Lab 11: PCR for Lupines

Today we performed PCR using ISSR primers on previously extracted Lupinus arboreus samples. ISSR stands for interspersed simple sequence repeats, which are microsatellites. Instead of using the microsatellites as the markers, we use them as primers to generate fragments of DNA through PCR. We will then compare the length of these fragments to better understand population genetics of Lupinus arboreus.

First we each received 5 samples. Then, for each sample, we made three 1:10 dilutions so that each table could work with each sample. Additionally, PCR for these ISSR primers works better with diluted gDNA.

My samples and ISSR primer
Every table worked with the same 60 samples, but each table used a different ISSR primer. My table worked with the primer HB10. I also included a negative control. Below is table showing my samples and their corresponding label on their PCR tube. I also labeled each strip with my intials, AJC, and HB10.

Label Sample ID
1 PSF01
2 PSF02
3 PSF03
4 PSF04
5 PSF05
6 CRA01
7 CRA02
8 CRA03
9 CRA04
10 CRA05
11 PRA01
12 PRA02
13 PRA03
14 PRA04
15 PRA05
16 Negative control


Master Mix
Vanessa prepped the master mix as shown below, working on ice. Except Prof Paul added the taq at the end just before we add the master mix to our PCR tubes and put them in the thermocycler. Vanessa made enough Master Mix for 80 samples (our table had 64 total)

Material per rxn (µL) per 80 rxns (µL)
pure H2O 12.5 1000
10x buffer + Mg 3.00 240
BSA 1.00 80
dNTPs 2.00 160
HB10 primer 0.25 20
Taq 0.25 20


PCR prep
We first prepped our PCR tubes by adding 1 µL gDNA to each appropriately labeled tube. Then we added 19 µL of master mix to each tube. I pipetted up and down to mix each tube. Samples were kept on ice until they were placed in the PCR machine and ran.


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