Microsatellites - Science topic

Treatment options depend on the extent of disease at presentation. While those with resectable tumors at presentation have traditionally undergone surgery first, a paradigm shift is moving toward neoadjuvant chemotherapy first with emerging evidence in favor of total neoadjuvant treatment (chemotherapy followed by chemoradiation). Surgical options now include both minimally invasive approaches in select centers where experience has accumulated. Those with borderline resectable disease will benefit from neoadjuvant chemotherapy and chemoradiation. Provided a favorable response, these patients can undergo surgery although a more extensive resection to include vascular structures is often necessary to achieve an R0 resection. Patients with locally advanced or metastatic disease on presentation should undergo definitive chemotherapy with FOLFIRINOX, gem-nabP or gemcitabine + capecitabine +/- radiation. If patients respond to a sufficient degree, resection can be considered. For those with distant metastases, intra-abdominal metastases should generally not undergo resection unless in a trial setting while metachronous isolated lung metastases can be resected with favorable outcomes. For PDAC patients with isolated liver metastases, hepatic artery infusion pump is currently under investigation. Targeted therapeutics in PDAC are under investigation with the help of next-generation sequencing that allows genomic mapping of tumor cells for the identification of treatment targets. Currently, PARP inhibitors are utilized for tumors with DDR deficiency, agents targeting certain KRAS mutations have been shown to be efficacious in select patients as well as TRK inhibitors. Immunotherapy is currently utilized in the small cohort of PDAC patients with dMMR and/or high microsatellite instability (MSI-H) and multiple studies are ongoing on combination immuno- and chemotherapy.

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

I used Beast to analyse COI sequence (741 bp) in a bat species, and the analysis clearly indicated that instead of one species, we had two different ones. I'd like to estimate the divergance date between these two genetic clades. I decided to use Beast. However, I have no fossil Datong information, so in BEAUti I fixed mean substitution rate to '1'. I received the tree with ages of nodes estimated in units: substitution per site (as stated in the manual). Is it possible to 'translate' this information into years, for example using the substitution rate for a particular gene?

Structure

multilocus gentoypes

microsatellites

population structure

Hi! I am genotyping several microsatellite loci in a nonhuman primate, and one in particular, LL1118, seems to have shifted from being monomorphic at around 142bp to monomorphic at 134 bp. At first I thought the individuals I was typing just had a different allele, but one of the individuals was done before and was homozygous for 142 and is now homozygous for 134. While I did change the size standard recently, this has not happened for any of the other 20 or so loci that I am using. Why could this have happened? Thanks!

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.

Hi everybody. May I ask you how to insert microsatellite data in GENETIX v 4.05 software?

Many thanks in advance!

Hello fellow researchers,

For my research I have acquired fragment size data for the analysis of microsatellites in Aspergillus fumigatus. I want to compare my data to other studies. wherein most data are represented in repeat numbers.

I have tried to convert the fragment size data by using the formula: Repeat number = Fragment size - (Forward primer length - forward spacer length)- (Reverse primer length - reverse spacer length) = X / repeat unit size.

However, I could not retrieve the spacer length from a reference A. fumigatus strain.

Can anybody help me further in finding a possible easier way to convert Fragment size to repeat number?

Thnx!

Dear,

I am looking for the MICROSAT software (Microsat (version 1.5): A computer program for calculating various statistics on microsatellite allele data) to insert it into a script, but the links on the internet are giving an error. Someone would have this software to send me (my email: adamrickbessa@gmail.com). Thank you so much.

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

Hello, it's my first work with microsatellite and the last one, I hope. I have 6 markers for some populations of Microtus gregalis from Transbaikal region. In some of them for big proportion of samples there are strange peaks patterns I can't explain. Unfortunately, I haven't time to sequence all the strange patterns, so maybe anyone has any reasonable explanation to them. Until it I decided just to remove these samples.

A,B,C pictures are for one microsatellite locus. As I understand these samples are heterozygous, but the place of the second peak is unclear. D,E for the second misat locus, and samples here have more than two peaks, which can be understood as the real locus sizes. Which explanation could be for these pictures?

I'm constructing a phylogenetic tree using microsatellite sequences in MEGA11. I have aligned the sequences using MUSCLE and now I can see a lot of "xxx" and gaps in many of the sequences. Kindly suggest whether I should remove the entire sequence or should just remove the part of the sequence. For better understanding provide an answer with an explanation.

Thank you in advance.

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.

