PUBLIC SEMINAR At Agro-Biotechnology Institute, ABI Serdang Prof J. S. “Pat” Heslop-Harrison, University of Leicester Academic Icon, University of Malaya Chromosomes, Crops and Superdomestication Crop improvement is reliant on the exploitation of new biodiversity and new combinations of diversity. I will discuss our work on genome structure and evolution, involving processes including polyploidy, introgression, recombination and repetitive DNA changes. Identification and measurement of diversity and relationships assists in use of new gene combinations or new crops, through synthesizing new hybrid species, by chromosome engineering or by transgenic strategies. We are studying crops including wheat, Brassica and banana, using genome sequencing, repetitive sequence comparison, and cytogenetics. Plants, pathogens and farmers have been involved in a three-way fight since the start of agriculture, and the concept of superdomestication involves systematic identification of needs from crops, only then followed by finding appropriate characters and bringing them together in new varieties. Crops will continue to deliver the products needed for food, fibre, fuel and fibre in an increasingly sustainable and safe manner.

1. Chromosomes, Crops and
Superdomestication
Pat Heslop-Harrison
phh4@le.ac.uk
www.molcyt.com and www.molcyt.org
Twitter, YouTube and Slideshare: pathh1
17 December 2013 10-12

2. Outputs
–CROPS
– Fixed energy
Inputs
–Light
–Heat
–Water
–Gasses
–Nutrients

3. Outputs
–CROPS
– Fixed energy
– Light
– Heat
– Water
– Gasses
– Nutrients
3
Inputs
–Light
–Heat
–Water
–Gasses
–Nutrients

5. Apollo 17 – The Blue Marble December 7, 1972
NASA
The Blue Marble
Apollo 17 7 Dec 1972

6. We’ve done that before …
Coming out of ice age at time of recognizably modern
humans 50,000 yrs ago
Coming up to the start of agriculture 10,000 yrs ago
During agricultural clearances 2,000 and 1,000 yrs ago
During better cultivation 150 yrs ago
20th Century: Drainage/fertilization/crop protection
… and nearly every other ‘species’ tries to do it …
goats, pines, viruses

7. Burren West Ireland
Mediaeval: Peat forest 1500 years of overgrazing
Eroded to bedrock (now a preserved landscape!)

8. st
21
C: Population increase
higher living standards / health
fossil fuel use
climate change
water …

9. Life on the edge …
Verge of stability for fire
with 20% oxygen
Water – quality and
quantity
Temperature – too
hot or cold
ABIOTIC FACTORS

11. 11

12. • Brazil slash and burn
• Malaysian cut out ganoderma plants

13. Ecosystems anchor slide
Largely
– Self-organizing
– Self-maintained
– Cycling
– Defined scope
– cf University
– Household
– Aircraft
–
13

14. Outputs
–CROPS
– Fixed energy
– Light
– Heat
– Water
– Gasses
– Nutrients
14
Inputs
–Light
–Heat
–Water
–Gasses
–Nutrients

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

16. Ecosystem cycling threatened
by stress and Abiotic
instability
Water
Fire
Wind
Biotic
Virus, bacteria, fungi
Weeds, insects
Nematodes etc.
Alien invasions
16

17. Rainfall
Distribution
mm/yr
17

18. 18
Occasional ‘extreme inputs’:
Limiting composition of ecosystems
more than ‘mean input’ - Robustness

20. 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
20

21. 21
Argenome mexicana: a goat-proof plant from
Mexcio introduced and successful in Africa

22. Anhalt, Barth, HH
Euphytica 2009 Theor App Gen 200

23. 23

24. 24

26. 50 years of plant breeding progress
4
Maize
Rice
Wheat
Human
Area
3.5
3
Agronomy
2.5
2
1.5
1
0.5
0
1961
1970
1980
1990
2000
2007

27. 27

29. • 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

32. Outputs
–Crops
(Chemical energy)
– Food
– Feed
– Fuel
– Fibre
– Flowers
– Pharmaceuticals
– Fun
32

33. 50 years of plant breeding progress
4
Maize
Rice
Wheat
Human
Area
Genetics
3.5
3
2.5
2
1.5
1
0.5
0
1961
1970
1980
1990
2000
2007

34. 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 website.

35. 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

36. 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

38. Inputs
–Light
–Heat
–Water
–Gasses
–Nutrients
–STRESSES
38

40. BIODIVERSITY and genetic resources
Red - AAA
Palayam codan AAB (two bunch yellow, one green)
Peyan ABB (green cooking banana),
Njalipoovan AB (yellow)
Robusta AAA (green ripe)
Nendran AAB
Poovan AAB (one yellow bunch)
Red AAA
Peyan
Varkala, Kerala, India

