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Editors
Kendall R. Lamkey, Michael Lee
Plant Breeding:
The Arnel R. Hallauer
International Symposium
Plant Breeding:
The Arnel R. Hallauer
International Symposium
Editors
Kendall R. Lamkey, Michael Lee
Kendall R. Lamkey, Ph.D., is the Pioneer Distinguished Chair Authorization to photocopy items for internal or personal use,
in Maize Breeding and Director of the Raymond F. Baker or the internal or personal use of specific clients, is granted by
Center for Plant Breeding, Agronomy Department, Iowa State Blackwell Publishing, provided that the base fee of $.10 per
University. His research is focused on the origin, maintenance, copy is paid directly to the Copyright Clearance Center, 222
and utilization of genetic variation for important agronomic Rosewood Drive, Danvers, MA 01923. For those organizations
and grain quality traits in maize. that have been granted a photocopy license by CCC, a separate
system of payments has been arranged. The fee codes for users
Michael Lee, Ph.D., is Professor and Chair of the Plant of the Transactional Reporting Service are ISBN-13: 978-0-
Breeding and Genetics Panel, Agronomy Department, Iowa 8138-2824-4; ISBN-10: 0-8138-2824-4/2006 $.10.
State University. Lee’s research focuses on developing and uti-
lizing genetic techniques and principles to complement the First edition, 2006
programs in maize breeding and genetics with the most recent
advances in applied plant molecular genetics. Library of Congress Cataloging-in-Publication Data
Chapter 5 Improving the Connection Between Effective Crop Conservation and Breeding 90
S. Kresovich, A.M. Casa, A.J. Garris, S.E. Mitchell, and M.T. Hamblin
Chapter 10 Integrating Breeding Tools to Generate Information for Efficient Breeding: Past, Present, and Future 141
M. Cooper, O.S. Smith, R.E. Merrill, L. Arthur, D.W. Podlich, and C.M. Löffler
Chapter 13 Perspectives on Finding and Using Quantitative Disease Resistance Genes in Barley 182
P.M. Hayes, L. Marquez-Cedillo, C.C. Mundt, K. Richardson, and M.I.Vales
Chapter 14 Breeding for Resistance to Abiotic Stresses in Rice:The Value of Quantitative Trait Loci 201
David J. Mackill
v
vi Contents
Chapter 16 The Historical and Biological Basis of the Concept of Heterotic Patterns in Corn Belt Dent Maize 219
W.F.Tracy and M.A. Chandler
Chapter 21 Improving Tolerance to Abiotic Stresses in Staple Crops: A Random or Planned Process? 293
Gregory Edmeades, Marianne Bänziger, Hugo Campos, and Jeffrey Schussler
Chapter 25 Derivation of Open-Pollinated Inbred Lines and Their Relation to Z-Lines for Cyclic Hybridization 345
Fidel Márquez-Sánchez
The Arnel R. Hallauer International Symposium on of plant breeders to evaluate more germplasm in
Plant Breeding was held in Mexico City on 17–22 more ways in more environments and to identify
August 2003. The chapters in this book resulted genotypes that exhibit optimal adaptation to the
from the papers presented at that symposium. The needs of society, the demands of nature, and the
chapters are organized in the book in the same desires of the market. Nascent developments in
order that they were presented at the symposium. basic biological and informational sciences, as ex-
Many people were responsible for organizing this emplified by the gradual annotation of entire
symposium and to list them all would mean that genomes and their gene products, have provided
some would be left out. We would all agree, how- additional tools and options for various aspects of
ever, that this symposium would not have hap- plant breeding.
pened without the vision, dedication, and hard Yet, the essential activity of plant breeding re-
work of Dr. Shivaji Pandey. Dr. Julien de Meyer mains constant: the development of germplasm
was responsible for organizing all aspects of the with a superior aggregate phenotype for a given
conference. The success of the conference was due target environment. As the mediation of many im-
to Dr. de Meyer’s organizational skills and atten- portant phenotypes will likely remain unknown to
tion to detail, and for that we owe him a debt of contemporary science, direct selection on a con-
gratitude. tinuous basis using well-established methods by
The world of plant breeding has experienced well-supported and integrated plant-breeding
dramatic changes during the span of Arnel Hal- programs may be the best choice of approaches to
lauer’s career. At the institutional level, interna- crop improvement.
