SSR - Science topic

I am using SSR and cytochrome markers

Dear all,

Considering that for diploid organisms, each microsatellite locus is represented by as much as 2 alleles, is would be possible that for species with huges genomes some microsatellites are repeated rendering more than 2 alleles?

Thanks beforehand.

Regards

Good afternoon. Please tell me, are there molecular markers of zeina genes for the purpose of genotyping lines and varieties? There are Asid-PAGE and SDS-PAGE methods for studying the polymorphism of zein-coding loci in maize. But I have not yet been able to find molecular markers based on the PCR reaction (ISSSR, SSR, etc.)

For phylogenetic analysis using SSRs, normally we don't use just one SSR, but a set of multiple SSRs to ensure accuracy. So how can we input these data into NTSYS? I know input for one SSR is as followed:

1 3 4 0

A B C D

1 0 1 1

1 1 0 1

1 1 1 0

Then how about multiple SSRs for the same samples (A, B, C, D)?

Hello everyone,

I'm currently conducting genetic analyses using SSR markers, and I'm looking for software recommendations that support GLM (General Linear Model) and MLM (Mixed Linear Model) analyses with SSR markers. I've previously used TASSEL, but I understand it no longer supports SSR markers. Could anyone suggest alternative software or tools that I could use for my analysis? Any recommendations or insights would be greatly appreciated.

Thank you in advance!

In the SSR method, I used the same pair of primers (forward and reverse) in two different individuals, but I observed different band patterns in PCR.

Dear All

I am trying to amplify the SSR markers on genomic DNA of date palm but it always gives smeared, diffused and fuzzy bands in gel electrophoresis. I have standerdized them as much as the posible ways but still I am getting same result. Why such result is happening> I am attaching gel image herewith for reference. Please suggest.

Regards

Chet Ram, Ph.D.

Hello Everyone.

Greetings:

I would like to ask about gene-marker software to study population genetic analysis. I will be highly thankful if someone who are using this software and working on population genetic analysis via SSR markers.

In the context of cross-species amplification of SSR markers, is it possible for the number of alleles detected to be consistent with or equivalent to that observed in species-specific amplification? What factors influence the similarity or divergence in the number of alleles between cross-species and species-specific SSR marker amplification?

My name is Huiyeon and I am using STRUCTURE 2.3.3 software for or Population structure analysis. But I have a problem.

I have genotype data scored as 0 and 1 for SSR marker in formats available on the NTSYSpc program.

First, I converted my Excel files into TxT file format (Tab delimited).

Next, I tried to import the file into a new project.

And I specified according to instruction and number of my sample is 105.

When I finish setting and want to proceed, error "Bad Format in Data Source: Expect 27 data entries at line 1" occurs, and clicking "OK", a window says "The data file is expected to have following format: 1 row with 24 entries(marker name)/1 rows with 27 entries (data)".

Though I turned back to the setting and modified Number of loci several times, almost the same error occurs.

How can I convert my genotype data file into STRUCTURE input data file for Population structure analysis?

Kindly advise.

Thank you.

Hello..

I identified SSRs using the web server MISA and now I want to asses whether they are single copy or multi copy loci.

I found that read mapping is an insilico method that can be used for this purpose.

I'm very new to this field and I highly appreciate any help on how to do read mapping for my task.

Thanks in advance..

I need a suggestion. I am working on molecular characterization by using an SSR marker. I have recorded data in 1, 0 in format. What will be the input file for association mapping?

I would appreciate it very much if RG members could suggest any good and (preferably GPL) alternative to GeneMapper and Geneious software for microsatellite (SSR) analysis. Thanks.

We're performing genetic diversity studies using SSR and RAPD markers and we're done with the experiments, but we're finding it difficult to get this software for the data analysis.

I am carrying out polymorphism studies using ssr markers and running them on 6% polyacrylamide gel using 1x tbe buffer. But I'm facing smearing type of bands and multiple bands in certain samples can anyone kindly answer why this problem is encountering

How to calculate PIC value for SSR?

I'm working with microsatellite (SSR) and get different allele sizes from the same primer.

The difference in alleles ranges from 1 - 4 bp. For example, in the first experiment I got alleles of 150 bp, 152 bp in the second, 150 bp in the third, and 154 bp in the fourth.

Is there any suitable software to analyze these different allele sizes so that a valid number is obtained which can be concluded from the different allele sizes?

Thank you

We had a problem in the process of running DNA with SSR primer in 10% polyacrylamide gel and in our result, no clear DNA bands were formed. Do you have any suggest for us?

Thank you

information : Our SSR primer can't separate in 2% gel agarose because of the small size of different DNA (1-5 bp).

