A student of mine taking AGH635. Molecular and Cellular Analysis in Plant Breeding Course, once asked me the following question: “Is there any specific requirement we should follow about the plant population used in molecular marker analysis and evaluation?” Instead of directly answering the question, I would rather discuss what common by descend is, in relation to molecular marker analysis and evaluation.
In molecular analysis, the term “common by descend” is an important issue. Therefore, we should understand what this terminology means. So, what is “common by descend” anyway? and what is not?
Consider several cases below:
All the 200 individuals in the Case # 1 – 5 above are commonly descended from the parents (in this case the P1 and the P2). Therefore, the genetic materials of the 200 individuals in the Case #1, #2, #3, #4, and #5 are common by descend, since they are descended from either from P1 or P2.
On the other hand, 200 individuals in the Case # 6 might probably not be descended from common parents as in the case # 1-5, respectively. Hence, the genetic materials of the 200 individuals in the Case #6 might probably not common by descend.
The 200 individuals in the Case #1-#5 can be used as mapping populations to study linkage analysis using molecular markers (i.e. linkage map construction) and study association between molecular markers and certain plant characters (i.e. gene mapping). Although it has 200 individuals, as many as those in the Case #1-#5, individuals within the population in the Case #6 can not be used as mapping population to study linkage analysis using molecular markers nor suitable for studying association between molecular markers and certain plant characters.
Why is “common by descend” important in studying linkage analysis using molecular markers and in association studies? It is because the genotype and phenotype variations existed among individual members of the populations are the results of either (1) segregation, (2) recombination, or (3) mutation events. However, in just one or two generation – mutations is a rare event. Therefore, the existing variations in a given F2 population most probably are the result of either segregation or recombination event or both.
By analyzing segregation and recombination events, one can determine whether two loci are located in the same chromosome (i.e. linkage) or in different one (i.e. independently segregating). If the two loci are in one chromosome – then the two loci are linked. On the other hand, if the two are not in the same chromosome, then the loci are not linked and they are segregated independently. One can not determine whether the two loci are either linked or segregated independently unless one use population with a number of individual members (i.e. mapping population) that are “common by descend” (i.e. they are descended from common parents).
In conclusion, back to answer the question my student has asked me, it is necessary to develop certain kind of population to answer certain objectives of using molecular marker. If one want to study linkage analysis using molecular markers, then a population with individuals commonly descended from the same parents (mapping population) is needed because only from such a population we can analyze the co-segregation among markers. Hence, one will be able to determine which molecular markers are linked and which are independently segregated. However, if one objective is only to study genetic distance among individual members of the population then it is nod required to have a population with individuals commonly descended from the same parents.