Through Arlequin, I'm hoping to learn how to study population genetics (e.g., Fst values, Hardy-Weinberg analyses) using DNA sequences. Perhaps you could give screenshots of the files you have or a step-by-step guide on how to perform it. All I know is how to use Arlequin to analyze microsatellite data.

Your response will be greatly appreciated!

if samples are limited, e.g., less than 10 samples per population, which molecular markers are suitable(Microsatellites or SNPs generated by RAD-seq)? If you can provide some references for your opinion, it would be better. Thank you for your attention!

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

The STR markers I am working on are linked to Cystic Fibrosis Transmembrane (CFTR) gene and I wonder where should I check if these STR have previously been reported or not.

Cheers,

We are working with DNA samples extracted from faeces, so we are trying to find the optimal PCR conditions to amplify microsatellite markers, as the nature of the samples require quite an effort.

On the image with the stuttering zones is represented the second test we performed in order to see what conditions are optimal.

We used the same PCR conditions with the expection of the following:

-Finan Extension was a)68 ^oC b)72 ^oC for both for the duration of 30min as stated by the Qiagen PCR Multiplex Kit protocol

-T annealing both times was 60 ^oC

What could cause such an utter mess? Is it possible the higher temperature on the final extension step do this?

I would like to construct a dendrogram by microsatellite data, I have progeny trials that consist of 72 individuals, 2 from location A, 2 from location B, 63 from location 5 from location D. Is that okay to run the analyses to omit the tree, if possible is there any justification?

Hi, I have a study in which I have approximately 250 samples (plant material). Microsatellite makes have already been developed and tested for this species, and I would like to know if anyone have experience with sending away material for isolation and sequencing, and if yes - the name of the company/institution? I just don't have the time to do it myself, and also no time to train lab-tech for the task...

Hello, I am doing a microsatellite PCR and the bands appear with a few definition, the electrophoresis conditions are the following, TBE buffer 0.5X pH 8.4 (according to Sambrook, Molecular Cloning), 45 mA constant or 100 V constant (I've try both conditions), 8% polyacrylamide gel (according to Sambrook, Molecular Cloning) (8 cm long), loading of pPCR 3uL + 1uL Gel Red [1: 2000]. What can be my mistake that the bands are thick and have little definition?

Thank you.

I am running DIYABC on microsatellite data and all the data that was accumulated over the last 8 days still exists (the project file is over 25GB now), but the program is not recognizing the last run.

It has crashed before, and restarted without a problem. Now, when I re-open the microsatellite project it is starting me from 0 "Number of already simulated data sets in the reference table". Has anyone encountered this before? Any ideas?

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?

unlike amplifies coding region or gene via PCR which shows simple single band pattern in single well but microsatellite is some what confusing that shows multiple banding pattern while screening on gel electrophoresis. so how can i interpret the screening results of ssr via gel electrophoresis. as the attached image shows multiple band in same well.

I am having an assembled fasta file (~3.7 GB in size). I tried using the web based MISA v2.1, but it accepts fasta upto 2Mb only. Is there any other alternate software which can be used for a large size dataset for filtering SSRs?

I am interested in assessing the inter- and intra-specific variations in fish using genetic markers. RAPD, cytochrome b, COI, microsatellites are mostly used for the evaluation of genetic variations. Can you please recommend me the best marker to be used.

Thank you.

Hello,

I have developped 4 markers to detect microsatellite instability in a cancer type using digital PCR.

I would like to determine the discriminatory power of each marker, meaning the cut-off (mutant allelic frequency) to classify a tumor as microsatellite instable (MSI) or microsatellite stable (MSS). For each marker, I performed ROC analysis using 7 MSI tumors and 20 MSS tumors but I was wondering if ROC is the right analysis for this purpose. Could you help please ?

Best,

Khadidja

I am running DIYABC for both microsatellite and mtDNA data and testing 3 scenarios. Once I start the analysis I get the following error message:

"Something happened during the reftable generation :

Program of thread 'Species_ABC reference table generation' exited (with return code -6) unsuccessfully.

not priormusmoy.fixed"

Does anyone new the reason and a way to fix it?

Thank you

Assume a hypothetical microsatellite region with the sequence AGTA. Towards the middle of the set of repeats, there is a repeat where the first A is replaced with a T.

Would that insertion split the microsatellite region into two separate regions, one with the original AGTA sequence and one with GTAA?

...AGTA-AGTA-AGTA-AGTA-AGTA-AGTA-AGTA-AGTA...