I'm using SSR　to analysis population genetic structure of P. aphanidermatum. Now i want to know  why we need AMOVA to analysis? what we can know from AMOVA result? Hope someone can help me. thank you. 

Can anyone tell me if there is any free software to create dendrogram for SSR marker analysis?

Fellow researchers,

I am trying to carry out an experiment on thermoplasticity in heat treatment of Steel cylinders. I want to set up my own heat treatment apparatus. I came across a readily affordable DIY equipment on the internet and I am pretty convinced it will suffice my needs. It is the popular ZVS (Zero Volt Switching) driver. I bought one for me, which is described here https://www.banggood.com/1000W-20A-ZVS-Induction-Heating-Machine-Cooling-Fan-PCB-Copper-Tube-12-36V-p-1089662.html?rmmds=myorder&cur_warehouse=CN . In my experiment I have to control the heat supply according to temperature. When the temperature reaches a threshold then the device should turn off. When the temperature goes below this threshold then it should switch back on. At first I thought of doing this with an SSR (Solid State Relay) where I would control the on/off function to the ZVS driver from Arduino. In regards to using SSR I have the following two questions:

1. I found in a YouTube video that the workpiece should not be inserted in the coil before turning on the driver. I don’t exactly have the link to the video but he said the reason was to avoid cross conduction in MOSFETs. This is not a problem for the initial insertion. However, as I plan on using the relay with the workpiece still inside the coil I may not be able to take out the workpiece (already hot) in and out.

2. What could be an alternative technique to control the power to the ZVS driver?

I have an SSR marker that shows what looks like one allele remaining fixed while the other allele is variable. I have run this marker in about 100 samples of dikaryotic (n+n) fungal spores and the pattern has held up so far.

The picture included below shows the pattern. I thought perhaps the larger product variants were stutter products, but the same three 'hills' are present with the rightmost being the highest peak and called by the software. And the peaks are very clear.

How is this explained?

I need to create a phylogenetic tree using the microsatellite data from the paper I attached below. Kindly advice me to how to start and software that can be used.

i am trying to do genetic diversity analysis (allele frequency, PIC, Nei genetic diversity and shanon information index etc..). in my data some locus have 1 alleles other have 2, 3 and 4 alleles per locus. when i used Genalex it analyze only Binary and data have locus with two alleles only.

Thank you all!

Best Regards,

Haftom

Dear statistic experts

I am developing a model to predict the behavior of around 30000 data. I use 2 different approaches to calculate the R2 and each one gives a completely different value.

The first approach: R2 = SSR/SST = 0.95

Whereas the second approach: R2=1-SSE/SST= 0.00

where SSR is Sum Square Regressions, SST is the Sum Squared Total, and SSE is Sum Squared Errors.

Any comment is highly appreciated.

Cheers,

Bahman

I have used 10 microlitre forward and 10 microlitre reverse sequence stock to make 100 microlitre working primer solution is that the reason for these kind of bands what is dimer ?

I have been doing diversity analysis of sugarcane crop using SSR markers can someone tell how to analyse the gel documentation photos and what is the need for diversity analysis using markers?

I have to study the genetic diversity among the germplasm of finger millet using SSR markers. But before SSR I want to check the banding pattern of isolated genomic DNA with one RAPD primer (10 bp long Tm 39C). But after running PCR ( 25 uL reaction primer conc. 2 uL , template 2 uL) I got a smeared pattern , there was no any clear band. So please can anyone suggest me the logic behind this and what to do next thing because it is very new for me working on molecular biology.

Recently, I have worked on genetic diversity analysis in mango genotypes using SSR markers. I can do it well as it is diploid. However, I have a question in my mind. If I worked on the triploid or tetraploid organism for genetic diversity analysis using SSR markers, how I count allele bands in gel image and make input files for GeneAlex, Darwin and other statistical software.?

If anybody worked with the triploid and more allelic organisms, please help me.

I am working on SSR markers.I have used Genodive software for analysis of tetraploid data. To check the genetic differentiation in 12 populations I applied AMOVA and the result file has attached. What conclusion I can make from this? Also does the sample size of a population would alter the result?

I want to analysis my SSR data for diversity study, I

NTSYS pc 2.02 software, any help? My email 2017201100@njau.edu.cn

Hi dears,

Hope everyone doing best. Anyone has access to Excel Microsatellite Toolkit (Park, 2001).

I need it for analysis of SSR markers data.

Thanks, and Regards

I got my fragment analysis results of Microsatellite markers designed using haploid species. I am using a gene marker to analyze the peaks. I read that since it is haploid, i should see only one peak (means one allele per locus?). But i see many for types of markers ( di, tri , ...) . I want to select polymorphic markers and want to score them for population analysis.

