FOREST GENETICS. The role of genetics in domestication, management and conservation of forest tree populations

Transcription

1 FOREST GENETICS The role of genetics in domestication, management and conservation of forest tree populations Yousry A. El-Kassaby Department of Forest and Conservation Sciences Forest Sciences Centre, 2424 Main Mall University of British Columbia

2 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)

3 Gregor Mendel ( ) Laws of segregation and independent assortment

4 Walter Flemming ( ) Cell division and chromosomes discovery

5 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

6 Fisher s Infinitesimal Model (1918) Genetics of Complex Traits

7 Watson and Crick 1953 (Nature 171: ) DNA structure

8 Venter et al (Science 291: ) Human genome sequence

9 Tuskan et al (Science 313: ) Poplar genome sequence

10 Plant Breeding Teosinte Maize

11 Value of Genetics in Maize 140 U.S Average Corn Yields since Single Cross Hybrid Open Pollinated Double Cross Hybrid Pioneer Hi-Bred (2002)

12 Dairy industry prized bull 12

13 Radiata Pine Unimproved Improved

14 Plantation Forestry High Yield High Uniformity

15 Pine plantations in USA 15

16 Eucalyptus plantations in Brazil 16

17 Natural Variation: assessment

18 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)

19 Molecular Markers Going after the causal genes

20 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)

21 Understanding Natural Variation: wide continuous distribution (white spruce)

22 Understanding Natural Variation: wide but fragmented distribution (Ponderosa pine)

23 Understanding Natural Variation: regional distribution (Longleaf pine)

24 Understanding Natural Variation: endemic distribution (very localized) (Bigcone Douglas-fir)

25 Development of Seed Planning Zones: results from reciprocal transplanting and long-term assessment

26 Lodgepole pine testing, Prince George, BC Ministry of Forests, Lands and Natural Resource Operations

27 Role of Provenance Testing Populations perform differentially in contrasting environments

28 Development of Seed Planning Zones Ministry of Forests, Lands and Natural Resource Operations

29 Domestication Steps

30 Tree Improvement Delivery System Tree Improvement = Breeding + Delivery Maximize gain per unit time, effort, cost Rate of conversion to high gain

31 Recurrent Selection Selection Testing M Breeding Breeding/Testing/Selection

32 Traditional Breeding Recurrent Selection Quantitative Genetics Analyses & Rank 1- Phenotypic selection 2- Genotypic selection Selection Progeny Testing Testing Breeding Structured Pedigree

33 Testing Multiple sites within the breeding zone

34 Testing Multiple sites within the breeding zone

35 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...

36 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

37 Seed Orchards

38 Breeding Essentials - Recurrent Selection Selection Testing M Breeding Breeding/Testing/Selection El-Kassaby and Lstiburek 2009

39 Simplifying Breeding Assembled Pedigree: Pedigree Reconstruction One open-pollinated family genotyping

40 Assembled Pedigree: Pedigree Reconstruction Paternity assignment

41 Assembled Pedigree: Pedigree Reconstruction Pedigree reconstruction (2D): One HS family Full-sib family size Paternal half-sib families

42 Assembled Pedigree: Pedigree Reconstruction Pedigree Reconstruction (3D) Full-sib family size Males Females El-Kassaby et al 2015

43 Data Analysis BLUP: Best Linear Unbiased Prediction

44 El-Kassaby et al 2011 Assembled Pedigree Comparing classical pedigree with reconstructed pedigree Offspring height breeding values

45 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

46 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)

47 Pedigree-Free Models Comparing Pedigree-based vs. Genomic-based Information Offspring Klapste et al 2014

48 Breeding Essentials - Recurrent Selection Selection Testing M Breeding Breeding/Testing/Selection

49 Marker Assisted Selection/Breeding Genomic Selection Transition from phenotype-dependence to phenotype-prediction

50 Genomic Selection Hypothetical Genome 5 chromosomes

51 Causal gene/qtl Genomic Selection Fisher s Infinitesimal Model

52 Genomic Selection Random Locations of Markers (SNPs) Causal gene/qtl Marker (SNP) Linkage disequilibrium

53 Genomic Selection Simple regression: relationship between one independent and one dependent variables

54 1- Training population 2- Validation population 3- Genotyping 4- Phenotyping Genomic Selection What is needed?

55 Genomic Selection in space Wood density (white spruce) PGTIS ALL 0.53 Quesnel Aleza Lake 0.53 Gamal El-Dien et al 2015

56 Genomic Selection What can be done? 1- Reliable predictive models 2- Predict the phenotype of young seedling e.g., wood density at age Eliminating the breeding and testing phases from the TI cycle 4- Massive reduction of time for selecting desirable parents

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