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Evolution, biodiversity and the banana pangenome
The document discusses the challenges facing banana production, including biotic and abiotic stresses, and emphasizes the need for new genetic traits to enhance resistance, yield, and nutritional quality. It outlines a strategy for improvement that involves identifying challenges, useful genetic variants, and testing new varieties while highlighting the evolution and diversity within the Musa and Ensete species. The ultimate goal is to leverage this genetic diversity for the sustainability and benefit of farmers in the banana economy.
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Evolution, biodiversity and the banana pangenome
- 1. The banana pangenome, evolution,and exploiting biodiversity PAT HESLOP-HARRISON TWITTER: @PATHH1 AND SLIDESHARE PHH@MOLCYT.COM
- 3. Map DongLi Cui,Qing Liu & HH SCBG Musa – Banana distribution warm, humid tropics Sister genus Ensete
- 4. • World BananaProduction • Almost all tropical • India: 30Mt but no export • “Banana economy” is praise
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- 6. Musa and Musaceae– banana and the banana taxonomic family Musaceae Charles Darwin 1859 The Origin of Species And notebook
- 7. Ensete ventricosum 2ndgenus in Musaceae enset, ensete, false banana Staple food in Ethiopia
- 8. What is abanana? • Musa – Musaceae – Zingiberales • Monocotyledon – Giant Herb (grass not tree!) 1.1 Banana – Taxonomic position Zingiberales Order Bed, National Botanic Garden of Wales
- 9. green plants land plants vascular plants seedplants flowering plants diversification of angiosperms ANA ε Ginkgo Taxus Pinus Cedrus Sequoia Welwitschia Ephedra Lycophytes (ca. 1200 species) Physcomitrium sp. Chlorophytes (ca. 4300 species) 0 100 200 300 400 1500 Mya 500 AGF Charophytes (ca. 12,000 species) Sphagnum sp. Physcomitrella Monilophytes (ca. 13,000 species) Cretaceous–Tertiary extinction event Vitis (grapevine) Solanum (tomato, potato) Arabidopsis Carica (papaya) Populus (poplar) Linum (flax) Brassica (rapeseed) Glycine (soybean) Malus (apple) Musa (banana) Oryza (rice) Triticum (wheat) Zea (maize) β α γ ρ σ τ Nicotiana (tobacco) Petunia ζ Bryophytes (20,000 spp) Gymnosperms (1000 spp) Green algae ‘Pteridophytes’ Angiosperms (400,000 spp) Eudicots Monocots Basal Angiosp. Karine Alix et al., Ann Bot 2017
- 10. Challenges for banana •Abiotic stress • Water (drought and waterlogging) • Temperature • “Climate change” • Biotic stress • Fungal, bacterial & viral • Insects & nematodes • Agronomy changes • Growing in new areas • Post-harvest • Quality • Transportability and Storage • Nutritional • Socio-economic changes • More people to feed on less land • Urbanization of population • New uses • Processing • Ultra-processing (eg “plant-meats”) • Waxes • Fibre • Starch • Medical • Enhancing current properties • New properties (vaccines, antibiotics) Additions from farmers and growers welcome: What is your most pressing need? The F s of Farming Food, Fibre, Feed, Fuel Flavours, Flowers, Fun, Pharmaceuticals Pat Heslop-Harrison phh@molcyt.com For Malaysia National Banana Congress 2021
- 11. Disease resistance – fieldtrial in Malaysia China
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- 16. "The banana pangenome,evolution, and exploiting biodiversity" • i) identification of the challenge; • ii) identification of useful genetic variants; • iii) potentially bringing together useful variants in a single plant; • iv) testing of characteristics of a new variety; and • v) propagation and planting.
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- 19. “Fingerprint” gels showingdiversity in different Musa banana varieties
- 20. 07/09/2021 20 Phylogenetic analysis ofMusa genomes – separating species. Teo, Schwarzacher et al.