Also, gene marker has the option only to analyze plant dinucleotide and plant fragments. So i am not sure what settings should i select for fungal species?

i would appreciate if someone could clear my doubts?

I am using SSR marker data to construct phylogenetic tree through NTSYS, bt there is no option for boot strap.

Is there any option to add bootstrap in results obtained from NTSYS software..?

For molecular aspects study

I am working on SSR markers. I applied AMOVA and it showed 100% variation within a population and 0% variation among the populations. Is it possible to get this result? If not, what can be the possible reasons for this outcome?

some SSR markers are giving fade bands irrespective of change in Tm, while in the same configuration other markers give good results.

We have SSR marker (150) based genotypic data of 190 rice landraces. Want to prepare a research article. Which kind of analysis may be performed with these data? Kindly give your opinion and suggestions.

Regards

Parmeshwar

STRUCTURE, DARWIN, NTsys software are frequently used for SSR diversity estimation, is there any package in R-studio that can also be used for the same

I have to study the genetic diversity among the accessions of millets using SSR markers, so can I use the boiling lysis method for DNA extraction instead of CTAB.

What open-source softwares are available to generate a heat map of the Jaccard similarity coefficient for SSR diversity from the available data set?

Which new/modern softwares are being used for SSR analysis ? i mean for genetic diversity, to estimate inbreeding or out breeding guess of population in plants

I am trying to find polymorphic SSR markers. I got a few markers that amplified my 8 fungal isolates with the same size of bands but for 1 or 2 samples there is no band. Could they be considered polymorphic markers?

I ran an agarose gel with 8 fungal isolates to check the polymorphism. I am not sure if I can consider the marker with the missing band as polymorphic?

I m working on probiotic bacterial isolates, is there any importance to using SSR to determine bacterial diversity, I need some relevant literature.

I am trying to select microsatellite markers from the database for assessing genetic diversity and DNA fingerprinting for germplasm. The database has consisted of Di-, Tri-, Tetra-, Penta- and Hexa-repeats along with the compound type of repeats. So what type of repeats are more potent as utilize in molecular analysis of germplasm. Whether I should choose perfect SSR markers or compound (imperfect) type or both? Kindly suggest to select the SSR markers.

Thank you

Regards

Chet Ram

I just want to know whether we can utilize the DNA barcoding approach to check genetic variation among species, eg: Sorghum bicolor

I am planning to use SSR markers to check the variability among the population, apart from that I would like to conduct phylogenetic analysis with DNA barcoding. Would it be possible? Has anybody conducted both approaches?

Your valuable comments are highly appreciated.

Just to learn the procedure (if possible) and to prepare the GD and GM data files. If anyone done GWAS in GAPIT using SSR marker data, please share (or help me to prepare) GD and GM files.

Thanks.

I am trying to determine the usefulness of the marker shown in the attached photo. You will see that in one sample there appears to be 3 alleles (this is a diploid, or more precisely a dikayotic spore). I have seen this in other samples too and have eliminated the possibility that it is DNA contamination by looking at other markers that don't show this pattern.

I have already gone through the step of Pig-tailed reverse primer (these are the results for this) and a longer final extension in the PCR (30 minutes) to try to eliminate stutter on the 'rooster comb' peaks you see. Any other suggestion, or just don't use this marker?

To take a barcoding approach I need to amplify rbcL/matK/ITS of Sterculia villosa and some other members of Sterculiaceae (Chronquist, 1981). How should I select a suitable primer for a particular plant for proper amplifiation? Please suggest? Also if I want to test genetic diversity using ISSR, SSR or RAPD, what are the things I should do to select a marker? Thanks in advance.

Large germplasm collections may have several duplicates which need to be removed from the set. DUS characterization based on morphological traits are the best way to differentiate them. But it is very tough to DUS characters in large germplasm lines. Is there any method in molecular breeding to identify the duplicates in huge germplasm collections of rice? Kindly give your opinion and suggestions.

I have made detection for microsatellite SSR markers in patient with plasmodium...

for statistical analysis, I have used genalex 6.5 ...

I still need to make confirmation with another software...

can anyone help me within this point?

As SSR are most widely used markers in major cereals. They are highly reliable (i.e. reproducible), co-dominant in inheritance, relatively simple and cheap to use and generally highly polymorphic. What other factors can affect polymorphism in case of SSR markers?

I have SSR data for 32 genotypes. In some case getting more no of allele for the markers. even hetro also coming . Now How to create input file for these in Darwin software.

I have previously designed primers and now I have done SSR mining and primer designing. So I want to check if the newly designed primers have the old same primers in the excel file.

I have both the query and subject in excel files.

