Genetic Markers - Many genetic marker systems are used for recognizing the haploids. The basic principle involved is that the hybrids and nonhybrids should differ, so that any failure of fertilization and parthenogenetic development of embryo can be recognized in the progeny at the seed stage, seedling stage or adult plant stage.

For instance, if a female parent in a cross carries a recessive marker and is pollinated by dominant stock, then any recessive progeny would be generally a maternal haploid, although possibility also exists of its being a diploid of one of the following types

This technique of genetic markers has been extensively used in developing maize monoploids. Most extensively used markers include a 1 for brown coloured aleurone, plant and root and 1g for liguleless, their corresponding dominant markers being 'A' for purple colour and '1g' for liguled character.

If the female parent carries 'a' and/or 1g, then the monoploids will be recognized by lack of purple colour and/or ligule, in crosses with male parent carrying 'A' and/or '1g' Another critical marker gene is 'R' allele (Rnj-cudu), which produces deep pigmentation of aleurone, and thus allows screening at the dormant seed stage. Other markers included purple plumule (A, Put, Pu2), scutetllum colour (A, C, R genes, and S1, S2 and 53 genes), and purple coleorrhiza (Pc1, PC2, PC3 and PC4).

In most of the above cases when genetic markers are used, 90-98% of the progeny can be discarded rather early and a very high frequency of haploids is recovered in the remaining population.

The above technique of using genetic markers is particularly useful for the development of inbred lines in maize, but in crops like barley and wheat which are self pollinated and where doubled haploids need to be used for cultivation, the availability and utility of genetic markers may be limited.