Word order in question with very long subject
Solution 1:
What might the consequences of the loss of diversity of plant genetic resources be?
What might be the consequences of the loss of diversity of plant genetic resources?
In the first question, the subject is the consequences of the loss of diversity of plant genetic resources. The interrogative word what is the complement of the verb BE. Because it has moved to the front of the sentence it has triggered subject auxiliary inversion, and we see might change places with the subject.
In the second sentence, what is the subject of the sentence. The noun phrase the consequences of the loss of diversity of plant genetic resources is the complement of the verb BE. Because what is already at the front of the sentence, it doesn't cause any inversion.
In short both sentences are perfectly grammatical.
We can make the difference clear by showing the following in situ versions of questions 1 and 2:
1'. The consequences of the loss of diversity of plant genetic resources might be what?
2'. What might be the consequences of the loss of diversity of plant genetic resources?
Sentence 2' has the same word order as sentence 2, because what is already in the subject position. In sentence 1', however, we see what in a position that would have been filled by a specific value or word in the corresponding declarative sentence. It therefore looks quite different from 1.