Allele Mining of Seed-Related Genes Reveals Early movement, Selection and Adaptation of Asian Rice Landraces

Abstract

Background Asian cultivated rice is one of the most important crops in the world. According to archaeological studies, carbonated rice grains in Taiwan were quite small before 3300 BP, but rice seeds from excavated sites became much larger later on. In the current study, we explored seed size differences by using genome re-sequencing, followed by allele mining of several seed- and adaptation-related genes to propose the early movement, selection and adaptation of Asian rice landraces. Results Taiwan indigenous people are descendants of early Austronesians. We collected 116 rice accessions from Taiwan indigenous villages and used whole-genome re-sequencing to explore the mutations, early movement, selection and adaptation of world rice landraces together with landraces collected from all rice-growing areas in Asia. The morphology of Taiwan indigenous rice accessions featured huge variations, and the most primitive accessions were tropical japonica. Also, some grain size-related genes could explain grain size differences. Allele analyses revealed that some mutations in grain morphology-controlling genes may have been targets for selection. Mutation, movements, selection and adaptation occurred in early Asian rice cultivation. Our findings do not conflict with the “out-of-Taiwan” theory. Conclusion The grain sizes of all rice subgroups studied had been selection targets, and seed size gradually changed along with the improvement of rice cultivation, via introgression and expansion (i.e., by human beings), over thousands of years. Supplementary Information The online version contains supplementary material available at 10.1186/s12284-025-00854-9.