1. Pat Heslop-Harrison
Talk 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.uk
www.molcyt.com pw/user: ‘visitor’
Social media: pathh1 Twitter/YouTube
PAU, Ludhiana 21 – 2 – 12

2. Brassica
Wheat
Banana
Others
Crocus
Panicum
Drosophila
Arachis
Medicago

4. Genomics & Genome
organization in
chromosomes
Hybrids/polyploids
Biodiversity
Systems biology
Introgression and
breeding
Socio-economics and
applications

5. l Those where people control their
reproduction and nutrition
lMany alternatives
People control their access to space
People have selected the variety
They are different from wild species
They would die out in the wild
02/03/2012 Species useful to humans 5

6. l Those where people control their
reproduction and nutrition
What about
Weeds
Commensuals
Diseases
?
02/03/2012 6

7. ¡ 350,000 plants
¡ 4,629 mammals
¡ 9,200 birds
¡ 10,000,000 insects
¡ 500,000 fungi
7

8. ¡ 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
8
¡ Are there many candidate species?

9. ¡ 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
9 2 insects are domesticated

10. ¡ 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 ...
10
§ Two ferns are invasive problem

11. ¡ 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

12. 12

13. About 10,000 years before
present
Plants and animals
In context:
Humans 6,000,000 years since
divergence from apes
or 50,000 years since recognizably
‘modern’
02/03/2012
Worldwide! 13

14. 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 toxic
All still a challenge today – and many
improvements are still coming

15. ¡ 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

17. ¡ 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 ...

18. ¡ 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

19. Population increase
Population increase
Chicken
↑
Farming
Competitive Advantage
↓
Farming
Egg
02/03/2012 19

20. (Not Archaeology and Anthropology!)
Hunter-gatherer no longer sustainable
Over-exploitation?
Habitat destruction/extinction?
Population growth?
Climate change? Food stability?
Diet change? sf
(Is farming reaching its end now?)
02/03/2012 20

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

23. ¡ 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
23

28. 4
3.5 Maize
3 Rice
2.5
Wheat
2
Human
1.5
Area
1
0.5
0
1961 1970 1980 1990 2000 2007

29. 4
GM
3.5
maize Maize
3
Genetics Rice
2.5
Agronomy Wheat
2
Human
1.5
Area
1
0.5
0
1961 1970 1980 1990 2000 2007

30. 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.

31. lOther people’s cultivars
31

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

33. lLandraces
33

34. lLandraces
lWild and cultivated relatives
34

35. 35

37. Inheritance of Chromosome 5D
Aegilops ventricosa × Triticum persicum Ac.1510
DDNN AABB
ABDN
AABBDDNN × Marne
AABBDD
VPM1 × Hobbit Dwarf A
CWW1176-4 × Virtue
Rendezvous × {Kraka × (Huntsman × Fruhgold)}
dpTa1
pSc119.2 Piko 96ST61
Genomic Ae.ventricosa

38. ¡ 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

39. Crop standing
Lodging in cereals
Crop fallen

40. Susanne Barth, Ulrike Anhalt, Celine Tomaszewski

41. n Formidable
genetic and
environmental
interactions
Anhalt, Barth, HH
Euphytica 2009
Theor App Gen 2008

42. Anhalt UCM, Heslop-Harrison JS, Piepho HP, Byrne S, Barth S. 2009. Quantitative trait loci

44. 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)

46. Cell fusion
hybrid of two
4x tetraploid
tobacco
species
Patel, Badakshi, HH,
Davey et al 2011
Annals of Botany

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

50. ¡ Increased sustainability
¡ Increased value
¡ Uses genes outside the
conventional genepool
Benefits to all stakeholders:
Breeders, Farmers, Processors,
Retailers, Consumers, Citizens
in developed and developing countries
and to all members of society.
50

51. 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

52. ¡ 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

53. ¡ 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
53

54. ¡ The additions to the FAO list of
crops since 1961
§ Triticale
§ Kiwi fruit
§ Jojoba
+ two split categories:
popcorn, feed legumes
54

55. ¡ The additions to the FAO list
§ Triticale (Genome engineering)
§ Kiwi fruit (High value niche)
§ Jojoba (New product)
§ Popcorn is split (High value)
55

56. • 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

57. ¡ 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

59. 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. 1125 Mbp 38 4 Cotyledon oil/protein
napus
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

60. ¡ Sequences
¡ Genes / motifs
¡ Repetitive DNA
¡ Chromosomes ¡ Mutation
¡ Chromosome sets ¡ Rearrangement
(‘Genomes’) ¡ Duplication
¡ Genotypes/CVs ¡ Deletion
¡ Species ¡ Homogenization
¡ Genera and above
¡ Crops / wild species
¡ Selection
¡ Speciation

61. ¡ 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.

62. ¡ It is interesting to contemplate … many
plants of many kinds … and to reflect
that these elaborately constructed
forms, so different from each other …

63. ¡ 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.

64. 1: Genes, genomes and genomics in crops
2: Species, crops and domestication
3: Diversity sources: mutations and germplasm
4: Genome & chromosome organization
5: Markers, mapping and QTL analysis
6: DNA markers from genomics
7: Markers for biodiversity
8: Superdomestication and breeding
9: Agriculture, food and Millennium Dvlpmnt Goals
10: PCR for genes and diversity

66. • Targeted breeding and transgenic
strategies
• Increase in high value niche crops
66

67. ¡ Technology underpins developments
§ Complexity
§ Direction
§ Safety
¡ Germplasm collection and diversity
¡ Statistical methods
¡ Screening
67

68. ¡ Genes, gene combinations and species with
limited exploitation in agriculture
¡ Present in non-domesticated species,
unimproved cultigens and crops with
different characteristics
68

70. ¡ 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)

71. ¡ 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

72. ¡ 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

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

74. ¡ 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

75. Pat Heslop-Harrison
Talk 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.uk
www.molcyt.com pw/user: ‘visitor’
Social media: pathh1 Twitter/YouTube
PAU, Ludhiana 21 – 2 – 12