In case a technology is protected and the institute is serious about these rights, an agreement may have to be concluded with the patent holder. Such licenses are the result of negotiations between the user and the right holder and may contain almost any provision that the two parties agree upon. Such licenses are commonly granted for research only; i.e. during the research processes the technology may be used, but as soon as something comes out that may be commercialized, the right holder reserves the right to re-negotiate the license contract.
In the short run this is very good for the scientist; but in the long run, the paten holder may reap the main benefits: at the ‘end’ of the research process (s)he is more able to gauge the commercial value than at its start, so he will be able to negotiate a fair profit when the research resulted in something that may be widely applied. Perhaps even a greater danger is that the provider of the technology may never lift the "research only" provision because it may fear, for example, that the technlogy will escape from its control. This would leave the whole research project without a product (and a waste of energy).
On the other hand, at that stage, the breeder would very much like to take his new varieties to market, and relatively easily agree with less favourable benefit sharing arrangements. Such agreements may include monetary and non-monetary benefits for the patent holder.
Monetary benefits generally include royalties. Non-monetary restrictions may for example deal on the geographic area (the breeder gets the right to commercialise the variety in the country where he resides, but the patent holder gets all the rights in the rest of the world), with the time (the first 5 years, the breeder may commercialise it, after that the patent holder will claim license fees) the use of technology (the breeder is allowed to use this technology, but when the patent holder develops an improvement, the breeder is forced to use that improved technology), etc.
A license contract is a civil law contract so parties may agree on virtually anything that they choose to agree on within the boundaries of national law (e.g.in the EU it is not allowed to use IPRs for geographic segmentation of markets - it is important to check with a lawyer locally when designing such license contracts). In reality, many patent holders have better negotiation skills than public research institutes, and the latter need to be aware of this difference.