42. Genomes and
genomics

43. Genomics
• Study of the structure, diversity, function and
behaviour of all the DNA in an organism, organelle
or virus
ata clone MuG9, genomic, 73268bp
gaaatccaatcaatccagatcaatattgatcgggttctg
tgacgaagcagtcaaactgatcactaaaattcaatacat
ggagtgctgatttcagaaacttaatcccttctgatagaa
ccaacttacactaattagtcttaaaactcattaaggttg
aataaatgtcatattacccttccaggtcataaacagctt
aatgctgaagctattggcattacacttagtcttaacttc
atttaacgatatgacaatcaataatgagataggcaaata
aaaatgacatttttttgaactctgcagaattagctccta
atcctttagtgaatgcagacaaggaatcagtaaccactg

45. Triticale: wheat x rye hybrid

46. Wheat evolution and hybrids
Triticum uratu
2n=2x=14
AA
Aegilops speltoides
relative
2n=2x=14
Triticum tauschii
BB
(Aegilops squarrosa)
Triticum dicoccoides
2n=4x=28
AABB
Einkorn
Triticum monococcum
2n=2x=14
Rye
AA
Secale cereale
2n=2x=14
RR
Durum/Spaghetti
Triticum turgidum ssp durum
2n=4x=28
AABB
2n=2x=14
DD
Bread wheat
Triticum
aestivum
2n=6x=42
AABBDD
Triticale
xTriticosecale
2n=6x=42
AABBRR

47. Crop standing
Lodging in cereals
Crop fallen

48. Use of repetitive DNA sequences as
chromosome markers

49. Satellite DNA probe green

51. Differences between genomes
Major differences in the nature and amount of
repetitive DNA
• dpTa1 tandem repeat • 45S rDNA

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

53. Multiple repeat (dpTa1) variants
of each chromosome
e.g. 5DL
Bardsley, Schwarzacher & HH

54. S
1A L
Multiple dpTa1 variants
of each chromosome
S
2A L
S
e.g. 5DL
3A L
S
4A L
S
5A L
S
6A L
S
7A L
5BS.
5BL.
7BS
7BL
Bardsley, Schwarzacher & HH

55. Proportion of chromosome arms with
identical in situ signal
Correlation between genetic relationships and
similarity of dpTa1 hybridization
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
0
0.1
0.2
0.3
0.4
0.5
0.6
Coefficient of parentage
0.7
0.8
0.9
1

56. •
•
•
•
Tandem Repeats
Where each arrow is a single unit of a repeat –
- often a multiple of 180 bp but up to 10kb long
Head-to-tail organization
TCGCTAGA TCGCTAGA TCGCTAGA TCGCTAGA
TCGCTAGA TCGCTAGT TCGCTAGA TCGCTAGA

57. ancestral
High-copy number
A
High-copy number
B
Low-copy number
High-copy number
C
High-copy number
D
Low-copy number
High copy spp: homogenized, amplification from a limited number of master
copies
Low copy spp: much variation
Kuhn, Schwarzacher, PHH

58. Use of repetitive DNA sequences as
chromosome markers

59. Wheat Streak Mosaic Virus in North America
Bob Graybosch, USDA

60. Wsm-1: only highly effective source of resistance to WSMV

61. Mace wheat
Graybosch et al. 2009
In situ: Niaz Ali & Schwarzacher

64. Retroelements
Sequences which amplify through an RNA intermediate
•50% of all the DNA!

65. Retroelement Markers
Insertion
LTR
Retrotransposon
LTR
IRAP – InterRetroelement PCR
LTR
LTR
Retrotransposon
Retrotransposon
LTR
LTR
LTR
LTR
LTR
Retrotransposon
Retrotransposon
LTR
Retrotransposon
LTR
LTR

66. UPGMA dendrograms of the relationships based on IRAP analysis of (A) accessions of Ae.
tauschii subsp
Copyright restrictions may apply.
Saeidi, H. et al. Ann Bot 2008 101:855-861; doi:10.1093/aob/mcn042

68. Retroelements
•Homologous BAC sequences from Calcutta 4
Homologous over the full length
•except for a 5kb insert
•a Ty1-copia retroelement

69. Musa balbisiana (MBP 81C12)
hAT 1
1676 TE
Musa acuminata (MA4 82I11)
384 bp TE + 781 MITE
Microsatellite (AT)
hAT 2
Transposed Element
621 bp MBT
hAT 3
4192 bp TE
Sr. No.
Primer Pairs
Product Size
(bp)
Sequence
hAT 4
1.
hAT18486
hAT19037
560
ACCCACCTGGCTCTTGTGTC
AGCGAATGTGTTTTGACCAC
Microsatellite (AT)
MBP 81C12 (M. balbisiana) x MA4 82I11 (M. acuminata) BACs.69
16/12/2013

70. 1KB
800
600
400
200
HP-1
1
2 3 4 5
6
7 8 9 10 11 12 13 14 15 16
17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
hAT1 insertion sites in Musa diversity collection
hAT486F and hAT037R
Top bands (560-bp) amplified hAT element and lower bands amplifying the flanking
16/12/2013
70
sequences only – Menzel, Nouroz, Schmidt, Schwarzacher, Heslop-Harrison 2013/14

