Personal understanding is that ssr primer 1 amplified two bands (diploids) of ab, and the length of AB may be the same or different. If the length of band A is the same in all sample DNA, it is not a polymorphic band. If there are differences, do they belong to polymorphic bands? Let's get to know each other in our study. It takes a lot of time just to understand this problem. Polymorphic bands should be dominant markers, and it is said in the literature that ssr also has the concept of polymorphic fragments.
The following is the ISSR detection process. ISSR primers are both F and R, regardless of F and R. ISSR primers can be combined on two strands of dna. Two fragments of a sequence must have reverse and complementary repeat units, so that a single primer can amplify the fragment. In this way, this sequence between inverted and complementary repeat units should try not to show differences between samples. Therefore, ISSR is dominant, and a single ISSR primer can only amplify one band in the sample (theoretical situation), but it is not a band. As long as the above situation exists, it can be amplified.
The reference material is
Schulke, Marcus. "An economical method for fluorescent labeling of PCR fragments." Nature Biotechnology 18.2 (2000): 233-234.
The principle of PCR is not very clear. Draw a picture to understand: red is M 13 sequence, blue is F R primer, orange shaded part indicates primer and sequence annealing, QQQQ is target sequence, NNNN is non-target sequence.
F approaching 0 means that the random hybridization at the lower site conforms to Havin equilibrium? A large number of positive values indicate inbreeding.
Ideal population
Batch SSR primers can be obtained from transcriptome or genome data, or selected from previous papers for primer screening. Primer design uses oligo7 or primer, etc. Oligo is free, and primer has to pay.
The selected primers can be detected by agarose, polyacrylamide and capillary electrophoresis, and finally the primers with strong specificity are selected for genome amplification.
All the data of 2020090 1 have been completed.
Fluorescent capillary electrophoresis was used in this experiment. Taking the use of software as the experimental content. The specific usage of the software can be found in the software manual in the collection. Actually, the manual has been written in detail.
The final data results are as follows, and the specific length of the line segment will be obtained.
* * * Data for 24 locations are not available.
Genetic diversity parameters were analyzed by GenAlex, but I didn't quite understand the meaning of these parameters, and I was worried that I would miss the data in the calculation process, so I ran it twice again to see if the results were the same.
The differences of genetic diversity index of different provenances in different regions were compared. At present, the lowest classification is divided by province.
Is low heterozygosity related to self-pollination?
GenAlex can't calculate PIC, so he uses Powermarker.
Powermarker calculates the genetic distance and uses UPGMA or NJ method to make achievements.
Darwin also wrote articles using this software. Do many articles use Darwin? Powermarker is relatively simple.
Get the tree file and beautify it with itol. Count the population under each subgroup.
GenAlEx provides this function.
The variance component of the population is the genetic differentiation of the population.
This analysis can be carried out according to the population classification of region, cluster and structure, and the genetic differences and internal and external variation differences of populations under different classifications are compared.
(1) AMOVA analysis in genalex needs to determine the following parameters.
Some populations between clustering and structure are represented by venn diagram with samples.
GenAlEx is available,
Individuals in each population are divided into pure or admitted according to the probability score, and are divided into a subgroup separately.
According to the population divided for the first time, we can continue to divide subgroups.
(1) Use the structure collector to get the best K.
(2) Repeat sampling to obtain the results of multiple runs.
(3) exploded view