- 21. This work shows whatcan be achieved to measure diversity and relationships using SSR type of gel- based markers. By 2020s, whole- genome based survey sequencing and GBS (Genotyping by Sequencing) would be more appropriate • Yellow AA; Green ABB; Blue BB; Pink AAB; Orange AAA
- 22. Musa and Musaceae– banana and the banana taxonomic family Musaceae
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- 24. • Work with disease-related genesand resistance in Musa species • Azhar et al. Nuklear Malaysia / MINT
- 25. • LRRs inMusa compared to reference Rice • Azhar et al. Nuklear Malaysia / MINT
- 27. MT1 MT2 AWKW Primers : MLRR1-F and MLRR2-R 1000 bp 800 bp 600 bp MT1 and MT2 – Mutiara tolerance to FOC AW - Pisang Awak KW – Klutuk Wulung
- 28. BSV Banana StreakVirus
- 30. Nuclear Copies ofBanana Streak Virus in Banana
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- 32. Nuclear Copies ofBSV in Banana Harper, HH et al., Virology 1999 …
- 33. D’Hont, PHHet al. Nature2012 doi:10.1038/natu re11241
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- 35. • dinucleotide • ATATATATATATA •AGAGAGAGAG • trinucleotide • AATAATAATAAT • AAAGAAGAAG • tetranucleotide • AAAT; AGAT; AAAT; CCCT; Blue: monomorphic; Red: polymorphic Manosh Biswas et al The landscape of microsatellites in the enset (Ensete ventricosum) genome and web-based marker resource development. Scientific reports. 2020 Sep 17;10(1):1-1.
- 36. The genotypic andgenetic diversity of enset (Ensete ventricosum) landraces used in traditional medicine is similar to the diversity found in starchy landraces Gizachew Woldesenbet Nuraga, Tileye Feyissa, Kassahun Tesfaye, Manosh Kumar Biswas, Trude Schwarzacher, James S. Borrell, Paul Wilkin, Sebsebe Demissew, Zerihun Tadele, J.S. (Pat) Heslop- Harrison bioRxiv 2021 doi: https://doi.org/10.1101/2020.08.31.274852
- 37. NJ tree ofdiversity in Enset in Ethiopia with medicinal uses Green – non- medicinal starchy crop type But Landraces with medicinal uses have similar diversity (adjacent same colour are similar landrace accessions from different smallholdings) NM*, ‘non-medicinal’;BF for bone fracture; DP, discharge of placenta; BP, back pain; SD, skin itching and diarrhea; ET, expulsion of thorn and drainage of abscess from tissue; LD, liver disease; OD, other diseases
- 38. NJ tree ofdiversity in Enset in Ethiopia with medicinal uses Non-medicinal starchy crop type But Landraces with medicinal uses have similar diversity (adjacent same colour are similar landrace accessions from different smallholdings) NM*, ‘non-medicinal’;BF for bone fracture; DP, discharge of placenta; BP, back pain; SD, skin itching and diarrhea; ET, expulsion of thorn and drainage of abscess from tissue; LD, liver disease; OD, other diseases
- 39. A chromosome-level referencegenome of Ensete glaucum gives insight into diversity, chromosomal and repetitive sequence evolution and diversity in the Musaceae Ziwei Wang, Mathieu Rouard, Manosh Biswas, Gaetan Droc, Dongli Cui, Nicolas Roux, Franc-Christophe Baurens, Xue-Jun Ge, Trude Schwarzacher, Pat (J.S.) Heslop-Harrison and Qing Liu
- 40. Biodiversity Oryza sativa Rice Musabalbisiana Musa acuminata Musa schizocarpa Ensete glaucum Phoenix dactlyifera Date A chromosome-level reference genome of Ensete glaucum gives insight into diversity, chromosomal and repetitive sequence evolution and diversity in the Musaceae Ziwei Wang, Mathieu Rouard, Manosh Biswas, Gaetan Droc, Dongli Cui, Nicolas Roux, Franc-Christophe Baurens, Xue-Jun Ge, Trude Schwarzacher, Pat (J.S.) Heslop-Harrison and Qing Liu
