Open Access A C P : inferring allele co‑ancestry in polyploids
Polyploids and Chromosomes Lecture Japanese Genetics Society Heslop-Harrison Okayama
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Transcript of Polyploids and Chromosomes Lecture Japanese Genetics Society Heslop-Harrison Okayama
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Pat Heslop-Harrison
www.molcyt.com89th Genetics Society of Japan MeetingCentennial of the discovery of the correct chromosome number and polyploidy in wheat
Polyploidy, its distribution and evolutionary significance
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H Kihara 1945
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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
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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
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Rye chromosomes 2n=2x=14
Satellite DNA probe green
45S rDNA probe (NORs) red
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Wheat and wild relatives
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Satellite DNA probe green
45S rDNA probe (NORs) red
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Lodging in cereals
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Triticum aestivum wheat ‘Rendezvous’ eyespot (Oculimacula/Pseudocercosporella) resistance from Aegilops ventricosa
pSc119.2 dpTa1
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Inheritance of Chromosome 5D
dpTa1
×Aegilops ventricosa 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
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Inheritance of Chromosome 5D
dpTa1
×Aegilops ventricosa 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
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Highest yielding group1 breadmaking
wheat in UK, released 2013
Includes pch1
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WHEAT EVOLUTION AND HYBRIDSTriticum uratu
2n=2x=14AA
EinkornTriticum monococcum
2n=2x=14AA
Bread wheatTriticumaestivum2n=6x=42AABBDD
Durum/SpaghettiTriticum turgidum ssp durum
2n=4x=28AABB
Triticum dicoccoides2n=4x=28AABB
Aegilops speltoidesrelative
2n=2x=14BB Triticum tauschii
(Aegilops squarrosa)2n=2x=14
DD
TriticalexTriticosecale
2n=6x=42AABBRR
RyeSecale cereale
2n=2x=14RR
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Wheat 5AS.5RL at meiosis
Schwarzacher 1997 Plant Sexual Reproduction 10, 324-331
Meiotic interphase Leptotene
Zygotene Pachytene MI
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SaffronCrocus sativus
2n=3x=24Minimal if any genetic variation
Vegetatively propagatedGrown (China), Kashmir, Europe, Iran
Most valuable agricultural/farmed product
AlSayied, HH et al. 2015. Ann Bot
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Identical patterns in fingerprint gel with diverse Saffron accessions (18=garden-hyb)
Nouf Alsayied, HH et al Ann Bot 2015
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Variable patterns in 11 Crocus species, including intra-specific variation
(19-21 and 22-24)
Saffron 1-5
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A garden plant in UK : Crocus ‘Golden Yellow’ triploid 2n=3x=14C. flavus 2n=2x=8 (8 yellow) C. angustifolius 2n=2x=12 (6 green)
Orgaard, Jacobsen & HH
‘Stellaris’ hybrid diploid 2n=2x=10C. flavus 2n=2x=8 (4 green)
C. angustifolius 2n=2x=12 (6 blue)Orgaard & HH, Ann Bot
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Metaphase I in triploid hybrid Golden Yellow Crocus
Four bivalents C. flavus (2n=2x=8)-origin chromosomes
Six univalents C. angustifolius (2n=2x=12)
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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
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Saffron: another triploid Crocus sativusPachytene: so no variation from meiosis
DAPI
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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
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(a) Interphase (b) Leptotene (c) Early Zygotene
CE
NH
3 T
RS
DA
PI
C
EN
H3 A
SY
1
CE
NH
3A
SY
1
CENH3 centromere
ASY1 associated with the lateral elements
ZYP1 central element of the synaptonemal complex
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Centromere dynamics and timing of chromosome synapsis (6x wheat)
Sepsi et al. Plant Journal 2017
0
5
10
15
20
25
30
35
40Interphase Leptotene Early Mid-late Pachytene Diplotene
Zygotene Zygotene
2n=423 x 14 chromosomes
21 bivalents3 x 7 pairs of chromosomes
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(a) (b) (c)
(d) (e) (f)
(g) (h) (i)
AS
Y1
CE
NH
3D
AP
I
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Mid Zygotene Pachytene DiploteneEarly Zygotene
Dynamics of centromeres during meiosis
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Mid Zygotene Pachytene DiploteneEarly Zygotene
Dynamics of centromeres during meiosis
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(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
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Recombination in alien fragments
Th. intermedium DNA-greenAfa Thin-red
Trude Schwarzacher, Niaz Ali
Ph-locus controls pairing with
strict homologous chromosomes
forming bivalents
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Thinopyrum (wheat grasses) is source for biotic and abiotic stress tolerance
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NO2Y5149 Mace Tomahawk
Wheat Streak Mosaic Virus resistance
From Thinopyrum intermedium in wheat
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Th. intermedium
DNA
pSc119.2/CS134D
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
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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
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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
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• 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
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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.
