Unit 6: Model Systems and Genetic Analysis of Development

Model organisms are species chosen because their biology, short life cycle and experimental tractability make them stand in for genetic processes shared across all life. This unit surveys the classic panel of models and then uses Drosophila to show how mutational analysis dissects embryonic development.

Defining criteria of a good model system:

• Short generation time: rapid succession of crosses (hours in E. coli, ~10 days in Drosophila).
• Large progeny number: enough offspring to detect rare recombinants or mutants.
• Small, mapped genome: ease of sequencing and gene localisation.
• Ease of culture and mutagenesis: cheap growth, response to agents like EMS, X-rays.
• Conserved pathways: homologues of human genes (e.g. Hox, cell-cycle, signalling genes).

II. Escherichia coli — Prokaryotic Workhorse

A Gram-negative gut bacterium that founded molecular genetics.

A. Genetic features

• Genome: single circular chromosome, ~4.6 Mb, ~4,300 genes, haploid.
• Generation time: ~20 minutes; overnight culture yields ~10⁹ cells/mL.
• Mapping tools: conjugation (Hfr strains transfer genes time-ordered), transduction and transformation.
• Selection: auxotrophic and antibiotic-resistance markers allow direct plating for rare events.

B. Contributions

• Operon model: lac operon defined gene regulation (Jacob and Monod).
• Cloning host: plasmids and phage vectors propagate recombinant DNA.
• Replication/repair: semiconservative replication (Meselson–Stahl) and mismatch repair worked out here.

III. Bacteriophage — Viral Genetic Probe

Viruses that infect bacteria, used to define the gene at molecular resolution.

A. Genetic features

• Phage λ and T-phages: small genomes (λ ≈ 48.5 kb) fully sequenced.
• Plaque assay: clear zones on a bacterial lawn quantify individual infective particles.
• Lytic vs lysogenic cycles: λ chooses between immediate lysis and integration as prophage.

B. Contributions

• Fine-structure mapping: Benzer's rII locus in T4 showed the gene is subdivisible by recombination to the nucleotide level.
• Nature of genetic material: Hershey–Chase used ³²P/³⁵S labelling to prove DNA, not protein, is hereditary.
• Complementation test: cis–trans test defined the cistron.

IV. Neurospora crassa — Filamentous Fungus

Orange bread mould that linked genes to enzymes.

A. Genetic features

• Haploid vegetative phase: phenotype directly reflects genotype; no dominance masking.
• Ordered tetrads: eight ascospores in an ascus record meiotic products in linear order.
• Simple medium: grows on minimal medium plus a carbon source; auxotrophs need supplements.

B. Contributions

• One-gene–one-enzyme hypothesis: Beadle and Tatum's X-ray-induced arg auxotrophs mapped biosynthetic steps to single genes.
• Gene conversion & centromere mapping: ordered asci allow tetrad analysis and first-division vs second-division segregation.

V. Saccharomyces cerevisiae — Budding Yeast

Single-celled eukaryote combining microbial ease with eukaryotic biology.

A. Genetic features

• Both ploidies stable: haploid a/α cells mate to form diploids; both can be studied.
• Genome: ~12 Mb, 16 chromosomes, ~6,000 genes; first eukaryotic genome sequenced (1996).
• Efficient homologous recombination: enables precise gene knock-out and replacement.

B. Contributions

• Cell-cycle control: cdc mutants defined CDKs and cyclins.
• Tools: yeast two-hybrid assay, artificial chromosomes (YACs), plasmid shuttle vectors.

VI. Arabidopsis thaliana — Plant Model

A small mustard-family weed, the reference organism for plant genetics.

A. Genetic features

• Small genome: ~135 Mb, 5 chromosomes; first plant genome sequenced (2000).
• Rapid cycle: seed-to-seed in ~6 weeks; thousands of seeds per plant.
• Self-fertile and transformable: Agrobacterium floral-dip introduces transgenes easily.

B. Contributions

• Flower development: ABC model of floral organ identity from homeotic mutants (apetala, agamous).
• Hormone & light signalling: genes for auxin, ethylene and phytochrome responses dissected here.

VII. Drosophila melanogaster — Fruit Fly

The historical foundation of chromosome and developmental genetics.

A. Genetic features

• Life cycle: ~10 days at 25 °C; hundreds of offspring per female.
• Chromosomes: only 4 pairs; giant polytene chromosomes in salivary glands give visible banding.
• Balancer chromosomes: suppress recombination and carry dominant markers to maintain stocks.

