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Plant DNA Replication & Mutation

Methylation may impair CG pairing during replication

cytosin -> methylcytosin (similar to thymine)

Transposons are mobile DNA elements, able to change their location, capable of destroying a protein/regulatory

DNA regulates “jumping genes” (transposons), via methylation of cytosin with histones. However, this can cause mutations as discussed earlier.

autopolyploid: duplication of ploidy within species allopolyploid: combination of genomes (e.g. rapeseed)

homologs vs homeologs in crossing over [LKUP]

All the above mentioned mutations are totally without the presence of any external mutagen!

Of course, external sources exist as well: - UV radiation - Dimerization of neighboring pyrimidins (T-T bond) with UV radiation - cannot be replicated! - Cytosines may hydratize - Strand breakage - Single strand breaks are very frequent, but easily repaired - Double strand breaks are much worse - Ionizing radiation can produce ROSes (reactive oxygen species, eg peroxide, oxygen, hydroxides) - ROSes - loss of bases - oxidation of bases - crosslinks between DNA and proteins (stuck to histones!) - Other chemicals - can intercalate with DNA and shift the reading frame (ethidium bromide does this!)

Mutation Prevention

Repair pathway depends on type of mutation: - mismatch repair - nucleotide excision repair - double strand break - nonhomologous end joining - worst case - join the next end you can find - single-strand annealing - used for repetitive DNA - reduces number of repetitions, so creates a variation but still functional - homologous recomb. - ideal solution - can’t happen in gametes, or during parts of mitosis with uncondensed chromatin

If damage is too severe, kys (programmed cell death to prevent cancer, retrovirus, etc.)

Patterns of Mutations

Most abiotic mutatagenesis sources are exacerbated by human activity

Law of Homologous Series

If you find a type of variant in species A, you’ll likely find that variantin species B

Similar colors between carrots, beets, potatoes, but different chemical dyes - No blue beets!

What about blue flowers? - Blue flowers exist, but no blue roses

Why is the law generally true? - Evolution starting with a similar starting material - chlorophyll as a photosynthetic dye, although phycobilin would also be possible - Physical boundaries - theoretical maximum tree size, limited by physics of transpiration v. gravity - minimal size limited by cell size - convergent evolution - CAM photosynthesis in bromeliads and cacti

Why would the law be wrong? - gene drift in small populations - alleles randomly lost, trait no longer expressed - domestication is a common example of this - divergent evolution - e.g. beech trees won’t have CAM photosynthesis, since they never faced extreme drought as a population

Types of Selection

  1. Negative selection (removal of harmful mutation, freq goes down)
  2. positive selection (freq incr.)
  3. genetic drift (random loss, freq. in small populations since an individual makes up a bigger proportion of the population)

Somatic Mutations

Lost in the next generation, unless they occur in the reproductive tissue. This is how floral dip transformation works, for example.

Mutation Harm/Benefit

As soon as a mut. reduces fitness of organism, it is harmful or deleterious

Fitness soleley describes the ability to produce viable offspring (hence you can end up with weird sexual selection towards traits that seem harmful and that doesn’t matter as far as “fitness” is concerned) - e.g. incel/manosphere behaviors that actually decrease likelihood of finding a mate lol

Most deleterious mutations block the formation of a functional RNA - start and stop codon - splicing sites - changing the reading frame (e.g. ethidium bromide shit)

Mutations in exons can be deleterious, whereas intron mutations generally don’t affect much - no signif. selection on introns, so you’ll find more mutations on them - exons are more highly conserved

How would a mutation be harmful?

[Insert graphic of the RNA Codon Sun]

  • Point mutations
    • genetic code is degenerate (redundant, there are more 3-base combinations than codons)
    • hence a a good amount of SNPs are synonymous mutations (tRNAs can vary in frequency, so this can still influence rate of translation and protein production)
    • non-synonymous mutations occur with e.g. CTT to ATT, but is still conservative, since their corresponding amino acids leucine and isoleucine are very chemically similar
    • mutation from CGG to CCG yields proline instead of arginine, which are different
      • hence, a radical mutation
    • Start and stop codon SNPs can make a big difference, though
      • premature stop codon
      • loss of stop with nonsense after the protein
  • Indel
    • deletion of 3bp deletes a full amino acid from the desired sequence, hence inframe
    • frameshift (1, 2, 4bp)
    • indels in nature are mostly in multiples of 3 for this reason (frameshifts are worse)

How can a mutation be positive? - mutation in promoter can change expr level or allow new or different regulation which may be beneficial to the individual - mutations within splicing sites can lead to new proteins entirely - within exon can improve structural or catalytic features of the protein w/r/t it’s interaction with other proteins

Positive selection can lead to new traits, and therefore contribute to speciation.

Mutation Speed

7x1e-08 in a. thaliana. with a genome size of 150Mbp, we expect ~20 mutations per generation. probability of being positive is unknown but very low (<1%) - therefore likely to be lost due to genetic drift - this is why speciation normally takes several million years - higher selection pressure also accelerates the process as the influence of genetic drift is reduced - breeding is always a process of purposeful high selection pressure

Ag Selection vs Natural Selection

  • nature selects for survival to reproduction
  • we select for yield
  • Plants want easily dispersed seed, ripening at different times to maximize their chances
    • we want even ripening, non-shattering cereal grain heads
  • We demand higher disease resistance (higher load than in mixed culture)
  • look attractive to dissemination species for pollen or seeds
    • we want them to taste good, look nice, and be easily processed

Domestication reduces genetic diversity due to strong selection pressure, but you trade off many potential beneficial traits (abiotic resistance, disease resistance, etc.) - important to keep the bank of genetic variation healthy alongside the domesticated varieties - depending on how climate change occurs, we’ll have more genes to draw from to adapt crops to new conditions

Phenotype = Genotype x Env x (Genotype by environment intrxns)

There is no clear relationship between genome and crop performance due to that third factor

Domestication is followed by adaptation which further reduces diversity

Genebanks store options for later, not for now! (Like a genetic “save state”)

Why do we need to know which changes are causal?

Forward and Reverse Genetics

Forward: which genetic factors influence a trait (pheno to gene) Reverse: Which phenotypes are influenced by the gene? (gene to pheno)

Linkage Mapping, Transcriptomics [LKUP]