- 41. Starch synthesis pathway- number of genes present in Musaceae species Ensete glaucum Ensete ventricosum Musa acuminata Musa balbisiana Musa schizocarpa Musa itinerans Gene EGL EVE MAC MBA MSC MIT AGPase 6 8 7 7 8 8 DBE 3 3 5 5 3 5 SBE 3 9 5 12 5 6 SS 21 10 17 14 14 12 Total 33 30 34 38 30 31 Cellulose Synthase Single Nucleotide Polymorphism SNP Provisional tree for GBSS Granule Bound Starch Synthase
- 42. Chromosome Evolution betweenbanana (x=11 chromosomes) and enset (x=9 chromosomes) eg01 eg02 eg03 eg04 eg05 eg06 eg07 eg08 eg09 ma01 ma02 ma03 ma04 ma05 ma06 ma07 ma08 ma09 ma10 ma11 45S 45S A chromosome-level reference genome of Ensete glaucum gives insight into diversity, chromosomal and repetitive sequence evolution and diversity in the Musaceae Ziwei Wang, Mathieu Rouard, Manosh Biswas, Gaetan Droc, Dongli Cui, Nicolas Roux, Franc-Christophe Baurens, Xue- Jun Ge, Trude Schwarzacher, Pat (J.S.) Heslop-Harrison and Qing Liu
- 43. Ensete glaucum Musa acuminata 0Mb 10 20 30 50 40 60 left right left right 0Mb 10 20 30 50 40 45SrDNA 5S rDNA Musa acuminata Ensete glaucum
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- 45. 60 years ofplant breeding progress – banana? Agronomy Genetics New breeding 0 500000000 1E+09 1.5E+09 1961 1965 1969 1973 1977 1981 1985 1989 1993 1997 2001 2005 2009 2013 2017 Production of major crops Wheat-p Rice-p Maize-p People/10 0 10000 20000 30000 40000 50000 60000 70000 1961 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 Yield of major crops Wheat-y Rice-y Maize-Y People(rel)
- 46. 60 years ofplant breeding progress – banana? Agronomy Genetics New breeding 0 1000000 2000000 3000000 4000000 5000000 6000000 1950 1960 1970 1980 1990 2000 2010 2020 2030 Banana Yield hg/ha
- 47. Super-domestication: The future ofbanana crops • The genepool has the diversity there which can meet these challenges • Breeders need to get better and faster • Banana has extra challenges • Staple food • Major income source in many communities • Sterile plant • Export has transport/ripening requirements
- 48. How to usediversity • 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 • Gene editing and Transgenic approaches
- 49. Yield – quality– sustainability Inputs: Agronomy, Genetics, Technology Climate change: extremes; water; temperature; salinity; CO2 Populations – urbanization, health Get better at what we do Partnerships with farmers, traders, processors, markets (marketing?), users, breeders, scientists Communicate and collaborate 49
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- 51. Outputs •CROPS • Fixed energy 51 Inputs –Light –Heat –Water –Gasses –Nutrients – Light –Heat – Water – Gasses – Nutrients
- 53. “The banana pangenome,evolution, and exploiting biodiversity“ Pat Heslop-Harrison phh@molcyt.com for Malaysian National Banana Congress 2021 • Banana production faces challenges from biotic (disease) and abiotic (environment) stresses. • New genetic characteristics are needed for stress resistance and to improve yield, agronomy, post- harvest quality, nutritional value, and even for new food or industrial uses. • Improvement requires i) identification of the challenge; ii) identification of useful genetic variants; iii) potentially bringing together useful variants in a single plant; iv) testing of characteristics of a new variety; and v) propagation and planting. • I will discuss our results measuring diversity in germplasm from banana and its sister species including the starchy Ensete, towards generating a pan-genome representing the entire genetic diversity within the Musaceae family. • I will consider how this diversity has evolved and how we might use it as a common gene pool to improve banana for the benefit of smallholder or commercial farmers, and for the sustainability in the environment.
- 54. The banana pangenome, evolution,and exploiting biodiversity PAT HESLOP-HARRISON TWITTER: @PATHH1 AND SLIDESHARE PHH@MOLCYT.COM