Genomics, mutation breeding and society

Trude Schwarzacher and

Pat Heslop-Harrison

TS32@le.ac.uk

PHH@molcyt.com www.molcyt.comTalk prepared for meeting May 2017 of

PatHH1Slideshare

Ensete ventricosum 2nd genus in Musaceae

enset, ensete, false banana

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

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

1000 bp

800 bp

• Find and create the diversity for breeding in crops, wild relatives and by mutation

• Apply genomic tools to measure and use biodiversity

• Use tissue culture to support breeding Document and make information accessible

Azhar M, Heslop-Harrison JS. Genomes, diversity and resistance gene analogues in Musa species. Cytogenetic and genome research. 2008, 121: 59-66.

i) assess Ensete genetic diversityii) conserve the Ensete gene pooliii) identify pathogens and soil biotaiv) compare Ensete genome and other speciesiv) apply genomics tools and tissue culture to support breeding and use biodiversityv) document and make information accessible.

Genomics changes study of taxonomy, phylogeny, diversity

Revolutionizes crop geneticsand breeding

Exploits Musa as a reference

i) assess Ensete genetic diversityii) conserve the Ensete gene pooliii) identify pathogens and soil biotaiv) compare Ensete genome and other speciesiv) apply genomics tools and tissue culture to support breeding and use biodiversityv) document and make information accessible.

Enseteventricosum

2n=181C ~600Mb

Ensete ventricosum ‘Maurelli’ 2n=18

5S rDNA 5S rDNA (AAC)7

OBJECTIVESFundamental and Practical

Explain major structures and features of the DNA in plant genomes

Understand the structure of chromosomes and genomes

Explain the nature and origin of molecular markers

Understand key events in evolution and generation of diversity including induced mutations

www.molcyt.com

OBJECTIVESFundamental and Practical

Manipulate and exploit diversity

Apply genomic knowledge to breeding

Develop markers for breeding –genome, chromosome, gene …

Use superdomestication in breeding to identify and provide solutions to problems facing breeders and farmers

www.molcyt.com

Collaboration critical: blue countries

• Dr Qing Liu, South China Botanical Garden

• Dr Adel Sepsi, EU Marie Curie Hungary

• Prof Roberto de la Herran, Granada, Spain

• Prof Lani Khalid, Kuala Lumpur, Malaysia

• Dr V Arunachalam, Goa, India

• Dr Shwet Kamal, Solan, India

• Dr Ijaz Rasool Noorka, Sargodha, Pakistan

• Dr Zubeda Chaudhry, Mansehra, Pakistan

• Dr Yifei Liu, South China Botanical Garden

• Dr Sara Saraswathi, Tamil Nadu, India

• Dr Mateus Mondin, Sao Paulo, Brazil

• Prof Asha Nair, Kerala, India

• Dr Kazumi Furakawa, Numazu, Japan

• Dr Anath Das, Orissa, India

• Dr Xianhong Ge, Wuhan, China

• Dr Ana Claudia Araujo, EMBRAPA, Brasilia, Brazil

Senior Visitors, Post-docs and collaborators

• Professor Jenni Harikrishna, Malaysia

• Dr Katja Richert-Poeggeler, JKI, Germany

• Prof Rachel , UTAD, Portugal

• Prof Thomas Schmidt and Gerhard Menzel, Dresden

• Alex Vershinin, Russia

• Olena Alkhimova, Ukraine

• Nicolas Roux, Mathieu Pinard, France

• Maria Madon, Malaysia

• Bob Greybosch, Nebraska

PhD students• Iza Mohd Zaki, Malaysia, 2nd year• Osamah Alisawi, Iraq, 3rd year• Sarbast Mustafa, Kurdistan, 3rd year• Rubar Salih, Kurdistan, 2017• Nauf Alsayaid, 2015• Jotyar Muhammed, Kurdistan, 2017• Chetan Patokar, India, 2015• Stuart Desjardins, 2015 & John Bailey

• Farah Badakshi, India, 2014• Worku Negash Mhiret, Ethiopia, 2014• Celine Tomazewski, France, 2012• Hojatollah Saeidi, Iran, 2010• Faisal Nouroz, Pakistan, 2012• Niaz Ali, Pakistan, 2012• Azhar Mohammad, Malaysia• Emmanuel Otwe, Ghana

• Navdeep Jamwal, India• Manica Balant, Croatia• Aude Aguzou, France• Frederica Raccis, Italy• Juceli Gouveia, Brazil• Fabiola Carvalho, Brazil• Natalia Melloni, Brazil• Laetitia Gaspar, Portugal• Ana Sofia Silva, Portugal• Israr Ahmad, Pakistan• Valentina Scrocca, Italy• Christos Kyprianou, UK• Acga Cheng, Malaysia• Salwa Sirajuddin, Malaysia• Emanuelle Ranieri, Italy• Pedrdo Campoy, Spain• Fengjiao Zhang, China

Major Genomic Components

• Tandem Repeats

• Simple Sequence Repeats

• Dispersed Repeats

• Functional Repeats

• Retroelements

• Genes

Typical Fraction

10%

5%

10%

15%

50%

10%

Analysis with RepeatExplorer

A978

Petunia

Ensete repetitive DNA distributionNot huge abundance of repetitive sequences in Ensete – 25% of genome

Taraxacum

Bombarely, … Schwarzacher, Heslop-Harrison, … et al. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nature plants. 2016 May 27;2:16074.