...AGTA-AGTA-AGTA-T-GTAA-GTAA-GTAA-GTAA-GTA...

I've seen literature regarding how to count repeat numbers in a situation like this, but I can't remember if there was a biological justification for the conclusion it drew (to only consider the longer remaining piece as the original microsatellite region) or if it was a shortcut to make computations easier.

selection DNA fragment for application microsatellites technicians, will be association in improvement performance of domestic population layers.

How to score microsatellites for analysis through NTSYS pc? Should I use some other program? which one is the best and available on line? Please guide me in details.

I have with me diploid data(genotypes)which is microsatellite markers.Can you suggest any software to produce the same fig,with pie chart as attached?

I'm working with sequence data from a set of closely related species and along with other indels and SNPs there are microsatellites regions in the sequences.

I was planning on building a character matrix using complex indel coding, which from my understanding requires the sequences to all share a 5' or 3' end. Where I'm running into trouble is that there is some variation in the repeats as well, with the occasional insertion or deletion giving me trouble aligning (ex. the repeats are mostly AT but there's the occasionally extra A or T).

I can't only rely on the microsatellite data, so is there a way to build a character matrix that differentiates the taxa based on the repeat number and the variations in them (insertions, deletions, and substitutions) rather than just depending on the length?

In my investigation on microsatellite I always get the results from Fig. E (the peaks around 160).

It looks like I have stutter pieks before the highest peak, but also after.

Before the highest peak there is a rising trend (normal). After de highest piek is a downward trend (not normal).

I used a tail-PCR. A forward primer with a tail at the 5' (around 40 bp), a reverse primer (around 20 bp), a fluorescent primer (around 20 bp). Each microsatellite has an other primerpair (I designed them).

I have done a PCR in simplex and a multiplex-PCR (with 3 fluorescent primers). Most microsat of both PCR's had the pattern of Fig. E.

Because this is a rare pattern, I was wondering how this can happen. What are possible causes?

Your sincerely

Thomas Raps

I have amplified the rpl32-trnL spacer region for five different grass species (trnL (UAG) and rpl32-F primers). Instead of seeing one consistent amplicon size, I have some fragments that differ by about 150 bp. Has anyone seen something similar in plants or grasses in particular? Could there be a microsatellite region that is being amplified that is causing this size difference?

There is three molecular pathway for sporadic colorectal cancer is Microsatellite instability (MSI), Chromosomal instability pathway (CIN), and CPG island methylation CIMP.

From my understanding, microsatellite repeats should be consistent (e.g. di-, tri-, tetra-); therefore, allele sizes should be consistently separated by 2, 3, or 4 nucleotides. I am working with a new locus that seems to have multiple repeat lengths. For example, there are repeats of 2 nucleotides, followed by repeats of 3, and then back down to 2. Has any one else had this experience with microsatellites? Is it a biological phenomenon, or likely just scoring error?

I am trying to estimate the null allele frequency in my Microsatellite data. For this purpose, I used Steven Kalinowski's software ML-Null.

You will find it here:

Has anyone ever used it? If yes, can anyone suggest it for publication purpose?

The software is quite easy to operate; uses a Genepop input file. However, it lacks the manual or description about wich approach or model is used for Null allele freq. calculation.

Dear all,

I am preparing a population genetics study at the moment, specifically a microsatellite-based approach to identify fly specimens from different regions. Currently I am at the step of establishing all of the microsatellite markers to assess which are suitable for the study - this requires a sufficient quantity of DNA to test all primers on the wild fly specimens.

As the wild fly samples are the most valuable in this experiment, I need to get as much yield as possible from the DNA extraction.

I have tried 2 protocols so far:

- Zymo research quick g-DNA miniprep kit: It delivers a low DNA yield when extracting from 6 fly legs; treatment with proteinase K for 1 hour before the standard protocol increases the yield around 5-fold to 30-40ng per μl. This would be barely enough for all PCRs, so I am looking for a way to increase the yield even more.

- in-house prepared homogenization buffer, consisting of TRIS-HCl, EDTA and NaCl. Following a quick and easy protocol to extract crude, non-purified DNA from single legs in 80 μl homogenization buffer, the leg is crushed, buffer added. The solution is vortexed and spun down, then 1.7 μl Proteinase K is added. The sample is incubated at 37 degrees C for at least one hour, followed by a short inactivation of Proteinase K at 98 degrees C. From this method, I could successfully amplify DNA with 1 μl template DNA from a fresh fly leg. However doing the same with a preserved wild fly leg, I don't receive the same result, even when using 4 μl template DNA.