tional centers of crop improvement have emerged The contents of this book reflect the status of
and declined, legal and ethical issues have become major challenges, approaches, and accomplish-
routine considerations, the private sector has de- ments of plant-breeding programs from around
veloped and consolidated, and the public sector the world as told by several hundred scientists of
(national programs, federal governments, univer- plant breeding who gathered to honor a great
sities) has diversified and placed greater emphasis teacher, practitioner, and researcher of that disci-
on basic research as opposed to varietal develop- pline, Arnel R. Hallauer.
ment. Changes in infrastructure (e.g., off-season
nurseries, service laboratories) and technology Kendall R. Lamkey
(e.g., computers, machinery, analytical methods, Michael Lee
transgenic methods) enable the declining number
vii
Plant Breeding:
The Arnel R. Hallauer
International Symposium
1
Plant Breeding: Past, Present, and Future
Theodore M. Crosbie,Vice President, Global Plant Breeding, Monsanto
Sam R. Eathington, Director of Breeding Applications, Monsanto
G. Richard Johnson, Sr., Science Fellow, Monsanto
Marlin Edwards, Global Lead, Breeding Technology, Monsanto
Robert Reiter, Director of High Throughput Genotyping, Monsanto
S. Stark, Lead, Seed Breeding and Biotech Statistical Services, Monsanto
Radha G. Mohanty, Senior Statistician, Seed Breeding and Biotech Statistical Services, Monsanto
Manuel Oyervides, R&D Director, Latin American Corn/Global Sorghum, Monsanto
Robert E. Buehler, Program Director,Trait Development Pipeline, Monsanto
Alan K.Walker, Global Soybean Breeding Director, Monsanto
Raymond Dobert, Regulatory Affairs Manager-Oilseeds, Monsanto
Xavier Delannay, Director, Ag Technology, Monsanto Protein Technologies
Jay C. Pershing, Corn Rootworm Project Lead, Monsanto
Michael A. Hall, Line Development Western Lead, North America Corn Breeding, Monsanto
Kendall R. Lamkey, Professor, Iowa State University
Introduction
Plant breeding has played a seminal role in the
As part of the Hallauer Symposium we have been advancement of human civilization. The domesti-
asked to address three questions on plant breeding: cation and continuous improvement of plants and
what is it? what has it done? and what can it do? We animals meant an ever-increasing segment of the
have approached these questions with graduate human population could focus their inventive cre-
education in mind and with the view that under- ativity on improving other aspects of civilization.
standing the context of any particular concept is es- The benefits of this phenomenon are completely
sential to understanding the details of science. Our obvious in well-developed countries, and the at-
objective is to lead the reader to the details of plant tending social unrest and anarchy in countries
breeding science but not to get lost in them. In this with severe food shortages are unquestionable.
chapter, we have described and contrasted the The smaller the percentage of people involved in
past, present, and future of plant breeding of im- food production the more rapidly a civilization
portant field crops from a commercial point of has advanced and, inversely, the less social strife its
view. Dozens of authors have offered definitions of people have endured. As the world moves from six
plant breeding in the published literature, and we billion people to a much larger number, the im-
have resisted the temptation to add yet another portance of plant breeding can only increase. We
personal nuance to the stack. Bernardo (2002) of- have divided plant breeding into three technical
fers the most universal description in our view: eras based on the methodology used to achieve ge-
“Plant breeding is the science, art, and business of netic gain. Throughout history, breeders have im-
improving plants for human benefit.” proved the harvested crop in the field primarily by
3
4 Chapter 1
phenotypic mass selection and replicated progeny rice (Oryza sativa L.) in China, sorghum (Sorghum
selection, and today direct genotypic selection is bicolor L.) in west Africa, millet (Pennisetum amer-
finally emerging as a reality. The breeding mission icanum L.) in Ethiopia, sugar cane (Saccharum sp.)
has been based on the concept that any given phe- and taro (Colocasia esculenta) in New Guinea,
notype is the summation of several factors. As maize (Zea mays L.) in Central America, and
plant breeders, we write P = G + E + G*E + e, squash (Cucurbita sp.) and sunflowers (Helianthus
where P is the phenotypic performance, G is con- annuus) in the eastern United States (Sykes, 2001).
