Polyploidy, its occurrence in plants, consequences and evolutionary significance. Lecture to Japanese Genetics Society, Okayama, September 2017. Covering wheat and its evolution

1. Pat Heslop-Harrison
phh@molcyt.com
www.molcyt.com
89th Genetics Society of Japan Meeting
Centennial of the discovery of the correct
chromosome number and polyploidy in wheat
Polyploidy, its distribution and
evolutionary significance

3. H Kihara 1945

5. Hsu, Tao-Chiuh. Mammalian chromosomes in vitro. I. The karyotype of man. J. Hered. 1952.
TC (Tao-chiuh) Hsu
April 17, 1917 – July 9, 2003
Tjio & Levan 1956: 2n=46

6. CHAPTER 24:
THE FUTURE
“Probably the most pressing
problem in chromosome
research is the understanding of
the molecular architecture of the
chromosomes”
“Evolutionary studies using
cytogenetic characteristics
should gain more sophistication
and momentum”
1979

7. Rye chromosomes 2n=2x=14
Satellite DNA probe green
45S rDNA probe (NORs) red

8. Wheat and wild relatives

9. Satellite DNA probe green
45S rDNA probe (NORs) red

12. Lodging in cereals

13. Triticum aestivum wheat ‘Rendezvous’
eyespot (Oculimacula/Pseudocercosporella) resistance from Aegilops ventricosa
pSc119.2 dpTa1

14. Inheritance of Chromosome 5D
dpTa1
×Aegilopsventricosa DDNN
ABDN
AABBDDNN Marne
AABBDD
VPM1
×
Triticum persicum Ac.1510 AABB
VPM1:
The entire original
chromosome from
Ae. ventricosa is not
transferred, but a
small is translocated
to the Marne 5D

15. Inheritance of Chromosome 5D
dpTa1
×Aegilopsventricosa DDNN
ABDN
AABBDDNN Marne
AABBDD
CWW1176-4
Rendezvous
Piko
VPM1 Dwarf A
96ST61
Virtue
×
×
×
Hobbit
× {Kraka×(Huntsman × Fruhgold)}
Triticum persicum Ac.1510 AABB
VPM1:
The original
chromosome from
Ae. ventricosa is not
transferred, but a
small segment is
translocated to the
Marne 5D
transferred to further
recombinant 5D chromosomes

16. Highest yielding group1 breadmaking
wheat in UK, released 2013
Includes pch1

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

18. Wheat 5AS.5RL at meiosis
Schwarzacher 1997 Plant Sexual Reproduction 10, 324-331
Meiotic interphase Leptotene
Zygotene Pachytene MI

20. Saffron
Crocus sativus
2n=3x=24
Minimal if any genetic variation
Vegetatively propagated
Grown (China), Kashmir, Europe, Iran
Most valuable agricultural/farmed product
AlSayied, HH et al. 2015. Ann Bot

21. Identical patterns in fingerprint gel with
diverse Saffron accessions (18=garden-hyb)
Nouf Alsayied, HH et al Ann Bot 2015

22. Variable patterns in 11 Crocus species,
including intra-specific variation
(19-21 and 22-24)
Saffron 1-5

24. A garden plant in UK : Crocus ‘Golden Yellow’ triploid 2n=3x=14
C. flavus 2n=2x=8 (8 yellow) C. angustifolius 2n=2x=12 (6 green)
Orgaard, Jacobsen & HH
‘Stellaris’ hybrid diploid 2n=2x=10
C. flavus 2n=2x=8 (4 green)
C. angustifolius 2n=2x=12 (6 blue)
Orgaard & HH, Ann Bot

25. Metaphase I in triploid hybrid Golden Yellow Crocus
Four bivalents C. flavus (2n=2x=8)-origin chromosomes
Six univalents C. angustifolius (2n=2x=12)

26. Origins of Crocus sativus
(Not only from C. cartwrightianus by
autotriploidy)
C. cartwrightianus crossed with a related
species involving unreduced gamete
F1 hybrid between 2 species crossed with
3rd species with an unreduced gamete
AAA AA’B ABC
5 III + 3 II + 3 I
8 III ?
John Bailey, Farah Badakshi, Nouf Alsayied, Trude Schwarzacher
Genomic constitution

27. Saffron: another triploid Crocus sativus
Pachytene: so no variation from meiosis
DAPI

28. Mid Zygotene Pachytene DiploteneEarly Zygotene
Dynamics of centromeres during meiosis in
6x wheat
CENH3 centromere
ASY1 associated with the lateral elements
ZYP1 central element of the synaptonemal complex
CENH3 centromere
ASY1 associated with the lateral elements
ZYP1 central element of the synaptonemal complex
Sepsi, Heslop-Harrison,
Schwarzacher et al.
Plant Journal 2017

29. (a) Interphase (b) Leptotene (c) Early Zygotene
CENH3TRSDAPICENH3ASY1CENH3ASY1
CENH3 centromere
ASY1 associated with the lateral elements
ZYP1 central element of the synaptonemal complex