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B. nigraBB
2n=2x=16 760Mbp
B. rapaAA
2n=2x=20 564Mbp
B. junceaAABB
2n=4x=36 1495Mbp
B. carinataBBCC
2n=4x=34 1544Mbp
B. oleraceaCC
2n=2x=18760Mbp
B. napusAACC
2n=4x=38 1324Mbp
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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
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• 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
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BIODIVERSITY and genetic resourcesRed - AAA
Palayam codan AAB (two bunch yellow, one green)Peyan ABB (green cooking banana),
Njalipoovan AB (yellow)Robusta AAA (green ripe)
Nendran AABPoovan AAB (one yellow bunch)
Red AAAPeyanVarkala, Kerala, India
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THE BANANA GENOME• Seven countries + international organization coordinated by Angelique D’Hont - France (CIRAD,
Genoscope)
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A D’Hont et al. Nature 000, 1-5 (2012) doi:10.1038/nature11241
Whole-genome duplication events.
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Bryophytes(ca. 20,000 species)
green plants
land plants
vascular plants
seed plants
flowering plants
diversification of angiosperms
Gymnosperms(ca. 1000 species)
ANITA
εGinkgo
Taxus
PinusCedrus
Sequoia sempervirens
WelwitschiaEphedra
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 papayaPopulus trichocarpaLinum usitatissimum
Brassica rapa
Glycine maxMalus domestica
Musa acuminata
Oryza sativaTriticum 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
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Petunia hybrida
P. inflata X P. axillaris2n=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
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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 SchranzTo Bomberley et al. 2016 Genomes of Petunia hybrida. Nature Plants 2: article number 16074
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• Alix et al. 2017. Annals of Botany
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NASA
The Blue Marble
Apollo 17 7 Dec 1972Apollo 17 – The Blue Marble December 7, 1972
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Use biodiversity in germplasm to meet challenges
Population increasehigher living standards / health
fossil fuel useclimate change
water …
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Outputs
–CROPS
– Fixed energy Inputs
–Light
–Heat
–Water
–Gasses
–NutrientsLand
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Inputs
–Light
–Heat
–Water
–Gasses
–Nutrients
–Light
–Heat
–Water
–Gasses
–Nutrients
(Ecosystem services)
Outputs
–CROPS
– Fixed energy
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Outputs
–Crops(Chemical energy)
– Food– Feed– Fuel
– Fibre– Flowers
– Pharmaceuticals– Fun
61
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2 End hunger, achieve food security, improve nutrition & promote sustainable agriculture
15 Protect, restore and promote sustainable use of terrestrial ecosystems … halt biodiversity loss
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Legislation: European Parliament & Commission
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EVOLUTION OF WHEATS - POLYPLOIDY
Common Ancestor2n=2x=14
Aegilops ventricosa2n=4x=28DDNN
Triticum tauschii2n=2x=14
DDAegilops uniaristata
2n=2x=14NN
Triticum aestivum2n=6x=42AABBDD
Triticum durum2n=4x=28
AABB
Triticummonococcum2n=2x=14
AA
Aegilops sp.2n=2x=14
BB
Aegilops2n=2x=14
Triticum2n=2x=14
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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
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Pat Heslop-Harrison
www.molcyt.com89th Genetics Society of Japan MeetingCentennial of the discovery of the correct chromosome number and polyploidy in wheat
Polyploidy, its distribution and evolutionary significance
Twitter: @pathh1Slideshare pathh1
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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
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• 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
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• 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
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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
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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
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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!
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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
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(Some text deleted to focus for IAEA/FAO CRP)
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Pat Heslop-Harrison
www.molcyt.com89th Genetics Society of Japan MeetingCentennial of the discovery of the correct chromosome number and polyploidy in wheat
Polyploidy, its distribution and evolutionary significance
Twitter: @pathh1Slideshare pathh1