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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