Lecture 7
Genetic variation:
- Why sequence more than one genome of a species? (1) You will find
genetic variation and phenotypic variation, with which you study function of
genes. (2) You can find genes that are
not functional in genome1, but are functional in genome2: develop ‘genetic
standard’.
Questions art 1
- What is wrong with the sentence ‘ the sequence of the human (or
Arabidopsis) genome ..’ ?
- Describe a few examples of genome variation. CNVs (copy number
variation (size can change)), SNPs, indels (insertions, deletions)
- How many SNPs are expected to be present in the Arabidopsis
genome?1 in 50 basepairs
- Describe the different effects of SNPs located in gene regulatory
sequences and in gene (coding) sequences. Gene regulatory
sequence, e.g. promotor (may cause higher or lower gene expression) or
coding sequence (may cause different proteins)
- Why is it a particular advantage that Arabidopsis is mostly self-
fertilizing? Less variation due to homozygous genome
- What are recombinant inbred lines(RILs)? Start with two homozygous
lines and combine them into F1. Then self-fertilize these lines, you end up with
genetic mosaics of the original (page 4, slide 1). If you search for a gene,
analyze the mosaics --> if the trait you are looking for is on one of the
mosaics, then you know the gene lays in that region of the mosaic and of the
original.
- What is a QTL? Quantative Trait Loci ??
Mutants
- How to make KO in plants? KO = knock-out, made in genes to study
their function. Make them using siRNAs (small-interfering RNAs, they can
interfere gene expression, called knock-down [gene has lower expression,
expression is not zero]), CRISPR/Cas (??), transposons(they can move DNA
across the genome), Ti DNA, chemicals
Random mutations: transposons, Ti DNA, chemicals
Targeted mutations: CRISPR/Cas and RNAi
With transposons, you can create a primer that acts on the transposon, so that
you can find back the transposon (where did it go?) see page 6, slide 1
- How do I find a tissue specific promoter? Tissue specific promotor:
promotor only functional in a certain type of tissue, not in other tissues.
Metabolomics
- How can we identify plant metabolites? Metabolites: Labile, chemical
diversity. They have a wide dynamic range (different concentrations, turnover
time, etc.) Identifying using MS-methods
- What do all these enzymes do/produce?
Metabolites are the small chemical components in every cell. Major traits such as
food quality, taste, nutritional value, toxicity, allergenicity etc. are all directly
correlated with the presence or absence of specific combinations of metabolites
in the plants.
Metabolomics technologies have therefore been developed to give us the
broadest possible overview of the biochemical composition of biological materials
without having to have prior metabolic knowledge
Genetic variation:
- Why sequence more than one genome of a species? (1) You will find
genetic variation and phenotypic variation, with which you study function of
genes. (2) You can find genes that are
not functional in genome1, but are functional in genome2: develop ‘genetic
standard’.
Questions art 1
- What is wrong with the sentence ‘ the sequence of the human (or
Arabidopsis) genome ..’ ?
- Describe a few examples of genome variation. CNVs (copy number
variation (size can change)), SNPs, indels (insertions, deletions)
- How many SNPs are expected to be present in the Arabidopsis
genome?1 in 50 basepairs
- Describe the different effects of SNPs located in gene regulatory
sequences and in gene (coding) sequences. Gene regulatory
sequence, e.g. promotor (may cause higher or lower gene expression) or
coding sequence (may cause different proteins)
- Why is it a particular advantage that Arabidopsis is mostly self-
fertilizing? Less variation due to homozygous genome
- What are recombinant inbred lines(RILs)? Start with two homozygous
lines and combine them into F1. Then self-fertilize these lines, you end up with
genetic mosaics of the original (page 4, slide 1). If you search for a gene,
analyze the mosaics --> if the trait you are looking for is on one of the
mosaics, then you know the gene lays in that region of the mosaic and of the
original.
- What is a QTL? Quantative Trait Loci ??
Mutants
- How to make KO in plants? KO = knock-out, made in genes to study
their function. Make them using siRNAs (small-interfering RNAs, they can
interfere gene expression, called knock-down [gene has lower expression,
expression is not zero]), CRISPR/Cas (??), transposons(they can move DNA
across the genome), Ti DNA, chemicals
Random mutations: transposons, Ti DNA, chemicals
Targeted mutations: CRISPR/Cas and RNAi
With transposons, you can create a primer that acts on the transposon, so that
you can find back the transposon (where did it go?) see page 6, slide 1
- How do I find a tissue specific promoter? Tissue specific promotor:
promotor only functional in a certain type of tissue, not in other tissues.
Metabolomics
- How can we identify plant metabolites? Metabolites: Labile, chemical
diversity. They have a wide dynamic range (different concentrations, turnover
time, etc.) Identifying using MS-methods
- What do all these enzymes do/produce?
Metabolites are the small chemical components in every cell. Major traits such as
food quality, taste, nutritional value, toxicity, allergenicity etc. are all directly
correlated with the presence or absence of specific combinations of metabolites
in the plants.
Metabolomics technologies have therefore been developed to give us the
broadest possible overview of the biochemical composition of biological materials
without having to have prior metabolic knowledge
