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Chromosomes, Crops and Superdomestication in Katowice Pat Heslop-Harrison [email protected] www.molcyt.com UserID/PW ‘visitor’ Pathh1: Twitter #PMC . Slideshare pathh1

Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

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Plant Molecular Cytogenetics www.molcyt.com Conference Katowice, Poland September 2014 Chromosomes, in situ hybridization, genome organization and evolution

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Page 1: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Chromosomes, Crops and Superdomestication in Katowice

Pat [email protected]

www.molcyt.comUserID/PW ‘visitor’

Pathh1:

Twitter #PMC .

Slideshare pathh1

Page 2: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

From Chromosome to Nucleus

Pat Heslop-Harrison [email protected] www.molcyt.com

Page 3: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Genome evolution• How do genomes evolve?

–Gene mutation very rarely (human: 10−8/site/generation)

–Chromosome evolution–Polyploidy and genome duplication (ancient &

modern)–Repetitive sequences: mobility & copy number

(10−4/generation in µsat)–Recombination–Epigenetic aspects: centromeres & expression

Page 4: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Genome evolution• How do genomes evolve?

– Gene mutation very rarely– Chromosome evolution– Polyploidy and genome duplication (ancient and modern)– Repetitive sequences: mobility & copy number– Recombination– Epigenetic aspects – centromeres & expression

• How can we exploit knowledge of genome evolution?– Biodiversity– Chromosome and genome engineering– Breeding– Markers

Page 5: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication
Page 6: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Musa biodiversity and genomes: x=11Red - AAA 2n=3x=33 – M. acuminata Palayam codan AAB (two bunch yellow, one green) Musa x Peyan ABB (green cooking banana) Njalipoovan AB (yellow) 2n=2x=22 M. acuminata x M. balbisiana Robusta AAA (green ripe) Nendran AAB Poovan AAB (one yellow bunch) Red AAA Peyan ABBVarkala, Kerala, India

Page 7: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication
Page 8: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

RetrotransposonsClass I transposable elementsRNA intermediate

DNA transposonsClass II transposable elements

Cut-and-paste

Page 9: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

RetroelementsSequences which amplify through an RNA intermediate

• 50% of all the DNA!

Page 10: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Retroelements

BAC sequences from Musa Calcutta 4 Homologous over the full lengthexcept for a 5kb insert• a Ty1-copia retroelement

Page 11: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Alignment of two homologous Musa BACs shows gaps in both B genome M. balbisiana and A genome M. acuminata

MA4_82I11

MBP_81C12

MuhAT1

MuhAT2a

XX TE (SINGLE)XX TE MITE

XX TE (AGNABI)

MuhAT3 MuhAT4 MITE(MBIR)

XX TE XX TE (MBT)

272 bp 102,190 bp

26, 410 bp 128,068 bp

DNA transposons hAT are particularly frequent

8 bp TSD, and short TIRs of 5–27 bptransposase (sometimes degenerate) including a DDE site.Non-autonomous (MITE) derivatives of hAT with deletion coding sequence

Menzel, Schmidt, Nouroz, HH Chr Res subject minor revision 2015

Page 12: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

13/04/2023 12

Sr. No. Primer Pairs Product Size (bp)

Sequence

1. hAT18486hAT19037

560 ACCCACCTGGCTCTTGTGTCAGCGAATGTGTTTTGACCAC

MBP 81C12 (M. balbisiana) x MA4 82I11 (M. acuminata) BACs.

Musa balbisiana (MBP 81C12)M

usa

acu

min

ata

(MA

4 82

I11)

Transposed Element

hAT 1

hAT 2

hAT 4

Microsatellite (AT)

hAT 3621 bp MBT

384 bp TE + 781 MITE

1676 TE

Microsatellite (AT)

4192 bp TE

Page 13: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

13/04/2023 13

Sr. No. Primer Pairs Product Size (bp)

Sequence

1. hAT18486hAT19037

560 ACCCACCTGGCTCTTGTGTCAGCGAATGTGTTTTGACCAC

MBP 81C12 (M. balbisiana) x MA4 82I11 (M. acuminata) BACs.

