1. BS2081
Ecology and Biodiversity
Pat Heslop-Harrison
University of Leicester, UK
phh4@le.ac.uk
www.molcyt.com UserID/PW „visitor‟
Twitter: pathh1 –
cytogenomics.wordpress.com
20/02/2013 1

2. 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

3. Biodiversity
What is biodiversity?
20/02/2013 3

4. Rio de Janeiro Conference in June 1992
Defined 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.”
4

5. Biodiversity
Agriculture brings in new
species and new genotypes
„Biodiversity‟ includes
weeds, pests, vectors,
predators
20/02/2013 5

6. Domesticated species
What are domesticated
species?
20/02/2013 6

7. What are domesticated species?
Those where people control their
reproduction and nutrition
Many 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
20/02/2013 7

8. Domesticated species
What?
Mammals
Plants
Other species
–Fungi, Insects
–Fish, Molluscs
20/02/2013 –Birds 8

9. Are there many candidates?
380,000 plants
4,629 mammals
9,200 birds
10,000,000 insects
But only 200 plants, 15 mammals, 5
birds and 2 insects are domesticated!
9

10. 10

11. 11

12. 12

13. 13

14. 14

15. 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
15

16. 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
16

17. Suite of
plant domestication traits
Seed dispersal – no!
Seed dormancy – yes then no!
Large harvested parts
– Gigantism
– High proportion useful
Determinate/synchronized growth
Edible and tasty
17

18. Examples
Wheat
Tomato
Cattle
Pigs
http://www.els.net/WileyCDA/
18

19. Tinyurl.com/domest
http://www.le.ac.uk/biology/phh4/p
ublic/PHH_AltmanHasegawa_ch001.
pdf
19

20. 20

21. S. Banga – Punjab Agricultural University
first determinate / terminal flowering
Brassica juncea / B. napus lines Feb 2012 21

22. 22

23. 23

24. When did domestication start?
About 8,000 years before
present
Plants and animals
In context:
Humans 6,000,000 years since
divergence from apes
or 50,000 years since recognizably
20/02/2013 „modern‟ 24

25. Why did domestication start?
(Not Archaeology and Anthropology!)
Hunter-gatherer no longer sustainable
Over-exploitation?
Habitat destruction/extinction?
Population growth?
Climate change? Food stability?
Diet change? sf
20/02/2013 25

26. Where?
After Diamond 2002

27. Domesticated species
What?
How?
When?
Why?
Where?
20/02/2013 27

28. 28

29. NASA
The Blue Marble
Apollo 17 7 Dec 1972

30. Ecosystems anchor slide
Largely
– Self-organizing
– Self-maintained
– Cycling
– Defined scope
– cf Household
– Aircraft
–
30

31. 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

32. Rainfall
Distribution
mm/yr
32

33. Ecosystems
Recognizing
– Inputs
– Outputs
– Networks / webs of organisms
– Cycles
– Scales
– Functions 33

34. Inputs
– Light
– Heat
– Water
– Gasses
– Nutrients
34

35. 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

36. Outputs
– Light
– Heat
– Water
– Gasses
– Nutrients
36

37. Outputs
Ecosystem
Services
Water, gasses,
nutrients
”nature‟s services, like flood control, water
filtration, waste assimilation”
37

38. Dynamic processes: turn-over
Outputs
– Limestone
38
– Made by marine organisms, formation and
stability affected by pH and temperature

39. Inputs - Biotic
– Diseases
– New organisms
• Aliens/invasives
– New genes and
genotypes of
existing
organisms
39

40. Outputs
– Light
– Heat
– Ecosystem services
– Chemical energy
– Long term storage
Required
and valued
40

41. Biotic Inputs
– New genes
– New species
• Diseases
• Alien species
Abiotic inputs
– Irrigation
– „Salt‟ (NaCl)
– Nitrogen
– Phosphorous
41

42. 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 42

43. Argenome mexicana: a goat-proof plant from
Mexcio introduced and successful in Africa 43

44. 44

45. Occasional ‘extreme inputs’:
Limiting composition of ecosystems
more than ‘mean input’ - Robustness 45

46. 46

47. 47

48. Anhalt, Barth, HH
Euphytica 2009 Theor App Gen

49. Light in ecosystems
Heat Information
Energy
Quantity Quality Direction Periodicity
Photosynthesis
Control of development

