Hello everyone, I would be very grateful if you could give me guidance on the use of transcription factors as molecular markers. I am studying senescence in fruits through the analysis of transcriptome and I´m looking for genes of interest that serve to explain the differences between the different varieties of fruits.
I´m interested in the transcription factors associated with the metabolic pathways that lead to the senescence of the fruit , but I'm not sure if studying it that way is the right thing to do, since many similar studies only focus on one metabolic pathway or one specific gene within the same pathway. I feel that it would be more interesting to study the transcription factor because it is capable of modulating multiple routes, so it can be a marker that defines whether a fruit has a more rapid maturation than another. I hope you understand my question, thank you very much to those who comment.
Success to all.
Hi Romina Moris, firstly you did not mentioned in which fruits you would like to investigate. However, if they are the flesh fruits you can try to look for the NAC transcription factor genes. For an example, if you are working on tomato then download all NAC TF genes of tomato from
http://planttfdb.cbi.pku.edu.cn/
Thereafter design the primers for qRT-PCR and synthesis the cDNA of your contrasting cultigens taking sample at different fruit ripening stages. In this way you could be identified the possible candidate for fruit senescence. Now you can try to do normal PCR using genomic DNA with new designed primers on the predicted candidate covring start to stop codon, or even including promoter for getting the variation on PCR amplicon between your contrasting cultigens. By these way you can do cloning and sequencing for the variations to be sure on the amount of either indel/synonymous SNPs/nonsynonymous SNPs. Indel could be used directly as markers, but SNPs could be used to develop HRM (high resolution melting) markers. You can validate those markers using any segregating genotypes or the diverse tomato genotypes. you can look the attached paper:
Hello Ujjal Kumar Nath thanks for your response.
I am working with fruits of the Prunus genus, specifically with peaches, plums and cherry trees. I'm doing RNA seq and studying the transcriptome of the fruits in different stages of maturation. I have already identified some NAC transcription factors that are repeated in my fruits of interest, but I am still unsure about whether it is better to use a transcription factor as a molecular marker or a gene within the routes that are affected during senescence (such as biosynthesis of flavonoids, lignification, etc.).
Thank you!
Yes you could use TFs as markes, There is studies that developed transcription factor gene-derived microsatellite markers (TFGMS) in chickpea https://academic.oup.com/dnaresearch/article/20/4/355/353793
and Medicago truncatula Article Development and Characterization of Transcription Factor Gen...
Please have a look of the following papers describing significance of TFs based molecular markers. These suggested articles will give you some basic information of TFGMS and their utility for improving crops.
Kujur et al. https://academic.oup.com/dnaresearch/article/20/4/355/353793
Liu et al. https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25988608/
Gahlaut et al. https://link.springer.com/article/10.1007%2Fs00122-016-2794-z
Kumar et al. Article Genome-wide identification and characterization of gene fami...
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