If you cannot judge the difference based on phenotype alone, you should be easily able to distinguish the nucellar seedlings from zygotic seedlings using molecular markers. The nucellar seedlings' genotypes will be identical to the seed parent, while the zygotic seedlings will be hybrids, containing half their alleles from the pollen parent.

Dr. Hoggard in case molecular markers are not option and we have to decide by phenotype only?

Infact , we talk about  polyembryonic nature of fruit species, but our field experience says something else. I can share our experience with citrus. we hardly see many seedlings from one seed of either acid lime or rough lemon. In the process , zygotic seedlings hardly gain any growth , just ruminant growth, while nucellar ones attain very good steady growth rate. therefore , field option based phenotypic character is still by far the best option . On the other hand , use of  molecular markers would be costlier and seems comparatively irrelevant .

Vikas said, "In Jamun there is no phenotypic differences in the growth of both nucellar and zygotic seedling". If there is no phenotypic difference, then by definition there is no way to distinguish the seedlings visually. His experience with Jamun must be different than yours with citrus, Anoop, making differentiation based on growth rate irrelevant (to borrow your slightly arrogant term).

Some other ideas:

Is the pollen parent known? Is it morphologically different from the seed parent? If so, then you may be able to distinguish them phenotypically at the stage of development when that difference manifests itself.

Could you perform isozyme analysis?

If the pollen parent is distantly related, you may be able to identify differences in chromosome pairing between the zygotic and nucellar seedlings.

What is the current state of art application to differentiate nucellar seedlings from zygotic ones , a cost effective method..?

Why are  zygotic seedlings  so weak , because they do not represent true-to-type to parent seedlings ..

Isozyme analysis will surely help . you are right Jack...but , again question comes to cost effectiveness and accessability to end users..?

My intention was merely to provide possible solutions to Vikas' problem. If his zygotic seedlings were weak, then he would have no problem differentiating them from nucellar ones.

I don't have any better suggestions, so I am going to excuse myself from this discussion. I wish you both the best of luck with your research!

Dear Mr. Vikas,

You may look for quantitative differences in phyto-chemicals between nucellar and zygotic seedlings at relatively early stages of seedling development. I am not sure which phytochemicals to look for.

Unfortunately, at field application level , differences in vigour of seedlings is still considee quite effective in polyembryonic seedlings. In nucellar selection, seedlings of uniform growth are selected and others with varying growth vigour are rogued out

Anoop Kumar Srivastava sir that practice is followed in citrus what about other fruit crops.

I think , this is the easiest method followed in all polyembryonic crops . Use of molecular markers is really difficult , where such mass scale production is required....

I agree with the answer of Dr AK Srivastava.

Why do we do this exercise for rovuing out the zygotic seedlings and picking up the only nuclear seedlings. We do this to produce true- to - type plant of mother tree...

In field where so large scale of seedlings are propagated, any other method , right now atleast looks impractical , despite the fact , it is often difficult ..

Vegetatively propagated crops including fruit species, in general, are highly heterozygous, and upon inbreeding the zygotic individuals display considerable extent of inbreeding depression. In polyembryonic cases, the ensuing seedling derived from nucellus cells will generically be exactly like its mother plant, maintaining the same degree of heterozygosity, and thereby expressing heterosis in terms of rate of growth, early vigor, etc. In contrast, zygotic embryo will have different genetic constitution compared to its mother plant, and suffers the ill effects of inbreeding associated with such crops. Such embryo will have slower growth. These phenotypic markers, which are highly cost effective, can be used to distinguish two types of seedlings during emergence and early seedling stages as Dr Srivastava has mentioned for citrus species, and that will also be true for Jamun as well.

If given the condition that both embryos have emerged identically, which can hardly be the case, biochemical and/or molecular markers can be used to distinguish them. However, it will not be a cost effective approach.