50. Threats to sustainability:
no different for 10,000 years
Habitat destruction
Climate change (abiotic stresses)
Diseases (biotic stresses)
Changes in what people want
MORE outputs needed
MORE stability in outputs from less
stable inputs / poorer environments

51. 51

53. How to exploit models
Increased sustainability
Increased value
Genetic improvement
Robustness („food security‟)
Benefits to all stakeholders:
Breeders, Farmers, Processors,
Retailers, Consumers, Citizens
53

54. 50 years of plant breeding progress
4
GM maize
Maize
Genetics
3.5
3 Rice
2.5
Agronomy Wheat
2
Human
1.5
Area
1
0.5
0
1961 1970 1980 1990 2000 2007

55. UK Wheat 1948-2007
52,909 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

56. Conventional Breeding
Cross the best with the best and hope for
something better
Superdomestication
Decide what is wanted and then plan how to
get it
– Variety crosses
– Mutations
– Hybrids (sexual or cell-fusion)
– Genepool
– Transformation

57. 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

59. 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

60. 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.)

61. Needs from Stochastic Models of Ecosystems
Outputs Inputs
Ecosystem – Light
services – Heat
– Chemical – Water
energy
– Gasses
– Long term
– Nutrients
storage
61

62. The major crops
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
62

63. Where do these
genes come from?
63

64. Other cultivars
Landraces
Wild and cultivated
relatives
Other species
Mutation breeding
Synthetic biology
64

65. Conventional Breeding
Cross the best with the best and hope for
something better
Superdomestication
Decide what is wanted and then plan how to
get it
 - variety crosses
 - mutations
 - hybrids (sexual or cell-fusion)
 - genepool
 - transformation

66. 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
66

67. 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

71. 50 years of plant breeding progress

72. 50 years of plant breeding progress
4
3.5 Maize
3 Rice
2.5
Wheat
2
Human
1.5
Area
1
0.5
0
1961 1970 1980 1990 2000 2007

73. 50 years of plant breeding progress
GM
4
maize
Maize
Genetics
3.5
3 Rice
2.5
Agronomy Wheat
2
Human
1.5
Area
1
0.5
0
1961 1970 1980 1990 2000 2007

74. Why exploit novel germplasm?
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.
74

75. Conventional Breeding
Cross the best with the best and hope for
something better

76. New crops
The additions to the FAO list
– Triticale (Genome engineering)
– Kiwi fruit (High value niche)
– Jojoba (New product)
– Popcorn is split (High value)
76

77. 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

78. 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. 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
Tinyurl.com/domest

79. Lolium Biomass production
Susanne Barth, Ulrike Anhalt, Celine Tomaszewski

81. Size and
location of
chromosome
regions from
radish
(Raphanus
sativus)
carrying the
fertility
restorer
Rfk1 gene
and transfer
to spring
turnip rape
(Brassica
rapa)

82. Chromosome
and genome
engineering
Cell fusion
hybrid of
two
4x tetraploid
tobacco
species

83. Nicotiana
hybrid
4x + 4x
cell fusions
Each of 4
chromosome
sets has
distinctive
repetitive
DNA when
probed with
genomic DNA
Patel et al
Ann Bot 2011

84. Exploiting novel germplasm
Superdomestication
• Targeted breeding and
transgenic strategies
• Increase in high value niche
crops
84

86. 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

87. Market demand “MORE”
 Food (people)
 Feed (animals)
- Major driver of volume
Enormous increase in pigs and poultry
Increases 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

88. 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.)

89. 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

90. 90

91. 91

92. 92

93. 93

94. 94

95. 95

96. 96

97. 97

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

100. 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

101. Crop standing
Lodging in cereals
Crop fallen

102. Rules for successful
domestication
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

103. 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

104. 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

105. 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

106. Do we need change?
Do we need faster change?
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

107. 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

108. 108

109. http://blog.ecoagriculture.org/2012/02/29/pac
109

110. 110