Musa balbisiana (MBP 81C12)M

usa

acu

min

ata

(MA

4 82

I11)

Transposed Element

hAT 1

hAT 2

hAT 4

Microsatellite (AT)

hAT 3621 bp MBT

384 bp TE + 781 MITE

1676 TE

Microsatellite (AT)

4192 bp TE

Page 14: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

A-genome specific hAT in three Musa accessions

(2n=3x=33)

Musa ‘WilliamsCavendish’ (AAA)

Musa (ABB)

Musa (ABB)

Page 15: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

13/04/2023 15Dot plot showing the complete Inverted repeat.

Page 16: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

13/04/2023 16

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

1KB800600400200

hAT1 insertion sites in Musa diversity collectionhAT486F and hAT037R

Top bands (560-bp) amplified hAT elementLower bands amplifying the flanking sequences only

Menzel, Nouroz, Heslop-Harrison, Schmidt 2014

Page 17: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Retroelement Markers

Retrotransposon LTRLTR

Retrotransposon LTRLTR

RetrotransposonLTR LTR

Retrotransposon LTRLTR

Insertion

IRAP – InterRetroelement PCR

Retrotransposon LTRLTR

RetrotransposonLTR LTR

Page 18: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

IRAP diversity in Musa

Teo, Tan, Ho, Faridah, Othman, HH, Kalendar, Schulman 2005 J Plant BiolNair, Teo, Schwarzacher, HH 2006 Euphytica Teo, Schwarzacher et al. in prep.

Page 19: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

13/04/2023 19

Phylogenetic analysis of Musa genomes – separating species. Teo, Schwarzacher et al.

Page 20: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

BSV Expression in Banana

Double stranded DNA is infective: Insect vectorUnexpected epidemiology: Appearance after cold or tissue culture

Page 21: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Nuclear Copies of Banana Streak Virus in Banana

Page 22: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Nuclear Copiesof BSV in banana

DNA Fibre in situ hybridization

Harper, HH et al., Virology 1999 … cf D’Hont et al., Nature, 2012

Page 23: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Whole genome shotgun sequencing

• Changing all cytogenomics (.org) work

• Easily obtaining several-fold sequence coverage

Page 24: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

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

Page 25: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Musa Bananan=11

Sequence:D’Hont, inc HH et al. Nature 2012

Haploid: Nair, HH 2013

Page 26: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication
Page 27: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Whole genome duplications

• The surprise to the sequencers: conserved synteny and relatively few breakpoints

• The surprise to the cytogeneticists: sequencing shows whole genome duplications (=polyploidy) deep in the phylogenetic tree

• The surprise to everyone: so few genes but multifunctional

Page 28: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

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

Page 29: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication
Page 30: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

BrachiariaLTR element families

Fabíola Carvalho SantosAndré Luiz Laforga VanzelaSee poster

Forage/pastureUrbanSavanna/cerrado

ForestSugar caneSoybean/corn

Brazil land use

Page 31: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Chromosomal evolution and the organization of repetitive DNA sequences in diploid and polyploid

Brachiaria forage grasses

Some probes show less hybridization to some chromosomes, perhaps indicating genome specificity.

Fabíola Carvalho SantosAndré Luiz Laforga VanzelaSee poster

Page 32: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

From Chromosome to Nucleus

Pat Heslop-Harrison [email protected] www.molcyt.com

Page 33: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Wheat evolution and hybridsTriticum uratu

2n=2x=14AA

EinkornTriticum monococcum

2n=2x=14AA

Bread wheatTriticum aestivum

2n=6x=42AABBDD

Durum/SpaghettiTriticum turgidum ssp durum

2n=4x=28AABB

Triticum dicoccoides2n=4x=28

AABB

Aegilops speltoidesrelative

2n=2x=14BB Triticum tauschii

(Aegilops squarrosa)2n=2x=14

DD

TriticalexTriticosecale

2n=6x=42AABBRR

RyeSecale cereale

2n=2x=14RR

Page 34: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Copyright restrictions may apply.

