Defining breeding goal(s)
The first priority – it's vital to know what you are trying to achieve.
It is probably not possible to fix every problem all at once, so it's important to decide what is the most important trait to be improved, and make a list of priorities.
If (for example) a variety has suddenly become susceptible to a disease but is otherwise well liked by the farmer and the consumer, then the priority will probably be to solve the resistance problem.
If (another example) the most important constraint to productivity is drought, then a high priority could be to improve the drought tolerance of the crop.
If (a third example) you are trying to improve a crop which at the moment is grown locally as landraces, you will need to understand what are the most important traits in the opinion of the farmers and the consumers. Often this involves end-use quality rather than yield. But it may be that you are competing with other breeding programmes, and that you need yield to be the #1 priority.