In Genotype, do the market rows for Tools, Pea plants and Assistants refill immediately or only at the end of each round?
Not until the end of the round. Pg. 10 of the rulebook:
(Assistant Cards are not refilled until the end of the Round.)
And pg. 12:
Discard the remaining Pea Plant Cards, Tool Cards, and Assistants. Refill Tool and Pea Plant Cards based on player count (see p. 3) and refill 3 face-up Assistants.
And reiterated on the "reminders and clarifications" section on pg. 13:
Tool Cards and Pea Plant Cards are only refilled during the End of the Round Reset, not when taken.