B. Contributions

• Chromosome theory of heredity: Morgan's white-eye mutant proved sex linkage; Sturtevant built the first genetic map.
• Developmental genetics: saturation mutagenesis identified genes patterning the body plan (below).

VIII. Caenorhabditis elegans — Nematode Worm

A 1 mm soil roundworm chosen for its cellular simplicity.

A. Genetic features

• Fixed cell lineage: invariant 959 somatic cells in the adult hermaphrodite, mapped cell by cell.
• Transparent body: every cell division watched under the microscope.
• Reproduction: self-fertilising hermaphrodites plus males allow both easy stock-keeping and crosses.

B. Contributions

• Apoptosis: ced genes defined programmed cell death (exactly 131 cells die during development).
• RNA interference: double-stranded RNA silencing discovered here (Fire and Mello).

IX. Danio rerio — Zebrafish

A vertebrate model bridging invertebrates and mammals.

A. Genetic features

• Transparent embryos: external fertilisation and clear eggs allow live imaging of organogenesis.
• High fecundity: ~200 eggs per clutch; development rapid (organs by 24–48 h).
• Forward genetics: large-scale ENU mutant screens isolate developmental mutants.

B. Contributions

• Vertebrate development: models heart, blood, and nervous-system formation with human gene homologues.
• Regeneration & disease modelling: fin and heart regeneration; transparent casper line for tumour imaging.

X. Genetic Analysis of Development in Drosophila — Building the Body Plan

Drosophila development proceeds through defined morphological stages, and a cascade of maternal and zygotic genes converts a uniform egg into a segmented larva.

A. Drosophila developmental stages

The fly undergoes complete metamorphosis through four life stages.

• Embryo: ~24 hours; fertilised egg develops into a segmented first-instar larva inside the eggshell.
• Larva: three instars (L1–L3) separated by moults; feeding and growth phase.
• Pupa: encased in a puparium; imaginal discs differentiate into adult structures during metamorphosis.
• Adult (imago): sexually mature fly emerges (eclosion); reproduction restarts the cycle.

B. Embryonic development

Patterning depends on gene classes acting in a temporal hierarchy along the anterior–posterior (A–P) axis.

1. Maternal-effect genes (axis set-up):

• Deposited before fertilisation: mRNAs localised in the oocyte by the mother's genotype.
• Anterior determinant — bicoid: mRNA anchored at the anterior; protein forms a concentration gradient that specifies the head/thorax. High Bicoid = anterior structures.
• Posterior determinant — nanos: localised posteriorly, represses hunchback to allow abdominal development.

2. Zygotic segmentation genes (read the gradient): act in sequence to subdivide the embryo.

• Gap genes: e.g. hunchback, Krüppel, knirps; mutants delete broad contiguous blocks of segments. Respond directly to maternal gradients.
• Pair-rule genes: e.g. even-skipped, fushi tarazu; expressed in seven stripes; mutants lose alternate segments.
• Segment-polarity genes: e.g. engrailed, wingless, hedgehog; define anterior/posterior compartments within each of the 14 segments.

3. Homeotic (Hox) selector genes (segment identity):

• Function: specify what each segment becomes, not its number.
• Two clusters: Antennapedia complex (head/anterior thorax) and Bithorax complex (posterior thorax/abdomen).
• Homeotic transformations: loss of Ultrabithorax converts the third thoracic segment into a second — producing four-winged flies; Antennapedia mutation makes legs grow where antennae should be.
• Homeobox: each Hox gene carries a conserved 180-bp homeobox encoding a 60-amino-acid DNA-binding homeodomain, conserved from flies to humans.

Colinearity principle:

Chromosomal order of Hox genes  ⟷  Anterior-to-posterior body order
3' end (expressed anterior) ────────► 5' end (expressed posterior)

Genes at the 3′ end of the cluster act in anterior segments; those at the 5′ end act posteriorly, matching physical gene order to body position.

Worked example — logic of a gap-gene screen:

• Cross setup: mutagenise males with EMS, cross to establish balanced lines carrying a lethal mutation.
• Phenotype: homozygous Krüppel embryos show deletion of central thoracic and anterior abdominal segments.
• Inference: the affected gene normally patterns that region — mapping the block of missing segments to a single gene, the strategy Nüsslein-Volhard and Wieschaus used to identify segmentation genes systematically.