plant bio 3

Traditional selective breeding

The artificial selection and propagation of individuals with desirable inherited phenotypic traits over generations without prior knowledge of underlying genetics.

Inefficiency of radiation-based crop mutagenesis

It causes random, genome-wide DNA lesions rather than targeted modifications, requiring extensive screening across large plant populations to locate desired mutations.

Recombinant DNA technology

A molecular biotechnology technique that enables the transfer and stable expression of genes across distant, unrelated branches of life.

Restriction enzyme

A specialized bacterial endonuclease that cleaves double-stranded DNA at specific palindromic recognition sequences.

DNA ligase

An enzyme that seals recombinant DNA fragments by catalyzing phosphodiester bond formation between adjacent nucleotides.

Plasmid

A small, circular, double-stranded extrachromosomal DNA molecule widely used as a vector to amplify or transfer inserted genes.

T-DNA (Transferred DNA)

The defined segment of the Agrobacterium tumefaciens Ti plasmid that is transferred and integrated into the host plant genome.

Purpose of removing auxin and cytokinin genes when disarming a Ti plasmid

To eliminate the physiological driver of crown gall tumor growth while preserving the plasmid's ability to transfer genes into plant cells.

Role of left and right border repeats in the Ti plasmid

Direct flanking repeat sequences that delineate and mark the boundaries of the DNA region destined for transfer into the plant.

Primary purpose of introducing a recombinant plasmid into Escherichia coli

To rapidly clone, replicate, and amplify large quantities of the plasmid DNA prior to downstream plant transformation.

Antibiotic selection in transformed bacteria

Demonstrates successful uptake and retention of a plasmid carrying the selectable resistance gene, without verifying the sequence accuracy of the insert.

PCR screening in recombinant cloning

A fast enzymatic amplification assay used to verify that colonies contain the expected gene insert based on amplified fragment size.

Electroporation

A transformation technique that applies brief, high-voltage electrical pulses to create transient membrane pores, enabling plasmid uptake into cells.

Two common methods for Agrobacterium-mediated plant transformation

Floral dip and in vitro plant tissue culture.

Green Fluorescent Protein (GFP)

A visual reporter marker that emits green fluorescence under blue or ultraviolet excitation to confirm and monitor in vivo gene expression.

Distinction between selection and screening post-transformation

Selection applies lethal agents to selectively kill untransformed cells; screening assays surviving cells visually or molecularly to confirm intended gene insertion or expression.

Natural evolutionary origin of CRISPR-Cas9

An adaptive immune defense mechanism in bacteria and archaea that identifies and degrades foreign viral or plasmid nucleic acids.

Cas9 nuclease

The RNA-guided endonuclease in the CRISPR system that creates targeted double-strand breaks in complementary DNA sequences.

Primary role of guide RNA in CRISPR-Cas9

Directs the Cas9 endonuclease to a precise genomic target sequence through complementary base pairing.

Single-guide RNA (sgRNA)

A synthetic, single chimeric RNA transcript fusing the targeting crRNA and structural tracrRNA elements into one molecule.

Key advantage of CRISPR-Cas9 over conventional random transgene insertion

It directs sequence-specific, targeted modifications at precise genomic loci rather than integrating unpredictably.

Primary molecular tool for engineering a targeted gene knockout

CRISPR-Cas9 genome editing.

Evolutionary benefit of sexual reproduction

Generates novel combinations of alleles and genetic diversity through independent assortment, crossing over, and fertilization.

Meiosis

A reductional cell division process in which a diploid ($2n$) cell undergoes two successive nuclear divisions to produce four haploid ($n$) products.

Fertilization

The union of two haploid ($n$) gametes that restores the diploid ($2n$) chromosome number in the resulting zygote.

Chromatin

The eukaryotic structural complex composed of genomic DNA wound around histone protein octamers and associated regulatory proteins.

Protein composition of the nucleosome core

An octamer made up of two molecules each of histones H2A, H2B, H3, and H4.

Electrostatic basis of DNA-histone binding

Positively charged basic amino acid residues on histones electrostatically attract the negatively charged phosphate backbone of DNA.

Metaphase chromosome

The maximally condensed, microscopically distinct structural state of chromatin achieved during nuclear division.

Homologous chromosomes

Chromosome pairs that carry the same gene loci in identical linear positions, derived from maternal and paternal parents, which may possess different alleles.

Distinctive chromosomal events of prophase I in meiosis

Synapsis of homologous chromosome pairs and reciprocal genetic exchange via crossing over.

Crossing over

The reciprocal exchange of homologous genetic segments between nonsister chromatids during meiotic prophase I.

