Population genomics of the rice landrace Acuce reveals exceptional dynamics of immune receptors
Abstract
In cultivated plants such as Oryza sativa, landraces harbour high levels of diversity, in sharp contrast with genetically uniform modern varieties. The Yuanyang terraces (China) are renowned for traditional farming involving landraces and low disease incidence. To understand the molecular basis of these resistance levels, we explored the genomic diversity of Acuce, one of the oldest landraces in the region. Based on whole-genome resequencing of over 200 Acuce plants, we evaluated the diversity of immunity and agronomical genes with respect to the rest of the genome. In parallel, we analysed the genetic basis of pathogen resistance and agronomical traits. Acuce exhibits high levels of diversity, reaching 38% of the worldwide levels. We uncovered an excess of diversity and signatures of balancing selection associated with immunity genes, in contrast with agricultural traits. Furthermore, cultures of mixed genotypes exhibited superior performances for both pathogen resistance and agricultural traits. We showed that, within one single landrace, traditional farmer practices may have favoured agronomically beneficial traits, while diversity in pathogen resistancerelated genes has been maintained. However, the extent to which this maintenance reflects active selection versus correlated outcomes of socio-cultural practices or pathogen-driven balancing selection remains to be determined. This study elucidates the complex interplay between genetic diversity, natural selection related to pathogens, and selection for agricultural traits within traditional landraces, providing insights into sustainable agricultural practices in diverse cropping systems.
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BibTeX
@article{mita2026population,
title = {{Population genomics of the rice landrace Acuce reveals exceptional dynamics of immune receptors}},
author = {Stéphane de Mita and Shengchang Duan and Xiang Li and Rémi Pélissier and Laura Mathieu and Jingyu Li and Linna Ma and Zihang Li and Jingjing Liao and Xiahong He and Youyong Zhu and Chengyun Li and Yang Dong and Jean-Benoit Morel and Huichuan Huang},
journal = {Plant Diversity},
year = {2026},
month = sep,
doi = {10.1016/j.pld.2026.08.010},
url = {https://hal.science/hal-05765515v1},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Population genomics of the rice landrace Acuce reveals exceptional dynamics of immune receptors
AU - Stéphane de Mita
AU - Shengchang Duan
AU - Xiang Li
AU - Rémi Pélissier
AU - Laura Mathieu
AU - Jingyu Li
AU - Linna Ma
AU - Zihang Li
AU - Jingjing Liao
AU - Xiahong He
AU - Youyong Zhu
AU - Chengyun Li
AU - Yang Dong
AU - Jean-Benoit Morel
AU - Huichuan Huang
PY - 2026
DA - 2026/09/12
JO - Plant Diversity
DO - 10.1016/j.pld.2026.08.010
UR - https://hal.science/hal-05765515v1
AB - In cultivated plants such as Oryza sativa, landraces harbour high levels of diversity, in sharp contrast with genetically uniform modern varieties. The Yuanyang terraces (China) are renowned for traditional farming involving landraces and low disease incidence. To understand the molecular basis of these resistance levels, we explored the genomic diversity of Acuce, one of the oldest landraces in the region. Based on whole-genome resequencing of over 200 Acuce plants, we evaluated the diversity of immunity and agronomical genes with respect to the rest of the genome. In parallel, we analysed the genetic basis of pathogen resistance and agronomical traits. Acuce exhibits high levels of diversity, reaching 38% of the worldwide levels. We uncovered an excess of diversity and signatures of balancing selection associated with immunity genes, in contrast with agricultural traits. Furthermore, cultures of mixed genotypes exhibited superior performances for both pathogen resistance and agricultural traits. We showed that, within one single landrace, traditional farmer practices may have favoured agronomically beneficial traits, while diversity in pathogen resistancerelated genes has been maintained. However, the extent to which this maintenance reflects active selection versus correlated outcomes of socio-cultural practices or pathogen-driven balancing selection remains to be determined. This study elucidates the complex interplay between genetic diversity, natural selection related to pathogens, and selection for agricultural traits within traditional landraces, providing insights into sustainable agricultural practices in diverse cropping systems.
SN - 2468-2659
ER -