Your question is based on the Babylonian Talmud that is more frequently studied than the Yerushalmi Talmud.
The reason we don't have a Gemara for most of the Mishnayot in Zeraim (Seeds) and Taharot (Purity) is because none was ever found among the manuscripts composed for the other four Orders of the Mishna (Sedarim). Most commentators suggest that the concepts and regulations pertaining to agriculture (Zeraim) and the laws of purity (Taharot) were not deemed applicable to Jewish life in Babylonia, and were therefore not recorded by the Sages there.
One might ask, then, if so why are there Tractates of Gemara for Seder Kodashim (Sacred Objects) which deals largely with the many procedures and rituals of Korbanot (Sacrifices), which were also no longer applicable at that time? The answer is that the Sages recorded these subjects and laws in the Gemara because of the concept that one who learns about the laws of a Korban is deemed (in a sense) to have actually offered the Korban.
