Genomics assisted Genetic enhancement – Applications and...
Transcript of Genomics assisted Genetic enhancement – Applications and...
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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
# Provides food and materials# A source for timber and fuel# Maintain elemental composition of air# Source of recreation and pleasure
Forests contribute to
82% of continental biomass50% of terrestrial biodiversity
AND
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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…
Wood for construction
FAO-2008
Global paper and paperboard
There is a tremendous demand on tree products including rubber
Wood fuel Natural rubber
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What are the possibilities of attaining the demand?
Scenario 1: No increase in productivity with slow increase in areaScenario 2: Slow increase in area but productivity increasesScenario 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 ?
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Constraints in Tree Breeding research:
Long generation times
Large genomes
Lack of well characterized mutants
Limited funding
Any effort that enhances selection efficiency while reducing generation interval has great relevance
ΔG Accuracy of selection X intensity of selection X genetic std dev.
Generation interval =
Genetic gain/improvement is a function of:
Resources
Light C02 H20 Nutrient
I0 X RUE T X WUE NU X NUE
These resources must be efficiently used in order to attain a balance
Balance (efficiency)
CO2H20Nutrients
11/1/2012
Carboxylation Efficiency
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Tremendous genetic variability in these traits is available.
These variations have never been assessed and documented systematically in several important tree species.
Min Max Mean CD CV
Total leaf area 9644 19222 13171 3880 17.67
Root biomass 92 416 235 123.21 21.30
Total biomass 273 689 412 165.18 24.04
Total water used 150 205 179 49.51 16.56
WUE 1.44 3.39 2.30 0.50 12.96
Δ13C 19.47 21.92 20.67 0.98 2.84
We assessed the variability in around 45 clones of Ecalyptus…
Mohanraju et al 2012 (unpublished)
Breeding for these traits in trees is extremely complex!!
Can genomics help in solving the problem?
Genomics
Structure of tree genomes
genotype-phenotype relationship
Monitor adaptive gene diversity
Adopt appropriate tools
QTL discovery has greatly revolutionized crop breeding
Trees are out breeding and QTL discovery is not easy
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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.
The large genomes of tree species
Lack of validation of the QTL
Co-dominant SSR markers also failed to change the outcome.
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
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Sequencing efforts also resulted in the discovery of large numbers of SNP and SSR markers
SSR based maps were developed…
Large genome sizeCost 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
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These efforts paved way for assessing gene diversity and trait dissection
(http://dendrome.ucdavis.edu/ccgp) (http://dendrome.ucdavis.edu/crsp)
Efforts are now being made for Comparative genomics (Conifers)
With these genomic resources, what should be our approach?
What is linkage Disequilibrium (LD)?
Non random association of alleles located either on the same or different linkage groups
What causes LD ?1. Linkage2.Multi locus selection3.Mutation4. Random drift in small populations5. Bottlenecks in population size
LD based association genetics approach might provide the impetus.
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Extensive out crossing among trees results in
Higher recombination frequency
Faster decay of LD over the genome
Thus tree species are excellent candidates for association mapping to discover QTL
(Neale & Ingvarsson, 2008)
Gene pool
Accuracy of Selection Intensity of selection
Selection for breeding
Increase in genetic gain
Hardy Weinberg equilibrium population
Mutation
Hardy Weinberg disequillibrium population
regulate inbreeding
Regulate Genetic drift
Characteristics of selection programme
Extinction
Fixation
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To increase the genetic gain we need to increase the breeding value
What is breeding value?
An estimate of the additive genetic merit for aparticular trait that an individual will pass on to itsdescendents.
How to estimate Breeding value?
X
10 litre
12 litre8 litre 10 litre0.5 litre
What is the Breeding value of this cow for milk production?
Breeding value =h2(milk production-average)
= (12-7.625)*h2= 4.35 L
Traditional selection
SD is high
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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
The SNP haplotyping is done and LD is calculated .
With precise phenotyping for a trait we can associate markers for a trait.
Haplotyping is finding the going together of two SNPS.The haplotype blocks is used for polymorphism
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Gail taylor-2002 Annals of Botany
QTL map for the leaf and growth traits in populus
Forward genetic strategy has remained the method of choice
Genomic Selection in oil palm in comparision with the phenotypic selection
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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
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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
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Consortium of plantation crop genomics – Overall structure
Assemble Germplasm
Transcriptome profiling or WGS
Expression analysis
Phenotyping for different traits
Stress tolerance Quality
QTL discovery
Introgression of traits - MAS
Allele mining
Novel genes
Transgenics
SNP and SSR
Genotyping
Develop mapping populations
Association mapping panel
Yield
What needs be done… URGENTLY
Genomic resources
Whole genome sequencingTransriptome 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
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It is certain that Genomics can significantly enhance the breeding
success in Tree improvement
Thank you
Especially the RUBBER tree