Q&A in AGH635 Course: What Conclusion Can We Draw from Molecular Markers Analysis of a Group of Plant Accessions?

One of my student taking AGH635. Molecular and Cellular Analysis in Plant Breeding Course, raised the following case: “I have analyzed 200 plants for different morphological and yield associated characters. The same plants were also subjected to analysis using 100 loci of molecular markers.” The student also raised the following question: “What conclusion can one draw from such molecular markers, morphological, and yield associated characters analysis of a group of plant accessions?”

Before you read further my answer to this case, I would suggest you to read my previous posting about “common by descend” and about “associating markers with phenotypes.” Some of the contents in those two postings may help you understand my answer for the question above.

Since the studied population, consisted of 100 plants, was not descended from common parents, one can not conclude any association either among one character/phenotype with the other characters/phenotypes, among character/phenotype with the markers, or among one marker with the others. Since they were not descended from the same parents, it would be improper to draw any conclusion about any linkage among the characters, the markers or the characters and markers, respectively.

Let’s consider the following results of analysis:

Freq of markersFrom Table 1, the “+” allele of the M1, M5, and M6 markers occurred in the majority of the resistance plants (Group A). However, since the members of the plant population were not descended from common parents (not a mapping population), one could not conclude that the “+” allele of the M1, M5, and M6 were linked to the resistance character.

Similarly, the “+” allele of the M2, M3, and M7 markers occurred in the majority of the large fruited plants (Group B). However, since the members of the plant population were not descended from common parents (not a mapping population), one could not conclude that the “+” allele of the M2, M3, and M7 were linked to the large fruited character.

The “+” allele of the M4 and M100 markers occurred in the majority of the high yielding plants (Group C). However, since the members of the plant population were not descended from common parents (not a mapping population), one could not conclude that the “+” allele of the M4 and M100 were linked to the high yielding character. It could neither conclude that the “+” allele of the M4 and M100 were linked to the high yielding character.

Finally, the “+” allele of M1 and M8 markers occurred in the majority of the dwarf stature character (Group D). However, since the members of the plant population were not descended from common parents (not a mapping population), one could not conclude that the “+” allele of the M1 and M8 were linked to the dwarf stature character (Group D).

So… what one could conclude from such data in Table 1:

  • The M1, M5, and M6 were examples of resistance specific markers
  • The M2, M3, and M7 were examples of large fruited specific markers
  • The M4 and M100 were examples of high yielding specific markers
  • The M1 and M8 were examples of dwarf stature specific markers

Considering what has been discussed previously, one should be cautious about making too far a conclusion about data in Table 1. Phenotype specific markers did not necessarily linked markers, i.e. resistance specific markers were not the same as markers that were linked to the resistance characters. They only meant that the markers occurred specifically on resistance plants. The markers might be linked with the resistant character or they might be segregating independently. To determine whether or not the markers and characters were the subject of further investigations.

Furthermore, the molecular marker data could be used to group the 100 plants into a number of clusters using certain software for that purpose, such as NTSys or DarWIN. The following was just an example of output of such cluster analysis:

Cluster analysisNote: A-H=groups of plants with certain set of characters; Rs=resistant, rs=susceptible; Hy=high yielding, hy=low yielding; Lf=large fruit, lf=small fruit; Dw=dwarf stature, df=normal stature.

The genetic distance among groups indicated how genetically different among them. Plants belonging to the H and I groups were very closely related genetically. The same for those belonging to the A and B groups, they were closely related genetically. In contrast, plants belonging to the A and H groups were the most distant genetically.

If we consider the phenotype, i.e. the resistance vs. the susceptible plants, plants in the A group (resistance) and the H group (susceptible) exhibited the most distant genetically. As for the high yielding one, plant in the B group (high yield) and those in the H group (low yield) exhibited the most distant genetically. For large fruited plant vs. small one, plants in group I (large fruited) and in group A (small fruited) were the most distant genetically. Lastly, for dwarf stature, plants in group B (dwarf stature) and in group I (normal stature) were the most distant genetically.

If ones would like to identify which markers linked to either resistance, high yield, large fruit, or dwarf stature, they need to developed a mapping population descended from common parents. Which parents should one used to generate the mapping population? The answer to this question is:

  • The plants that would be used as parents should exhibit a contrasting phenotype (i.e. resistance vs. susceptible; high yielding vs. low yielding; large fruited vs. small fruited; and dwarf stature vs. normal stature), and
  • The plants should exhibit as large genetic distance as possible.

Using the results of cluster analysis presented in Figure 1 and the requirement for prospective parents to generate mapping population, one should be able to conclude the following:

  • For all combinations between resistance vs. susceptible character, the plants in the Group I and the Group B or Group A and the Group H can be used as prospective parents for generating mapping population to study markers linked to resistance character
  • For all combinations between high yielding vs. low yielding character, the plants in the Group B and the Group H or Group I and the Group A can be used as prospective parents for generating mapping population to study markers linked to high yielding character
  • For all combinations between large fruited vs. small fruited character, the plants in the Group A and the Group H or Group I and the Group B can be used as prospective parents for generating mapping population to study markers linked to large fruited character
  • For all combinations between dwarf stature vs. normal stature character, the plants in the Group B and the Group H or Group B and the Group I can be used as prospective parents for generating mapping population to study markers linked to dwarf stature character

In conclusion:

  • When one analyzes a population that are not descended from common parents for phenotype and for molecular marker, one can only use the data to determine the genetic distance among the plants
  • When one analyze a population that are not descended from common parents for phenotype and for molecular marker, one can only use the data to determine markers that are specific for the evaluated phenotype, i.e. resistance specific, high yielding specific, large fruited specific, and dwarf stature specific markers. However, those markers might not necessarily be linked to the characters
  • When one analyze a population that are not descended from common parents for phenotype and for molecular marker, one can use the molecular marker data to do cluster analysis
  • When one analyze a population that are not descended from common parents for phenotype and for molecular marker, results of the cluster analysis could be used to select prospective parents to generate mapping population. The mapping population is a necessary mean for identifying markers linked to the targeted characters

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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