The wild fly samples are conserved in propylene glycol as well as Ethanol. Before the extraction I take out the fly, let it dry and rehydrate the leg.

Any suggestions on how to enhance the DNA yield for one of those protocols?

Hi everyone, How can i input microsatellite loci data into nexus file? Or maybe theres a way to convert popgen file into nexus?

I want to construct a NJ tree for my microsatellite data which should be supported with bootstrap values. I downloaded the software Populations 1.2.31. I did not find any manual for that so tried to deal with the short guidlines section in the software webpage but couldnt get any result. even I could not open the input into the software. Can sombody help me to get through this?

Hi! I'm analyzing microsatellites to hybrid fish (triploid, sometimes even tetraploid). I'm not sure if I do enough good. I send two pictures. Do you agree with my analysis? I think that the first specimens on the left are residuals.

I am currently trying to create a dendogram from my microsatellite data, which consists of alleles from nine strains of nile tilapia using nine primers/loci. It has been recommended to me to use Phylip to infer the trees and then using either Tree Explorer or Dendroscope to make a reasonable image. Does anybody know if there is a better/newer method of creating dendograms or am I better off sticking with this software? Thanks!

I look for databases concerning morphometric measurements or goat microsatellites, either a database in EXEL form or a site from which I find what I'm looking for

📷

Fst is used in many genetic studies which involve different markers (mtDNA, microsatellites, SNPs...) as methodologies and next-generation genetics improve. I was wondering if it would be correct to compare Fst values obtained from microsatellites with Fst obtained by SNPs or rather should simply compare results qualitatively.

Thank you very much.

Most of my microsatellite markers are dinucleotides, therefore they show stuttering. In regular stuttering is easy to identify the allele, which is the highest peak on the right, after the shorter stutter peaks (Fig. A). But in some samples, usually in larger alleles, the highest peak varies the position or all peaks show similar highs (Figs. B, C, D, E). In these cases, what is the allele: the highest peak (independently of position) or the peak on the right (following the position pattern)? Fig. E is an extreme case, with confusing peaks. In a specific marker, some samples show a central highest peak with two other shorter peaks: one ~30 pb smaller and the other ~30 pb larger (Fig. F). Is one of the shorter peaks a true allele or are both a type of artifact ("ghost peaks")? Finally, can I consider weak amplifications? Probably these shorter peaks are because of low quantity/quality of DNA or due to large allele dropout (Fig. G). I am scoring microsatellite data manually in Peak Scanner 1.0 (labels show height (H) and size (S) of peaks). In the PCRs, was used Platinum Taq DNA Polymerase, cycles with 30 min of final extension and primers forward tailed with M13. Due to limitations of time and resources, we won't be able to rerun the fragment analysis. Thanks for your attention.

Which is one is better in between 16S rRNA and microsatellite phylogentic study?

I am trying to determine if a highway is too much of a barrier for shrews to cross and breed freely. What I have to work with is ~1080 bp of the mitochondrial cytochrome b gene (we did not do microsatellites which most researchers do use and I think it is the source of a lot of my troubles using common programs and R packages). I have 3 sites north and 3 sites south of a highway and I want to see if the Fst values I have calculated through DNAsp are significantly different from zero or each other. Does anyone suggest a way I can organize my data so that I can put it in R to determine the significance or another route I should take? Thank you for your time!

I ran a three scenario analysis using DIYABC. Some output files attached. PCA looks ok and the 95% PP clearly indicates that scenario 3 is the most supported one, with no CI overlap. However, either I am not doing it well but the error is lower for scenario 2 than 3. Any idea why this happens when the remaining analyses clearly indicate that scenario 3 is the best one?

Thank you in advance

I am using a trinucleotide SSR primer (169 pb). I expected that the allele sizes would be in 3 pb (e.g. 157/166) but GeneMapper software also detected sizes 156/165. More details about the allele sizes can be viewed in the attached file.

Should I round the allele sizes? Could anyone help me how to score this?

Male birds (30 generations of selection) belonging to three homozygous genotypes (DD, CC, BB) at ADL0176 microsatellite and females (4 dams to each sire) having corresponding homozygous genotypes were crossed avoiding mating between full and half-sibs with the help of pedigree record. The pullets raised out these straight-run chicks (progeny) when genotyped revealed 7 genotypes (AC, AD, BD, CC, CE, DD, EE) at ADL0176 locus. What could be the explanation behind the appearance of extra A and E alleles in the progeny?