Saeidi, H. et al. Ann Bot 2008 101:855-861; doi:10.1093/aob/mcn042

Inter-retroelement (IRAP) analysis of Triticum tauschii ssp tauschii from Iran

SSR/Microsats: all are different and no tree is supported

Different sequence classes evolve at different rates

Page 35: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Crop standing

Lodging in cereals

Crop fallen

Page 36: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Use of repetitive DNA sequences as chromosome markers

Page 37: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

dpTa1pSc119.2Genomic Ae.ventricosa

Inheritance of Chromosome 5DAegilops ventricosaDDNN

ABDN

AABBDDNN MarneAABBDD

CWW1176-4

Rendezvous

Piko

VPM1 Dwarf A

96ST61

Virtue

×

×

×

×

Hobbit

× {Kraka × (Huntsman × Fruhgold)}

Triticum persicum Ac.1510AABB

Page 38: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Wheat Streak Mosaic Virus in North AmericaBob Graybosch, USDA

Page 39: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

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

Page 40: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Mace wheatGraybosch et al. 2009In situ: Niaz Ali & Schwarzacher

Page 41: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Chromosome evolution - Polyploidy

• Selected natural– Wheat– Banana – Brachiaria – Proso millet

• Synthetic– Triticale– Nicotiana

Page 42: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Proso millet (Panicum miliaceum): origins, genomic studies and prospects

Pat Heslop-Harrison, Farah Badakshi and Harriet Hunt

Page 43: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Panicum sensu stricto c. 100 species; x=9Evolution of Panicum miliaceum Proso millet

P. miliaceum 2n=4x=36

P. capillare2n=2x=18

P. repens2n=4x=36

also 2n=18 to 54

P. sumatrense2n=2x=18 or 4x=36

Global North-temperateLow genetic diverstiyWeedy forms

P. virgatum2n=4x=36 or 2x=18

? ? ? ? ??

• Hunt , HH et al. 2014. Reticulate evolution in Panicum (Poaceae): the origin of tetraploid broomcorn millet, P. miliaceum. J Exp Bot. 2014

Page 44: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication
Page 45: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

• P. miliaceum: allotetraploid with maternal ancestor P. capillare and one genome shared with P. repens (also allotetraploid)

Hunt , HH et al. 2014. Reticulate evolution in Panicum (Poaceae): the origin of tetraploid broomcorn millet, P. miliaceum. J Exp Bot. March 2014

Page 46: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Chromosome and genome engineering

Cell fusionhybrid of two4x tetraploidtobaccospecies

Patel, Badakshi, HH, Davey et al 2011 Annals of Botany

Page 47: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Nicotiana hybrid4x + 4x

cell fusions

Each of 4chromosome

sets hasdistinctiverepetitiveDNA when

probed withgenomic DNA

Patel et alAnn Bot 2011

Cell fusionhybrid of two4x tetraploidtobaccospecies

Four genomesdifferentiallylabelled

Patel, Badakshi, HH, Davey et al 2011 Annals Botany

Page 48: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Arachis hypogaea - PeanutTetraploid of recent origin,

ancestors separated only 3 My ago

• Ana Claudia Araujo, David Bertioli, TS & PHH EMBRAPA, Brasília. Annals Botany 2013

Page 49: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

•Arachis hypogea 2n=4x=40 probed with •(green) A. duranensis; (red) A. ipaënsis

Bertioli et al. Annals of Botany 2013

Page 50: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

BAC in situ hybridization

Page 51: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication
Page 52: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Primula BAC mapping

Gilmartin, Lu, HH & Badakshi 2015?

