Chromosomes, Crops and Superdomestication

17 December 2013 10-12

Pat Heslop-Harrisonphh4@le.ac.uk

www.molcyt.com and www.molcyt.orgTwitter, YouTube and Slideshare: pathh1

Outputs–CROPS

– Fixed energy Inputs

–Light–Heat–Water–Gasses–Nutrients

Outputs–CROPS

– Fixed energy

3

Inputs

–Light–Heat–Water–Gasses–Nutrients

– Light– Heat

– Water– Gasses

– Nutrients

Chromosomes, Crops and

Superdomestication What do we want?

What have we done?

NASAThe Blue Marble

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

We’ve done that before …Coming out of ice age at time of recognizably modern

humans 50,000 yrs agoComing up to the start of agriculture 10,000 yrs ago

During agricultural clearances 2,000 and 1,000 yrs agoDuring better cultivation 150 yrs ago

20th Century: Drainage/fertilization/crop protection

… and nearly every other ‘species’ tries to do it …goats, pines, viruses

Burren West IrelandMediaeval: Peat forest 1500 years of overgrazingEroded to bedrock (now a preserved landscape!)

21st C: Population increasehigher living standards / health

fossil fuel useclimate change

water …

Life on the edge …

Verge of stability for fire with 20% oxygen

Water – quality and quantity

Temperature – toohot or cold

ABIOTIC FACTORS

11

• Brazil slash and burn

• Malaysian cut out ganoderma plants

Ecosystems anchor slideLargely

– Self-organizing– Self-maintained– Cycling– Defined scope

– cf University– Household– Aircraft–

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Outputs–CROPS

– Fixed energy

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Inputs

–Light–Heat–Water–Gasses–Nutrients

– Light– Heat

– Water– Gasses

– Nutrients

OutputsEcosystem ServicesWater, gasses,nutrients”nature’s services, like flood control, water filtration, waste assimilation”

Ecosystem cycling threatenedby stress andinstability Abiotic

WaterFireWind

Biotic Virus, bacteria, fungiWeeds, insectsNematodes etc.Alien invasions

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RainfallDistribution

mm/yr

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Occasional ‘extreme inputs’:Limiting composition of ecosystemsmore 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

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Argenome mexicana: a goat-proof plant fromMexcio introduced and successful in Africa

Anhalt, Barth, HH Euphytica 2009 Theor App Gen 2008

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Chromosomes, Crops and

Superdomestication What do we want?

What have we done?

50 years of plant breeding progress

1961 1965 1970 1975 1980 1985 1990 1995 2000 2005 20070

0.5

1

1.5

2

2.5

3

3.5

4

MaizeRiceWheatHumanArea

Agronomy

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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

Outputs

– Crops(Chemical energy)

– Food– Feed– Fuel

– Fibre– Flowers

– Pharmaceuticals– Fun 32

50 years of plant breeding progress

1961 1965 1970 1975 1980 1985 1990 1995 2000 2005 20070

0.5

1

1.5

2

2.5

3

3.5

4

MaizeRiceWheatHumanArea

Genetics

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.

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

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

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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 AAB Poovan AAB (one yellow bunch) Red AAA PeyanVarkala, Kerala, India

Chromosomes, Crops and

Superdomestication Genomes and

genomics

>AY484588 Musa acuminata clone MuG9, genomic, 73268bpgggatccaacctgttttctaggaaatccaatcaatccagatcaatattgatcgggttctgatctatgcgctgaggaatatgtgacgaagcagtcaaactgatcactaaaattcaatacatactcagtccaagttatgaaggggagtgctgatttcagaaacttaatcccttctgatagaacccaagaatttctattgcatcccaacttacactaattagtcttaaaactcattaaggttgagctatttaaacattctaagtaataaatgtcatattacccttccaggtcataaacagcttagaccaaacacaaaagcaaataatgctgaagctattggcattacacttagtcttaacttcatgttatctctgacaaggcaaatttaacgatatgacaatcaataatgagataggcaaataaaaaacaatatcttaaagacaaaaatgacatttttttgaactctgcagaattagctcctaaatgcaagaagaggcacatctatcctttagtgaatgcagacaaggaatcagtaaccactgtcacttgtatgttcagtgaatcctcatataggaaaatgcagtatgaccattttgtacgaacaatcatcatttgatcatttaaagagataataccaggagaaatggcagtgctgatctgcttcgatgctgaataaatgtgcctcacaaaaggcattcgttttataaaccactctcccaccc

