SYLLABUS INTRODUCTION TO PLANT …

1 SYLLABUS INTRODUCTION TO PLANT quantitative GENETICS Tucson, 8 10 Jan. 2018 INSTRUCTORS: Mike Gore, Cornell University, Lucia Gutierrez, Department of Agronomy, University of Wisconsin, Madison Bruce Walsh, Department of Ecology & Evolutionary Biology, University of Arizona References B = Bernardo,Breeding for quantitative Traits in Plants, 2nd ed. LW = Lynch & Walsh: Genetics and Analysis of quantitative Traits (book) WL = Walsh & Lynch: Evolution and Selection of quantitative Traits (website) LECTURE SCHEDULE Monday, 8 Jan 8:30 10:00 am 1. Introd to Modern PLANT Breeding (Gore, Gutierrez, Walsh) Background reading: B Chapter 1 10:00 10:30 am Break 10:30 12:00 am 2.

2 Basic Genetics (Walsh, Gore) Background reading: LW Chapter 4 12:00 1:30 pm Lunch 1:30 3:00 pm 3. Basic Statistics (Walsh) Background reading: LW Chapters 2, 3 Additional reading: LW Appendix A4 3:00 3:30 pm Break 3:30 5:00 pm 4. Allelic Effects and genetic Variances (Walsh) Background reading: B Chapters 3, 6 Additional reading: LW Chapters 4, 5 Tuesday, 9 Jan 8:30 10:00 am 5. Resemblance Between Relatives (Walsh) Background reading: B Chapter 6 Additional reading: LW Chapter 7 10:00 10:30 am Break 10:30 12:00 am 6. Heritability and Field Designs (Gutierrez) Background reading: B Chapters 6, 7 Additional reading: LW Chapters 17, 18, 20, 22 Holland, J.

3 , Nyquist, Cervantes-Martinez. 2010. Estimating and Interpreting Heritability for PLANT Breeding: An Update. PLANT Breeding Reviews 22: 9-112. 12:00 1:30 pm Lunch 1:30 3:00 pm 7. QTL Mapping (Gutierrez) Background reading: B Chapter 5 Additional reading: LW Chapters 12-15 3:00 3:30 pm Break 3:30 5:00 pm 8. Association Mapping (Gore) Background reading: B Chapter Additional reading: LW Chapter 16 Wednesday, 10 Jan 8:30 10:00 am 9. Inbreeding, Heterosis (Gore) Background reading: B Chapter 12 Additional reading: LW Chapter 10, 10:00 10:30 am Break 10:30 12:00 am 10.

4 Mass and Family Selection (Walsh) Background reading: B Chapters 9, 10 Additional reading: WL Chapters 12, 13, 19, 20, 35 ADDITIONAL BOOKS ON quantitative GENETICS General Falconer, D. S. and T. F. C. Mackay. INTRODUCTION to quantitative Genetics, 4th Edition Lynch, M. and B. Walsh. 1998. Genetics and Analysis of quantitative Traits. Sinauer. Mather, K., and J. L. Jinks. 1982. Biometrical Genetics. (3rd Ed.) Chapman & Hall. PLANT Breeding Wricke, G., and W. E. Weber. 1986. quantitative Genetics and Selection in PLANT Breeding. De Gruyter. Mayo, O. 1987. The Theory of PLANT Breeding.

5 Oxford. Stoskopf, N. D. T. Tomes, and B. R. Christie. 1993. PLANT breeding: Theory and practice. Westview, Boulder. Sleper, D. A., and J. M. Poehlman. 2006. Breeding Field Crops. 5th Edition. Blackwell Bernardo, R. 2010. Breeding for quantitative Traits in Plants, 2nd Ed Stemma Press. Hallauer, A. R., M. J. Carena, and J. B. Miranda Filho. 2010. quantitative Genetics in Maize Breeding. Iowa State Press. Statistical and Technical Issues Bulmer, M. 1980. The Mathematical Theory of quantitative Genetics. Clarendon Press. Kempthorne, O. 1969. An INTRODUCTION to genetic Statistics. Iowa State University Press.

