Polyploids and Chromosomes Lecture Japanese Genetics Society Heslop-Harrison Okayama

Pat Heslop-Harrison

phh@molcyt.com

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

H Kihara 1945

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

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

Rye chromosomes 2n=2x=14

Satellite DNA probe green

45S rDNA probe (NORs) red

Wheat and wild relatives

Satellite DNA probe green

45S rDNA probe (NORs) red

Lodging in cereals

Triticum aestivum wheat ‘Rendezvous’ eyespot (Oculimacula/Pseudocercosporella) resistance from Aegilops ventricosa

pSc119.2 dpTa1

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

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

Highest yielding group1 breadmaking

wheat in UK, released 2013

Includes pch1

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

Wheat 5AS.5RL at meiosis

Schwarzacher 1997 Plant Sexual Reproduction 10, 324-331

Meiotic interphase Leptotene

Zygotene Pachytene MI

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

Identical patterns in fingerprint gel with diverse Saffron accessions (18=garden-hyb)

Nouf Alsayied, HH et al Ann Bot 2015

Variable patterns in 11 Crocus species, including intra-specific variation

(19-21 and 22-24)

Saffron 1-5

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

Metaphase I in triploid hybrid Golden Yellow Crocus

Four bivalents C. flavus (2n=2x=8)-origin chromosomes

Six univalents C. angustifolius (2n=2x=12)

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

Saffron: another triploid Crocus sativusPachytene: so no variation from meiosis

DAPI

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

(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

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

(a) (b) (c)

(d) (e) (f)

(g) (h) (i)

AS

Y1

CE

NH

3D

AP

I

Mid Zygotene Pachytene DiploteneEarly Zygotene

Dynamics of centromeres during meiosis

Mid Zygotene Pachytene DiploteneEarly Zygotene

Dynamics of centromeres during meiosis

(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

Recombination in alien fragments

Th. intermedium DNA-greenAfa Thin-red

Trude Schwarzacher, Niaz Ali

Ph-locus controls pairing with

strict homologous chromosomes

forming bivalents

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

NO2Y5149 Mace Tomahawk

Wheat Streak Mosaic Virus resistance

From Thinopyrum intermedium in wheat

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

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

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

• 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

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.

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

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

• 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

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

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

Genoscope)

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

Whole-genome duplication events.

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

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

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

• Alix et al. 2017. Annals of Botany

NASA

The Blue Marble

Apollo 17 7 Dec 1972Apollo 17 – The Blue Marble December 7, 1972

Use biodiversity in germplasm to meet challenges

Population increasehigher living standards / health

fossil fuel useclimate change

water …

Outputs

–CROPS

– Fixed energy Inputs

–Light

–Heat

–Water

–Gasses

–NutrientsLand

Inputs

–Light

–Heat

–Water

–Gasses

–Nutrients

–Light

–Heat

–Water

–Gasses

–Nutrients

(Ecosystem services)

Outputs

–CROPS

– Fixed energy

Outputs

–Crops(Chemical energy)

– Food– Feed– Fuel

– Fibre– Flowers

– Pharmaceuticals– Fun

61

2 End hunger, achieve food security, improve nutrition & promote sustainable agriculture

15 Protect, restore and promote sustainable use of terrestrial ecosystems … halt biodiversity loss

Legislation: European Parliament & Commission

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

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

From Chromosome to Nucleus

Pat Heslop-Harrison phh4@le.ac.uk www.molcyt.com

Pat Heslop-Harrison

phh@molcyt.com

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

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

• 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

• 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

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

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

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!

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

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

Pat Heslop-Harrison

phh@molcyt.com

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