Hi, I need suggestion, I am working on association mapping of 220 genotypes. I used SSR primers. Kindly tell me how I recorded Data like 1 or 0 in excel sheet. if any dummy file is available please share for guideline.

than you

Is this use molecular weight or binary data for this software. I was using molecular weight and got error 32.

If we want to study the population genetics/population structure of 30 genotypes by employing SSR markers. How we have to prepare input data file of SSR markers data to analyse in POPGENE Software.

Hi researchers!

I extracted DNA from Cocoa leaves and amplified some fragments (SSRs markers), the thing is I get those bands! (attached image), and don't have a defined band. I'm using a new TBE 1X with the gel, running with TBE 1X buffer, 3% Agarose gel, and running it 60V/150 min. But I can't get defined bands!

Maybe it's because of the thermal PCR program? should I use a TouchDown PCR or something? any idea to get defined bands would be Helpful! Thank you!

I need to genotype an association panel using simple sequence repeat (SSR) marker loci. As expected number of alleles in the panel cannot be predicted unlike in the case of segregating populations derived from bi-parental crosses; kindly suggest to me as to which is the better method for resolving the size-based SSR alleles? Metaphor agarose gel electrophoresis OR Polyacrylamide gel electrophoresis (PAGE)?

Dear friends,

Please explain how to find allele frequencies for the case of obtaining multiple bands for SSR markers and how to do scoring for the multiple bands? or Shall I exclude the results of a SSR marker that gives multiple bands in scoring for data analysis?

Hi all,

I'm looking for pieces of software that could compute Maximum Likelihood and Parsimony on mixed-ploidy SSR data (2n though 6n). I can devise sequences, but the crucial points are (1) handling more than 1n data; (2) ability to assess phylogeny among the mixed-ploidy dataset. Thank you for your suggestions!

-Marcin

GenAlex SSR data input file

I am studying the SSR genetic variation in a diploid fungus. For one fungal isolate I have got 5 repeats of a di-motif SSR marker in one chromosome. However, the other chromosome in the pair shows an allele size with zero repeats for the locus. Is this absence of a SSR locus possible? I could not find any research evidence to prove it.

If anyone has got any explanation or evidence to prove this please do share.

Thank you.

I have identified SSR from some function gene sequence. Further I have done blast N to check sequence similarity which give 90 % query coverage but the part of sequence containing SSR is not lie in alignment with other sequence found in blast analysis. In that case how to proceed for PCR .

Hi,

any one please guide me; SSR primers are species specific or trait specific. i have few primer which was reported in articles for wheat yield can i use these similar primer for lentil yield or other yield related traits.

Thank you

How to find SSR markers associated with hair loss in cotton?

I have data from SSR markers that have 2-10 bands each. I was able to run analysis wherein the program consider each band as single loci. The program gave me the following data (as in attached photo):

Band Frequency, Estimated Allele Frequency (p & q), Samples Size, No. Alleles, No. Effective Alleles, Information Index, Expected and Unbiased Expected Heterozygosity

for each band within an SSR marker. Will taking the average of the resulting value of each bands per SSR marker will give me the value of that SSR Marker? If not, may I ask what set of useful data for multi-locus binary data I can obtain in GenAlEx aside from the AMOVA?

Thank you!

Each time this SSR primer show band like that other show one or two band . Is it polymorphic ?

I have a set of SSR, SNPs, DArT markers of wheat pre-harvest sprouting resistance of about 300 in number and I wish to check their sequences, get their positions and integrate them.

Secondly, I will use the above to determine major stable loci for PHS-R by rich cluster, identify candidate genes in each QTL rich clusters and predict according to gene annotation of wheat reference genome and previous information of validated genes.

Please my major issue now i want to get the sequences of each marker how can i do that please?

How to identify SSR markers associated with quality and quantity characters in cotton?

Hi everybody,

I am just wondering - would anybody care to share their experience with using an AATI fragment analyzer for microsatellites (especially the binucleotide type)? Did you achieve the advertized 2 bp resolution (with which kit)? Are you worried to "miss" alles varying by only 2 (or 3, if trinucs) bp? From you experience, would you recommend it to replace, say an ABI CEQ 8000 capillary sequencer?

Best regards,

Klaus

I have SSR and SNP data and I am looking for a free software to construct a genetic map for each of these data

I have added the controls and want to analyse the sub synchronous effect in DFIG with increase and decrease of wind speed. Please help if anyone has an idea, its urgent

Nanodrop result of my DNA samples extracted from fresh finger millet leaves showed 260/280 ratio ranged from 1.7-2.2 whereas 260/230 ratio ranged from 1.1-2.2. How can I assess the quality of such DNA samples? Are all these samples good enough for SSR work?