Beyond Arabidopsis - model systems

These slides provide some resources to get started with a selection of model plants. These slides were generated by the speakers at the "Beyond Arabidopsis" workshop, hosted by Kaisa Kajala and Michael T. Raissig at ICAR 2018 in Turku. The slides are openly shared with the permission of the speakers.

Specifically, the slides cover:
Brachypodium - Michael T. Raissig
Populus, birch and conifers - Ykä Helariutta
Sunflower - Stacey Harmer
Tomato - Javier Brumos
Soybean - Mariko Nonogaki
Chlamydomonas - Josep Vilarrasa-Blasi

Transcript

1. Beyond Arabidopsis - Advantages and Challenges of Emerging Plant Models June 26th 2018 | ICAR | Turku, Finland https://speakerdeck.com/kaisakajala
2. Tomato Birch Brachypodium Sunflower Soybean Wheat Chlamydomonas Chlorophyceae Stacey Harmer Javier Brumos Ykä Helariutta Mariko Nonogaki Josep Vilarrasa-Blasi Kaisa Kajala Michael Raissig
3. Brachypodium Chlorophyceae Michael Raissig
4. Brachypodium distachyon - purple false brome Generation time From seed to seed in 3-4 months Genome 272 Mb (smallest grass genome to date) High quality assembly and annotation https://doi.org/10.1038/nature08747 & https://phytozom e.jgi.doe.gov/jbrowse/index.htm l Whole-genome de novo assembly and annotation of 54 lines -> pangenome! https://doi.org/10.1038/s41467-017-02292-8 https://brachypan.jgi.doe.gov/ Biotechnology: Efficient tissue-culture based transformation (HygR) http://1ofdm q2n8tc36m 6i46scovo2e- wpengine.netdna-ssl.com /wp-content/uploads/2015/05/Brachypodium -distachyon-transform ation-protocol.pdf Also with nptII (KanR) resistance gene and paramomycin selection https://doi.org/10.3389/fpls.2016.00716 Other protocols like crossing, mutagenesis, etc. https://jgi.doe.gov/our-science/science-program s/plant- genom ics/brachypodium / Cloning vectors: pANIC series (Gateway) https://doi.org/10.1111/j.1467-7652.2011.00658.x pIPKb series (Gateway) https://doi.org/10.1104/pp.107.111575 Single guideRNA CRISPR system from rice (Goldengate/Gateway) https://doi.org/10.1038/cr.2013.123
5. Brachypodium distachyon - purple false brome Germ plasm: Collection of natural accessions from Turkey & Spain https://doi.org/10.1186/1471-2229-9-88 https://naldc.nal.usda.gov/download/38162/PDF http://www.jstor.org/stable/20869171 RIL populations https://www.ars.usda.gov/ARSUserFiles/1931/GarvinLabCoreBrachypodium distachyonLineSet(2).pdf T-DNA lines https://jgi.doe.gov/our-science/science-program s/plant-genom ics/brachypodium /brachypodium -t-dna-collection/ Genome-wide sequence-indexed collection of grass mutants (M3/M4 individuals, >800 of 2000 done and released) https://phytozom e.jgi.doe.gov/jbrowse/index.htm l?data=genom es% 2FBdistachyonBd21_3_er% 2F&loc=Bd2% 3A51544003..51556072&trac ks=Transcripts% 2CM utant_Sites&highlight= Other species with sequenced genome: B. stacei, B. hybridum (allotetraploid of B. distachyon and B. stacei), B. sylvaticum (perennial) https://phytozom e.jgi.doe.gov/pz/portal.htm l Why Brachypodium as model? It's a wild grass (humanitarian importance, no domestication effects) Grass stomata have a major developmental innovation - subsidiary cells! Personal "best" and "worst" +simple leaves with a strict developmental gradient - Crossings (1 flower = 1 seed)
6. Birch (and other trees) Ykä Helariutta
7. Hybrid aspen (Populus tremula x tremuloides Michx, clone T89) as a model system for wood formation Advantages: - An angiosperm forest tree - Deciduous, hardwood trees - Economically important - Diploid sequenced genome (Tuskan et al. 2006) - Easy in vitro propagation - Agrobacterium-mediated transformation (Nilsson et al. 1996) - DNA and RNA isolation methods - Unique growth habits in comparison to annual species (ray cells, seasonal activity-dormancy cycle of cambial activity, tension wood formation) - Wood forming zone transcript profiling (http://aspwood.popgenie.org, Sundell et al. 2017)
9. Silver birch (Betula pendula) - A novel model system for tree genetics Advantages: - An angiosperm forest tree - Economically important - Monoecious, and out-crossing - Diploid sequenced genome, no WGD (Salojärvi et al. 2017) - Easy in vitro propagation - Agrobacterium-mediated transformation (Lemmetyinen et al. 1998) - DNA and RNA isolation methods - Can be self-pollinated - Can be induced “artificially” to flower (Longman et al. 1959) - Naturally occurring wood formation and morphology mutants - Wood forming zone transcript profiling Silver birch - Betula pendula
