Pat Heslop-HarrisonTalk 2: Genome evolution: perspectives from billions of years to plant breeding timescales, from the base pair to trillions of bases, and from the cell to the planet and beyond

phh4@le.ac.ukwww.molcyt.com pw/user: ‘visitor’Social media: pathh1 Twitter/YouTube

PAU, Ludhiana 21 – 2 – 12

Brassica

Wheat

Banana

OthersCrocusPanicumDrosophilaArachisMedicago

Genomics & Genome organization in chromosomes

Hybrids/polyploidsBiodiversitySystems biologyIntrogression and

breedingSocio-economics and

applications

02/03/2012 5

l Those where people control their reproduction and nutritionlMany alternatives

People control their access to spacePeople have selected the variety

They are different from wild speciesThey would die out in the wild

Species useful to humans

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l Those where people control their reproduction and nutrition

What about Weeds

CommensualsDiseases

?

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¡350,000 plants¡4,629 mammals¡9,200 birds¡10,000,000 insects¡500,000 fungi

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¡ 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¡ Are there many candidate species?

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¡ 350,000 plants¡ 4,629 mammals¡ 9,200 birds¡ 10,000,000 insects¡ 500,000 fungi

¡But only 200 plants, 15 mammals, 5 birds, c. 5 fungi and 2 insects are domesticated

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¡ Spread of these few species¡ Little change since early agriculture¡ Repeated domestication of these species

(sometimes)¡ Lack of new species even with attempts

with species known to be valuable

¡ Some groups of good candidates with no domestication eg ferns, sub-Saharan mammals ...§ Two ferns are invasive problem

¡ New uses and demands – biofuels, animal feed, medicinal/neutraceutical, water/climate, food changes¡ Knowledge why species aren’t suitable for

domestication or were not useful¡ Better understanding of genetics and

selection¡ Sustainability of production¡ Reliability of production

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02/03/2012 13

About 10,000 years before present

Plants and animalsIn context:

Humans 6,000,000 years since divergence from apes

or 50,000 years since recognizably ‘modern’

Worldwide!

Genetic:¡ No seed dormancy¡ Determinate and synchronized growth¡ Gigantism in the harvested parts¡ No seed dispersal (after Hammer)

¡ Increased harvest index¡ Sweetness no bitterness ¡ Productivity high¡ Not toxicAll still a challenge today – and many

improvements are still coming

¡ Technology:

¡ Tilling, planting, watering, feeding, weeding, disease control, ‘growing’, harvesting, threshing, storing, packaging, transporting, propagating, fields, cooking and preparation

¡ All still a challenge today – with many changes and opportunities – worldwide

¡ Human: a tiny part of history¡ Many animals plan ahead: store food, make

nests, post guards/lookouts, plan battle strategies, broker marriages, build sanitation systems/toilets ... But only two farm

¡ Ants: clearing weeds, farming insects and fungi, feeding them, maintaining fungal cultures ...

¡ And its worse ...

¡ If you put goats on an island, after 10 years you will only have goat-proof plants left!

¡ Humans too have strong tendency to overexploitation § Dodo§ Cape Cod

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Population increase

Farming

Chicken

Egg

Population increase↑

Competitive Advantage↓

Farming

02/03/2012 20

(Not Archaeology and Anthropology!)

Hunter-gatherer no longer sustainableOver-exploitation?

Habitat destruction/extinction?Population growth?

Climate change? Food stability?Diet change?sf

(Is farming reaching its end now?)

¡Habitat destruction¡ Climate change (abiotic stresses)¡Diseases (biotic stresses)¡ Changes in what people want¡ Blindness to what is happening¡Unwillingness to change

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¡ Will not be displaced¡ Continue to need 1 to 1.5% year-on-year

productivity increase¡ Increased sustainability essential¡ Major breeding targets§ Post-harvest losses§ Water use§ Disease resistance§ Quality

0

0.5

1

1.5

2

2.5

3

3.5

4

1961 1970 1980 1990 2000 2007

MaizeRiceWheatHumanArea

0

0.5

1

1.5

2

2.5

3

3.5

4

1961 1970 1980 1990 2000 2007

MaizeRiceWheatHumanArea

Agronomy

Genetics

GMmaize

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.

