Molecular Soil Biology 2025, Vol.16, No.2, 91-102 http://bioscipublisher.com/index.php/msb 91 Case Study Open Access Breeding Rice Varieties for Low Nitrogen Environments QifuZhang1 , Danyan Ding2 1 Hier Rice Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China; 2 Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, China Corresponding email: qifu.zhang@hitar.org Molecular Soil Biology, 2025, Vol.16, No.2 doi: 10.5376/msb.2025.16.0010 Received: 23 Feb, 2025 Accepted: 05 Apr., 2025 Published: 23 Apr., 2025 Copyright © 2025 Zhang and Ding, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Zhang Q.F., and Ding D.Y., 2025, Breeding rice varieties for low nitrogen environments, Molecular Soil Biology, 16(2): 93-102 (doi: 10.5376/msb.2025.16.0010) Abstract Nitrogen is an essential nutrient for rice growth, but the excessive use of nitrogen fertilizers has led to environmental degradation, increased costs, and diminishing returns. Root structure and the ability to maintain chlorophyll content are key indicators of nitrogen use efficiency (NUE), while genes such as OsTCP19, OsNAC68, and TOND1 play important roles in nitrogen uptake and assimilation. Field and hydroponic trials, combined with high-throughput phenotyping technologies, are effective in evaluating genotypic variation and selecting superior varieties. Breeding strategies include conventional selection, marker-assisted selection (MAS), genomic selection (GS), and the introgression of favorable traits from wild or traditional rice varieties. The case of Swarna-Sub1 demonstrates the potential of integrated breeding for enhancing both stress resistance and NUE. Despite significant progress, breeding efforts still face challenges such as balancing high yield with NUE, shortening breeding cycles, and adapting to diverse ecological zones. Integrating genetic improvement with sustainable agronomic practices—such as precision fertilization and organic fertilizer application —can reduce nitrogen input while maintaining yield, offering a promising path toward green, economical, and efficient rice production. Keywords Nitrogen use efficiency (NUE); Low nitrogen stress; Rice breeding; Genome editing; Sustainable agriculture 1 Introduction Nitrogen is one of the essential nutrients for rice and has a great impact on yield and quality. Since the "Green Revolution", the large-scale use of nitrogen fertilizers has indeed increased yields, but it has also caused problems such as environmental pollution, resource waste and rising costs (Lee, 2021; Wang et al., 2021). Therefore, improving the efficiency of nitrogen fertilizer use has become a key issue that needs to be urgently addressed in global rice cultivation. The process of rice absorbing and utilizing nitrogen is controlled by multiple genes, involving root structure, related enzyme activity, and signal regulation mechanisms in the body (Li et al., 2022a; Lee, 2021; Kasemsap and Bloom, 2022). In recent years, with the development of molecular breeding and genomic technologies, researchers have found some genes and quantitative trait loci related to nitrogen efficiency (Li et al., 2022a; Xin et al., 2021; Liu et al., 2021). In many developing countries, farmers often use nitrogen fertilizers poorly or even suffer from nitrogen shortages due to high prices, unstable supply or lack of technical guidance (Liu et al., 2021; Jyoti et al., 2024). Excessive use of nitrogen fertilizers not only increases economic pressure, but also easily causes environmental problems such as water pollution and greenhouse gas emissions (Lee, 2021; Wang et al., 2021). In areas with poor land and limited inputs, rice often faces low nitrogen stress (Castro-Pacheco et al., 2024; Jyoti et al., 2024). Some rice varieties can maintain good growth and yield even in the absence of sufficient nitrogen fertilizers. These varieties have strong low nitrogen tolerance (Liu et al., 2021; Ajmera et al., 2022; Qi et al., 2023; Zhou et al., 2025). This is mainly due to their more reasonable root structure, more efficient nitrogen absorption and assimilation ability. For example, optimizing the root angle, root number and distribution can significantly improve the absorption efficiency and yield performance in a low nitrogen environment (Ajmera et al., 2022; Zhou et al., 2025). At present, scientists have discovered some key genes and QTLs related to low nitrogen, such as OsTCP19 and OsNAC68, which provide strong support for the breeding of new rice varieties with high nitrogen efficiency (Liu
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