Genomics• Study of the structure, diversity, function and behaviour of all the DNA in an organism, organelle

or virus

Triticale: wheat x rye hybrid

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

Crop standing

Lodging in cereals

Crop fallen

Use of repetitive DNA sequences as chromosome markers

Satellite DNA probe green

• 45S rDNA

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

• dpTa1 tandem repeat

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

Multiple repeat (dpTa1) variantsof each chromosome

e.g. 5DL

Bardsley, Schwarzacher & HH

S

1A L

S

3A L

S

2A L

S

4A L

S

5A L

S

6A L

S

7A L

5BS.

7BS

5BL.

7BL

Multiple dpTa1 variantsof each chromosome

e.g. 5DL

Bardsley, Schwarzacher & HH

Correlation between genetic relationships and similarity of dpTa1 hybridization

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1

Coefficient of parentage

Prop

ortio

n of

chr

omos

ome

arm

s w

ith

iden

tical

in s

itu s

igna

l

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

ancestral

A B C D

High-copy number High-copy number High-copy number High-copy number

Low-copy number Low-copy number

High copy spp: homogenized, amplification from a limited number of master copies Low copy spp: much variationKuhn, Schwarzacher, PHH

Use of repetitive DNA sequences as chromosome markers

Wheat Streak Mosaic Virus in North AmericaBob Graybosch, USDA

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

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

RetroelementsSequences which amplify through an RNA intermediate

•50% of all the DNA!

Retroelement Markers

Retrotransposon LTRLTR

Retrotransposon LTRLTR

RetrotransposonLTR LTR

Retrotransposon LTRLTR

Insertion

IRAP – InterRetroelement PCR

Retrotransposon LTRLTR

RetrotransposonLTR LTR

Copyright restrictions may apply.

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

UPGMA dendrograms of the relationships based on IRAP analysis of (A) accessions of Ae. tauschii subsp

Retroelements

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

13/04/2023 69

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

13/04/2023 70

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 hAT037RTop bands (560-bp) amplified hAT element and lower bands amplifying the flanking sequences only – Menzel, Nouroz, Schmidt, Schwarzacher, Heslop-Harrison 2013/14

Size and location of chromosome regions from radish (Raphanus sativus) carrying the fertility restorer Rfk1 gene and transfer to spring turnip rape (Brassica rapa) Tarja Niemelä, Mervi Seppänen, Farah Badakshi,Veli-Matti Rokka and J.S.(Pat) Heslop-Harrison

Chromosome Research (subject to minor revision Feb 2012)

Chromosome and genome engineering

Cell fusionhybrid of two4x tetraploidtobaccospecies

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

Nicotiana hybrid4x + 4x

cell fusions

Each of 4chromosome

sets hasdistinctiverepetitiveDNA when

probed withgenomic DNA

Patel et alAnn Bot 2011

Diploid 2n=2x=22 Musa / banana metaphase probed red with transposable elementTeo & Schwarzacher

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

Six-way Venn diagram showing the distribution of shared genefamilies (sequence clusters) among M. acuminata, P. dactylifera,Arabidopsis thaliana, Oryza sativa, Sorghum bicolor and Brachypodiumdistachyon genomes.

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

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

Whole-genome duplication events.

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

Arachis hypogaea - PeanutTetraploid of recent origin,

ancestors separated only 3 My ago

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

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 PMB 2005

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

Bertioli et al. Annals of Botany 2013

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

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

• 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

• Stable cAMP oscillations in the cells with other molecules/ions

Valeyev et al. Mol Biosyst 2009

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

From Chromosome to Nucleus

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

Outputs

– Crops(Chemical energy)

– Food– Feed– Fuel

– Fibre– Flowers

– Pharmaceuticals– Fun 90

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

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

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!

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

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

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

50 years of plant breeding progress

1961 1965 1970 1975 1980 1985 1990 1995 2000 2005 20070

0.5

1

1.5

2

2.5

3

3.5

4

MaizeRiceWheatHumanArea

Agronomy

Genetics

GM maize

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

Chromosomes, Crops and Superdomestication

17 December 2013 10-12

Pat Heslop-Harrisonphh4@le.ac.uk

www.molcyt.com and www.molcyt.orgTwitter, YouTube and Slideshare: pathh1

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