Allele Mining of Seed-Related Genes Reveals Early movement, Selection and Adaptation of Asian Rice Landraces
Journal
Rice (New York, N.Y.)
Journal Volume
18
Journal Issue
1
Start Page
95
ISSN
1939-8425
Date Issued
2025-10-21
Author(s)
Wu, Cheng-Chieh
Tseng, Yi-Tzu
Tsai, Yuan-Ching
Liu, Chun-Kai
Huang, Lin-Tzu
Hsu, Tze-Fu
Chen, Yi-Fang
Dai, Nai-Chiang
Wang, Ying-Hao
Lo, Jeng-Chung
Shung, Dah-Pyng
Wu, Chih-Wen
Tsang, Chen-Hwa
Li, Kuang-Ti
Chu, Whei-Lee
農業部農業試驗所
Wu, Dong-Hong
農業部農業試驗所
Chang, Su-Jein
Chen, Kai-Yi
Chiou, Wan-Yi
Yu, Su-May
Ho, Tuan-Hua
Sagart, Laurent
Yang, Jun-Yi
Hsing, Yue-Ie C
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.
Subjects
Adaptation
Carbonated rice grain
Genetic diversity
Population structure
Rice grain-related genes
Selection
Publisher
Springer
Type
journal article