The Role of Genetics and Genomics The Role of Genetics and Genomics in XXI Century Agriculturein XXI Century Agriculture

M. Enrico PèM. Enrico PèInstitute of Life SciencesInstitute of Life Sciences

Scuola Superiore Sant’AnnaScuola Superiore Sant’Anna

ISSSEESISSSEESParma September 21Parma September 21stst 2015 2015

Food Security: FactsFood Security: Facts• Human population projections: 9 billions in 2040Human population projections: 9 billions in 2040

80% in Developing /E merging Countries80% in Developing /E merging Countries• 790 milion people classified as undernourished 790 milion people classified as undernourished + 17% from 1970 + 17% from 1970 • 650 milions of the poorer live in rural areas650 milions of the poorer live in rural areas

but rapid and constant urbanizationbut rapid and constant urbanization• Arable land will stay at 1.4 billion hectarsArable land will stay at 1.4 billion hectars

but challeged by urbanization, soil erosion,but challeged by urbanization, soil erosion, pollutionpollution• Agriculture MUST BE sustainableAgriculture MUST BE sustainable

environmentally friendly BUT productiveenvironmentally friendly BUT productive++

Climate changes already at workClimate changes already at work

1.1. High yield potential High yield potential 2.2. High quality for nutrition and industrial transformationHigh quality for nutrition and industrial transformation3.3. Yield stability Yield stability tolerance/resistance to biotic tolerance/resistance to biotic and and

abiotic stressesabiotic stresses4.4. Efficient use of Efficient use of

resources resources metabolism, N, P, photosynthesismetabolism, N, P, photosynthesis translocation of photosynthatestranslocation of photosynthates HOW?HOW?

Genetic ResourcesGenetic Resources BreedingBreeding

The Role of Plant Genetics: to The Role of Plant Genetics: to Contribute New (better?) Varieties Contribute New (better?) Varieties

Plant Breeding is an accelerated evolutive Plant Breeding is an accelerated evolutive process directed by humansprocess directed by humans

Plant breeding is a slow and costly process based on Plant breeding is a slow and costly process based on controlled sexual reproduction and crosses between selected controlled sexual reproduction and crosses between selected individuals (artificial selection)individuals (artificial selection)

Plant hight reduction one of the pillars of the Plant hight reduction one of the pillars of the GreenGreen RevolutionRevolution in the ’70s in the ’70s

Bruegel the old XVI sec.

GENOMEGENOME

GENESGENES

RNARNAmRNAmRNA

PROTEINSPROTEINS

PHENOTYPEPHENOTYPE

TRANSCRIPTIONTRANSCRIPTION

TRANSLATIONTRANSLATION

METABOLISMMETABOLISMPHYSIOLOGYPHYSIOLOGY

HOW TO IDENTIFY IDENTIFY PLANTS TO BE HOW TO IDENTIFY IDENTIFY PLANTS TO BE SELECTED? SELECTED?

Development; Yield; ResponseDevelopment; Yield; Responseto stresses; etc.to stresses; etc.

ENVIRONMENTENVIRONMENT

1 cm

B73

F1

H99

1 cm1 cm

B73

F1

H99

Genome complexity Genome complexity described as number of described as number of paia base-pairs (bp)paia base-pairs (bp)1 Mbp = 1 milion bp1 Mbp = 1 milion bp

Homo sapiens Homo sapiens = 3,200 Mbp= 3,200 Mbp 24,000 genes24,000 genesDurum Wheat = 13,000 MbpDurum Wheat = 13,000 Mbp

40,000 genes40,000 genes

MODERN MEANING of GENOMEMODERN MEANING of GENOME The whole content of The whole content of GENETIC MATERIAL GENETIC MATERIAL -- DNA -DNA -

in a cell, in an organism, or in a speciesin a cell, in an organism, or in a species

It reprsents the POTENTIAL It reprsents the POTENTIAL in terms of functionality of an in terms of functionality of an

organismorganism

GeneGene: : 1. Hereditary unit1. Hereditary unit 2. Functional unit of DNA2. Functional unit of DNAAllelesAlleles: : ALTERNATIVE forms of the same geneALTERNATIVE forms of the same gene

