FOREST GENETICS The role of genetics in domestication, management and conservation of forest tree populations Yousry A. El-Kassaby y.el-kassaby@ubc.ca Department of Forest and Conservation Sciences Forest Sciences Centre, 2424 Main Mall University of British Columbia
What is Genetics? Branch of Biology that deals with heredity (mechanisms of hereditary transmission of variation among generations) Causes for resemblances and differences among related individuals (presence or absence of genes) It is the product of genes, the environment and their interaction (P = G + E + GxE)
Gregor Mendel (1822-1884) Laws of segregation and independent assortment
Walter Flemming (1843-1905) Cell division and chromosomes discovery
Hardy-Weinberg 1908 Genes in Populations Hardy-Weinberg Equilibrium Law Rediscovered 1943 Evolution is simply a change in frequencies of alleles in a population s gene pool In the absence of evolution, the gene pool frequencies remain unchanged Conditions for NO evolution 1- Populations are large 2- Random mating among all individuals 3- No mutation, selection, migration
Fisher s Infinitesimal Model (1918) Genetics of Complex Traits
Watson and Crick 1953 (Nature 171: 737-734) DNA structure
Venter et al. 2001 (Science 291:1304-1352) Human genome sequence
Tuskan et al. 2006 (Science 313:1596-1604) Poplar genome sequence
Plant Breeding Teosinte Maize
Value of Genetics in Maize 140 U.S Average Corn Yields since 1920 1994 120 100 1993 80 Single Cross Hybrid 1983 1988 60 1970 1974 40 Open Pollinated Double Cross Hybrid 20 1936 1947 1934 0 Pioneer Hi-Bred (2002)
Dairy industry prized bull 12
Radiata Pine Unimproved Improved
Plantation Forestry High Yield High Uniformity
Pine plantations in USA 15
Eucalyptus plantations in Brazil 16
Natural Variation: assessment
Natural Variation: adaptive vs. neutral Leaf colouring in Birch as affected by geographic source (northern and southern sources are arranged from left to right) (SLU) DNA neutral molecular markers Microsatellites: Simple Sequence Repeats (SSRs)
Molecular Markers Going after the causal genes
Factors Affecting Genetic Variation Among and Within Populations Life History Attributes: Life forms (annual, short-lived perennial, long-lived perennial) Taxonomic status (gymnosperms, angiosperms) Geographic range (endemic, narrow, regional, widespread) Regional distribution (boreal, temperate, tropical) Breeding system (selfing, mixed (animals/wind), outcrossing (animals/wind)) Seed dispersal (gravity, attached, explosive, ingested, wind) Mode of reproduction (sexual, sexual and asexual) Successional status (early, mid, late)
Understanding Natural Variation: wide continuous distribution (white spruce)
Understanding Natural Variation: wide but fragmented distribution (Ponderosa pine)
Understanding Natural Variation: regional distribution (Longleaf pine)
Understanding Natural Variation: endemic distribution (very localized) (Bigcone Douglas-fir)
Development of Seed Planning Zones: results from reciprocal transplanting and long-term assessment
Lodgepole pine testing, Prince George, BC Ministry of Forests, Lands and Natural Resource Operations
Role of Provenance Testing Populations perform differentially in contrasting environments
Development of Seed Planning Zones Ministry of Forests, Lands and Natural Resource Operations
Domestication Steps
Tree Improvement Delivery System Tree Improvement = Breeding + Delivery Maximize gain per unit time, effort, cost Rate of conversion to high gain
Recurrent Selection Selection Testing M Breeding Breeding/Testing/Selection
Traditional Breeding Recurrent Selection Quantitative Genetics Analyses & Rank 1- Phenotypic selection 2- Genotypic selection Selection Progeny Testing Testing Breeding Structured Pedigree
Testing Multiple sites within the breeding zone
Testing Multiple sites within the breeding zone
Seed Orchards To function properly, they must act as a closed, perfect populations (i.e., reproductive synchrony and equality, minimal migration/contamination (remember Hardy-Weinberg law) BUT...
Tree Improvement Delivery System Biological Constraints Natural Populations Selection Products Plus-trees Time & cost Breeding Testing Elite genotypes El-Kassaby 1995 Reproductive phenology Parental imbalance Contamination Seed handling & storage Germination Dormancy Thinning Culling Seed orchards Nurseries Regeneration Seeds Seedlings
Seed Orchards
Breeding Essentials - Recurrent Selection Selection Testing M Breeding Breeding/Testing/Selection El-Kassaby and Lstiburek 2009
Simplifying Breeding Assembled Pedigree: Pedigree Reconstruction One open-pollinated family genotyping
Assembled Pedigree: Pedigree Reconstruction Paternity assignment
Assembled Pedigree: Pedigree Reconstruction Pedigree reconstruction (2D): One HS family Full-sib family size Paternal half-sib families
Assembled Pedigree: Pedigree Reconstruction Pedigree Reconstruction (3D) 63 61 59 57 55 53 51 49 47 45 43 41 39 37 35 33 31 29 27 25 23 21 19 17 15 13 11 9 7 Full-sib family size Males 5 3 1 1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 51 53 55 57 59 61 63 Females El-Kassaby et al 2015
Data Analysis BLUP: Best Linear Unbiased Prediction
El-Kassaby et al 2011 Assembled Pedigree Comparing classical pedigree with reconstructed pedigree Offspring height breeding values
Genomics & Quantitative Genomics Genomic-based relationship Accounts for: contemporary pedigree historic pedigree Substituting pedigree-based with genomic-based in BLUP analyses Structured-pedigree = Unstructured-pedigree Watershed moment in genetics Pedigree-free models
Pedigree-Free Models Test Case Breeding Values Comparison: known pedigree (FS) vs. Relationship (no pedigree) W: Wang (2002) L & R: Lynch & Ritland (1999) L: Li et al. (1993) Q & G: Queller & Goodnight (1989)
Pedigree-Free Models Comparing Pedigree-based vs. Genomic-based Information Offspring Klapste et al 2014
Breeding Essentials - Recurrent Selection Selection Testing M Breeding Breeding/Testing/Selection
Marker Assisted Selection/Breeding Genomic Selection Transition from phenotype-dependence to phenotype-prediction
Genomic Selection Hypothetical Genome 5 chromosomes
Causal gene/qtl Genomic Selection Fisher s Infinitesimal Model
Genomic Selection Random Locations of Markers (SNPs) Causal gene/qtl Marker (SNP) Linkage disequilibrium
Genomic Selection Simple regression: relationship between one independent and one dependent variables
1- Training population 2- Validation population 3- Genotyping 4- Phenotyping Genomic Selection What is needed?
Genomic Selection in space Wood density (white spruce) PGTIS 0.51 0.32 0.34 0.24 0.23 0.62 ALL 0.53 Quesnel 0.31 0.30 Aleza Lake 0.53 Gamal El-Dien et al 2015
Genomic Selection What can be done? 1- Reliable predictive models 2- Predict the phenotype of young seedling e.g., wood density at age 40 3- Eliminating the breeding and testing phases from the TI cycle 4- Massive reduction of time for selecting desirable parents