymorphism markers. Theor. Appl. Gen/83:765–774.

Edwards, M.D., C.W. Stuber, and J.F. Wendel. 1987. Molecular-marker-facilitated investigations of quantitative-trait loci in maize. I. Numbers, genomic distribution, and types of gene action. Genetics 116:113–125.

Frei, O.M., C.W. Stuber, and M.M. Goodman. 1986. Yield manipulation from selection on allozyme genotypes in a composite of elite corn lines. Crop Sci. 26:917–921.

Frei, O.M., C.W. Stuber, and M.M. Goodman. 1986. Use of allozymes as genetic markers for predicting performance in maize single cross hybrids. Crop Sci. 26:37–42.

Geric, I., M. Zlokolica, C. Geric, and C.W. Stuber. 1989. Races and populations of maize in Yugoslavia International Board for Plant Genetic Resources, Rome, Italy.

Goodman, M.M., K.J. Newton and C.W. Stuber. 1981. Malate dehydrogenase: viability of cytosolic nulls and lethality of mitochondrial nulls in maize. Proc. Nat. Acad. Sci. USA