A FEW IMPORTANT DEFINITIONSA FEW IMPORTANT DEFINITIONS

……C C C C AA T T G A C T T G A C……

……C C C C GG T T G A C T T G A C…………G G G G TT A A C T G A A C T G……

……G G G G CC A A C T G A A C T G……

Allele 1Allele 1

Allele 2Allele 2

PROBLEMPROBLEM::How to determine the functional How to determine the functional significance of genetic variationsignificance of genetic variation• identificationidentification• measurement of variabilitymeasurement of variability• genetic analysisgenetic analysis

Grapevine genomeGrapevine genome500 Mbp500 Mbp

Shotgun sequencingShotgun sequencing (genomes equivalents)(genomes equivalents)

AssemblyAssembly

Gene PredictionGene PredictionAnnotationAnnotation

13 milion euros13 milion euros2 years2 years

THE FIRST GENOMIC REVOLUTION (1985-2005) THE FIRST GENOMIC REVOLUTION (1985-2005)

SECOND GENOMIC REVOLUTIONSECOND GENOMIC REVOLUTION

3,000 euros in 3 weeks3,000 euros in 3 weeksIdentification of genetic variationIdentification of genetic variation

NO LONGER NO LONGER the bottleneckthe bottleneck

Single NucleotideSingle NucleotidePolymorphismPolymorphism

Molecular CharacterizationMolecular Characterization DNA-chipsDNA-chips

Re-sequencing individual plantsRe-sequencing individual plants

……C C C C AA T T G A C T T G A C……

……C C C C GG T T G A C T T G A C…………G G G G TT A A C T G A A C T G……

……G G G G CC A A C T G A A C T G……

Single Nucleotide PolymorphismSingle Nucleotide Polymorphism - SNP - - SNP - - Identified by sequencing- Identified by sequencing- Their frequency depends on- Their frequency depends on several factors (several factors (1 in < 100 bp1 in < 100 bp))

1.1. High yield potential High yield potential 2.2. High quality for nutrition and industrial transformationHigh quality for nutrition and industrial transformation3.3. Yield stability Yield stability tolerance/resistance to biotic tolerance/resistance to biotic and and

abiotic stressesabiotic stresses4.4. Efficient use of Efficient use of

resources resources metabolism, N, P, photosynthesismetabolism, N, P, photosynthesis translocation of photosynthatestranslocation of photosynthates HOW?HOW?

Genetic ResourcesGenetic Resources BreedingBreeding

The Role of Plant Genetics: to The Role of Plant Genetics: to Contribute New (better?) Varieties Contribute New (better?) Varieties

Each dot is an alellic variantEach dot is an alellic variantBlue = Parent 1Blue = Parent 1Pink= Parent2Pink= Parent2

MAIZE RECOMBINANT GENOTYPEMAIZE RECOMBINANT GENOTYPE

MAPPING PHENOTYPES: COMBINING MAPPING PHENOTYPES: COMBINING GENOMIC CHARACTERIZATION WITH GENOMIC CHARACTERIZATION WITH

MEASUREMENTSMEASUREMENTS

Structured Structured Population Population

i.e. Bi-i.e. Bi-parental parental

populationpopulation

Not Not structured structured populationpopulation

MAPPING PHENOTYPES: COMBINING MAPPING PHENOTYPES: COMBINING GENOMIC CHARACTERIZATION WITH GENOMIC CHARACTERIZATION WITH

MEASUREMENTSMEASUREMENTS

Zooming Zooming on the on the

genomegenome

Modified form Mackay et al., 2009

Statistical Statistical analysisanalysis

Region controlling yieldRegion controlling yield

MAIZE RECOMBINANT GENOTYPEMAIZE RECOMBINANT GENOTYPE

Each dot is an alellic variantEach dot is an alellic variantBlue = Parent 1Blue = Parent 1Pink= Parent2Pink= Parent2

1.1. High yield potential High yield potential 2.2. High quality for nutrition and industrial transformationHigh quality for nutrition and industrial transformation3.3. Yield stability Yield stability tolerance/resistance to biotic tolerance/resistance to biotic and and

abiotic stressesabiotic stresses4.4. Efficient use of Efficient use of

resources resources metabolism, N, P, photosynthesismetabolism, N, P, photosynthesis translocation of photosynthatestranslocation of photosynthates HOW?HOW?

