Sorry, do you mean how they are reproducible between Labs and experiments? or how to measure the coincidence between SSR and phenotype /other genetic markers?.
If you want the correlation between ssr markers you have to use PCA which meseaures correlation and then give principal components based on engine vectors and values.
Actually it would have been better if u would have elaborated your question
SSR markers are linked to specific trait, so, identify trait for which you are looking for. Then, identify no.of markers which may be co-related with trait of interest. Principle Component Analysis (PCA) is one of the tool which can be used for that. In addition to that, if you are unaware of the markers which are linked to specific trait in a plant species for which you are looking, go for comparative use of markers. Such as markers linked to same trait in same genus or different. Sequencing of such trait specific gene may reveal new dimension for correlation.
SSR markers are useful for selection of our desired trait. so that,,after conclusion,,we can select our desired one,,,e.g. YMV resistant lines, salt tolerant lines etc.
ssr data analysis is used usually for getting number of genetic information, including estimation of the polymorphism for number of phenotypic traits. which can be used further for estimation of genetic diversity and similarity between the different screened plant species or for individuals within the same species. moreover, the SSRs molecular markers are used for construction of genetic mapping, fingerprinting crop varieties, etc...also could be used in gene cloning,
With the use of SSRs
1. You can analyze extent of genetic diversity and population structure within your plant species.
2. Phylogenetic relationship and evolutionary track can be identified
3. You can go for trait specific characterization for one/many specific traits.
4. Material with tolerance/resistance to biotic and abiotic stresses can be identified. Also you can study the allelic diversity withing a particular QTL describing a trait.
All these and many more can be done, provided what kind of markers have been used.
There are the terms like "LINKAGE" among molecular markers, "LINKAGE" among markers and certain functional gene, and or "LINKAGE" among markers and certain phenotypes or QTL. If two loci of molecular markers OR a molecular marker and a gene OR a molecular marker and phenotype or QTL are linked, then those by definition indicate that they exist in the same chromosome, with certain distance from one to another.
If the two are linked, we can use one to indirectly predict the existence of the other.
(1) If marker M1 is linked to marker M2 then the presence of marker M1 in one individual will in turn indicate that the individual also carry marker M2 in its genome. (2) If marker M1 is linked to the GENE-1 then the presence of marker M1 in an individual also indicate the presence of GENE-1 in that individual's chromosome
(3) If marker M1 is linked to the PHENOTYPE-1 or QTL-1, then individual carrying marker M1 will also has PHENOTYPE-1 or QTL-1
Using that line of thinking, one can relate to your question : "What are the results to be concluded from Simple sequence repeats (molecular marker) data analysis of plants?"
For one, from the marker analysis - you can generate linkage map among SSR markers, among SSR markers and important genes, and SSR markers and phenotype or QTL across the plant genome. Once you generate such linkage map, you can use the associated marker as indirect predictor for the others (i.e. the other markers, genes, or phenotypes/QTLs that are in the same linkage groups). Such association among markers, genes, and phenotypes have been used by plant breeders to assist in their selection activities (i.e. marker assisted selection - MAS; marker assisted back-crossing - MAB)
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