I have Microsatellite Data of buffalo and i want to associate with milk yield. Please guide me the exact model for this analysis?

I've run a couple hundred samples using a microsatellite panel, and recently some of the runs show very exaggerated stutter peaks smaller than the true allele size. To troubleshoot the issue, I've rerun the same PCR product multiple times on our ABI 3500. The problem appears to arise from the fragment analysis, rather than the PCR step, since the same product produces very different results from run to run. Some samples look fine in one run but the same PCR product shows the mystery peaks on a second run. Since some of them are showing up in each run, and the peaks are often much larger than the true allele peak (sometimes the true allele is even absent), this makes accurate scoring impossible.

I've posted three examples from three different samples and 3 different loci. The lower run for each is the one depicting the correct alleles, the upper run shows the large stutter peaks and small true peaks. In one case, the ghost peaks are 4bp smaller for a 4bp repeat, but in the other two they are 10.5bp smaller and 7bp smaller for a 3bp and 4bp repeat, respectively.

I've never had this problem before, but also am relatively new to running the ABI machine myself. I'm loading:

7ul of MClab orange size standard in SuperDi

1ul each of 3 PCR products (topped with mineral oil). They are diluted 2x first before loading.

the product was stored for ~1wk in the fridge before loading.

I've tried heating the plate to 95deg for 5 min then chilling and loading, to no avail. I've also tried re-running PCRs and the problem returns. Some plates look fine, and others are all bad.

Any suggestions on what is going on or how to fix it?

Thanks!

Kevin

I have calculated the distance matrix in populations software. The data which i used is microsatellite data. I saved the distance matrix file in .txt format.But when I chose this same file to develop phylogenetic tree with distance matrix, showing "Matrix file format is not recognized.....".

Could somebody help me to sort this issue.

Previously for genotyping from mouse tissue, I have used an extraction method which involved SDS-proteinase k, followed by RNAse A and Isopropanol, then resuspension of remaining pellet in buffer for PCR. We never had an issue with amount of DNA with this method.

My current lab uses a phenol-chloroform extraction, which seems like 'overkill' for DNA extraction for the purposes of PCR and microsatellite analysis. Plus, there are the health and environmental impacts of using these materials.

Has anyone tried both methods - are there additional drawbacks or considerations to think about?

statistical analysis with microsatellite data markers

I'm studying the polymorphism of a microsatellite related productive performance in 4 goat breeds and I would like to represent the distances between them according to its polymorphism (alleles and genotypes), which method is the most appropriate: PCoA, dendrogram,...? . Thank you in advance

I have read that sequence based data are not powerful for analyze isolation by distance between population. However, I want to know if is possible to analyze the effect of environmental variables as elevation, temperature or land use on the genetic differentiation between lineage or cryptic species using sequence based data as mitochondrial DNA and nuclear DNA (ITS2)?

If yes. Which metric should I use as a measure of genetic differentiation between lineage or cryptic species?

If not. I know that ITS data can have microsatellites, it is possible to use these microsatellites as a source of genetic information for landscape genetics?

Hi All, we have a bioinformatics challenge and we would love any help this community can offer. We have data from a target-enrichment experiment that was supposed to capture certain microsatellite motifs. The three enriched libraries were sequenced in a rapid run on Illumina Hiseq 2500 (paired end mode) and our data is in the standard illumina fastq output. Our three libraries come from three different sources. The first library is developed from fresh fish tissue; the second one is mammal tissue; and the third one is the same mammal species but from fecal samples. For the fecal samples, we need to somehow filter out sequences belonging to the mammal only (i.e. not prey or microbiome). We have a reference genome for the mammal, but not for the fish. The data has been demultiplexed already (so for the fish we have 40 individual fish each with its own .fq file containing all the read data). Now, we are facing the challenge of how to deal with this data. Although we are familiar with most basic bioinformatic tools and analyses we do not have advanced programming skills. We need to find a way not only to find and identify the length of our microsats within the reads but also (for the fecal library) somehow be able to identify unique flanking sequences that would correspond to our mammal, in such a way that the reads of other species in the fecal libraries can be excluded. Would anyone have a suggestion on what approach(es) we could use? We have already (unsuccesfully) attempted to tackle this with SSR_pipeline. Thank you in advance for any help you can offer - it is very much appreciated! Daniel & Vania

When scoring a couple of tetranucleotide microsatellite loci, I noticed in a few samples the allele length is inconsistent with the repeat modulus. For example, I have sizes 369-373-377… up to 417 following a nice 4bp repeat pattern. Then, the next alleles are 422-430-435-439 and 447 (verified by 2 different software). Question is…should I keep these sizes as is or do I fix them to fit a 4bp-repeat motif? Thanks.