Structures separated during anaphase I of meiosis

Homologous chromosomes (sister chromatids remain conjoined at their centromeres).

Structures separated during anaphase II of meiosis

Sister chromatids.

Typical cellular yield of meiosis from one diploid progenitor cell

Four genetically distinct haploid ($n$) cells or nuclei.

Direct cellular product of meiosis in land plants

Haploid spores that divide mitotically to produce multicellular gametophytes.

Cellular basis of Mendel's law of independent assortment

The random, independent alignment and orientation of nonhomologous chromosome pairs on the metaphase I plate.

Phenotypic outcome of crossing true-breeding tall and short plants

All $F_1$ progeny are tall because the tall allele exerts complete dominance over the masked recessive allele.

Expected $F_2$ phenotypic ratio from a standard monohybrid cross of heterozygotes

$3:1$ (dominant to recessive phenotype).

Cellular mechanism underlying Mendel's law of segregation

The physical separation of homologous chromosomes and their constituent alleles into separate daughter nuclei during anaphase I.

Inheritance behavior of genes on nonhomologous chromosomes

Independent assortment, segregating into gametes completely at random relative to one another.

Genetic linkage

The coinheritance of gene loci located physically close to each other on the same chromosome due to a low probability of crossing over between them.

Silent substitution

A single-base substitution in a coding region that changes a codon into a synonymous codon without altering the encoded amino acid.

Missense substitution

A point mutation that alters a single codon, resulting in the incorporation of a different amino acid residue into the polypeptide chain.

Nonsense substitution

A point mutation that converts an amino-acid-specifying codon into a premature stop codon, leading to truncated translation.

Frameshift mutation

An insertion or deletion of a number of nucleotides not divisible by three, disrupting the triplet reading frame downstream.

Chromosomal inversion

A structural chromosome rearrangement in which a segment breaks, flips $180^\circ$, and reinserts in reverse orientation.

Recombination suppression in inversion heterozygotes

Crossover events inside an inversion loop yield structurally unbalanced gametes bearing duplications and deletions that are typically nonviable.

Aneuploidy

An abnormal chromosomal condition characterized by the loss or gain of individual chromosomes rather than complete chromosome sets.

Polyploidy

The condition of possessing three or more complete haploid sets of chromosomes ($3n$, $4n$, $6n$, $8n$, etc.).

Ploidy level of bread wheat (Triticum aestivum)

Hexaploid ($6n$).

Ploidy level of cultivated strawberry (Fragaria \times ananassa)

Octoploid ($8n$).

Barbara McClintock

The cytogeneticist who discovered transposable elements ("jumping genes") through studies of chromosome breakage and kernel variegation in maize.

Apomixis

A form of asexual reproduction in angiosperms where viable seeds develop maternally without meiosis and fertilization.

Vegetative asexual reproduction via horizontal stems

Clonal propagation through modified horizontal vegetative stems, such as runners, stolons, or underground rhizomes.

Main genetic disadvantage of obligate asexual reproduction

Generation of near-zero novel genetic variation among clonal progeny, increasing vulnerability to environmental and biotic stressors.

Self-fertilization (selfing)

A plant mating system in which female ovules are fertilized by pollen originating from the same individual plant.

Primary adaptive advantage of self-fertilization

Provides reproductive assurance when potential mates, population densities, or insect pollinators are scarce.

Gene expression

The multistep process by which information encoded in DNA is transcribed into RNA and frequently translated into functional protein products.

Primary level of gene expression regulation in plants

Transcriptional regulation, controlling the recruitment of RNA polymerase and initiation of mRNA synthesis.

Promoter

A specific noncoding DNA regulatory region upstream of a gene where the core transcription machinery and RNA polymerase bind to initiate transcription.

Transcription factors

Sequence-specific DNA-binding regulatory proteins that activate or repress the transcription rate of designated target genes.

MYB transcription factor family

A large family of plant transcription factors that regulates flavonoid and anthocyanin pigment biosynthesis as well as developmental cell identity.

WRKY transcription factor family

A conserved zinc-finger-like transcription factor family that mediates plant defense responses to biotic and abiotic stress.

Ethylene Response Factor (ERF) family

A family of transcription factors that operate in the terminal steps of the ethylene phytohormone signaling pathway.

Euchromatin

Loosely packaged, decondensed chromatin that is accessible to transcription factors and actively transcribed.

Heterochromatin

Tightly packed, highly condensed chromatin that is transcriptionally silent and inaccessible to RNA polymerase.