tribution of the genotype, E is the environmental Given social roles in these early societies, it is likely
effect, G*E is the interaction of the genotype with that many of the first plant breeders were women
its environment, and e represents accumulated and that their children served as their field techni-
measurement errors. All breeders, regardless of cians while the most able men were off hunting.
their century, have devised various methods to Within a few thousand years, without any under-
cope with the frustratingly elusive nature of the standing of genetics and with the power of visual
components of phenotypic performance in an ef- selection, our ancestral mothers created the germ-
fort to estimate the genotypic or breeding value of plasm base for modern food production.
individuals. Since the arrival of flowering plants, So profound was the importance of maize to
these components have remained timeless pieces early South American civilizations that it was given
of the puzzle. The quest for genetic improvement religious meaning and significance. It is nearly im-
has not changed but the methodological choice to possible to imagine our modern world without
estimate breeding value and to achieve genetic domesticated maize, which is used directly or indi-
gain through selection has changed and continues rectly to produce much of the food on our tables
to change even today. as well as for fuel to deliver it to us. Once domesti-
cated, maize spread from its center of origin to the
agricultural corners of the globe to feed and be im-
Era 1: Domestication and phenotypic mass proved by all of the world’s farmers.
Upon his retirement as president of the Univer-
selection sity of Chicago, Dr. George W. Beadle resumed his
In the first era, early humans domesticated our early interest in the ancestry of maize. As a gradu-
current crops by mass selection of the female phe- ate student with R.A. Emerson, he began studying
notype. The domesticators essentially invented the cytogenetics of maize–teosinte crosses in 1928,
agriculture and transformed human civilization and they concurred with A. Vinson’s 1877 hypoth-
from one of nomadic hunting to a more sedentary esis that wild teosinte was the direct ancestor of
lifestyle based on gardening. Farming and farming cultivated maize (Beadle, 1980). In the mid-1970s,
tools were invented during the Neolithic or New after 40 years of debate in the literature about the
Stone Age, and by 10,000 years ago, our hunter– origin of maize, he reconstructed their 1930s hy-
gatherer ancestors had reached all but the most re- pothesis using a primitive Mexican maize variety,
mote areas of the globe (Sykes, 2001). In the blink Chapalote, and Chalco, the most cornlike variety
of a geological eye, human life had been changed of Mexican teosinte (Figure 1.1). We are indebted
beyond recognition for all time. Small bands of to Dr. Linda Pollak at Iowa State University, Walter
people across the globe originally survived on Goeppinger, a Boone, Iowa, farmer, and Mrs.
whatever they could gather, and then, according to George Beadle for preserving Figures 1.1 and 1.2.
Sykes (2001), the domestication of wild crops and In the mid-1980s, Mr. Goeppinger introduced Dr.
animals began independently in several different Pollak to Mrs. Beadle who gave her all of Dr.
parts of the world. Beadle’s seed, breeding records, and photographs.
As the glaciers retreated for the last time, cereal Dr. Beadle personally took these photographs as
grains were domesticated about 11,000 years ago part of the breeding experiments for his 1980
from wild grasses in the Near East in what is now paper in which he showed that Chalco and
known as the Fertile Crescent. Early people also in- Chapalote differed by only about five major genes.
evitably used mass selection with without control Seventy years after Beadle and Emerson found
of the male (Hallauer and Miranda Fo, 1981) to normal chromosome pairing during meiosis in
domesticate beans (Phaseolus vulgaris L.) in India, maize–teosinte crosses, Matsuoka et al. (2002)
Plant Breeding: Past, Present, and Future 5
used microsatellite-based phylogenetic analyses to a regulatory locus on the short arm of chromo-
confirm the Vinson–Emerson–Beadle hypothesis some 4 would have been required to affect the
and showed that a single domestication event of complicated genetic array involved in this trans-
Zea mays ssp. parviglumis resulted in cob maize in formational event.
