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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