bs2081 heslop-harrison summary lecture ecology and biodiversity - agricultural systems

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BS2081Ecology and Biodiversity

Pat Heslop-HarrisonUniversity of Leicester, UK

phh4@le.ac.ukwww.molcyt.com UserID/PW

‘visitor’Twitter: pathh1 –

cytogenomics.wordpress.com

Flip – teaching : Wiki “Flip teaching is a form of blended learning which encompasses any use of technology to leverage the learning in a classroom, so a teacher can spend more time interacting with students instead of lecturing. This is most commonly being done using teacher-created videos that students view outside of class time.” 2

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BiodiversityWhat is biodiversity?

Rio de Janeiro Conference in June 1992Defined biological diversity as “the

variability among living organisms from all sources including, among other things, terrestrial, marine, and other aquatic ecosystems and the ecological complexes of which they are part: this includes diversity within species, between species and of ecosystems.”

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BiodiversityAgriculture brings in new species and new genotypes‘Biodiversity’ includes weeds, pests, vectors, predators

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Domesticated species

What are domesticated species?

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What are domesticated species?Those where people control their

reproduction and nutritionMany alternatives

– People control their access to nutrition/space– People have selected the variety– They are different from wild species– They would die out in the wild– Species useful to humans– Those with molecular signatures of selection/bottlenecks

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Domesticated speciesWhat?

MammalsPlantsOther species–Fungi, Insects

–Fish, Molluscs

–Birds

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Are there many candidates?

380,000 plants4,629 mammals9,200 birds10,000,000 insects

But only 200 plants, 15 mammals, 5 birds and 2 insects are domesticated!

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How? The biological changes(others think of the anthropology)

Animals and plants–Not ‘fussy’ for diet, soil, climate–Control reproduction

• Fast and fertile–Fast growing–Doesn’t die–Thrives in monoculture–Not aggressive/unpleasant

The first steps to domestication

Being worthwhile to grow– Can propagate: Seeds germinate, eggs hatch,

young produced– Can harvest: Seeds not dispersed/can catch,

doesn’t rot, don’t die – Reasonably persistent (but the odd extinction

does not matter)– Determinate growth / uniform ripening– Large yield - seed/fruits/meat/milk

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Suite ofplant domestication traits

Seed dispersal – no!Seed dormancy – yes then no!Large harvested parts

– Gigantism– High proportion useful

Determinate/synchronized growth

Edible and tasty17

Examples

WheatTomatoCattlePigs

http://www.els.net/WileyCDA/

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Tinyurl.com/domest

http://www.le.ac.uk/biology/phh4/public/PHH_AltmanHasegawa_ch001.pdf

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S. Banga – Punjab Agricultural Universityfirst determinate / terminal floweringBrassica juncea / B. napus lines Feb 2012

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When did domestication start?

About 8,000 years before present

Plants and animalsIn context:

Humans 6,000,000 years since divergence from apesor 50,000 years since recognizably ‘modern’

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Why did domestication start?(Not Archaeology and Anthropology!)

Hunter-gatherer no longer sustainableOver-exploitation?

Habitat destruction/extinction?Population growth?

Climate change? Food stability?Diet change?sf

Where?

After Diamond 2002

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Domesticated speciesWhat?

How?When?Why?Where?

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NASAThe Blue Marble

Apollo 17 7 Dec 1972

Ecosystems anchor slide

Largely– Self-organizing– Self-maintained– Cycling– Defined scope

– cf Household– Aircraft–

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Ecosystems

Living components– Plants and cyanobacteria (primary producers)– Bacteria, fungi, animals

Interacting with abiotic components– Light– Water– Wind, soil, nutrients, toxins, gasses ...

Recognizable homogeneity in one ecosystem 31

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RainfallDistribution

mm/yr

Ecosystems

Recognizing–Inputs–Outputs–Networks / webs of organisms–Cycles–Scales–Functions

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Inputs– Light– Heat– Water– Gasses– Nutrients

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50% of the world's protein needs are derived from atmospheric nitrogen fixed by the Haber-Bosch process and its successors.

Global consumption of fertilizer (chemically fixed nitrogen) 80 million tonnes

<<200 million tonnes fixed naturally

Outputs– Light– Heat

– Water– Gasses

– Nutrients

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OutputsEcosystem ServicesWater, gasses,nutrients”nature’s services, like flood control, water filtration, waste assimilation”

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Dynamic processes: turn-over

Outputs– Limestone

–Made by marine organisms, formation and stability affected by pH and

temperature

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Inputs - Biotic– Diseases– New organisms

• Aliens/invasives– New genes and

genotypes of existing organisms

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Outputs– Light– Heat

– Ecosystem services– Chemical energy

– Long term storage

Requiredand valued

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Biotic Inputs– New genes– New species

• Diseases• Alien species

Abiotic inputs– Irrigation– ‘Salt’ (NaCl)– Nitrogen– Phosphorous

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Water hyacinth – Eichornia: an invasive alien plant from South America, fills water courses (a surface habitat not used by any native species) in Asia and Africa

