HCS 825 Advanced Plant Breeding

1
Introduction to Plant Breeding ...
HCS 625
2
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 421568-570. 2004.
Symposium. Crop Science 441839-1919
3
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.

4
So what is plant breeding all about?

• Livingston and the Tomato

5
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.

6
Do we still need to train students in plant
breeding?
7
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

8
Projected population increase under different
assumptions of reproduction and mortality
9
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

10
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. 441907-1913).
•   Green revolution varieties have increased
  yields 2 to 3 fold in many developing nations
  (Knight, 2003).

11
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)

12
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.

13
What are appropriate targets
stress resistance
Value added
Herbicide resistance
aesthetics
Grain quality
Yield ?
Insect resistance
neutraceuticals
Fungal resistance
Virus resistance
14
The traits that are most easily altered with
transgenics are easily manipulated with
traditional breedingwith some key exceptions

• Transgenic
• Single genes
• Anti-sense
• Expanded gene pool

• Traditional
• Single genes
• Gene knock out by mutation
• Quantitative traits
• Yield
• Quality

15
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)

16

• Concerted effort to break with proprietary
  approach to intellectual property.
• Open-source crop-improvement.
• More expensive, so an efficiency must be gained.

17
(No Transcript)
18
The challenge of scale - computational

• High-throughput
• Pipelines
• Standardization
• Controlled vocabulary
• Validation

19
How can we use new information ?
20
The results of Structural Genomics gives us
many new tools to improve crops through
map-based breeding
21
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
22

• 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.

23
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

24
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
25
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?

26
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

27
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.

28
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

29
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