Genetic ResourcesGenetic Resources BreedingBreeding

The Role of Plant Genetics: to The Role of Plant Genetics: to Contribute New (better?) Varieties Contribute New (better?) Varieties

Domestication, Breeding and Domestication, Breeding and AgrobiodiversityAgrobiodiversity

““Bottleneck” effectBottleneck” effectduring domestication during domestication GENETIC EROSIONGENETIC EROSION

Molecular analysis confirms thatMolecular analysis confirms thatmodern cultivars have lost a huge modern cultivars have lost a huge part of genetic variabilitypart of genetic variability

Natural Populations

Cultivated Species

Genetic Genetic variabilityvariability ExploitabilityExploitability

Gene Pool: Crop genetic diversityGene Pool: Crop genetic diversity

Stem RustStem RustLeaf RustLeaf RustStripe RustStripe RustPowdery MildewPowdery MildewEyespotEyespot

Aegilops speltoides Aegilops tauschii Aegilops triuncialisAegilops umbellulataAegilops uniaristata Aegilops ventricosa

(85)(182)(290)

(31)(5)(50)

Resistance genes to pathogens in wild speciesResistance genes to pathogens in wild species

ETHIOPIA: Exploitation of durum ETHIOPIA: Exploitation of durum wheat genetic resourceswheat genetic resources AgriculturalAgricultural society society Food production affected by climate changesFood production affected by climate changes 40% of 40% of populationpopulation undernourished (FAO, 2012)undernourished (FAO, 2012)

• Higher Temperatures Higher Temperatures • More drought and floodingMore drought and flooding• More extreme eventsMore extreme events• Greater year-to-year Greater year-to-year variabilityvariability

There is a great amount of untapped diversity in EthiopiaThere is a great amount of untapped diversity in Ethiopia

SPECIFIC OBJECTIVESSPECIFIC OBJECTIVES Identify and evaluate local varieties of durum Identify and evaluate local varieties of durum wheat from Addis Abeba’s genebankwheat from Addis Abeba’s genebank Improve farmers’ access to genebank information and Improve farmers’ access to genebank information and materialsmaterials Merge phenotypic and genotipic information withMerge phenotypic and genotipic information with farmers’ knowledge farmers’ knowledge

• 450 Ethiopian landraces450 Ethiopian landraces• In field evaluation by breedersIn field evaluation by breeders• Involvement of local farmersInvolvement of local farmers• Molecular characterizationMolecular characterization• Crosses and selectionCrosses and selection

FOCUS GROUPS FOCUS GROUPS and identificationand identificationof traits of interestof traits of interest

GENETIC VARIATION BASED ON GENETIC VARIATION BASED ON MOLECULAR DATAMOLECULAR DATA

Mediterranean durumMediterranean durum

European breadEuropean bread

Ethiopian breadEthiopian bread

Ethiopian durumEthiopian durum

MAIN MESSAGESMAIN MESSAGES

• The The methodology is methodology is soundsound• Ethiopian wheat Ethiopian wheat germplasm is germplasm is peculiarpeculiar

Ethiopian Durum Wheat: Landraces vs Ethiopian Durum Wheat: Landraces vs Improved varietiesImproved varieties

Imrpoved varietiesImrpoved varietiesMAIN MESSAGESMAIN MESSAGES

• Ethiopian landraces Ethiopian landraces are very differentare very different• Most improved Most improved varieties are varieties are genetically similargenetically similar• Ethiopian Ethiopian germplasm is mostly germplasm is mostly untappeduntapped

LandracesLandraces

Solanum pennelliiSolanum pennelliiNatural HabitatNatural Habitat

Atico Arequipa-PeruAtico Arequipa-PeruUnexpected SurpriseUnexpected Surprise

Landscape Genomics: chasing genes for plant adaptation

GEOGRAPHICDATA

FIELD DATA

STATISTICALMODELLING

Geografic Information Systems (DIVA, QGIS…)

• Evolution• Adaptation• Historical trends• …

QUANTITATIVE DATAGenotyping

Climate, barriers…

Real world

If the plant grows it can cope with that specific environment

ENVIRONMENT as the BREEDER

The Group at Sant’Anna:The Group at Sant’Anna:PhD Students in PhD Students in AgrobiodiversityAgrobiodiversity

HUSNA

To Double Yield by 2050 We Need To Double Yield by 2050 We Need AGEAGE

Population increasePopulation increase > 7 billions in 2015> 7 billions in 2015 9 billions in 2040 (UN)9 billions in 2040 (UN)

Climate changesClimate changes already presentalready present

Sustainable agricultureSustainable agricultureEnvironment friendlyEnvironment friendlybut productivebut productive NutritionNutrition and health and health food qualityfood quality

XXI Century Agriculture: the XXI Century Agriculture: the challangeschallanges