6 Sorensen, D., and D. Gianola. 2002. Likelihood, Bayesian, and MCMC Methods in quantitative Genetics. Springer. Saxton, A. M. (Ed). 2004. genetic Analysis of Complex Traits Using SAS. SAS Press. Wu, R., Ma, and G. Casella. 2007. Statistical Genetics of quantitative Traits: Linkage, Maps. and QTL. Springer, 1 Lecture 1 INTRODUCTION to Modern PLANT Breeding Bruce Walsh Notes INTRODUCTION to PLANT quantitative Genetics Tucson. 8-10 Jan 2018 2` Importance of PLANT breeding PLANT breeding is the most important technology developed by man. It allowed civilization to form and its continual success is critical to maintaining our way of life Problem.

7 Feeding 9 billion (+) people with the same (or fewer) inputs Same or less acreage Same or less fertilizer, pesticides, water Adapting to climate and environmental change 3 Goals of PLANT breeding Increase the frequency of favorable alleles within a line Additive effects Increase the frequency of favorable genotypes within a line Dominance and interaction effects Better adapt crops to specific environments Region-specific cultivars (high location G x E) Stability across years within a region (low year-to-year G x E) 4 Objectives Development of pure ( highly inbred) lines with high per se performance Development of pure lines with high hybrid performance (either with each other or with a testcross) Less emphasis on developing outbred (random-mating) populations with improved performance Development of lines with high regional G x E, low year G x E 5 Animal and tree breeding Similar goals, but since mostly outcrossing, the goal is to create high-performing populations, not inbred lines Generally speaking, inbreeding is bad in animals and many trees Focus on finding those parents with the best transmitting abilities (highest breeding values)

8 Less of a G x E focus with animals, less of a focus on line and hybrid breeding 6 Special features exploited by PLANT breeders Selfing allows for the capture of specific genotypes, and hence the capture of interactions between alleles and loci (dominance and epistasis) Homozygous for selfed lines Heterozygous for crossed lines Often high reproductive output (relative to animal breeding) Seeds allow for multigeneration progeny testing, wherein individuals are chosen on the performance of their progeny, or of their sibs Allows for better control over G x E by testing over multiple sites/years 7 Historical PLANT breeding Early origins Creation of new lines through species crosses (allopolyploids) Visual selection Early domestication (selection for specific traits for ease of harvesting)

9 Biometrical school Using crosses to predict average performance under inbreeding or crossing or response to selection Better management of G x E 8 Modern tools Molecular markers Initially low density for QTL mapping, introgression of major genes into elite germplasm With high-density markers, association mapping and MAS/genomic selection New statistical tools Mixed model methods Bayesian approaches to handle high-dimensional data sets New methods to deal with G x E Other technologies Better standardization of field sites (laser-tilled fields, GPS, better micro- and macro-environmental measurements) High throughput phenotypic scoring DH lines 9 Diversity PLANT breeders face the conundrum of using inbred lines to concentrate elite genotypes, but requiring a very large collection of such lines to store variation for further selection Landraces or local cultivars may be highly adapted to specific environments, but otherwise not elite Issue with keeping germplasm elite while introgressing genes/regions of interest.

10 10 Integrated Approaches How do we best combine the rich history of quantitative genetics and classical PLANT breeding with the new tools from genomics and other advances? Key: quantitative genetics has all of the machinery needed to fully incorporate these new sources of information The goal of this course is to show how this is done. 1 Lecture 2 Basic PLANT Genetics Bruce Walsh Notes INTRODUCTION to PLANT quantitative Genetics Tucson. 8-10 Jan 2018 2 Overview Ploidy Linkage Linkage disequilibrium (LD) genetic markers Mapping functions Organelle inheritance Mating systems and types of crosses Gene actions Dominance and Epistasis Pleiotropy 3 Ploidy Most animals are diploid (2n), with their gametes (eggs, sperm) containing a haploid set of n chromosomes Polyploids are much more common in plants.