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 421:568- 570. 2004. Symposium. Crop Science 44:1839-1919

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. 44:1907-1913). “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: Yield ? Herbicide resistance Insect resistance Grain quality neutraceuticals Virus resistance aesthetics Fungal resistance stress resistance Value added

14. 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

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.

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. Functional Genomics is the attempt to understand the function of all genes... The methodology of breeding has something to offer emerging fields... 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