Genomics assisted Genetic enhancement Applications and potential in tree improvement

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1 Genomics assisted Genetic enhancement Applications and potential in tree improvement Sheshshayee MS, Sumanthkumar K and Raju BR Dept. of Crop Physiology and Genetics and Plant breeding UAS, GKVK, Bangalore Forests have innumerable uses Forests contribute to 82% of continental biomass 50% of terrestrial biodiversity AND # Provides food and materials # A source for timber and fuel # Maintain elemental composition of air # Source of recreation and pleasure 1

2 Recognizing the value of tree species, scientists identified and domesticated a few of them Teak, Eucalyptus, Poplus, Pines, and Rubber Sir Wickham s efforts in collecting seeds of Rubber plants led to the present day industry Rubber is an inseparable part of human daily life Ranging from the feeding bottles to the aircraft tyres to the gaskets in space crafts There is a tremendous demand on tree products including rubber Wood for construction Global paper and paperboard Wood fuel Natural rubber FAO

3 What are the possibilities of attaining the demand? Scenario 1: No increase in productivity with slow increase in area Scenario 2: Slow increase in area but productivity increases Scenario 3: Slow increase in area but productivity increases with modern technological intervention: Genetic & management With the extension of area becoming difficult, enhancing productivity appears to be the only option Hence, genetic enhancement is inevitable What are the constraints in Tree breeding programs? 3

4 Constraints in Tree Breeding research: Long generation times Large genomes Lack of well characterized mutants Limited funding Genetic gain/improvement is a function of: ΔG = Accuracy of selection X intensity of selection X genetic std dev. Generation interval Any effort that enhances selection efficiency while reducing generation interval has great relevance Resources Light C0 2 H 2 0 Nutrient Carboxylation I 0 X RUE T X WUE NU X NUE Efficiency These resources must be efficiently used in order to attain a balance Nutrients H20 CO2 11/1/2012 Balance (efficiency) 4

5 Tremendous genetic variability in these traits is available. We assessed the variability in around 45 clones of Ecalyptus Min Max Mean CD CV Total leaf area Root biomass Total biomass Total water used WUE Δ 13 C Mohanraju et al 2012 (unpublished) These variations have never been assessed and documented systematically in several important tree species. Breeding for these traits in trees is extremely complex!! Can genomics help in solving the problem? genotype-phenotype relationship Structure of tree genomes Genomics Monitor adaptive gene diversity Adopt appropriate tools QTL discovery has greatly revolutionized crop breeding Trees are out breeding and QTL discovery is not easy 5

6 Attempts to discover QTL in tree species was made two decades ago. Markers such as RFLP; RAPD and AFLP were used These markers were costly, not reproducible and failed to recognize heterozygotes. Co-dominant SSR markers also failed to change the outcome. The large genomes of tree species Lack of validation of the QTL Major cause for the lack of increased efforts This initiated the efforts in sequencing tree genomes Till now 7 genra have been sequenced. David B.Neale et al. Nature:2011 6

7 Sequencing efforts also resulted in the discovery of large numbers of SNP and SSR markers SSR based maps were developed Large genome size Cost of SSR development Hindered the further development The focus hence shifted towards transcriptome analysis This initiated gene discovery in trees for certain traits that are easy to phenotype 7

8 These efforts paved way for assessing gene diversity and trait dissection Efforts are now being made for Comparative genomics (Conifers) ( ( With these genomic resources, what should be our approach? LD based association genetics approach might provide the impetus. What is linkage Disequilibrium (LD)? Non random association of alleles located either on the same or different linkage groups What causes LD? 1. Linkage 2. Multi locus selection 3. Mutation 4. Random drift in small populations 5. Bottlenecks in population size 8

9 Extensive out crossing among trees results in Higher recombination frequency Faster decay of LD over the genome (Neale & Ingvarsson, 2008) Thus tree species are excellent candidates for association mapping to discover QTL Characteristics of selection programme Gene pool Hardy Weinberg equilibrium population Mutation Hardy Weinberg disequillibrium population Accuracy of Selection Intensity of selection Fixation Selection for breeding Increase in genetic gain regulate inbreeding Regulate Genetic drift Extinction 9

10 To increase the genetic gain we need to increase the breeding value What is breeding value? An estimate of the additive genetic merit for a particular trait that an individual will pass on to its descendents. How to estimate Breeding value? Traditional selection X 10 litre What is the Breeding value of this cow for milk production? 0.5 litre 8 litre 10 litre 12 litre Breeding value =h 2 (milk production-average) = ( )*h 2 = 4.35 L SD is high 10

11 A phenotype based estimate of Breeding value is time consuming and not accurate Genomics to the rescue!!! A strategy of estimating the breeding value based on genomics is Genomic selection This is a combination of Association mapping and MAS Genomic information SNP marker SNP is a biallelic marker They are many in number SNP marker through out the genome Haplotyping is finding the going together of two SNPS.The haplotype blocks is used for polymorphism The SNP haplotyping is done and LD is calculated. With precise phenotyping for a trait we can associate markers for a trait. 11

12 QTL map for the leaf and growth traits in populus Forward genetic strategy has remained the method of choice Gail taylor-2002 Annals of Botany Genomic Selection in oil palm in comparision with the phenotypic selection 12

13 How to initiate the program Extreme scenario: If all the genes affecting a QTL would be known then breeding values can be estimated without information on phenotypic observations Selections can take place in laboratory 13

14 Now, what should be our strategy? Generate SNP data base for the crop of your choice Assemble an excellent panel of diversity Device techniques and tools to measure the traits Identify stable trait donor genotypes Apply genomic tools for improving your species. Five priority research areas for genomics research in trees: Reference genome sequences for many genera of tree species Ecological functions of trees in terrestrial ecosystems. NGS technologies should be used for assessing adaptive differentiation and species divergence in natural populations. Greater investment in genome database resources Develop improved Phenotyping technologies 14

15 Consortium of plantation crop genomics Overall structure Assemble Germplasm SNP and SSR Transcriptome profiling or WGS Expression analysis Association mapping panel Genotyping Develop mapping populations Phenotyping for different traits QTL discovery Novel genes Stress tolerance Yield Quality Introgression of traits - MAS Allele mining Transgenics What needs be done URGENTLY Genomic resources Whole genome sequencing Transriptome sequencing SNP and SSR markers Genetic resources Germplasm: Diversity and Association mapping panels; Reference collections Mapping populations: Trait specific populations Phenotyping options Identify component traits and device accurate strategies for phenotyping 15

16 It is certain that Genomics can significantly enhance the breeding success in Tree improvement Especially the RUBBER tree Thank you 16