In addition to the potential end-user drawbacks discussed earlier, for the plant breeder, polyploid induction has its own set of potential problems.
Poisons: Polyploid induction chemicals are mitotic spindle inhibitors. As such, they are inherently cytotoxic, potentially mutagenic, and potentially carcinogenic. That said, with the same care, safe use practices, and personal protective devices that you would use in any chemical laboratory, any breeder can induce polyploids.
Conversion problems: For some species, inducing polyploids is simple and straight-forward. For others, it can be quite frustrating. You will find different species sensitivities to various polyploid induction chemicals. You will find different species sensitivities to various additives such as surfactants used to enhance the penetration of the chemicals through the plant cell wall and membrane. You will find different species responses to the stage at which you dose the plant. Each of these issues will be addressed in a later post, one in which I describe my conversion protocols.
Fertility or fecundity problems: Induced polyploids frequently display both decreased fertility and decreased fecundity, especially in early generations. When you double the chromosome number of a plant, there become more opportunities for the chromosomes to pair up incorrectly during meiosis. Until you go through enough seed generations to eliminate these pairing errors, fertility is going to be negatively affected. The good news is: you can readily select for increased fertility. However, decreased fecundity may or may not be so easy a problem to select against. Why not? Polyploid seeds are typically larger than diploid seeds, and as such, contain more biomass. Under ideal conditions, partitioning of plant biomass into seeds is likely to favor more and smaller seeds, rather than fewer and larger. It is as though the plant can produce a finite amount of biomass for seed production, and if it is making larger seeds, it is also making fewer of them.
If your crop is vegetatively-propagated, this is probably not an issue. If your crop is seed-produced, however, decreased fecundity could be a serious limitation. Especially if your crop is being hand-pollinated as an F1 hybrid.
Genetic instability: Forgive the anthropomorphism, but not all plant species seem to "like" being polyploid. More than just taking a few seed generations to clean up the genetic junk, these species tend to be very unstable when doubled, and during subsequent seed generations continue to eliminate the additional chromosomes. Unfortunately, as this occurs, extra chromosomes (aneuploidy) or extra pieces of chromosomes are likely to be working their way through your breeding project. You may think that you are selecting a particular phenotype, only to discover that your desired phenotype only occurs in a particular aneuploid form, and that that form is neither seed-stable nor vegetatively-stable.
"Mixoploid production": One of the problems with inducing polyploids is that plants are comprised of multiple layers of cells, and that you can convert one layer while leaving the rest at a diploid level. People often (and informally) refer to these incomplete conversions as "mixoploids".
Technically, a mixoploid is a cytochimera. Imagine that you are wearing a glove on your hand. In a plant chimera, the glove may be of one genotype (or one ploidy) while your hand is a different genotype. This is often the physical explanation for plant variegation. But it is also very possible to have the outer tissue layer (or layers) of a plant be at a different ploidy level than the inner tissue layer(s).
Imagine that you are attempting to convert a vegetative bud. You apply the chemical to the outside of the bud. If the chemical does not penetrate deep into the bud and convert the actual meristematic cells, you may convert only the outer layers, leaving the innermost layers diploid. In my hand-in-glove example, the glove would be tetraploid, while your hand --- the central tissue --- remains diploid.
Why is this a problem? Germ cells --- ovules and pollen --- are produced by the inner cell layers. If your goal is to breed with your induced polyploid, you need the tissues producing germ cells to be converted. Otherwise you have a plant that looks like a tetraploid, but breeds like a diploid --- and does not transmit the tetraploid condition to the next generation. Let me repeat that statement: a ploidy cytochimera can look like a tetraploid but breed like a diploid.
Please realize that unless you can determine the actual ploidy of these inner cell layers (and there will be posts on ploidy verification coming), you cannot identify a cytochimera from a "solid" conversion. A solid conversion is one in which all cell layers are converted --- the ideal result. Unfortunately, cytochimerae are not stable, and if a plant is not stable, it should neither be protected nor released to market. Cytochimerae can sport to solid diploid forms; they can sport to solid polyploid forms; they can sport to a form with is outside-diploid, inside-tetraploid. And as a breeder, you may or may not be able to distinguish these forms.
Polyploid genetics are more difficult: Polyploids are generally more challenging to work with as a breeder. In the simplest consideration, there are now 4 alleles segregating at a tetraploid level compared to 2 at the diploid. More possibilities for recombination are good, but finding those possibilities in a segregating population requires growing out much larger populations, and thus, much more bench space or field space, and much more labor for the observation of the increased population size. More, in order to find the desired phenotypes, the phenotypes resulting from additive effects of the additional alleles available in a polyploid are very likely to require more generations of recombination. More space, more labor, more time. Polyploid breeding is inherently slower than diploid breeding.