30. Centromere dynamics and timing of chromosome synapsis (6x wheat)
Sepsi et al. Plant Journal 2017
0
5
10
15
20
25
30
35
40
Interphase Leptotene Early Mid-late Pachytene Diplotene
Zygotene Zygotene
2n=42
3 x 14
chromosomes
21 bivalents
3 x 7
pairs of
chromosomes

31. (a) (b) (c)
(d) (e) (f)
(g) (h) (i)
ASY1CENH3DAPI

32. Mid Zygotene Pachytene DiploteneEarly Zygotene
Dynamics of centromeres during meiosis

33. Mid Zygotene Pachytene DiploteneEarly Zygotene
Dynamics of centromeres during meiosis

34. (b) Centromere depolarisation and SC formation during Zygotene
Interphase Leptotene Zygotene Late ZygoteneTelomere
bouquet
Homologue chromosome pairs Centromeres ZYP1
Early Zygotene
1 2 3
Subtelomeric synapsis Interstitial alignment Interstitial elongation
(a) Centromere, telomere and chromosome arm dynamics in meiotic prophase I
Sepsi et al. Plant Journal 2017

35. Recombination in alien fragments
Th. intermedium DNA-green
AfaThin-red
Trude Schwarzacher, Niaz Ali
Ph-locus controls pairing with
strict homologous chromosomes
forming bivalents

36. Thinopyrum (wheat grasses) is source for
biotic and abiotic stress tolerance

37. NO2Y5149 Mace Tomahawk
Wheat Streak Mosaic Virus resistance
From Thinopyrum intermedium in wheat

38. Th. intermedium
DNA
pSc119.2/CS13
4D
4D
4D T4DL*4Ai#2S
DAPI Afa Thin all
(blue) (green) (red)
Presence of T4DL recombinant
chromosome correlated with
resistance …
but some lines showed some
resistance without T4DL
Ali N, Heslop-Harrison JS, Ahmad H, Graybosch RA,
Hein GL, Schwarzacher T. (2016) Introgression of
chromosome segments from multiple alien species in wheat
breeding lines with wheat streak mosaic virus
resistance. Heredity 117: 114–123 10.1038/hdy.2016.36

39. SOME LINES ALSO
CARRY A THIN OR RYE
FRAGMENT ON
CHROMOSOME 1B
Th. intermedium
DNA
pSc119.2/CS13
Rye DNA
dpTa1/Afa
Ali N, Heslop-Harrison JS, Ahmad H, Graybosch RA,
Hein GL, Schwarzacher T. (2016) Introgression of
chromosome segments from multiple alien species in wheat
breeding lines with wheat streak mosaic virus
resistance. Heredity 117: 114–123 10.1038/hdy.2016.36

40. WHEAT TH. BESSARABICUM TRANSLOCATIONS
Patokar C, Sepsi A, Schwarzacher T, Kishii M, Heslop-
Harrison JS (2016) Molecular cytogenetic characterization of
novel wheat-Thinopyrum bessarabicum recombinant lines
carrying intercalary translocations. Chromosoma 125: 163-
172. 10.1007/s00412-015-0537-6

41. • Recent polyploidy
• Revealed by cytogenetics and hybridization
• Recent rearrangements or duplications
• Revealed by molecular cytogenetics
• Ancient, evolutionary polyploidy
• Revealed by sequencing
• Understanding polyploidy is important for speciation, evolution and
breeding
• Different sequence classes evolve at different rates and many are
saltatory rather than clocks
• Consequences and applications

42. Dasypyrum breviaristatum
2n=4x=28
Is it AAAA or AABB?
D. villosum (genomic DNA
green) × D. breviaristatum
(red)
Meiotic metaphase I in a F1
hybrid showing autotetraploid
nature
Galasso, Heslop-Harrison et al.

43. B. nigra
BB
2n=2x=16
760Mbp
B. rapa
AA
2n=2x=20
564Mbp
B. juncea
AABB
2n=4x=36
1495Mbp
B. carinata
BBCC
2n=4x=34
1544Mbp
B. oleracea
CC
2n=2x=18
760Mbp
B. napus
AACC
2n=4x=38
1324Mbp

44. Fertility restorer
Rfk1 gene BAC
(yellow probe) in
turnip rape
(Brassica rapa)
2n=2x=20A+2R
metaphase with
radish (Raphanus)
chromosomes
(red)
Radish genomic red (labels 2
radish chromosomes and 45S
rDNA)
Rfk1 carrying BAC green labels
sites on radish and
homoeologous pair in Brassica
Tarja Niemelä,
Seppänen, Badakshi,
Rokka HH
Chromosome Research
2012

45. • Recent polyploidy
• Revealed by cytogenetics and hybridization
• Recent rearrangements or duplications
• Revealed by molecular cytogenetics
• Ancient, evolutionary polyploidy
• Revealed by sequencing
• Understanding polyploidy is important for speciation,
evolution and breeding
• Different sequence classes evolve at different rates and
many are saltatory rather than clocks
• Consequences and applications

47. 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
PeyanVarkala, Kerala, India

48. THE BANANA GENOME• Seven countries + international organization coordinated by Angelique D’Hont - France (CIRAD,
Genoscope)