DNA methylation

The covalent addition of a methyl group ($-\text{CH}_3$) directly to cytosine bases, commonly associated with epigenetic transcriptional silencing.

Transcriptional effect of promoter hypermethylation

Severe repression or complete silencing of transcription by obstructing the binding of transcription factors.

Primary mechanism for transposable element repression in plants

Epigenetic silencing mediated by dense cytosine DNA methylation and small interfering RNAs (siRNAs).

Mechanism behind variegated kernel spotting in maize

Somatic excision of a transposable element from an anthocyanin biosynthesis gene in individual cells, restoring localized pigment production.

ROSEA gene in snapdragons (Antirrhinum)

A MYB regulatory gene responsible for directing broad, diffuse anthocyanin pigmentation across flower petals.

VENOSA gene in snapdragons (Antirrhinum)

A MYB regulatory gene specifically directing restricted anthocyanin pigment accumulation along petal venation.

Cause of distinct pigmentation patterns in petals sharing identical genomes

Spatially regulated differential gene expression of specific regulatory transcription factors in distinct petal cell layers.

Quantitative trait variation from regulatory point mutations

Subtle changes in promoter binding affinity or transcript dosage that alter trait intensity (e.g., pale pink versus magenta) rather than causing binary loss.

Agronomic utility of loss-of-function alleles

Inactivation of certain genes can produce desirable commercial traits (such as waxy endosperm starch) or reduce the synthesis of unwanted compounds.

Neofunctionalization

An evolutionary process following gene duplication in which one duplicated paralog acquires mutations that confer an entirely novel biochemical function.

Subfunctionalization

An evolutionary process following gene duplication where ancestral functions are partitioned between the two duplicated paralogs, requiring both for full function.

ABC model of floral organ development

A combinatorial developmental model driven by duplicated MADS-box transcription factors that establish sepal, petal, stamen, and carpel identities.

Supergene mechanism mediated by chromosomal inversions

Suppressed recombination inside the inverted chromosomal segment maintains tightly linked cassettes of co-adapted alleles as a single inherited block.

Phenotypic suite linked to the high-elevation Boechera stricta inversion ecotype

Slower vegetative growth, delayed flowering phenology, and enhanced cold and freezing tolerance.

Consequence of crossing over within an adaptive supergene inversion

The breakdown of co-adapted multi-locus allele combinations, producing maladaptive intermediate recombinant phenotypes.

Autopolyploidy

The multiplication of whole chromosome sets originating from within a single biological species.

Allopolyploidy

Polyploidy arising from interspecific hybridization between two divergent species followed by whole-genome doubling.

Primary cause of sterility in an initial interspecific hybrid

Divergent parental homeologous chromosomes fail to pair properly during meiotic prophase I, leading to irregular segregation and aneuploid gametes.

Diploidization

The progressive evolutionary restructuring and gene loss in a polyploid genome that returns it to disomic inheritance and diploid-like behavior.

Hemizygosity

A genetic state where a gene locus or chromosomal region exists in only a single copy within an otherwise diploid or polyploid organism.

Functional purpose of heterostyly in Primula

Promotes obligate outcrossing and disassortative mating between pin and thrum floral morphs to prevent self-fertilization.

Microevolution

Heritable shifts in allele frequencies occurring within a single population or species over successive generations.

Macroevolution

Large-scale evolutionary patterns and divergence events occurring at or above the species level over geological timescales.

Gene flow

The movement and incorporation of alleles between distinct populations or species via gamete dispersal, seed migration, or hybridization.

Gene pool

The total aggregate collection of all alleles across all gene loci present in an interbreeding population at a given time.

Relative prevalence of interspecific hybridization in plants versus animals

Considerably more frequent, viable, and significant as a speciation mechanism in plants than in animals.

Introgression

The permanent incorporation of alleles from one taxon into the gene pool of another through recurring backcrossing of fertile interspecific hybrids.

Major evolutionary outcomes of plant hybridization

Formation of novel homoploid or allopolyploid species, adaptive introgression between lineages, or reinforcement of prezygotic barriers.

Reinforcement

Natural selection strengthening prezygotic reproductive isolating barriers in response to selection against low-fitness hybrid offspring.

Genetic drift

Random, stochastic changes in population allele frequencies resulting purely from sampling error across generations.

Relationship between population size and genetic drift intensity

Genetic drift exerts significantly stronger and more rapid evolutionary changes in small, isolated populations than in large ones.

Mechanism driving natural selection

Heritable phenotypic differences among individuals that result in differential survival and reproductive success.

Biological fitness

The relative lifetime reproductive success of an individual or genotype, quantified by its proportional genetic contribution to future generations.