10. Accelerated Flowering 6 month old trees 2 month dormancy 1 week Flowering Induction + Crossing • LD: (20 h light/4 h dark) at 30-36°C • CO2 level: 12.00 - 2000 ppm 2-3 month Seeds Ripening 1 month Seeds Cold Treatment Germination test: University of Helsinki Natural Resources Institute Finland (Luke) Unripenedcatkins Ripened catkins TOTAL 12 months • LD: (16 h light/8 h dark) • 20-24°C *pollen collection Longman and Wareing 1959, Nature Tree architecture and wood formation/Birch as a model/elimäki phenotype Juan Alonso Serra Chang Su Juha Immanen Kaisa Nieminen
12. Umeå Plant Science Center
13. congenie.org – our database With the permission of Ove Nilsson (Umeå Plant Science Center)
14. 14 With the permission of Ove Nilsson (Umeå Plant Science Center)
15. Sunflower Stacey Harmer
16. Why study sunflower? Helianthus annuus is an excellent model for studying key evolutionary processes including: • domestication • adaptation • speciation Numerous wild extremophile sunflowers cross-compatible with cultivated sunflower • Excellent genetic/genomic resources Fascinating developmental phenotypes not found in Arabidopsis thaliana Salt & drought tolerant sunflower Flooding & salt tolerant sunflower Low-nutrient tolerant sunflower photos courtesy of Loren Rieseberg
17. Helianthus annuus – sunflower Generation time • From seed to seed in 3-4 months Genome • 3.6 Gb (~80% retrotransposons) • High-quality assembly required Illumina + PacBio sequencing High quality assembly and annotation • https://www.nature.com/articles/nature2 2380 and https://www.heliagene.org and https://www.sunflowergenome.org • Reference transcriptomes with organ- specific expression patterns • High density genetic map
18. Helianthus annuus – sunflower Association mapping panel • 288 genotypes re-sequenced; >85% of the allelic diversity in cultivated germplasm; available from the GRIN of the National Plant Germplasm System • http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003378; • https://npgsweb.ars-grin.gov/gringlobal/taxonomydetail.aspx?id=27923 Sequences & seeds from dozens of wild Helianthus species are available • https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12023 Numerous RIL populations • https://link.springer.com/article/10.1007/s00122-005-1934-7 • https://onlinelibrary.wiley.com/doi/full/10.3732/ajb.1400097 • http://www.genetics.org/content/176/4/2589 • https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.14202
19. Helianthus annuus – sunflower Extant TILLING populations • https://plantmethods.biomedcentral.com/articles/10.1186/1746-4811-7- 20 • https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-13- 38 Extensive genetic resources in development • Re-sequencing of hundreds of wild H. annuus, H. petiolarus, H. argophyllus individuals in progress • Generation and genotyping of Multiparent Advanced Generation Inter-Cross (MAGIC) mapping populations that include both cultivated and wild sunflower donors • Generation of two large mutagenized populations (EMS and gamma-irradiated) in domesticated sunflower Transgenics • Possible, but currently challenging Nicky Creux, UC Davis
20. Tomato Javier Brumos
21. Solanum lycopersicum - Tomato Generation time Approximately 3-5 months seed-to-seed (depending on the variety) Genome 950 Mb - 12 chromosomes – 30,868 genes https://solgenomics.net/search/locus & JBrowse High quality assembly and annotation ITAG 3.2 https://solgenomics.net/organism/Solanum_lycopersicum/genome http://plants.ensembl.org/Solanum_lycopersicum/Info/Index Whole-genome sequencing projects: https://solgenomics.net/organism/Solanum_lycopersicum/inbred_geno mes Inbred lines http://www.tomatogenome.net/index.html Wageningen UR Tomato 150 ReSequencing Jbrowse AGI Shenzhen Tomato 360 Tomato Expression Atlas and e-FP Browser http://tea.solgenomics.net/ http://bar.utoronto.ca/efp2/ http://tomexpress.toulouse.inra.fr/ Biotechnology: Efficient transformation and tissue-culture plant regeneration. Cloning propagation by cuttings and grafting. http://www.hos.ufl.edu/meteng/HansonWebpagecontents/Tomatotransformatioprotocol.html http://lippmannsf.labsites.cshl.edu/outreach/virtual-greenhouse/ Cloning vectors: Depending on requirements countless dicot binary-vector possibilities: Gateway/GoldenGate/GoldenBraid/Multiplexed gRNAs CRISPR Other protocols like crossing, mutagenesis, etc. http://tgrc.ucdavis.edu/ http://solcap.msu.edu/videos.shtml
