SNP's

Question 1

what are SNP’s?

Answer 1

• single nucleotide polymorphisms
• substitutions of one base for another
• means: error occurred during replication

Question 2

characteristics

Answer 2

• single varying base along DNA is unique of an individual
• many SNP’s distributed in genome
• very frequent
• stable –> can be inherited

Question 3

SNP’s vs Microsattelites

Answer 3

• SNP’s more frequent but less variability

Question 4

are all mutations SNP’s?

Answer 4

• no, but all SNP’s are mutations

Question 5

different groups of SNP’s

Answer 5

• linked SNP’s: no effect on protein function
• causative SNP’s: affect protein function

Question 6

how are SNP’s isolated and identified?

Answer 6

1. Library Preparation:
   - Genomic DNA is extracted from the samples of interest.
   - The DNA is then fragmented using a restriction enzyme that recognizes specific DNA sequences
   - The restriction enzyme cuts the DNA at these recognition sites, producing fragments with sticky ends.
2. Adapter Ligation:
   - Adapters (short DNA sequences) are ligated to the ends of the DNA fragments
   - These adapters serve as priming sites for subsequent steps in the sequencing process
3. PCR Amplification:
   - The DNA fragments, now with adapters attached, undergo PCR (Polymerase Chain Reaction) amplification to selectively amplify the regions of interest.
4. Sequencing:
   - The library of PCR-amplified fragments is then subjected to high-throughput sequencing.
   - This can be done using various sequencing platforms.
5. Data Analysis:
   - The obtained sequencing data are analyzed to identify SNPs and genomic variations.
   - The presence or absence of specific DNA fragments in different samples allows for the identification of genetic polymorphisms.

Question 7

what do you do after the sequencing?

Answer 7

• look at the common areas
• See, if there are differences in the nucleotide sequence of the locus

Question 8

Answer 8

• we have two loci (site 1 and site 2)
• we are comparing fragments of 6 individuals coming from 3 populations (blue, green, red)
• we can see that in all fragments the sequence of nucleotides is almost the same
• but there are some SNPs

Question 9

pros

Answer 9

• SNPs and RAD are good because they can be used for groups of species that are relatively phylogenetically distant
• we can find in different populations thousands of loci/markers/SNPs
• they are becoming cheaper with time (cost competitive with microsats)

Question 10

cons

Answer 10

• sequencing error rates are still moderately high
• we require data storage in order to compare the sequence and be sure that there really is a SNPs at that location