contrast to the multiple and independent domesti- Less clear are studies on changes in spikelet pair-
cations of most crops and animals. Matsuoka et al. ing and ear disarticulation. According to Doebley
(2002) also presented evidence that this most likely (1994), most studies have been complicated by the
happened around 9188 BP in the highlands be- concurrent distichous-polystichous segregation
tween the states of Oaxaca and Jalisco in Mexico across teosinte maize crosses made with maize
and that the early diversification of maize occurred lines of variable kernel row numbers. Most of the
in the highlands before spreading to the lowlands evidence, however, suggests that the principal ge-
at a later date. Interestingly, today ssp. parviglumis netic factors reside on the long arm of chromo-
is not found in the highlands where its nearest some 3 and the short arm of chromosome 5, re-
maize relatives are found today, but it is found in spectively (Doebley and Stec, 1991).
the Balsas River drainage below 1800 m altitude, Figure 1.2 is another reconstruction by Dr.
leaving an unwritten chapter in the history of Beadle and depicts his theory on the effect of selec-
maize (Matsuoka et al., 2002). tion for a second set of mutations underpinning
Mutational changes in as few as five restricted the evolution of primitive cob maize into modern
genomic regions account for most of the inflores- maize. The oldest, most primitive cobs recovered
cence differences between teosinte and maize and from several caves in the Tehuacán Valley are quite
likely facilitated the transformation to cob maize uniform, less than 2 inches in length, and have
(Beadle, 1939; Doebley and Stec, 1991). A locus on eight rows of six to nine kernels each. Comparative
the long arm of chromosome 1, purportedly Tb1, morphologic studies indicate that primitive maize
ensures that the primary lateral inflorescence de- farmers using phenotypic mass selection were re-
velops into a female rather than a male flower. A sponsible for 2, 5, and 2 increases in the
change from a two-ranked to a four-ranked inflo- number of kernel rows, ear length, and kernel
rescence was necessary for cob formation to occur, weight, respectively.
and Doebley (1994) attributes genetic control to a Both waves of genetic improvement by primi-
locus on the short arm of chromosome 2. Suppres- tive farmers formed the foundation for a signifi-
sion of teosinte cupulate fruitcase formation was cant portion of the world’s current food and feed
necessary for cob formation in the origin of maize, supply. However it occurred, the selection and
and Doebley (1994) speculated that a mutation in breeding of cob maize turned out to be a corner-
6 Chapter 1
stone of immense value to recorded civilization observed variations in plants and animals. Conse-
and was extraordinary by any scientific standard. quently, Mendelian genetics formed the founda-
The efforts of these early breeders resulted in a tion for modern plant breeding.
dramatic 20-fold increase in yield potential, albeit Throughout the time Mendel’s work gathered
over many millennia, which dwarfs even the most dust in a monastery, farmers in the United States
amazing accomplishments of modern science. were practicing a form of mass selection by saving
Using this germplasm base, modern maize breed- the best seed ears from their own fields. U.S.
ers quadrupled national maize yields in the United government estimates of national corn yields
States since breeding became an organized science (http://www.usda.gov/nass/pubs/histdata.htm)
a century ago, based on replicated progeny selec- show that national yields from 1866 to 1910
tion systems. Without the feats of these early arti- changed little as a result of farmer selection, as ev-
sans, we would have a very different global econ- idenced by a regression coefficient near zero (b =
omy today. 0.065; Figure 1.3). Yields may actually have
The cost and value of these two epic events in trended down (b = -0.165; Figure 1.3) for the next
early plant breeding is difficult, if not impossible, 25 years, despite the improvements in husbandry
to quantify but are easily seen and appreciated. usually associated with the change from horses to
The cost was simply the labor of multitudes of mechanically powered farming methods. Perhaps
people, within a rather short period of geologic the expansion of corn production into western
time, trying to survive the very elements of nature Corn Belt dry land areas, such as Kansas and Ne-
that propel natural selection. Whereas, small braska, contributed to this slight decrease.
grains were the main plant food staple for other While selection for simply inherited traits had
economies, maize was central to the physical and been very successful in domesticating corn and in
religious nourishment of the peoples of South selection of modern maize types, farmer selection
America. Without it, it is not clear how or how well in the U.S. Corn Belt was not successful in produc-
these cultures would have survived and flourished. ing noticeable genetic gains. Apparently, mass se-
As is well known, an Austrian monk, Gregor lection of individual plants was not successful in
Mendel, conducted studies and made observations improving quantitative traits such as yield.