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Argenome mexicana: a goat-proof plant fromMexcio introduced and successful in Africa

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Occasional ‘extreme inputs’:Limiting composition of ecosystemsmore than ‘mean input’ - Robustness

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Anhalt, Barth, HH Euphytica 2009 Theor App Gen

2008

Light in ecosystems

Energy

Photosynthesis

Information

Quantity Quality Direction Periodicity

Control of development

Heat

Threats to sustainability:no different for 10,000 years

Habitat destructionClimate change (abiotic

stresses)Diseases (biotic stresses)Changes in what people wantMORE outputs neededMORE stability in outputs from

less stable inputs / poorer environments

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How to exploit modelsIncreased sustainabilityIncreased valueGenetic improvementRobustness (‘food security’)

Benefits to all stakeholders:Breeders, Farmers, Processors,Retailers, Consumers, Citizens

50 years of plant breeding progress

1961 1965 1970 1975 1980 1985 1990 1995 2000 2005 20070

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MaizeRiceWheatHumanArea

Agronomy

Genetics

GM maize

UK Wheat 1948-200752,909 data points, 308 varieties

From Ian Mackay, NIAB, UK. 2009. Re-analyses of historical series of variety trials: lessons from the past and opportunities for the future. SCRI website.

Conventional Breeding

Superdomestication

Cross the best with the best and hope for something better

Decide what is wanted and then plan how to get it– Variety crosses– Mutations– Hybrids (sexual or cell-fusion)– Genepool– Transformation

Economic growth

Separate into increases in inputs (resources, labour and capital) and technical progress

90% of the growth in US output per worker is attributable to technical progress Robert Solow – Economist

Market Demand “MORE”

Food production volume–No possibility of market collapse

–Only slow market increase–Reduced post-harvest loss–Some crops gain/hit by global trends

Inputs

Better genetically– Harvest more– Stress resistant (Disease = biotic and

environment – abiotic)Higher

– Weed control improving for 8000 yearsLower

– Production loss less than cost decrease– Better agronomy (cropping cycles etc.)

Needs from Stochastic Models of Ecosystems

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Outputs

Ecosystem services

– Chemical energy

– Long term storage

Inputs

– Light– Heat– Water– Gasses– Nutrients

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The major cropsWill not be displacedContinue to need 1 to 1.5% year-

on-year productivity increaseIncreased sustainability essentialMajor breeding targets

– Post-harvest losses– Water use– Disease resistance– Quality

Where do these genes come from?

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Other cultivarsLandracesWild and cultivated relatives

Other speciesMutation breedingSynthetic biology

Superdomestication

Cross the best with the best and hope for something better

Decide what is wanted and then plan how to get it

- variety crosses - mutations - hybrids (sexual or cell-fusion) - genepool - transformation

Conventional Breeding

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Exploiting novel germplasm

Optimistic for improved crops from novel germplasm

Benefits for people of developed and developing countries

Major role for national and international governmental breeding

Major role for private-sector local, national and multi-national breeders

United Nations Millennium Development Goals-MDGs

• Goal 1 – Eradicate extreme poverty and hunger

•Goal 2 – Achieve universal primary education

• Goal 3 – Promote gender equity and empower women

• Goal 4 – Reduce child mortality

• Goal 5 – Improve maternal health

• Goal 6- Combat HIV/AIDS, malaria and other diseases

• Goal 7 - Ensure environmental sustainability

• Goal 8 - Develop a global partnership for development

50 years of plant breeding progress

50 years of plant breeding progress

1961 1965 1970 1975 1980 1985 1990 1995 2000 2005 20070

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1.5

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2.5

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3.5

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MaizeRiceWheatHumanArea

50 years of plant breeding progress

1961 1965 1970 1975 1980 1985 1990 1995 2000 2005 20070

0.5

1

1.5

2

2.5

3

3.5

4

MaizeRiceWheatHumanArea

Agronomy

Genetics

GMmaize

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Why exploit novel germplasm?Increased sustainabilityIncreased valueUses genes outside the conventional genepool

Benefits to all stakeholders:Breeders, Farmers, Processors,Retailers, Consumers, Citizens

in developed and developing countriesand to all members of society.

Conventional BreedingCross the best with the best and hope

for something better

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New crops

The additions to the FAO list

–Triticale (Genome engineering)–Kiwi fruit (High value niche)–Jojoba (New product)–Popcorn is split (High value)

Farming – the seven Fs• Food (people)• Feed (animals)• Fuel (biomass and liquid)• Flowers (ornamental and horticulture)• Fibres & chemicals

• Construction (timber)• Products (wood, ‘plastics’)• Fibres (paper, clothing)

• Fun – Recreational/Environmental• Golf courses, horses, walking etc.• Environmental - Water catchments,

Biodiversity, Buffers, Carbon capture, Security

• Pharmaceuticals

Nothing special about crop genomes?