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

52. Bryophytes
(ca. 20,000 species)
green plants
land plants
vascular plants
seed plants
flowering plants
diversification of angiosperms
Gymnosperms
(ca. 1000 species)
ANITA
ε Ginkgo
Taxus
Pinus
Cedrus
Sequoia sempervirens
Welwitschia
Ephedra
Lycophytes
(ca. 1200 species)
Physcomitrium sp.
Chlorophytes
(ca. 4300 species)
01002003004001500
-700
Mya500
AGF
Charophytes
(ca. 12,000 species)
Sphagnum sp.
Physcomitrella patens
Green algae
Monilophytes
(ca. 13,000 species)
‘Pteridophytes’
Cretaceous–Tertiary extinction event
Vitis vinifera
Solanum
Arabidopsis thaliana
Carica papaya
Populus trichocarpa
Linum usitatissimum
Brassica rapa
Glycine max
Malus domestica
Musa acuminata
Oryza sativa
Triticum aestivum
Zea mays
β
α
γ
ρσ
τ
Angiosperms
(ca. 400,000 species)
Nicotiana
Petunia
ζ
Eudicots
Monocots
Basal Angiosperms
337. Alix K, Gérard PR, Schwarzacher T, Heslop-Harrison JS. 2017. Polyploidy and interspecific
hybridisation: partners for adaptation, speciation and evolution in plants. Annals of Botany 120: 183-194.
https://dx.doi.org/10.1093/aob/mcx079 (freely available)
α

53. Petunia hybrida
P. inflata X P. axillaris
2n=14 x 2n=14
Bomberley, Kuhlemeier et al. 2016 Insight into the
evolution of the Solanaceae from the parental
genomes of Petunia hybrida. Nature Plants 2: article
number 16074.
See Supplementary paper 2 - Heslop-Harrison,
Schwarzacher, Richert-Poeggeler
www.molcyt.org/tag/Petunia
Diploid hybrid
Petunia Genome
Landscape

54. Sol-alpha:
Palaeohexaploidy in
Solanaceae
Paleopolyploidy events
followed by massive gene
loss and chromosomal
structural rearrangements
Gene fractionation is less
profound in Petunia
compared to tomato
Supplementary Paper 5
Incomplete gene fractionation
after paleopolyploidy: Petunia
Grandont, Tang, Johns, Lyons
and Schranz
To Bomberley et al. 2016
Genomes of Petunia hybrida.
Nature Plants 2: article number
16074

55. • Alix et al. 2017. Annals of Botany

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

58. Use biodiversity in germplasm
to meet challenges
Population increase
higher living standards / health
fossil fuel use
climate change
water …

59. Outputs
–CROPS
– Fixed energy
Inputs
–Light
–Heat
–Water
–Gasses
–NutrientsLand

60. Inputs
–Light
–Heat
–Water
–Gasses
–Nutrients
–Light
–Heat
–Water
–Gasses
–Nutrients
(Ecosystem services)
Outputs
–CROPS
– Fixed energy

61. Outputs
–Crops
(Chemical energy)
– Food
– Feed
– Fuel
– Fibre
– Flowers
– Pharmaceuticals
– Fun61

63. 2 End hunger, achieve food security, improve nutrition & promote
sustainable agriculture
15 Protect, restore and promote sustainable use of terrestrial
ecosystems … halt biodiversity loss

64. Legislation: European Parliament & Commission

65. EVOLUTION OF WHEATS - POLYPLOIDY
Common Ancestor
2n=2x=14
Aegilops ventricosa
2n=4x=28
DDNN
Triticum tauschii
2n=2x=14
DD
Aegilops uniaristata
2n=2x=14
NN
Triticum aestivum
2n=6x=42
AABBDD
Triticum durum
2n=4x=28
AABB
Triticum
monococcum
2n=2x=14
AA
Aegilops sp.
2n=2x=14
BB
Aegilops
2n=2x=14
Triticum
2n=2x=14

66. 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

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

68. Pat Heslop-Harrison
phh@molcyt.com
www.molcyt.com
89th Genetics Society of Japan Meeting
Centennial of the discovery of the correct
chromosome number and polyploidy in wheat
Polyploidy, its distribution and
evolutionary significance
Twitter: @pathh1
Slideshare pathh1

69. 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

70. • Abiotic stresses – water, wind, nitrogen, plant
nutrition
• Biotic stresses – disease – competition,
nematodes, fungi, bacteria, viruses, rodents
• Environmental challenges
– Soil, water, climate change, sustainability
• Social challenges
– Urbanization, population growth, mobility of
people, under-/un-employment
– Farming is hard, long work – increased standard of
living

72. • 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

75. 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

76. 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

78. 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!

79. 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

80. (Some text deleted to focus for IAEA/FAO CRP)

82. Pat Heslop-Harrison
phh@molcyt.com
www.molcyt.com
89th Genetics Society of Japan Meeting
Centennial of the discovery of the correct
chromosome number and polyploidy in wheat
Polyploidy, its distribution and
evolutionary significance
Twitter: @pathh1
Slideshare pathh1