SignificanceThis paper contributes to understanding how traditional agriculture can maintain large genetic diversity. We quantify the effects of traditional farmer activities on the genetic diversity of an indigenous common carp in the 1,200-y-old agriculture heritage rice−fish system. We show that small farmer households interdependently incubating fish fry for their rice−fish farming shape the genetic pattern and help to maintain high genetic diversity of this local common carp. We also show how the traditional practice of mixed culturing of diverse color types potentially promotes genetic diversity. We suggest that the locally adapted ways of traditional farmers obtaining and using local genetic resources for their farming play an important role in the biodiversity of farmed crops and animals. It can become a “hotspot” for genetic diversity conservation in agriculture.
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