Which method gives more reliable results to identify a typical variety of citrus SCAR, FAFLP, SCoT, RAPD, RFLP, AFLP etc
Hi,
first of all I would ask you which species of citrus are you working with, since the avaiability of markers is related to the citrus specie. Some markers can be available in literature, depending on which gene are you looking at and depending on which part of a gene more specifically are you looking at. If you want to search for variety-specific differences I would suggest you to analyse your samples with SSR markers, SCAR or SCoT which work generally well in those cases. I would strongly suggest you to have a look at literature before choosing your markers and then select accordingly.
Here you can find some info:
Article Potential of Start Codon Targeted (SCoT) Markers to Estimate...
https://www.omicsonline.org/ssr-markers/articles.php#:~:text=Microsatellites%2C%20otherwise%20called%20Simple%20sequence,Microsatellites%20are%20commonly%20co%2Dprevailing.&text=SSR%20markers%20are%20important%20in%20various%20gene%20studies.
https://www.frontiersin.org/articles/10.3389/fgene.2018.00192/full
For some information about citrus:
Article A quick methodology to identify sexual seedlings in citrus b...
Article Assessment of genetic variability in grapefruits (Citrus par...
https://www.sciencedirect.com/science/article/abs/pii/S0304423811003050
Chapter Markers, Maps, and Marker-Assisted Selection
https://www.actahort.org/books/535/535_1.htm
https://www.jstage.jst.go.jp/article/jsbbs/66/1/66_3/_article/-char/ja/
Best regards
If available SSR marker is the best for identification of genotypes.
Hi
If the taxa of interest (in the case Citrus cultivars) offer analysis by all available techniques, SSR will be the best provided, they are able to discriminate among the cultivars of your interest. It would be good to go through some points
1) How many types of DNA markers are available for analysis of citrus cultivars in literature.
2) What is the discriminatory power of each marker type.
3) If a particular trait needs to be identified, SCAR or SSR may be more useful.
4) If DNA fingerprint needs to be generated, AFLP and RAPD may be useful, AFLP will be a little bit more technically intensive
SO use of a technique for genotype differentiation should be carefully decided
What about identifying different citrus cultivars by GBS (genotyping by sequencing) can you please guide me a bit
Hi,
you can find some interesting articles linked here:
Article Genotyping by sequencing reveals the interspecific C. maxima...
https://academic.oup.com/aob/article/123/7/1231/5423114?login=true
https://link.springer.com/content/pdf/10.1007/s11295-012-0542-3.pdf
https://www.mdpi.com/1999-4915/13/2/168
https://www.nature.com/articles/s41598-020-73321-8
Best regards
Ammara Masood I'd recommend you to address our papers:
Golein B, Vahdati K, Nematollahi A (2013) Analysis of the genetic diversity in Citrus (Citrus spp.) species including unknown variants using SSR markers. Journal of Plant Physiology and Breeding. 3(2): 39-47.
Nematollahi A, Vahdati K, Golein B, Nabipour A, Danesh M (2009) Assessment of genetic variation in citrus germplasm of south of iran using SSR markers. Acta Horticulturae. 839:549-554.
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