Q&A in AGH635 Course : If I can not Use Them for Linkage Analysis, what Are They For ?

One of my student raised the following matter: “I have analyzed 200 individuals collected from different places. I evaluated the accessions for resistance against plant disease and also for approximately 100 loci of molecular markers (m1-m100). Results of the analysis indicated there were 50% resistance (R) and 50% susceptible (r) individuals. For those two groups (“R” or “r” group), I also noticed various degrees of polymorphism for (+) and (-) in the respective loci. Moreover, a number of “R” individuals were also scored (+) for a number of the marker loci. Similarly, some of the susceptible individuals were also scored (-) for a number of the evaluated marker loci. Summary of the collected data were presented in Table 1.” My question was: “If I can not conclude the M (+) markers were linked to the resistance character based on those data, what can I use the generated information for?”

Before you read my answer for the above question, I would suggest you to read my previous posting about “common by descend” and about “associating markers with phenotype characters.” As indicated previously, the data in the Table 1 summarize the score for resistance phenotype and for the evaluated markers.

Table 1. Percentage of responses against disease and the model of their marker  scores

Table 1 - variant1Grouping of the plant responses after inoculation with the target pathogens:

  1. Res M(+) is resistant – no visible symptoms and (+) score for the marker;
  2. Res M(-) is resistant – no visible symptoms and (-) score for the marker;
  3. Sus M(+) is Susceptible – visible symptoms and (+) score for the marker;
  4. Sus M(-) is Susceptible – visible symptoms and (-) score for the marker;

Grouping of the score of evaluated molecular marker for m1-m100 loci for each individual are resemble either the model M1, M2, M3, or M4 as shown in Table 1. The model M1-M4 could be described as follows:

  1. The M1 marker model : The neutral marker, the (+) score is similarly distributed as the (-) score, both in the resistance and in the susceptible individuals.
  2. The M2 marker model : The resistance specific marker, the (+) score is more frequently found in the resistance individuals than in the susceptible ones. On the other hand, the (-) score is more frequently found in the susceptible individuals than in the resistance ones.
  3. The M3 marker model : The susceptible specific marker, the (+) score is more frequently found in the susceptible individuals than in the resistance ones. On the other hand, the (-) score is more frequently found in the resistance individuals than in the susceptible ones.
  4. The M4 marker model : The negative marker, both the resistance and the susceptible individuals show (-) score for the markers.

Although for the model M1, the marker is neutral in relation to the resistance/susceptible responses. However, some of the loci that are score (+) for resistance and (-) for susceptible might be associated (linked) to the gene controlling resistance characters in certain individuals. However, to come to this conclusion, one needs to further analyze the co-segregation between markers and the resistance phenotype using segregated population (mapping population).

In the model M2, the marker is resistance specific marker. It means that the score (+) of the markers is commonly found in the resistance individuals, while the score (-) is in the susceptible ones. It might not guarantee that the markers are ones linked to the gene(s) controlling resistance character. However, some of the loci that are score (+) for resistance and (-) for susceptible might be associated (linked) to the gene controlling resistance characters in certain individuals. However, to come to this conclusion, one need to further analyze the co-segregation between markers and the resistance phenotype using segregated population (mapping population).

In the model M3, the marker is susceptible specific marker. It meant that the score (+) of the markers is commonly found in the susceptible individuals, while the score (-) is in the resistance ones. It might not guarantee that they are the markers linked to the gene(s) controlling susceptibility characters. However, since some of the loci that are score (+) for susceptible and (-) for resistance might be associated (linked) to the gene controlling susceptible characters in certain individuals. However, to come to this conclusion, one need to further analyze the co-segregation between markers and the susceptible phenotype using segregated population (mapping population).

In the model M4, it is the negative marker, since both the resistance and the susceptible individuals showed (-) score. It means that there is no marker generated neither from both the resistance (it is score [-] for resistant individual) nor the susceptible individuals (it is also score [-] for the susceptible individuals). Such negative markers would have no used in the molecular marker analysis.

Back to the raised question : “If I can not conclude the M (+) markers were linked to the resistance character, what can I use the generated information for?”

It is true that based on the data in Table 1, we could not conclude that the model M2 markers, which are the resistance specific markers, are ones linked to the resistance characters. To be able to make such conclusion, ones needs to conduct more evaluations using what is called mapping population.

In all of the above explanation, however, the model M1, M3, and M4 markers has no use when we plan to generate linkage map among markers or among markers and the resistance characters. Only the model M2 markers would be useful for such purpose, since they are resistance specific markers. Once the mapping population is generated, all of the model M3 markers could then be tested and evaluated for all individuals in the population. Subsequently, the generated data are then be used to identify co-segregation among markers or among markers with the resistance characters. Co-segregation among markers or among markers and the resistance characters in the mapping population indicate they are linked in one linkage group (i.e. existed in the same chromosome).

If the objective of the study is to investigate genetic distance among accessions, only the model M1, M2, and M3 markers would be useful. However, the model M4 marker will have no used even in this type of study. Data generated using model M1, M2, and M3 markers could be used to estimate the distance  among individuals in the studied population. Once the distance among individuals are determined, they could be used to select parents for conducting genetic studies (i.e. for generating mapping populations, linkage analysis, or heritability studies). The selected parents could for example be either

  1. P1 (resistant) and P2 (susceptible) with the highest genetic distance between them or
  2. P3 (resistant) and P4 (high yielding) with the highest genetic distance, or
  3. P5 (resistant) and P6 (resistant) with the highest genetic distance.

In the case of (1) P1 (resistant) and P2 (susceptible) with the highest genetic distance between them, the parents could be used to generate segregating population (mapping population). The population could then be used to :

  • Generate linkage map among model M1, M2, and M3 markers,
  • Generate linkage map among markers and the resistance characters, or
  • Study genetic control of resistance characters contributed by P1 parent.

In the case of (2) P3 (resistant) and P4 (high yielding) with the highest genetic distance between them, the parents could be used to generate segregating population. The population could then be used to :

  • Generate individuals having a combine resistant and high yielding characters,
  • Study the linkage map among model M1, M2, and M3 markers,
  • Generate linkage map among markers and the resistance or the high yielding characters, or
  • Study genetic control of resistance and high yielding characters contributed by either P1 or P2 parents, respectively.

In the case of (3) P5 (resistant) and P6 (resistant) with the highest genetic distance between them, the parents could be used to generate segregating population. The population could then be used to :

  • Evaluate alleles interaction among genes controlling the resistance in the P5 and P6 individuals (i.e. are they controlled by the same locus or by different one?),
  • Study pyramiding of two or more resistance loci, if the genes controlling resistant phenotype are non-allelic (i.e. they are in different – two or more – loci),
  • Generate linkage map among markers and the resistance genes, or
  • Study genetic control of resistance characters contributed by either P1 or P2 parents, respectively.

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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