In which cancer patients do you determine the microsatellite instability (MSI)? What are the new studies in this area?

Can someone suggest any research paper for a complete understanding of genotyping by microsatellites in fungus?

Hello,

I have an excel sheet with microsatellite data, I would like to make a NJ tree out of it. I have a basic level in bioinfo.

Can someone please guide me through the steps to get the tree?

Thank you

Tamara

I'm working on optimizing three panels of sand lance for multiplex PCR. I'm essentially starting from scratch and first ran gradients on each individual marker to determine annealing temperature and size range, and I then created a multiplex plan.

The first panel went really well, and all the samples worked, which is why I can say that the DNA is fine.

For the second panel, I used the same samples, and am getting variable results. Some samples work pretty well, others have no amplification for any of the three markers within the panel. I'm not sure what my next step would be. This is my second try on this panel. The first was a standard PCR at the determined annealing temp, and the second time I tried a touchdown protocol and lowered the concentration of primers a bit.

Anyone have any suggestions on where to go from here?

I am conducting a population genetic study on several species of fishes using microsatellite alleles. I have used BayesAss (http://www.rannala.org/software/) to estimate migration percentages to and from each population in my datasets for each species. Superficially, the outputs provided seem to be apparently correct and adhere to pre-conceived hypotheses. However, the output data do not provide me with p-values to indicate if the estimates are statistically significant. For each estimate (mean) the SD is provided in the output file, and after reading the generated Trace file (https://www.beast2.org/tracer-2/ ) several other outputs are calculated (SE, SD, variance, upper and lower 95% CIs) but no p-value. Could anyone help me either a) identify the p-value in the output that I am somehow missing? or b) calculate the p-value from the outputs provided? Unfortunately statistics aren't my strong suit so I feel like the answer might be obvious with the results I've been given but I can't figure it out from what I've looked up so far.

Thanks!

What is the relevance of Microsatellites or Simple Sequence Repeats (SSRs) based markers in the era of genomics for their utilization in plant molecular breeding ?

What proportion of plant molecular breeders are using them (SSRs) for their breeding activities ?

Are there any better DNA molecular markers systems evolved apart from SNPs ?

Did the development of SNPs marker system significantly reduced the use of SSR based markers in plant molecular breeding ?

Dear researchers,

I am currently using BEAST to infer TMRCA  from 10 microsatellite loci that I have genotyped for one population where I have cases and controls, so my question is:

What is the best way to estimate the TMRCA of the cases considering the 10 loci all together for the taxa previously described? How do I do this?

Thanks in advance!

I have analyzed the length of microsatellite PCR products by means of capillary electrophoresis and, basing on the results, I estimated the number of shorts tandem repeats (STRs). Then I created a matrix, where number of STRs are placed in columns (values 1-33) and names of strains are put in rows. Which clustering method would the best to create a distance tree? I've been thinking of UPGMA algorithm with Euclidean similarity index. But please advise me anything better if I'm wrong. So far I've worked with PAST Software. Thank you in advance!

There's this PCR product on all my samples of one species (first image) that amplified and is detectable but does not look the way the other alleles look so I don't know if I should be including it as an allele for the analyses or is this how a null allele looks? And if that's the case, should I include it with my dataset? The second image shows the PCR products for the second species I'm analyzing. You can see that the same product amplifies but looks almost exactly as the other alleles.

Hello,

I'm doing PCR and gel electrophoresis on tetranucleotide microsatellite repeat of a species of diploid salamander. The gel results yield three bands in two sample (attached; red arrows), and I'm confused about how should I interpret this. Other samples (not shown) also display three bands. I only expect from one to two bands in diploid organism. There are a lot of non-specifics, but the microsatellite alleles are highly pronounced.

Thank you

This is all the data I have for PCR products of 102 samples for this specific locus. I'm not sure if I should be counting the fragments on that range (more that 175 bp) because it is too far from the original one reported for the microsatellite. How do I know if the articles that have been published for my species actually use alleles that amplify over the top range number?

Hello,

I'm using PCR to assess the differences between the banding patterns of a microsatellite in different salamander species. In my resulting gel, there's extra unclear bands underneath the clear bands in the A.texanum and A. laterale samples, and above A. jeffersonianum's clear bands. What do these unclear bands indicate?