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

72. Chromosome
and genome
engineering
Cell fusion
hybrid of two
4x tetraploid
tobacco
species
Patel, Badakshi, HH, Dav
ey et al 2011 Annals of
Botany

73. 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

74. Diploid 2n=2x=22 Musa / banana metaphase probed red with transposable element
Teo & Schwarzacher

76. Six-way Venn diagram showing the distribution of shared gene
families (sequence clusters) among M. acuminata, P. dactylifera,
Arabidopsis thaliana, Oryza sativa, Sorghum bicolor and Brachypodium
distachyon genomes.
A D’Hont et al. Nature 000, 1-5 (2012)
doi:10.1038/nature11241
A D’Hont et al. Nature 2012 doi:10.1038/nature11241

78. Whole-genome duplication events.
A D’Hont et al. Nature 000, 1-5 (2012)
doi:10.1038/nature11241

79. A D’Hont et al. Nature 2012
doi:10.1038/nature11241

81. Arachis hypogaea - Peanut
Tetraploid of recent
origin, ancestors separated only 3
My ago
Ana Claudia Araujo, David Bertioli, TS & PHH EMBRAPA, Brasília. Annals of Botany 2013

82. Retroelement abundance and
diversity in barley
Gypsy elements are present in 25% of all BAC clones
Barley gypsy: Vershinin, Druka, Kleinhofs, HH: PMB 2002; cf Brassica Alix & HH PM

83.  Bertioli et al. Annals of Botany 2013
•Arachis hypogea 2n=4x=40 probed with
•(green) A. duranensis; (red) A. ipaënsis

84. Oscillations: noise and stability
• Stochastic fluctuations
– preserve stable oscillations
– ensure robustness of the oscillations to cell-to-cell variations
• Robustness analysis requires stochastic simulation
JongRae Kim et al. Stochastic noise and synchronisation during Dictyostelium
aggregation make cAMP oscillations robust. PLoS Computational Biology 2007

85. Weak
Stronger
Coupling
Kim J-R, Shin D, Jung SH, Heslop-Harrison P, Cho K-H. 2010. A design principle underlying the
synchronization of oscillations in cellular systems. Journal of Cell Science 123(4): 537-543

86. • Dynamic interactions between dependent modules
•
•
Valeyev et al. Mol Biosyst 2009 5: 612
Kim J-R, Kim J, Kwon Y-K, Lee H-Y, Heslop-Harrison P, Cho K-H. 2011. Reduction of complex signaling
networks to a representative kernel. Science Signaling 4, ra35. doi: 10.1126/scisignal.2001390

87. • Stable cAMP oscillations in the
cells with other
molecules/ions
Valeyev et al. Mol Biosyst 2009

88. •
•
•
•
“Biochemistry explains biology”
“Chemistry explains biochemistry”
“Physics explains chemistry”
“Mathematics explains physics”

89. From Chromosome to Nucleus
Pat Heslop-Harrison phh4@le.ac.uk www.molcyt.com

90. Outputs
–Crops
(Chemical energy)
– Food
– Feed
– Fuel
– Fibre
– Flowers
– Pharmaceuticals
– Fun
90

91. The genepool has the diversity to
address these challenges …
New methods to exploit and
characterize germplasm let use make
better and sustainable use of the
genepool
Molecular cytogenetics …

92. How to use diversity
• Cross two varieties
• Genome manipulations
•
Cross two species and make a new one
•
Cell fusion hybrids
• Chromosome manipulation
•
Backcross a new species
• Generate recombinants
•
Chromosome recombinations
• Transgenic approaches
• Use a new species

93. Are there many candidates?
•
•
•
•
250,000 plants
4,629 mammals
9,200 birds
10,000,000 insects
• But only 200 plants, 15 mammals, 5 birds
and 2 insects are domesticated!

94. 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/B9780-12-381466-1.00001-8
Tinyurl.com/domest

95. Rules for successful domestication
• There aren’t any!
• Crops come from anywhere (new/old world;
temperate/tropical; dry/humid)
• They might be grown worldwide
• Polyploids and diploids (big genomes-small
genomes, many chromosomes-few
chromosomes)
• Seeds, stems, tubers, fruits, leaves

96. Probably not many more
(at least for plants)
• Spread of the few species
• Little change since early agriculture
• Repeated domestication of these species
(sometimes)
• But wider use of current species with suitable
genetic changes, or of newly created hybrids
• A few species where wild-collections must be
replaced sustainably
• New needs – biofuels, neutraceuticals

97. 50 years of plant breeding progress
GM maize
4
Maize
Rice
Wheat
Human
Area
Genetics
3.5
3
Agronomy
2.5
2
1.5
1
0.5
0
1961
1970
1980
1990
2000
2007

101. 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

102. Chromosomes, Crops and
Superdomestication
Pat Heslop-Harrison
phh4@le.ac.uk
www.molcyt.com and www.molcyt.org
Twitter, YouTube and Slideshare: pathh1
17 December 2013 10-12