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Genomics, mutation breeding and society - IAEA Coffee & Banana meeting - Schwarzacher Heslop-Harrison

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Presentation on genomics, plant breeding and society for the IAEA / FAO joint Coordinated Research Programme CRP Research Coordination Meeting RCM Efficient screening techniques to identify mutants with disease resistance for coffee and banana CRP D22005 Lisbon June 2017 Pat Heslop-Harrison and Trude Schwarzacher. Emphasizing use of germplasm resources and mutation induction to meet challenges facing farmers, including overview of our work in the Molecular Cytogenetics lab. and plans for Ensete, Ethiopian banana. We discuss genotyping and phenotyping: areas where there have been huge improvements in the last decade. We discuss the need for superdomestication: consideration of traits needed by farmers and society in new crop varieties before generation of these varieties using appropriate genes and technologies to meet the challenges of sustainable, productive agriculture. Collaboration and education are needed globally to generate new sustainable crop varieties. see www.molcyt.com for more information about our research
Slide 6 Table 9 from http://www.fao.org/docrep/007/ae216e/ae216e08.htm Biotechnology and in vitro mutagenesis for banana improvement - Mak Chai, YW Ho, KW Liew, JM Asif

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Genomics, mutation breeding and society - IAEA Coffee & Banana meeting - Schwarzacher Heslop-Harrison

  1. 1. Genomics, mutation breeding and society Trude Schwarzacher and Pat Heslop-Harrison TS32@le.ac.uk PHH@molcyt.com www.molcyt.com Talk prepared for meeting May 2017 of PatHH1 Slideshare
  2. 2. Ensete ventricosum 2nd genus in Musaceae enset, ensete, false banana
  3. 3. 2 End hunger, achieve food security, improve nutrition & promote sustainable agriculture 15 Protect, restore and promote sustainable use of terrestrial ecosystems … halt biodiversity loss
  4. 4. 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.
  5. 5. i) assess Ensete genetic diversity ii) conserve the Ensete gene pool iii) identify pathogens and soil biota iv) compare Ensete genome and other species iv) apply genomics tools and tissue culture to support breeding and use biodiversity v) document and make information accessible.
  6. 6. Genomics changes study of taxonomy, phylogeny, diversity Revolutionizes crop genetics and breeding Exploits Musa as a reference i) assess Ensete genetic diversity ii) conserve the Ensete gene pool iii) identify pathogens and soil biota iv) compare Ensete genome and other iv) apply genomics tools and tissue cult support breeding and use biodiversity v) document and make information acc
  7. 7. Ensete ventricosum 2n=18 1C ~600Mb
  8. 8. Ensete ventricosum ‘Maurelli’ 2n=18 5S rDNA 5S rDNA (AAC)7
  9. 9. OBJECTIVES Fundamental 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
  10. 10. OBJECTIVES Fundamental 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
  11. 11. Collaboration critical: blue countries
  12. 12. • 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
  13. 13. 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
  14. 14. Major Genomic Components • Tandem Repeats • Simple Sequence Repeats • Dispersed Repeats • Functional Repeats • Retroelements • Genes Typical Fraction 10% 5% 10% 15% 50% 10%
  15. 15. Analysis with RepeatExplorer A978 Petunia Ensete repetitive DNA distribution Not 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.
  16. 16. 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 sequence Menzel et al. 2014 and Nouroz et al. Mol Gen Genet 2017 subject to revision
  17. 17. Episomal forms of PVCV Virions immunogold labeled Viroplasm in PVCV infected P. parodii IB Mi V V
  18. 18. Centromere DNA sequence TE Tandem repeat monomer TE 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)
  19. 19. • Project on Boesenbergia lead by Norzulaani Khalid & Jennifer Ann Harikrishna Genome sequence Secondary products Tissue culture changes Epigenetics – DNA and chromatin modification Histone H3 dimethylated lysine K4 (49-1004) euchromatin mark Labels ends of chromosomes: centromeric heterochromatin not stained Histone H3 mono-methylated lysine K9 (49-1006) heterochromatin mark
  20. 20. Organelle sequences from 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 repeats Satellite sequences DNA transposonsRetrotransposons 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 genome After 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
  21. 21. Outputs –CROPS – Fixed energy Inputs –Light –Heat –Water –Gasses –NutrientsLand
  22. 22. Outputs –Crops (Chemical energy) – Food – Feed – Fuel – Fibre – Flowers – Pharmaceuticals – Fun28
  23. 23. Outputs Ecosystem Services Water, gasses, nutrients ”nature’s services, like flood control, water filtration, waste assimilation”
  24. 24. Inputs –Light –Heat –Water –Gasses –Nutrients –Light –Heat –Water –Gasses –Nutrients (Ecosystem services) Outputs –CROPS – Chemical energy
  25. 25. Phenotyping and genotyping • Huge advances in last 5 years • Drones (including IAEA) • Sequencing
  26. 26. • 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
  27. 27. Agricultural production • Agronomy • Genetics • Genetics for production systems – technological solutions for sustainable agriculture
  28. 28. Legislation: European Parliament & Commission
  29. 29. (Some text deleted to focus for IAEA/FAO CRP)
  30. 30. 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’
  31. 31. 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
  32. 32. 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 diversity ii) conserve the Ensete gene pool iii) identify pathogens and soil biota iv) compare Ensete genome and other species iv) apply genomics tools and tissue culture to support breeding and use biodiversity v) document and make information accessible.
  33. 33. Socio-economic • High value crops: niche bananas • Urbanization of populations • Larger farms • Education – MSc level • Genetic resource conservation
  34. 34. Genomics, mutation breeding and society Trude Schwarzacher and Pat Heslop-Harrison TS32@le.ac.uk PHH@molcyt.com www.molcyt.com Talk prepared for meeting May 2017 of PatHH1 Slideshare
  35. 35. Molecular Cytogenetics Group www.molcyt.com Pat Heslop-Harrison Trude Schwarzacher and colleagues Impacts outside academia Legislation: 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 superdomestication strategies to exploit biodiversity for sustainable agriculture Work on hybrids and alien introgression with novel quality / disease resistance characters Wheat with virus resistance identified 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 for biotechnology Food fraud and safety detection Reviewing research programmes Editing Journals

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