Crop Genome size 2n Ploidy Food

Rice 400 Mb 24 2 3x endosperm

Wheat 17,000 Mbp 42 6 3x endosperm

Maize 950 Mbp 10 4 (palaeo-tetraploid) 3x endosperm

Rapeseed B. napus

1125 Mbp 38 4 Cotyledon oil/protein

Sugar beet 758 Mbp 18 2 Modified root

Cassava 770 Mbp 36 2 Tuber

Soybean 1,100 Mbp 40 4 Seed cotyledon

Oil palm 3,400 Mbp 32 2 Fruit mesocarp

Banana 500 Mbp 33 3 Fruit mesocarp

Heslop-Harrison & Schwarzacher 2012. Genetics and genomics of crop domestication. In Altman & Hasegawa Plant Biotech & Agriculture. 10.1016/B978-0-12-381466-1.00001-8 Tinyurl.com/domest

Lolium Biomass production

Susanne Barth, Ulrike Anhalt, Celine Tomaszewski

Size and location of chromosome regions from radish (Raphanus sativus) carrying the fertility restorer Rfk1 gene and transfer to spring turnip rape (Brassica rapa) Tarja Niemelä, Mervi Seppänen, Farah Badakshi,Veli-Matti Rokka and J.S.(Pat) Heslop-Harrison

Chromosome Research (subject to minor revision Feb 2012)

Chromosome and genome engineeringCell fusionhybrid of two4x tetraploidtobaccospecies

Patel, Badakshi, HH, Davey et al 2011 Annals of Botany

Nicotiana hybrid4x + 4x cell fusions

Each of 4chromosomesets hasdistinctiverepetitiveDNA whenprobed withgenomic DNA

Patel et alAnn Bot 2011

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Exploiting novel germplasmSuperdomestication

• Targeted breeding and transgenic strategies

• Increase in high value niche crops

Click icon to add picture

Market Demand “MORE”

Food production volume– No possibility of market collapse– Only slow market increase– Reduced post-harvest loss– Some crops gain/hit by global trends

Market demand “MORE”Food (people)Feed (animals)

- Major driver of volume

Enormous increase in pigs and poultryIncreases in farmed fish

Smaller changes in cattle

… animals with the same diet as us are increasing

… to feed a person meat means the farmer sells 2½ to 11 times more grain than in the person eats the grain

Inputs

Better genetically– Harvest more– Stress resistant (Disease = biotic

and environment – abiotic)Higher

– Weed control improving for 8000 years

Lower– Production loss less than cost

decrease– Better agronomy (cropping cycles

etc.)

Better stress resistance:– From the genepool– From engineering genes

– Existing crops will be the major food sources

New crops– Some will become important– Many niche crops will make money

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dpTa1pSc119.2Genomic Ae.ventricosa

Inheritance of Chromosome 5DAegilops ventricosa

DDNNABDN

AABBDDNNMarneAABBDD

CWW1176-4

Rendezvous

Piko

VPM1 Dwarf A

96ST61

Virtue

×

×

×

×

Hobbit

× {Kraka × (Huntsman × Fruhgold)}

Triticum persicum Ac.1510AABB

Eyespot (fungus Pseudocercosporella) resistance from Aegilops ventricosa introduced to wheat by chromosome engineering

Many diseases where all varieties are highly susceptible

Alien variation can be found and used7

Host and non-host resistances

Crop standing

Lodging in cereals

Crop fallen

Rules for successful domestication

There aren’t any!

Crops come from anywhereThey might be grown anywherePolyploids and diploids (big

genomes-small genomes, many chromosomes-few chromosomes)

Seeds, stems, tubers, fruits, leaves

55% of the world's protein needs are derived from atmospheric nitrogen fixed by the Haber-Bosch process and its successors.

Global consumption of fertilizer (chemically fixed nitrogen) 80 million tonnes

<<200 million tonnes fixed naturally

What have farmers done?

Over the last 150 years,

1.5% reduction in production costs per year

similar across cereals, fruits, milk, meat … coal, iron

With increased quality and security

Remarkable total of 10-fold reduction in costs

What have farmers done?Over the last 4500 years:Long-term ‘effort’ reduction:4500 years ago, getting food was full-time

job for everyone = 365*12 = 4380 hr/yr/person

(Minimal towns, few wars, few monuments, few records: all these need time-out from farming!)

Now:In Europe and North America, 2% of the

population are farmers = 0.02*8*300 = 48 hr/yr/person spent farming

0.1% per year cumulative reduction

Crop varieties- High yield- High quality and safe- Easy to grow agronomically- Disease resistant- Insect/nematode resistant- Efficient water use- Secure, stable production- Environmentally friendly

- Not invasive

Do we need change?Do we need faster change?

Genomics …

The genepool has the diversity to address these challenges …

New methods to exploit and characterize let use make better and sustainable use of the genepool

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http://blog.ecoagriculture.org/2012/02/29/pacs/

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