Q&A in AGH635 Course: Associating Molecular Markers with Phenotypic Characters

A student who took AGH635. Molecular and Cellular Analysis in Plant Breeding Course, once raised the following case: I have analyzed 100 plants for their resistance against a particular plant disease. The same plants were also subjected to molecular analysis using molecular markers (let’s just say marker M). The results indicated that a number of plants that were resistance (R), also exhibited M “+” Meanwhile, a number of plants that were susceptible, also exhibited M1 “-” He asked the following question: “Can it be concluded that M1 “+” was an indicator of the presence of R gene? In other word, can one used the M1 “+” allele as a marker linked to or associated with the resistance characters?”

Before answering that question, lets evaluate the following model plant. Please note, for simplifying explanations, genome of the model plants was represented by two sets of chromosomes (Chr.#1 and Chr.#2) and in the chromosome only contained two loci (the M and the R loci), respectively. In the R locus, there are “R” allele conferring resistance phenotype and the “r” one conferring susceptibility to a certain plant pathogen. In the M locus, there are “+” allele indicating the presence and “-” allele indicating its absent of molecular marker.

Lets also assume the individual Plant A and Plant B are both resistance against those particular disease and “+” for the M locus. On the other hand, Plant C and Plant D are both susceptible against that particular disease and “-” for the M locus. Since in these model plants, the genome were represented by two chromosomes and in the genome there only be two loci; therefore, the arrangement of the “R” and the “M” loci could be represented in the following figures.

Slide1 Slide2

If we evaluated the plants in the above figure against the target plant pathogen and for the molecular marker M, the expected results of the evaluation will be as presented in the following table.

Slide3Based on the above results, Plant A and Plant B were both resistant against the targeted pathogen while Plant C and Plant D were susceptible, respectively. Moreover, both Plant A and Plant B that were resistance, also “+” for marker M while Plant C and Plant D that were susceptible, also “-” for. marker M.

However, examining closely the above figure, we should notice the following:

  • Plant A: The R locus and the M locus were in the same chromosome or they were linked (both in Chr. #1)
  • Plant B: The R locus and the M locus were in different chromosomes or they were independently segregated (the R locus in Chr. #1 and the M locus in Chr. #2)

Examining Plant A and Plant B, they both were scored resistance and M “+” but genetically the R and the M loci were in the same chromosome (linked) in Plant A and they were in different chromosome (independently segregated) in Plant B.

  • Plant C: The R locus and the M locus were in the same chromosome or they were linked (both in Chr. #1)
  • Plant D: The R locus and the M locus were in different chromosomes or they were independently segregated (the R locus in Chr. #1 and the M locus in Chr. #2)

Examining Plant C and Plant D, they both were scored susceptible and M “-” but genetically the R and the M loci were in the same chromosome (linked) in Plant C and they were in different chromosome (independently segregated) in Plant D.

To summarize:

  • If one take a number of accessions, evaluate them for their individual phenotype and for molecular marker,
  • If one can group the accessions into two contrasting phenotypes (i.e. Resistance vs. Susceptible) and into two contrasting score of marker (i.e. “+” vs. “-“),
  • Even if we found the resistant (R) individual was almost always carries the M “+” and the susceptible (r) carries the M “-“
  • Those finding did not guarantee the conclusion that the M and the R loci were linked or they were in one chromosome

So, what was the correct conclusion ones can draw considering such results? Well, you are correct to conclude the following:

  • The marker M “+” were existed in a resistance specific way or the M “+” specifically occurred in the resistance plant. The M “+” can be called as the “resistance specific marker” but can not be called as “linked to the resistance character”
  • Whether the R and the M loci were linked (in the same chromosome) or not, can not be concluded based on the results of this evaluation
  • To be able to conclude either the two loci were linked or independently segregated, one need to have a mapping population descended from common parents (common by descend)

About PMB Lab: Prof. Sudarsono

This blog is dedicated as a communication media among alumni associated with PMB Lab, Dept. of Agronomy and Horticulture, Fac. of Agriculture, IPB, Bogor – Indonesia. It contains various information related to alumni activities, PMB Lab’s on going activities and other related matters.
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One Response to Q&A in AGH635 Course: Associating Molecular Markers with Phenotypic Characters

  1. Pingback: Q&A in AGH635 Course: Associating Molecular Markers with Phenotypic Characters « AGH635: ANMOL

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