Genomics, mutation breeding and society
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i) The document discusses applying genomics tools and techniques like sequencing, mutation breeding, and tissue culture to assess genetic diversity in Ensete, conserve the Ensete gene pool, and support breeding. It aims to identify pathogens and soil biota, compare the Ensete genome to other species, and document and make information accessible. ii) Genomics is revolutionizing the study of taxonomy, phylogeny, and diversity in crops. It enables exploiting biodiversity for breeding through tools like markers, mutation induction, and tissue culture. iii) The research has impacts outside academia through legislation, breeding more sustainable varieties, sequencing whole genomes, risk assessment, and advising on biotechnology and food safety.
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Genomics, mutation breeding and society
- 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. Ensete ventricosum 2nd genus in Musaceae enset, ensete, false banana
- 4. 2 End hunger, achieve food security, improve nutrition & promote sustainable agriculture 15 Protect, restore and promote sustainable use of terrestrial ecosystems … halt biodiversity loss
- 6. 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.
- 7. 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.
- 9. 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
- 12. Ensete ventricosum ‘Maurelli’ 2n=18 5S rDNA 5S rDNA (AAC)7
- 14. 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
- 15. 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
- 16. Collaboration critical: blue countries
- 17. • 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
- 18. 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
- 19. Major Genomic Components • Tandem Repeats • Simple Sequence Repeats • Dispersed Repeats • Functional Repeats • Retroelements • Genes Typical Fraction 10% 5% 10% 15% 50% 10%
- 21. 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.
- 22. 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
- 23. Episomal forms of PVCV Virions immunogold labeled Viroplasm in PVCV infected P. parodii IB Mi V V
- 24. 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)
- 25. • 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
- 26. 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
- 28. Outputs –Crops (Chemical energy) – Food – Feed – Fuel – Fibre – Flowers – Pharmaceuticals – Fun28
- 30. Outputs Ecosystem Services Water, gasses, nutrients ”nature’s services, like flood control, water filtration, waste assimilation”
- 33. Phenotyping and genotyping • Huge advances in last 5 years • Drones (including IAEA) • Sequencing
- 34. • 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
- 35. Agricultural production • Agronomy • Genetics • Genetics for production systems – technological solutions for sustainable agriculture
- 36. Legislation: European Parliament & Commission
- 37. (Some text deleted to focus for IAEA/FAO CRP)
- 38. 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’
- 39. 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
- 43. 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.
- 44. Socio-economic • High value crops: niche bananas • Urbanization of populations • Larger farms • Education – MSc level • Genetic resource conservation
- 46. 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
- 47. 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