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lOther people’s cultivars

¡ Cross the best with the best and hope for something better

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lLandraces

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lLandraceslWild and cultivated relatives

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dpTa1pSc119.2Genomic Ae.ventricosa

Inheritance of Chromosome 5DAegilops ventricosaDDNN

ABDN

AABBDDNN MarneAABBDD

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 allvarieties are highly susceptible¡ Alien variation can be

found and used7¡ Host and non-host

resistances

Crop standing

Lodging in cereals

Crop fallen

Susanne Barth, Ulrike Anhalt, Celine Tomaszewski

Anhalt, Barth, HHEuphytica 2009Theor App Gen 2008

n Formidable genetic and environmental interactions

Anhalt UCM, Heslop-Harrison JS, Piepho HP, Byrne S, Barth S. 2009. Quantitative trait loci mapping for biomass yield traits in a Lolium inbred line derived F2 population. Euphytica 170: 99-

Size and location of chromosome regions from radish (Raphanussativus) carrying the fertility restorer Rfk1gene 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)

Cell fusionhybrid of two4x tetraploidtobaccospecies

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

¡ How many genes are there?¡ 1990s: perhaps 100,000¡ 2000: 25,000¡ How does this give the range of functions and

control?

Najl Valeyev

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¡ Increased sustainability¡ Increased value¡Uses genes outside the

conventional genepoolBenefits to all stakeholders:Breeders, Farmers, Processors,Retailers, Consumers, Citizensin developed and developing countriesand to all members of society.

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

¡ 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

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¡ 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

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¡The additions to the FAO list of crops since 1961§Triticale§Kiwi fruit§ Jojoba

+ two split categories:popcorn, feed legumes

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¡ The additions to the FAO list

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

• 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

¡ 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

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

¡ Mutation¡ Rearrangement¡ Duplication¡ Deletion¡ Homogenization

¡ Sequences¡ Genes / motifs¡ Repetitive DNA¡ Chromosomes¡ Chromosome sets

(‘Genomes’)

¡ Genotypes/CVs¡ Species¡ Genera and above

¡ Crops / wild species¡ Selection¡ Speciation

¡ Farmers and agriculture underpin the well-being of the world’s population. Agriculture is changing continuously: every year for the last 10,000 years, farmers have improved their weed control and water management, and each decade, farmers have won and lost battles with pests and diseases, and adopted new varieties of their crops. Over a longer timescale of 50 to 100 years, they introduce new species to cultivation and the food supply, even if the exchanges of old-world and new-world crops in the 16th and 17th centuries – including maize and potato from tropical America with wheat from the middle-east and sugar cane from southeast Asia – are unlikely to be repeated. ‘Novelty’ in crops can come from finding and exploiting new diversity in existing major crops or from improving and introducing species not previously used on a significant scale. The exploitation of new diversity is important to the livelihood of subsistence farmers and commercial growers. Modern genetics, mutation and molecular methods, and plant breeding can benefit producers, consumers and the environment.

¡ It is interesting to contemplate … manyplants of many kinds … and to reflectthat these elaborately constructedforms, so different from each other …

¡ There is grandeur in this view of life, with its several powers ... whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.

1: Genes, genomes and genomics in crops2: Species, crops and domestication3: Diversity sources: mutations and germplasm4: Genome & chromosome organization5: Markers, mapping and QTL analysis6: DNA markers from genomics7: Markers for biodiversity8: Superdomestication and breeding9: Agriculture, food and Millennium Dvlpmnt Goals10: PCR for genes and diversity

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• Targeted breeding and transgenicstrategies

• Increase in high value niche crops

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¡ Technology underpins developments§ Complexity§ Direction§ Safety¡ Germplasm collection and diversity¡ Statistical methods¡ Screening

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¡ Genes, gene combinations and species with limited exploitation in agriculture

¡ Present in non-domesticated species, unimproved cultigens and crops with different characteristics

¡ Make more money - OUTPUT¡ Sell more for the same per unit¡ Sell the same units for more¡ Sell different (produce or service)

¡ Spend less money - INPUT¡ Less inputs¡ Less labour¡ Less capital (land and equipment)

¡ There aren’t any!

¡ Crops come from anywhere¡ They might be grown anywhere¡ Polyploids and diploids (big genomes-small

genomes, many chromosomes-few chromosomes)¡ Seeds, stems, tubers, fruits, leaves

¡ 40% 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

¡ Farm§ Not wild-collected§ Mostly kept land in production▪ No slash/burn▪ Erosion control▪ Intelligent irrigation

¡ 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

Pat Heslop-HarrisonTalk 2: Genome evolution: perspectives from billions of years to plant breeding timescales, from the base pair to trillions of bases, and from the cell to the planet and beyond

phh4@le.ac.ukwww.molcyt.com pw/user: ‘visitor’Social media: pathh1 Twitter/YouTube

PAU, Ludhiana 21 – 2 – 12