Page 53: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

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

DAPI metaphase blueRadish genomic red (2 radish chromosomes) far-red 45S rDNARfk1 carrying BAC green labels sites on radish and homoeologous pair in Brassica

Tarja Niemelä, Seppänen, Badakshi, Rokka HHChromosome Research 2012

Page 54: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

BACs from different species have different repeat distributions – and hence different patterns of hybridization

Page 55: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Organelle sequencesfrom chloroplasts or

mitochondria

Sequences from viruses, Agrobacterium or other

vectors

Transgenes introduced with molecular biology

methods

Genes, regulatory and non-coding single copy sequences

Dispersed repeats:Transposable Elements

Repetitive DNA sequences

Nuclear Genome

Tandem repeats

DNA transposons copied and

moved via DNA

Retrotransposons amplifying via an RNA intermediate

Centromeric repeats

Structural components of chromosomes

Telomeric repeats

Simple sequence repeats or

microsatellites

Repeated genes

Subtelomeric repeats

45S and 5S rRNA genes

Blocks of tandem repeats at discrete chromosomal loci

DNA sequence components of the nuclear genomeHeslop-Harrison & Schmidt 2012. Encyclopedia of Life Sciences

Other genes

Page 56: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

X MuTRR

MuTRF220 bp

• The original 177bp repeat fits nicely around the nucleosome allowing a tight coiling

• The repeat unit with the retroelement foot print, the 63bp box, has a much more open configuration

• It is maintained as it brings a CG and CNG site that allows control via methylation

MuTRR

MuTRF180 bp

Insertion and subsequent loss

Monkey retroelement

C.H Teo and Schwarzacher

Page 57: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

A

B

C

Centromere

DNA sequenceTE

Tandem repeat monomerTE Transposable element

Single copy DNA

Spindle microtubules pulling apart chromatids

Metaphase chromosome

147bp plus 5-70bp linker = 150-220bp

100bp plus 55bp linker = 155bp

D

E

F

G

H

I

Kinetochore

Heslop-Harrison & Schwarzacher 2013. Nucleosomes and centromeric DNA packaging. Proc Nat Acad Sci USA. http://dx.doi.org/10.1073/pnas.1319945110. See also http://wp.me/p2Ewqp-7h

Henikoff et al 2013

C: antibody to CENH3 variant

Page 58: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Domestication

• Most species domesticated 10,000 years ago: cereals, legumes/pulses, brassicas, fruits, cows/sheep/pigs, silkworm/bees)

• Few species more recently (rabbits, fish; trees, biofuel crops)

• A few dropped out of production

• First steps: productive, reproduce easily, disease-free, edible/tasty, harvestable …

Heslop-Harrison & Schwarzacher Domestication genomics www.tinyurl.com/domest and review of rabbits www.tinyurl.com/rabdom

Page 59: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Domestication

• …• A few dropped out of production

• Second steps: more productive, harvestable

• Third step: fitting for sustainable intensification• Proso millet: the most water-efficient cereal• Superdomestication and design of crops

Heslop-Harrison & Schwarzacher Domestication genomics www.tinyurl.com/domest and review of rabbits www.tinyurl.com/rabdom www.tinyurl.com/superdom

Page 60: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Outputs–CROPS

– Fixed energy Inputs

–Light–Heat–Water–Gasses–Nutrients

–Light–Heat

–Water–Gasses

–Nutrients

(Ecosystem services)

Page 61: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

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

Page 62: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

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

Page 63: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

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 49 50 51 52 530

200000000

400000000

600000000

800000000

1000000000

1200000000

Maize Rice, paddy

Wheat Population /10

1961 1970 1980 1990 2000 2010 2013

52 years of plant breeding progress

Agronomy

Genetics

GM maize

Page 64: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

United Nations Millennium Development Goals-MDGs1990 to 2015

• 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

Page 65: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

From Chromosome to Nucleus

Pat Heslop-Harrison [email protected] www.molcyt.com

Page 66: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Genome evolution• How do genomes evolve?

– Gene mutation very rarely – Chromosome evolution– Polyploidy and genome duplication (ancient and modern)– Repetitive sequences: mobility & copy number– Recombination– Epigenetic aspects – centromeres & expression

• How can we exploit knowledge of genome evolution?– Biodiversity– Chromosome and genome engineering– Breeding– Markers Pat Heslop-Harrison & Trude Schwarzacher

www.molcyt.comPathh1 on slideshare

Page 67: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Chromosomes, Crops and Superdomestication in Katowice

Pat [email protected]

www.molcyt.comUserID/PW ‘visitor’

Pathh1:

Twitter #PMC .

