Population structure dynamics of Taiwan rice accessions over thousands of years as revealed by archaeological, morphological and genome sequencing information

Abstract

Abstract Background Cultivation of rice (Oryza sativa) started in Taiwan about 5000 years ago. Here we studied changes in the rice population during this period by using archaeological, morphological, genetic and genomic strategies. We studied the grain size changes of carbonized rice from excavated sites. We also revealed the variations in landraces collected from the indigenous villages and landraces that arrived in Taiwan from southern China about 400 years ago. Some modern varieties were also used in the current study. Results The very early cultivated rice must have been temperate japonica type, and the seeds were relatively small. Rice seeds became relatively bigger around 1500 BP, with some indica or tropical japonica ones. Most, if not all, of the indica rice were not primitive types, suggesting they arrived in Taiwan rather late. Together, temperate, subtropical, tropical japonica and indica rice have been cultivated by indigenous people for a long period, with all in upland practice. However, only indica landraces were cultivated in the plain region from the early 17th century to about 100 years ago, when japonica rice accessions become dominant. We illustrated huge differences in genetic diversity among the subpopulations of Taiwan rice accessions, and many of these lines showed stress resistance to drought, flooding and ABA treatments. Conclusion We show how civilization, human migration, taste preference, natural introgression and breeding programs have shaped the population structure of Taiwan rice accessions over thousands of years. We also indicate that Taiwanese indigenous peoples and traditional farmers have kept the rice landraces for hundreds and up to thousands of years. With many old traits preserved, they are good resources for future breeding programs.