Slide #1.

Arabidopsis Experiments Developmental Screen and Phase Changes Reverse Genetics PCR Genotyping
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Slide #2.

Phase Changes flower development gametophyte development zygote to embryo germination vegetative to reproductive juvenile to adult
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Slide #3.

Phase Change Studies • Genetic and molecular genetic approaches, – isolate mutants that fail in some way to change phase properly, – study genes, gene products and associated molecules, and resulting structures.
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Slide #5.

Forward vs. Reverse Genetics • Treat thousands of organisms with a mutagen, – random mutagenesis, • Identify an individual with a phenotype of interest, • Identify the gene. Forward • Treat thousands of organisms with a mutagen (usually), – random mutagenesis, • Identify an individual with a genotype of interest, • Identify the phenotype. Reverse
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Slide #6.

Proton Pumps in planta Anthers cell elongation Stems transport; sucrose hormones Arabidopsis Pollen tip growth Leaves stomata (gas exchange) sucrose transport Roots root hair growth mineral Embryo/Seeds loading
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Slide #7.

+ H (protons) ATP synthase Transporters - carriers, - channels. ATP hydrolase (ATPase) Adapted from Biochemistry and Molecular Biology of Plants, pp. 115
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Slide #8.

Arabidopsis Genome ~125 Mb (Megabases, million base pairs), – Rice: 420 Mb, Human: 3 Gb, 25,498 genes from 11,000 gene families, – Rice: 32,000 - 50,000, Human: 25,000 - 66,000.
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Slide #9.

Phylogenetic Family Tree Arabidopsis H -ATPase + (ClustalW --> Phylip: protdist, fitch) Gene Family Gene AHA1 AHA2 AHA3 AHA4 AHA5 AHA6 AHA7 AHA8 AHA9 AHA10 AHA11 AHA12 Location whole plant root cortex phloem root endodermis whole plant anthers seeds hypocotyl - Function ? ? ? nutrient uptake ? ? ? ? ? ? ? psuedogene Baxter et al. , Plant Physiol, 123, (2003)
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Slide #10.

Reverse Genetics Functional Genomics Gene DNA Sequence Gene Disruption Phenotype Analysis Function Mutate DNA Sequence Genetically Link Development Physiology Cell Biology
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Slide #11.

Nature Ti-Plasmid T-DNA Plant Cells Hormones Opines Agrobacterium Lab T-DNA Out: Ti genes, opine genes, In: DNA of choice. Selectable Markers Reporter Genes Genes
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Slide #12.

Agrobacterium tumefaciens Ti Plasmid (Tumor inducing) Mother Nature wt plant chromosome hormone genes (i.e. auxins) Ti Plasmid (from agro) opaline virulence genes nopaline neoplastic transformation opaline, nopaline virulence genes hormone genes Agro food
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Slide #13.

T-DNA (Transfer DNA) Laboratory Construct T-DNA selection genes virulence genes …can put other genes. transform, select for agro with T-DNA Agrobacterium infect plant, select for plants with T-DNA …if the T-DNA lands in a gene, the gene is disrupted.
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Slide #14.

Probability of Finding an Insert in a Specific Gene p = 1-(1-f)n p = probability of insertion event f = 1-(Genome/Size of Gene) n = number of T-DNA inserts thousands of inserts
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Slide #15.

Knockology Plants/Pools DNA/Pools
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Slide #16.

Set-Up DNA Pooling Maintain lines as pools of seed. Seeds (9) Germinate and grow seeds in liquid culture. Seedlings (225) Extract DNA, DNA (225) Super Pool DNA, 1 2 3 4 5 PCR Screen 6 …30 Super Pools (2025)
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Slide #17.

QuickTime™ and a Cinepak decompressor are needed to see this picture.
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Slide #18.

5’--GCATGCATTAT 5’--GCATGCATTAGGCTACATCGACATCGACTAGCACTG--3’ 5’--GCATGCATTAGGCTACATCGACATCGACTAGCACTG--3’ 3’--GCTACGTAATCCGATGTAGCTGTAGCTGATCGTGAC--5’ 5’--GCATGCATTAGGCTACATCGACATCGACTAGCACTG--3’ 3’--GCTACGTAATCCGATGTAGCTGTAGCTGATCGTGAC--5’ 3’--CGTACGTAATACGATGTAGCTGTAGCTGATCGTGAC--5’ CTGATCGTGAC--5’ o 94 Denature Step ~30 seconds Synthesis ~1 minute/kb 72o PCR ~65o Annealing Step ~30 seconds 5’--GCATGCATTAGGCTACATCGACATCGACTAGCACTG--3’ CTGATCGTGAC--5’ 5’--GCATGCATTAGGCTACATCGACATCGACTAGCACTG--3’ 5’--GCATGCATTAT 3’--CGTACGTAATACGATGTAGCTGTAGCTGATCGTGAC--5’ 5’--GCATGCATTAT 3’--CGTACGTAATACGATGTAGCTGTAGCTGATCGTGAC--5’ CTGATCGTGAC--5’
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Slide #19.

PCR Strategy • Polymerase Chain Reaction (PCR), – with oligonucleotide primers with homology to the 5’ and 3’ ends of your gene, amplify the DNA sequence between the primers. Reaction: Product: 5’ Your gene Your gene amplified 3’
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Slide #20.

Reverse Genetic PCR Strategy Reaction: Product: Reaction: Product: none. T-DNA
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Slide #21.

PCR Screens for Mutants
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Slide #22.

PCR Strategy Reaction: T-DNA Product: Reaction: Product: T-DNA
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Slide #23.

Find the Plant You are ~here.
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Slide #24.

tagged tagged seed seedline line T-DNA Mutants Genetic Analysis tt x TT (wt) isolate isolate homozygous homozygous mutant mutant 2x backcross backcross to towildtype wildtype phenotype phenotype analysis analysis Tt T-DNA Segregation T t T TT Tt t Tt tt F2
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Slide #25.

PCR Genotyping L t T homozygote wt 5’ 5’ 3’ 3’ L t 5’ 3’ 5’ 3’ T heterozygote L t T homozygote mutant 5’ 3’ 5’ 3’
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Slide #26.

Genetic Analysis F2 Segregation T t T TT Tt t Tt tt T t T TT Tt t Tt tt T t T TT Tt t Tt tt 1:2:1 1 wt : 2 het 1 wt : 1 het Not Lethal Lethal Gametophyte Lethal
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Slide #27.

To Do • Tuesday: – Extract Plant DNA – PCR, – Continue Developmental Screen, • Thursday: – Run PCR fragments on gels, – Continue Developmental Screen, – Thin Developmental sceen plants.
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