Superdomestication and feed-forward plant breeding:

Genomic and molecular cytogenetic approaches

http://molcyt.org/2012/11/29/superdomestication-feed-forward-breeding-and-climate-proofing-crops/

Trude Schwarzacher and Pat Heslop-Harrisonts32@le.ac.uk and phh4@le.ac.uk

www.molcyt.comThese are the slides that go with the talk on YouTube and some text on molcyt.com for commentary. See: http://molcyt.org/2012/11/29/superdomestication-feed-forward-breeding-and-climate-proofing-crops/

• The talk on http://molcyt.org/2012/11/29/superdomestication-feed-forward-breeding-and-climate-proofing-crops/ starts with my personal approach to climate proofing!

• Climate Proofing of Food Crops: Genetic Improvement for Adaptation to High Temperatures in Drought Prone Areas and Beyond: an IAEA/FAO Coordinated Research Programme (CRP)

Contribution from Pat Heslop-Harrison andTrude Schwarzacher at www.molcyt.com to:

http://www-naweb.iaea.org/nafa/pbg/crp/drought-prone-areas.html archive: http://www.webcitation.org/6CKx3EVsw

http://www.iaea.org/newscenter/news/2012/feedbillions.html Archived URL at http://www.webcitation.org/6CKtUmjvr

7234 5 May 2012 7N33.558 38E40.120 North of Hawassa, Ethiopis

http://www.ncdc.noaa.gov/ homepage of 19 Nov 2012

Birth of Agriculture10,000 years ago

Domestication of cropshttp://www.ncdc.noaa.gov/paleo/globalwarming/paleobefore.html

Threats to sustainability:no different for 10,000 years

• Habitat destruction• Climate change (abiotic stresses)• Diseases (biotic stresses)• Changes in what people want• Blindness to what is happening

Phases of Domestication• Heslop-Harrison JS, Schwarzacher T. 2012.

Genetics and genomics of crop domestication In: Plant Biotechnology and Agriculture: Prospects for the 21st century. Eds Arie Altman, Paul Michael Hasegawa pp 3-18.

• http://tinyurl.com/cropdomestication • Arie Altman - extensive work with IAEA-Genetics and Plant Breeding

• See www.molcyt.com for full list of papers; all available on request, many downloadable with password and userID both ‘visitor’

Theme of my talkSuperdomestication and feed-forward plant breeding:

Climate Proofing of Food Crops: Genetic Improvement

• Planning ahead! What do we need?• How do we achieve these objectives?

– Knowledge of past– Biodiversity, mutation, hybrids/introgression– Abiotic focus, but diseases also change with

abiotic changes; sustainability critical– Approaches and technology

• Widely applicable and generic approaches

Genomic and molecular cytogenetic approachesSee: http://tinyurl.com/superdomestication

Recent molcyt.com research• Banana genome sequence (published 2012)

• Tri-species hybrid germplasm in Brassica• Wheat germplasm including introgression from wild

Thinopyrum with novel virus resistance loci• Somatic hybrids in Nicotiana for disease resistance (published 2011)

• Biomass gene identification in Lolium• Origin of Panicum miliaceum (broomcorn millet) – the worlds

most water-efficient crop• Genome evolution in Arachis – peanut/groundnut• Wild and landrace characterization of linseed/flax (including

farmer-led trials)

Banana genomesequence

• Fundamental importance to research since it allows us to compare banana with the related grasses and palms to understand genome evolutionary processes

• Led by Angelique D’Hont, France• 520 Mbp giving knowledge of ALL

36,000 genes including the agronomic and food-related properties

• Use for diversity access & breeding

http://www.nature.com/nature/journal/v488/n7410/pdf/nature11241.pdfhttp://molcyt.org/2012/08/16/banana-genome-sequence-in-the-news/

Brassica diversity• Important vegetable /oil worldwide• Irrigation water already limiting• Wide germplasm pool

• Tri-species hybrid in Pakistani Brassica juncea 2n=36 landrace

Faisal Nouroz & PHH 2013 (submitted 2012)

1000800600400200

B. oleracea (CC) B. juncea (AABB) B. napus (AACC)B. rapa (AA) B. juncea (AABB)

B. nigra (BB)c)

B. rapa AA genomes 2n=2x=20

B. nigra BB genomes 2n=2x=16

B. napus AACC genomes2n=4x=38

B. oleracea CC genomes2n=2x=18

B. carinata BBCC genomes2n=4x=34

B. juncea AABB genomes2n=4x=36

Wsm-1: only effective source of resistance to the virus WSMV

Viruses cannot be readily cured (as in human) and normally the control in wheat is by spraying insecticides to stop insect spread

Parental lines and hybrid derivatives:Yellow plants are infected

In situ hybridization showing (red) two chromosomes arms introgressed from the wild Thinopyrum into wheat