on the inheritance of certain characteristics of One positive outcome of the farmer selection
sweet peas. His work, finished in 1866, lay dor- era in the Corn Belt, however, was the fortuitous
mant and unnoticed for 40 years until its rediscov- formation of distinct heterotic groups in maize.
ery in 1900. Early geneticists recognized the value Farmers’ saving their “best ears” as their own seed
of his single-gene inheritance model in explaining and for corn contests at the local county fairs seg-
Plant Breeding: Past, Present, and Future 7
Figure 1.3 USDA-estimated average corn yield per acre for corn harvested for grain from 1866 to 1996.
mented and isolated gene pools across the Corn of methodological variations of the replicated
Belt. The resulting differences in gene frequency progeny test that often surface on Ph.D. prelimi-
and types of gene action among the hundreds of nary exams. Breeders innovated these approaches
populations formed a foundation for early breed- in an effort to (1) exploit various types of gene ac-
ing studies and progress. It also led to the forma- tion and genetic variance, (2) reduce cycle times,
tion and identification of the many heterotic (3) optimize crossing and testing schemes for self-
groups, such as Reid and Lancaster, that are ex- and cross-pollinated crops, and (4) find the most
ploited today by corn breeders. economical ways to maximize genetic gain. At the
heart of it, breeders attempt to cross “good-by-
good” and select the best as rapidly as possible. The
phenotypic simplicity and the statistical complex-
Era 2: Replicated progeny testing ity of this elegant concatenation have fueled late-
Crabb (1993) chronicled the early years of corn night discussions in graduate student offices and in
breeding in the United States. The leaders in hy- corporate offices alike for nearly a century.
brid corn are well known to all breeders. George Early corn breeders used Mendel’s model to
Shull, Edward East, Donald F. Jones, George N. analyze phenotypic variation, and early statistical
Hoffer, Merle Jenkins, James R. Holbert, and geneticists expanded the single gene model to
Henry A. Wallace are often mentioned. Their ef- explain continuous variation in quantitative traits
forts and accomplishments were extraordinary such as grain yield and other agronomic traits. By
and their lifetime spending on breeding would get necessity, breeders used a replicated progeny test to
lost as rounding error in any modern day corpo- study continuous variation and the practice be-
rate research budget. The concept of replicated came a common tool in virtually every breeding
progeny testing became a common tool in breed- program replacing phenotypic mass selection as
ing programs as these breeders and their counter- the primary breeding method. Inbreeding studies
parts studied the effects of inbreeding and pedi- and their implications prompted the use of dou-
gree selection. ble crosses, and national maize yields immediately
Popular textbooks such as Hallauer and Miranda began to improve steadily at a rate of nearly 1
Fo (1981) and Bernardo (2002) outline the dozens bushel/acre/year (b = 0.953) from the mid-1930s
8 Chapter 1
to about 1960, when single-cross use overtook slowdown was associated with little if any further
double crosses (Figure 1.3). During the so-called improvements in agronomic practices other than a
double-cross era, corn breeders also were making steady increase in plant density of 260 plants per
the improvements in inbred performance per se acre per year (Figure 1.4) because other factors
necessary for their use in profitable single-cross such as nitrogen fertilizer were declining (Figure
productions systems. 1.5) and very effective weed control had been
In the early 1960s an entirely new farming sys- achieved.
tem swept across the Corn Belt, boosting annual Figure 1.6 shows that the amount of yield vari-
improvements in maize yields to a rate of nearly ability across years has remained relatively constant
2.5 bushel/acre/year (b = 2.467, Figure 1.3). Major from 1866 to 1995, contrary to populist views that
improvements in weed control, increased plant monoculture and the use of single genotypes puts
density, earlier and more reliable planting dates, our total production more at risk than did the use
increased rates of nitrogen fertilizer and balanced of more heterogeneous varieties in crop rotations.
fertility programs coupled with modern single- Droughts and freezes account for most of the sig-
cross hybrids changed national corn yields at a nificantly lower years that visually appear in clus-
breathtaking rate. The increases in corn produc- ters of three in each half century. The residual
tion were also paralleled by a huge increase in analysis does not show any difference in yield vari-
breeding effort by the private sector. Companies ability among open-pollinated, double-cross, and
attracted by the profit potential of single-cross single-cross eras, suggesting that all of the science
seed corn rapidly built breeding, production, and in the world cannot completely counteract weather
sales capacities unseen in previous decades and as the dominant force on corn yields.