Slideshare pathh1

Page 68: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Major Genomic Components

• Tandem Repeats• Simple Sequence Repeats• Dispersed Repeats• Functional Repeats• Retroelements• Genes

Typical Fraction10%5%10%15%50%10%

Page 69: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication
Page 70: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

A D’Hont et al. Nature 2012

doi:10.1038/nature11241

Whole-genome duplication events.

Page 71: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Satellite DNA probe green

Page 72: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication
Page 73: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

• 45S rDNA

Differences between genomesMajor differences in the nature and amount of repetitive DNA

• dpTa1 tandem repeat

Page 74: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

146 bp around histones

Page 75: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

From Chromosome to Nucleus

Pat Heslop-Harrison [email protected] www.molcyt.com

Page 76: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

• Three copies of the Arabidopsis 180 bp repeat showing (dark purple, stepped line) GC content of the sequence and (red, smooth line) sequence curvature. While GC and AT rich regions of a sequence generally correlate with curvature, the kinked region shows curvature with low GC content.

Page 77: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

• How do genomes evolve?• How can we exploit knowledge of genome

evolution?– Biodiversity– Chromosome engineering– Markers

Page 78: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Genome engineering

• Introgression of chromosomes– Brassica – Raphanus– Wheat – Thinopyrum

Page 79: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Chromatin

• Packaging

Page 80: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

UK Wheat 1948-200752,909 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.

Page 81: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

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

Page 82: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

10 m

DNA methylation is unevenly distributed on Musa chromosomes

copia elements

in methylated regions, but also in some low methylated regions (arrows)

5MeC

Page 83: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

10 m

C.H Teo and Schwarzacher

5MeC

DNA methylation is unevenly distributed on Musa chromosomes

gypsy elements

in methylated regions, but also in some low methylated regions (arrows)

Teo & Schwarzacher in prep 2013

Page 84: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Genome evolution• How do genomes evolve?

– Mutation very rarely (human: 10−8/site/generation)

– Chromosome evolution– Polyploidy and genome duplication (ancient and modern)– Repetitive sequences – mobility & copy number (10−4 µsat)

– Recombination– Epigenetic aspects – centromeres & expression

• How can we exploit knowledge of genome evolution?– Biodiversity– Chromosome engineering– Breeding– Markers

Page 85: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Outputs

– Crops(Chemical energy)

– Food– Feed– Fuel

– Fibre– Flowers

– Pharmaceuticals– Fun 85

Page 86: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Molecular cytogenetics …

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

Page 87: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

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

Page 88: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

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

Page 89: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Centromere

DNA sequenceTE

Tandem repeat monomerTE Transposable element

Single copy DNA

Spindle microtubules pulling apart chromatids

Metaphase chromosome

147bp plus 5-70bp linker = 150-220bp

Kinetochore

Heslop-Harrison JS, Schwarzacher T. 2013. Nucleosomes and centromeric DNA packaging. Proc Nat Acad Sci USA. http://dx.doi.org/10.1073/pnas.1319945110. See also http://molcyt.org (Dec 2013)

Page 90: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Genes!

Page 91: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

EvolutionEpigeneticsDevelopment

PhenotypeMultiple abnormalities

Genetic changes  non-reverting

Changes seen, some reverting

(Male/Female)Normal Differentiation

CauseChromosomal loss, deletion or

translocationGene mutation / base pair

changesTelomere shortening

(Retro)transposon insertion Retrotransposon activation

SSR expansionMethylation

HeterochromatinizationChromatin remodelling

Histone modification

Page 92: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Outputs–CROPS

– Fixed energy Inputs

–Light–Heat–Water–Gasses–Nutrients

Page 93: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Outputs–CROPS

– Fixed energy

93

Inputs

–Light–Heat–Water–Gasses–Nutrients

– Light– Heat

– Water– Gasses

– Nutrients

Page 94: Plant Molecular Cytogenetics - Postgenomics, Chromosomes and Domestication

Chromosomes, Crops and

Superdomestication What do we want?

What have we done?