Independent genetic differentiation between upland and lowland rice ecotypes within japonica and indica subspecies during their adaptations to different soil‐nitrogen conditions

• Published in: Journal of systematics and evolution : JSE 2024-09, Vol.62 (5), p.915-927
• Main Authors: Zhou, Heng‐Ling, Wang, Lei, Yue, Yun‐Xia, Luo, Zhi, Wang, Shun‐Jie, Zhou, Li‐Guo, Luo, Li‐Jun, Xia, Hui, Yan, Ming
• Format: Article
• Language: English
• Subjects: Adaptation; Ammonium; Association analysis; Differentiation; Ecotypes; ecotypic adaptation; Environmental factors; Gene mapping; Genes; Genetic analysis; Genomic analysis; Nitrates; Nitrogen; nitrogen use efficiency; parallel evolution; Quantitative trait loci; Rice fields; Soil improvement; Soils; upland rice
• ISSN: 1674-4918; 1759-6831
• DOI: 10.1111/jse.13046

The soil‐nitrogen condition, which differs greatly between paddy fields (mainly in the form of ammonium, NH4+) and dry fields (mainly in the form of nitrate, NO3−), is a main environmental factor that drives the adaptive differentiation between upland and lowland rice ecotypes. However, the adaptive differentiation in terms of the nitrogen use efficiency (NUE) between upland and lowland rice has not been well addressed. In this study, we evaluated NUE‐related traits among rice landraces as well as the genetic differentiation between NUE‐associated genes and quantitative trait loci (QTLs). The japonica upland and lowland rice ecotypes showed large differences in their NUE‐related traits such as the absorption ability for NH4+ and NO3−. The indica upland and lowland rice exhibited similar performances when cultivated in solutions containing NH4+ or NO3− or when planted in paddy or dry fields. However, the indica upland rice possessed a greater ability to absorb NO3−. We identified 76 QTLs for 25 measured traits using genome‐wide association analysis. The highly differentiated NUE‐associated genes or QTLs between ecotypes were rarely shared by japonica and indica subspecies, indicating an independent genetic basis for their soil‐nitrogen adaptations. We suggested four genes in three QTLs as the candidates contributing to rice NUE during the ecotypic differentiation. In summary, the soil‐nitrogen condition drives the adaptive differentiation of NUE between upland and lowland rice independently within the japonica and indica subspecies. These findings can strengthen our understanding of rice adaptation to divergent soil‐nitrogen conditions and have implications for the improvement of NUE. The upland and lowland rice ecotypes were adapted to agroecosystems with contrasting soil‐nitrogen conditions. Upland and lowland ecotypes are independently differentiated within japonica and indica subspecies, resulting in rarely shared genetic bases and different appearances in the ability of NH4+/NO3− uptake.