began a shift from public to private enterprise in
nearly all aspects of breeding and agronomic re- Return on corn-breeding investment
search and development that has continued to the Russell (1993) summarized 10 papers covering 13
present day. studies showing genetic gain from breeding ac-
Sometime in the late 1970s, the rate of yield im- counted for 56–94% of the yield improvement
provement apparently slowed to 1.5 bushels/acre/ from the 1930s to the 1970s. On average, 75% of
year (b = 1.489; Figure 1.3). We speculate that this yield improvement in these studies was attributed
Figure 1.4 Average plant densities for U.S. corn production from 1964 to 1996.
Plant Breeding: Past, Present, and Future 9
to genetic gain from breeding, and the remainder funded 510 science person years (SYs) in corn
was generally attributed to improved farming breeding, which approximated the number of corn-
practices. breeding programs in these companies. Public in-
In a 1994 survey of plant breeding in the United stitutions accounted for an additional 35 SYs for
States, Frey (1996) reported that 91 companies corn, although nearly all public institutions con-
Figure 1.5 Nitrogen application rates per acre for U.S. corn production from 1964 to 1996.
Figure 1.6 Residual deviations from regression for average U.S. corn yield from 1866 to 1996 expressed as a percentage of predicted yields by year.
10 Chapter 1
duct research on breeding rather than on hybrid riod was chosen because it was possible to separate
development per se. Frey (1996) did not supply es- breeding and biotechnology program costs and be-
timates of plant-breeding spending by crop but cause yield improvements during this period were
did estimate that total plant-breeding spending by relatively unaffected by biotechnology.
the private sector was $338 million for all crops. We estimate that total spending on public and
An extrapolation of Frey’s numbers would predict private corn breeding was approximately $3.0 bil-
a total industry expenditure of $156 million in lion (1984 dollars) from 1930 to 1996 and that
1994 for corn breeding, which could account for 87% ($2.6 billion) was spent from 1960 to 1996
only direct costs and may not include normal (Figure 1.7). From 1930 to 1960, spending aver-
overhead and infrastructure costs. Frey’s numbers aged $12.8M/year in 1984 dollars, whereas the
probably do not include the cost of capital. We es- pace averaged $74.3M/year in 1984 dollars from
timate that in 1995, prior to major integration of 1961 to 1996. Virtually all of the total expenditure
breeding and biotech, the private and public sec- can be attributed to hybrid corn breeding.
tors spent $200 million annually on corn breeding Figure 1.8 shows the market year average price
per se. Our estimates are based on the published per bushel for #2 yellow corn in the United States
amounts in company annual reports and our own from 1930 to 1995 as dollars of the year and in
knowledge of the fully loaded costs associated with constant 1984 dollars. We conservatively assumed
private sector breeding programs. Applying a 30% that two-thirds of the yield improvements were
overhead factor to Frey’s survey results gives a due to genetic gain, and Figure 1.9 shows accumu-
spending estimate nearly identical to our estimate lated genetic gain as a percentage of total harvested
of $200 million for 545 programs, with larger com- grain production. The annual value of accumu-
panies spending between $400,000 and $500,000 lated genetic gain (1984 dollars) increased from
per year per breeding program in 1995. 1930 to 1950, slowly declined in value for the next
Using data from a number of sources, we esti- 20 years despite huge increases in yields annually,
mated annual corn-breeding spending from 1930 to and jumped to historic highs in the early 1970s,
1995 and expressed it in constant 1984 dollars based only to slowly decline in constant dollar value
on an agricultural price index from Huffman and (Figure 1.10). Even though both spending in real
Evenson (1993). Data sources were company annual terms (Figure 1.7) and accumulated genetic gain
reports for larger publicly traded companies, esti- (Figure 1.9) continued to increase over time, the
mates from Kalton and Richardson (1983), and U.S. value of accumulated gain did not show the same
Department of Agriculture (USDA) data (http:// increase in value (Figure 1.10).
www.usda.gov/nass/pubs/histdata.htm). This pe- The cumulative value of genetic gain from corn
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