Transcript HCS 825 Advanced Plant Breeding

Introduction to Plant Breeding ...
HCS 625
Outline:
• What is plant breeding?
• Human population growth, agricultural production,
and environmental impacts.
• Success of plant breeding.
• A crisis in plant breeding.
• Is conventional breeding obsolete?
• The Future of plant breeding
Sources:
Knight, J. 2003. “Crop Improvement: A Dying Breed” Nature 421:568570. 2004.
Symposium. Crop Science 44:1839-1919
What is plant breeding?
• Genetic improvement through crossing plants with
desired traits and selecting progeny with improved
performance and/or improved combinations of traits.
• “Accelerated” and “targeted evolution”.
• Application of genetics principles to crop improvement.
• Systematic procedures used to improve trait phenotypes
by crossing and selection, directed manipulation of the
genotype at the DNA sequence level, and introduction of
new genes.
So what is plant breeding all about?
• Livingston and the
Tomato
What is plant breeding?
• Modern plant breeding is an application of
genetic principles.
• Crop improvement is a cyclic process of
identifying new variation, crossing,
selection, and fixing favorable traits.
• Fundamentally breeding is evolution by
artificial selection.
Do we still need to train students
in plant breeding?
Agricultural food production
•Each year humans re-create the food supply that feeds
6.15 billion people
•Reserves of staple foods would feed the world for less
than two months and were as low as 48 days in 1995
•800 million people go to bed hungry every night
Food and Human nutrition
•http://www.harvestplus.org/
•Vitamin A deficiency
affects 750 million people
Projected population increase under different
assumptions of reproduction and mortality
4.00E+10
3.50E+10
Population
3.00E+10
2.50E+10
2.00E+10
1.50E+10
1.00E+10
5.00E+09
0.00E+00
1 2 3
4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
years from 2000
Projections
• We need to make as much progress in
production efficiency in the next 30 years as
we have made in the previous 12,000
• We need to double food production by 2050
The success of plant breeding
• Increases in yield are derived both from improved
varieties and from improved management.
• In vegetable crops, research suggests about a 50-50
split between genetic gain and gain attributed to
management.
• Genetic gain in grain yield of 75 Kg ha-1 yr-1 for corn
can be attributed to breeding.
– 1 ton/acre increase in yield every 30 years.
– Maize yields have increased 60% to 120% in the U.S. since
1940 (Cooper et al., 2004. Genomics, Genetics, and Plant
Breeding: A Private Sector Perspective. Crop Science.
44:1907-1913).
•
“Green revolution” varieties have increased yields 2 to
3 fold in many “developing” nations (Knight, 2003).
The crisis in plant breeding
• Public sector research into classical crop breeding is declining
dramatically (Knight, 2003).
• US, European, World Bank decreased funding for Consultative
Group on International Agricultural Research (CIGAR).
• Centro Internacional de Mejoramiento de Maiz Y Trigo
eliminated the Obregon part of the Toluca-Obregon shuttle used
in the two-cycle/year “shuttle breeding” wheat improvement
program.
• Number of students trained in plant breeding is decreasing.
• Shift from “public” to commercial sector than at Universities or
Government research organizations. (attributed to changes in
intellectual property laws)
Is conventional breeding obsolete?
• Easy traits to manipulate via GMO techniques are single gene –
these are also easily manipulated using conventional breeding.
• Conventional breeding can manipulate multiple traits
simultaneously
• Conventional breeding can manipulate genetically complex
“quantitative traits”
Traits that are influenced by the environment
Traits that are conditioned by multiple genes
• Selection on phenotype is a powerful approach to bring about
directed changes. (Robust but can be slow; requires that genetic
variation exist for the trait of interest)
• Complex genotype x environment systems that agriculture
operates under means that “methodology” of evaluation will
always be important.
What are appropriate targets:
Yield ?
The traits that are most easily altered with
transgenics are easily manipulated with traditional
breeding…with some key exceptions
• Transgenic
– Single genes
– Anti-sense
– Expanded gene pool
• Traditional
– Single genes
– Gene knock out by
mutation
– Quantitative traits
• Yield
• Quality
The Future:
• “Boost the power of conventional breeding by marrying
it to genomic and other molecular-genetic techniques”
• Build on strength of “incumbent strategy” e.g.
“molecular enhanced strategies”
• Adaptation of high-throughput approaches
– Breeding can benefit form genomics approaches e.g.
“ontolotgies” and emphasis on high througput
– Breeding can also offer genomics approaches e.g.
experimental designs for gene expression studies.
• Augment trait-based selection with knowledge-based
approach that targets selection at the level of DNA
sequence variation (Robustness will be determined by
rigor of marker-trait association)
• Concerted effort to break with proprietary
approach to intellectual property.
• “Open-source” crop-improvement.
• More expensive, so an efficiency must be
gained.
The challenge of scale - computational
• High-throughput
• Pipelines
• Standardization
– Controlled vocabulary
• Validation
How can we use new information ?
The results of “Structural Genomics”
gives us many new tools to improve
crops through “map-based” breeding
There is a broader context to the methodology e.g.,
quantitative methods used in plant breeding are currently
being applied to the analysis of “DNA chip” experiments
• “When considering the handling of
undesirable variation it is inevitable that the
discussion will centre on agricultural field
trials, since modern experimental technique
was initiated and has reached its greatest
elaboration in this realm”
• K. Mather, The Control of Error in Statistical Analysis in Biology,
University Paperbacks, Methuen & Co., LTD., London.
More research is needed for
“knowledge based approaches”
• (i) genetic architecture of the trait combinations we
seek to manipulate
• (ii) the nature of the genetic changes that were brought
about by phenotypic selection
• (anthropological genetics)
• (iii) the power that can be attained in conventional
breeding strategies
• (iv) the power that can be obtained by molecular
breeding strategies
• (v) the limits that will be faced in using genetics
(conventional or molecular) to improve crops
The methodology of breeding has something to
offer emerging fields...
Functional Genomics is the
attempt to understand the
function of all genes...
Clustering genes into functional groups
requires measuring gene expression under
many environmental conditions and
treatments
What is the most appropriate breeding
technology?
 How can new technologies enhance the all ready
proven techniques of traditional breeding without
diverting resources?
 Biotechnology advocates argue that the development of
new varieties through transformation is more precise
than introducing traits from wild species. Is there a
factual basis for this argument?
 How important are trans-genes to the future of crop
improvement?
Today selection is:
 guided by genetic principles
 guided by structural genetic information (map based
breeding)
 guided by genome sequences and functional
information
 guided by knowledge of metabolic pathways
 through laboratory manipulation
We can reconsider conventional wisdom
– “There is no way to measure the value … [of]
individual loci of a polygenic character.
Nevertheless, an understanding of their role in
determining the population mean is helpful for
evaluating the impact of selection on population
performance.” Fehr, 1996 pg.81.
Fundamentals of genetics
– Keep in mind how reproduction, mating scheme,
and selection unit affects your crop with respect to
segregation ratios and levels of heterozygosity for
genes, individuals, and populations.
– Phenotype = genotype + environment
» Phenotype is any measurable characteristic or
distinctive trait
» Genotype is all of the genes possessed by an
individual
Goals of Course:
• Grounding in conventional techniques
• Methods used for inbreeding and
outbreeding species
• Methods for maximizing or minimizing
recombination (and why we might want to
do this)
• Knowledge of new technologies (GMO)
• Integration of genome sequence and related
“genomics” technologies