L5: Exploring genetic diversity

- and - determine phenotypes

genotype, environment

how can we understand the function of a gene?

• sequence/structural similarity

• environmental perturbation

• genetic perturbation

homeotic genes determine -

organ identity 

perfect flowers have - whorls of organs

mutants revealed three sets of genes controlling -

four

floral organ identity

double flowered mutants are common in - flowers

ornamental

mutations can be artificially induced in a number of ways

• chemical

  • EMS (alkylating agent)

• physical

  • Xrays, gamma

• biological

  • transposons, virus, bacteria

forward genetics

start from phenotype of mutants to find gene

backward genetics

mutation of gene to find phenotype

mutant libraries for reverse genetics

saturated collections of mutants can be screened for genes of interest, looking for mutant phenotype

tilling populations

large collections of mutated organisms, most commonly plants, created for research to study gene function

Salk T-DNA lines

a collection of genetically modified Arabidopsis thaliana plants used for genetic research, where a piece of DNA called T-DNA has been randomly inserted into the plant's genome

direct gene manipulation

it is possible through transgenesis, gene editing to directly inactivate or manipulate the activity of a gene but transformation/transfection of organism of interest is required

mutations in coding sequences or regulatory elements are more likely to - that mutations in intergenic regions

disrupt gene function

semi-dwarf mutants and the green revolution

mutations producing semi-dwarf plants increase yield and reduce lodging

impaired ability to produce or respond to plant hormone, gibberellin

mutation breeding for crop improvement

breeders commonly induce mutations to generate new varieties

• gamma greenhouse

gene diversity allows organisms to adapt to -

different/changing environments

where does genetic diversity come from?

all new genetic variants arise from mutations

mutations are frequent, but only some are maintained in a population/species

whether a new variant is maintained or lost in a population depends on

selection: variants become more abundant or are lost due to their effect on the phenotype of individuals

drift: variants become more abundant or are lost due to chance events

genetic drift is when - determines the fate of an allele

chance

selection is when - determines the fate of an allele

phenotype

positive selection

the process where beneficial genetic variants spread through a population because they increase an organism's fitness

negative selection

the process of removing traits, alleles, or cells that are detrimental to an organism's survival or function

interaction between selection and drift

neutral variants?

non-neutral variants?

drift

selection

the effect of drift is much larger in - populations

deleterious mutations have a much higher chance to persist in - groups

smaller

small/isolated

two more sources of phenotypic and genetic diversity

sexual reproduction: generation of new genetic combinations through recombination

migration: introduction of new genetic variants through migration and/or hybridization

larger variants are important as well

SNV, SNP, inversions, translocations, indels, CNV

SNV

single nucleotide variant

SNP

single nucleotide polymorphism

CNV

copy number variation

insertions/deletions

indels can introduce or remove parts of genes, complete genes, regulatory sequences

• single nucleotide indels in gene can introduce frame-shifts in the coding sequence

• larger indels can affect whole genes or gene clusters

• several genetic disorders are due to very large chromosomal deletions

chromosomal inversions

effects of inversions

• disrupt genes or gene regulation at their boundaries

• suppress recombination between the two orientations

• by locally suppressing recombination, inversions keep together combinations of adaptive alleles

• inversions act as supergenes to maintain complex adaptations

Copy number variation

can affect short repeats or whole genes

can vary from zero, to few, to manychr

chromosomal translocations

• generally bad for individual

• can facilitate speciation

dispensable genes can be linked to

• disease resistance

• abiotic resistance

• secondary metabolites

• duplicated genes

• etc

reference bias in genomics

single reference genomes represent only one version the genome of a species, resulting in “invisible” genes

pangenomes

provide more complete representation of a species diversity

super pangenomes compare variation across related species

graph pangenomes

a sequence graph is a compressed way to represent multiple genome assemblies

• nodes: unique DNA sequences

• edges: ways in which nodes are connected in different genomes