J Syst Evol

• Research Article •    

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

Heng-Ling Zhou1,2†, Lei Wang1,3,4†, Yun-Xia Yue1, Zhi Luo1,2, Shun-Jie Wang1,2, Li-Guo Zhou1,3,4, Li-Jun Luo1,2,3,4,5, Hui Xia1,2,3,4,5*, and Ming Yan1,3,4*   

  1. 1 Shanghai Agrobiological Gene Center, Shanghai 201106, China;
    2 College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China;
    3 Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China;
    4 Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai 200240, China;
    5 National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China
    Heng-Ling Zhou and Lei Wang contributed equally to this work.
    *Authors for correspondence. Hui Xia. E-mail:hxia@sagc.org.cn;Ming Yan. E-mail:myan@sagc.org.cn
  • Received:2023-07-12 Accepted:2023-11-29 Online:2024-01-25

Abstract: 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.

Key words: ecotypic adaptation, nitrogen use efficiency, parallel evolution, upland rice