@maggie : Thank you for the answer. I am not looking for a particular loci as such because some of my initial chromosome substitution line studies indicated two chromosomes to be having a significant effect on the trait i am looking at. I am more interested in the nature of genetic architecture rather than the loci per se (at least at this point of time). So that means RILs followed by deficiency mapping is what I should be considering at this point and probably NILs can be looked into at a later point is it?

Near Isogenic Line are especially good for 'Mendelising' quantitative trait. This is achieved when selection is made for only one locus of interest after each repeated backcross with a recurrent parent. As suggested by Maggie, with Near Isogenic Line , you might miss out on other loci that may be of interest, except such loci are tightly linked to your selected locus. My PhD project started out with Double Haploid line ( which are genetically similar to RILs). And these allowed us to detect multiple loci that affect my trait of interest. We have now developed NILs for each of these loci. Although you are just interested in the genetic architecture of your trait, it might be a good idea to start developng NILs to look at each of your two chromosomal loci of interest separately.

@cristina: Well i get the point of inbred lines and since my populations are outbred, what I intend to do is, sample multiple sets of small sub-populations from my main outbred population and subject them to inbreeding. Then score all the inbred populations to see if they exhibit the phenotype of my interest and the use only the one that do so to move ahead and develop RILs or NILs. Any comments about this???

@ Oluwaseyi Shorinola : Given that my resolution is at the level of an entire chromosome (two such chromosomes) , don't you think instead of directly moving ahead to generate NILs for all the possible loci, I can first opt for a deficiency mapping study and then move on to NIL?

Hello Nikhil I am a bit more familiar with plant systems so apoplogies if I do not know about DH lines in Drosophila. Can you easily generate DH lines with Drosophila? If so, that is the fastest way to generate a population of what would be equivalent to a RIL population in order to determine the genetic architecture of whatever character you are studying, If you already know that there are two chromosomes that have a major effect on your character of interest, and you are not interested in the possible effect of the rest of the genome on your character, why not move to directly to deficiency mapping an then NILs (if there is need) to pin point your gene of interest?

Dear Nikhil,

I'm a plant geneticist; however, I may offer my two cents of suggestion. NILs are difficult and weak proposition in Drosophila as you have lab out-bred populations. RILs are therefore the next best thing. Even in RILs, please start with the initial ritual of looking out for parental polymorphism among your lines and select those which have the polymorphism for use as parents to generate series of RIL populations, extending Wagner's suggestion. If you can develop BC1F2 populations, thats still fine. If you try to inbreed too much, you may severely lose out many lines due to depression. As you have mentioned, since you are looking at gross architecture, you can do so by deficiency/substitution lines if available, or RILs are still very good if you do not have the former. Moreover, RILs populations are easy and quick to develop, maintain and study, be Drosophila or Arabidopsis. If you have parents with substitions/deficiencies in the trait, nothing like it for parental polymorphism. Never think of doubled haploids in Drosophila; Drosophila is not easy as plants!

@Margarita: well DH lines can be generated in drosophila but then will need a couple of crosses and does take a bit of time. But I am not aware of how easy is it in plants, going by the above comment by Vageeshbabu, it seems to be easier in plants than in flies.. But then, suppose I can generate DH lines with relative ease, what would be your suggestion?

@maggie: Thanks a lot for the help. Will contact you later in case I need further suggestions.

@vageeshbabu: Thanks for the answer but then regarding your statement ' if you try to inbreed too much" how do you exactly define/quantify that. The last time we set out with a huge number of isofemale lines and most of then crashed (probably due to inbreeding depression). Given that you are experienced in these methods, will be helpful if you can elaborate on how does one ensure there is no 'too much' of inbreeding? or How do i ensure the right levels of inbreeding? I know there is no definite answer for this but then would like to know about it.

The best reliable parameter of examining inbreeding depression (ID) is fecundity and survival rate of progenies. This is also experienced by you as stated. Although there are numerous genetic and molecular methods to quantify ID, practically all you can do easily is the variations in fecundity/sterility and survival of progenies in Drosophila (but then you maintain quantifiable records of different pair matings and their different progeny generations which will give you an approximate working idea). If it is easier for you to develop DHs in Drosophila, nothing like that. In fact, DHs are far more preferred and represent statistically better materials than RILs since each DH is itself a 100% homozygous RIL without the threat of residual recombination in further generations. As I had suggested earlier, instead of going for serial inbreedings, stop at BC1F2 and develop DHs out of this material. This should suffice your genetic studies. Even DHs of F2 are okay; however, try to generate a larger F2 population for each pair so as to get a more representative and statistically better and high resolution genetic analysis. I assume that you can generate BC1F2 populations and their respective DHs. If that is so, its more than sufficient for your work. For fine analysis, you can always use highly resolved regions after mapping.

Regards

Thank you @ all the discussants for sharing your knowledge with us, its wonderful.

Dear Dr KL Nikhil ,

Greetings and thank you for your question. Both methods could detect QTLs but for bi-parent you must have a wide parent in the traits under investigation and need time to develope these mapping population and this include F2:3, BC, DHLs or RILs mapping population. Both RILs and NILs came from bi-parent mapping populations

However for association mapping you must have a diverse collection from genotypes 100-200 genotypes.

Also, both need phenotyping and genotyping data

with best regards

Prof Dr Khaled F M Salem