Work led by RA Graybosch, USDA; hybrids made originally by his colleagues

http://dx.doi.org/10.3198/jpr2008.06.0345crc

dpTa1 digoxigenin

IWG genomic DNA biotin

http://dx.doi.org/10.3198/jpr2008.06.0345crc

Chromosome and genome engineering

Deval Patel, Badakshi,HH, Led by Mike Davey Annals of Botany 2011

Cell fusion hybrid of two tetraploid tobacco species, transferring fungus resistance

http://aob.oxfordjournals.org/content/108/5/809.full

Nicotiana hybrid

4x + 4x cell fusions

Each of 4chromosome

sets hasdistinctiverepetitiveDNA when

probed withgenomic DNA

Patel et alAnn Bot 2011

Four sets of chromosomes identified in Nicotiana somatic cell fusion hybrid

http://aob.oxfordjournals.org/content/108/5/809.full

Panicum miliaceumBroomcorn millet

• Among the first wave of domesticated species

• As important as rice 8,000 years ago• Now only 1% of the production of rice or

wheat• P. miliaceum: the worlds most water-

efficient crop• It is tetraploid; what are the parents?• Why did it not join modern staple crops?

• 2n = 4x = 36

• Led by Harriet Hunt, Cambridge withFarah Badakshi, PHH www.molcyt.com

Panicum miliaceumBroomcorn millet

• Among the first wave of domesticated species

• As important as rice 8,000 years ago• Now only 1% of the production of rice or

wheat• P. miliaceum: the worlds most water-

efficient crop• It is tetraploid; what are the parents?• Why did it not join modern staple crops?

• 2n = 4x = 36

• Led by Harriet Hunt, Cambridge withFarah Badakshi, PHH www.molcyt.com

The ancestral genomes in Panicum miliaceum

Arachis genome evolution• Peanut is a tetraploid arising from two

diploids maybe as little a 10,000 years ago• The diploids diverged from a common

ancestor 3.5 M years ago• The genes remain in a similar order, but a

few families of repeated, mobile DNA sequences, LTR retrotransposons, have diverged and amplified, distinguishing the genomes in the tetraploid

• Leaders: Ana Claudia Araujo, David Bertioli, EMBRAPA, Brazil 2013

Genomerepeatcontent

This work:https://pag.confex.com/pag/xx/webprogram/Paper3749.html

Related:http://aob.oxfordjournals.org/content/early/2012/11/05/aob.mcs237.full

Linum usitatissimum – Linseed/Flax• Project with Worku Mhiret, University of

Gondar, Ethiopia• 200 Accessions characterized by morphology

and molecular markers• 350 F2 plants from 6 crosses characterized by

morphology and markers• Farmer-led trials

established

Lolium ryegrass QTLs• Major grass for animal

production• Abiotic stress resistance

and biomass are key targets• Which genes are involved?• Field trial of segregating population shows location of

genes involved; now have candidate genes to select• Combining desirable

characters• Celine Tomaszewski, Ulrike Anhalt; Leader Susanne Barth (Ireland)HH (UK); publication in preparation • See molcyt.com; fine map and candidate genes in preparation• Thesis on-line: https://lra.le.ac.uk/jspui/bitstream/2381/10827/1/2012TomaszewskiCphd.pdf

United Nations United Nations Millennium Development Goals- Millennium Development Goals-

MDGsMDGs • Goal 1 – Eradicate extreme Goal 1 – Eradicate extreme

poverty and hunger poverty and hunger •

Goal 2 – Achieve universal primary educationGoal 2 – Achieve universal primary education

• Goal 3 – Promote gender Goal 3 – Promote gender equity and empower womenequity and empower women

• Goal 4 – Reduce child Goal 4 – Reduce child mortalitymortality

• Goal 5 – Improve maternal Goal 5 – Improve maternal health health

• Goal 6- Combat HIV/AIDS, malaria and Goal 6- Combat HIV/AIDS, malaria and other diseasesother diseases

• Goal 7 - Ensure Goal 7 - Ensure environmental sustainabilityenvironmental sustainability

• Goal 8 - Develop a global Goal 8 - Develop a global partnership for partnership for developmentdevelopment

Recent molcyt.com outputs• Training • Fellowships – Pakistan; Brazil; China; India + Europe/USA• PhD students – Ethiopia; Pakistan; India; Ghana; Saudi + Europe

• Courses and training• Refereeing• Programme reviews, advisory visits• Website development (help needed!)• Project development

• We are a research provider and not a research funder• Very keen to develop projects with CRP Partners

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• - genepool• - genes

Superdomestication• Learn what has been done

– Speciation timescales of millions of years– Hybridization timescale thousands of years– Breeding timescale hundreds of years

• Learn what we want to do– Sustainable crop production– High yield, low input (chemical, mechanical and

labour!)– Stable/Reliable/Robust/Buffered– Capital input? Transportable/storable?

• Do it!

50 years of plant breeding progress

CytoGenomics …

• 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

Welcome for collaborators

Superdomestication and feed-forward plant breeding:

Genomic and molecular cytogenetic approaches

http://molcyt.org/2012/11/29/superdomestication-feed-forward-breeding-and-climate-proofing-crops/

Trude Schwarzacher and Pat Heslop-Harrisonts32@le.ac.uk and phh4@le.ac.uk

www.molcyt.comThese are the slides that go with the talk on YouTube and some text on molcyt.com for commentary. See: http://molcyt.org/2012/11/29/superdomestication-feed-forward-breeding-and-climate-proofing-crops/