Figure M1-1: Dot plot of homoeologous BAC clones Musa balbisiana ‘MBP_81C12’ (horizontal) against Musa acuminata ‘MA4_82I11’

(vertical). The comparison of the BACs showed large homologous region with several gap-insertion pairs. The gaps showed transposon insertions

present in one BAC and absent in others. Different TEs are encircled and named. Several small insertions are not highlighted here.

Transposed MaN-hAT2

MaN-hAT1

MaN-hAT2

MbN-hAT3

MBT

MaMITE1

MAWA

Microsatellite

How do genomes differ?Dotplot of 50kb of sequenceMenzel et al. 2014 and Nouroz et al. Mol Gen Genet 2017 subject to revision

Episomal forms of PVCV

Virions immunogold labeled

Viroplasm in PVCV infected P. parodii

IB

Mi

V

V

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 SciUSA. http://dx.doi.org/10.1073/pnas.1319945110. See also http://molcyt.org (Dec 2013)

• Project on Boesenbergia lead by NorzulaaniKhalid & Jennifer Ann Harikrishna

Genome sequenceSecondary products

Tissue culture changes

Epigenetics –DNA and

chromatin modification

Histone H3 dimethylatedlysine K4 (49-1004)

euchromatin mark

Labels ends of chromosomes:centromeric heterochromatin

not stained

Histone H3 mono-methylated lysine K9 (49-1006)

heterochromatin mark

Organelle sequencesfrom chloroplasts or

mitochondria

Sequences from viruses

Transgenes introduced with molecular biology

methods

Genes, regulatory and non-coding low-copy sequences

Dispersed repeats

Repetitive DNA sequences

Nuclear Genome

Tandem repeatsSatellite sequences

DNA transposonsRetrotransposons

Centromericrepeats

Structural components of chromosomes

Telomericrepeats

Simple sequence repeats or

microsatellites

Repeated genes

Subtelomericrepeats

45S and 5S rRNA genes

Blocks of tandem repeats at discrete chromosomal loci

DNA sequence components of the nuclear genomeAfter Biscotti et al. Chromosome Research 2015

Other genes

Transposable elements

Autonomous/ non-autonomous

Dispersed repeats that we don’t know

about – except each is significant proportion

of genome

Outputs

–CROPS

– Fixed energy Inputs

–Light

–Heat

–Water

–Gasses

–NutrientsLand

Outputs

–Crops(Chemical energy)

– Food– Feed– Fuel– Fibre

– Flowers– Pharmaceuticals

– Fun28

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

Inputs

–Light

–Heat

–Water

–Gasses

–Nutrients

–Light

–Heat

–Water

–Gasses

–Nutrients

(Ecosystem services)

Outputs

–CROPS

– Chemical energy

Phenotyping and genotyping

• Huge advances in last 5 years

• Drones (including IAEA)

• Sequencing

• 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

Agricultural production• Agronomy

• Genetics

• Genetics for production systems – technological solutions for sustainable agriculture

Legislation: European Parliament & Commission

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

Precision farming

• Integration of genetics with agronomy

• Decision on crop requirements

• Biotic & abiotic stress resistances

• Yield, quality, post-harvest …

• Precision application of crop protection chemicals (even lasers)

• Giant and micro-vehicles –autonomous/intelligent/’big data’

Engagement• Publication and websites

• Press –(cf Stephan’s comments Monday)

• Blog posts – eg Julie Sardos and Bougainville collection mission http://www.promusa.org/blogpost506-Collecting-bananas-in-Bougainville

• Crowd sourcing: iNaturalist and feral banana

• Dr Adugna Wakjira, DDG, Ethiopian Institute of Agricultural Research (and co-author/colleague)

• “Our government recognizes biotechnology as one of the transformative tools to accelerate agricultural development … exemplified by Parliament’s amendment to a more progressive and permissive legislation of biotechnology”

• But needed quickly: training of new scientists to deliver local solutions. Certainty needed

i) assess Ensete genetic diversityii) conserve the Ensete gene pooliii) identify pathogens and soil biotaiv) compare Ensete genome and other speciesiv) apply genomics tools and tissue culture to support breeding and use biodiversityv) document and make information accessible.

Socio-economic

• High value crops: niche bananas

• Urbanization of populations

• Larger farms

• Education – MSc level

• Genetic resource conservation

Genomics, mutation breeding and society

Trude Schwarzacher and

Pat Heslop-Harrison

TS32@le.ac.uk

PHH@molcyt.com www.molcyt.comTalk prepared for meeting May 2017 of

PatHH1Slideshare

Molecular Cytogenetics Groupwww.molcyt.com

Pat Heslop-HarrisonTrude Schwarzacher

and colleagues

Impacts outside academiaLegislation: European Parliament & Commission

Breeding new, sustainable crop varieties

Sequencing of whole genomes

Discussing risk assessment and scientific advice with EU Health Commissioner Dr Vytenis Adriukaitis

We study genomes and evolution mechanisms to find, measure and exploit genetic variation in crops,

farm animals, and their wild relatives

Developing superdomesticationstrategies to exploit biodiversity

for sustainable agriculture

Work on hybrids and alien introgression with novel quality / disease resistance characters

Wheat with virus resistanceidentified in the group in breeding trials

Diversity, wild genes and recombination in species and landraces

DNA sequences we find confer stress resistance in crops

New methods forbiotechnology

Food fraud and safety detection

Reviewing research programmesEditingJournals