22. Germplasm: Collection of natural accessions http://tgrc.ucdavis.edu/ http://hos.ufl.edu/kleeweb/newcultivars.html http://tombreeding.ifas.ufl.edu/germplsm.htm http://traditom.eu/ https://www.ru.nl/bgard/solanaceae-collection/databases/solanaceae-database/ http://phenome-networks.com/ QTL and SNPs databases https://solgenomics.net/search/phenotypes/qtl https://solgenomics.net/qtl/population/14 https://solgenomics.net/qtl/population/18 https://solgenomics.net/qtl/population/12 http://www.kazusa.or.jp/tomato/ http://zamir.sgn.cornell.edu/Qtl/Html/home.htm http://archive.gramene.org/qtl/ Mutant lines http://zamir.sgn.cornell.edu/cgi-bin/mutation_site/mutant04_search.pl http://zamir.sgn.cornell.edu/mutants/ http://tomatoma.nbrp.jp/ https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.12728 http://www.agrobios.it/tilling/index.html http://urgv.evry.inra.fr/UTILLdb Related species with sequenced genome: Wild relatives-varieties mentioned, Potato, Pepper, Eggplant, 3 Nicotiana, 2 Petunia, Coffee Why Tomato as model? Tomato is one of the main fruits in the world, great economic impact. Model in the study of fleshy fruit development and ripening, stress and plant disease tolerance, carotenoid and cell wall biosynthesis, ethylene signaling pathway. Kaisa’s and my "best" and "worst" + Rapid transient expression in fruit, VIGS, and hairy root transformation. Farming direct applications. - Laborious plant maintenance, seed harvest, and long generation time. Solanum lycopersicum - Tomato
23. Soybean Mariko Nonogaki
24. Generation time From seed to seed in 4-8 months https://www.extension.umn.edu/agriculture/soybean/ Genome 1.1 Gb https://www.nature.com/articles/nature08670 Genetics and genomics information https://soybase.org/ http://soykb.org/ Biotechnology: Transformation https://www.jstor.org/stable/23387369?seq=1#page_scan_tab_contents https://link.springer.com/article/10.1007/s00299-005-0048-7 https://link.springer.com/article/10.1007/BF02632213 https://link.springer.com/article/10.1007/s001220051441 https://www.jstage.jst.go.jp/article/jsbbs/61/5/61_5_480/_article https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571417/ Gene editing http://www.plantphysiol.org/content/169/2/960.long https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.12758 https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.12201 Glycine max - soybean Gene expression tools Gene Chip http://seedgenenetwork.net/soybean RNA-seq http://seedgenenetwork.net/sequence
25. Germplasm: USDA-ARS https://www.ars.usda.gov/oc/np/soybeangermplasm/soybeangermplasmintro/ https://www.ars.usda.gov/midwest-area/urbana-il/soybeanmaize-germplasm-pathology-and- genetics-research/ Fast Neutron Mutant Population http://www.plantphysiol.org/content/156/1/240 https://www.ncbi.nlm.nih.gov/pubmed/21321255 High-density mutant library https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4662035/ Other species with sequenced genome Glycine soja (undomesticated ancestor) http://www.pnas.org/content/107/51/22032 Why soybean? "Direct” translational biology from Arabidopsis (dicot, oil/protein seeds, etc.) Personal "best" and "worst" +Have good collaborators/experts for transformation! - No experience with the species Glycine max - soybean
26. Chlamydomonas Chlorophyceae Josep Vilarrasa-Blasi
27. Adapted from Gutman and Niyogi 2004 Generation time; 8 hours Genome; Haploid 121 Mb, high GC de novo sequencing 39 common strain Assembly and annotation; Phytozone Chlamydomonas Biotechnology Efficient transformation; electroporation, glass beads (Paro, Hygro, Bleo) Protocols for crossing, maintenance.. Cloning vectors pLM, pRAM, pJM backbones Bicistronic vectors CRISPR vectors Chlamydomonas reinhardtii
28. Chlamydomonas reinhardtii Mutants collections - CLIP mutants library; genome wide, link to webpage (Jonikas lab). - Temperature sensitive (Cross lab). - CAL strains (Niyogui lab). All available Chlamy center Why Chlamy as a model? - Unicelular, generation time, haploid. - Biofuel, photosynthesis, flagella. - Basic mechanisms conserved, smaller gene families. Personal “best” and “worst” + Unicelular, generation time, genetics - Molecular genetics, expression.