The underground reserve (root) has been an uncharted research territory with its untapped genetic variation yet to be exploited. Identifying ideal traits and breeding new rice varieties with efficient root system architecture (RSA) has great potential to increase resource-use efficiency and grain yield, especially under direct-seeded rice, by adapting to aerobic soil conditions. In this review, we tried to mine the available research information on the direct-seeded rice (DSR) root system to highlight the requirements of different root traits such as root architecture, length, number, density, thickness, diameter, and angle that play a pivotal role in determining the uptake of nutrients and moisture at different stages of plant growth. RSA also faces several stresses, due to excess or deficiency of moisture and nutrients, low or high temperature, or saline conditions. To counteract these hindrances, adaptation in response to stress becomes essential. Candidate genes such as early root growth enhancer PSTOL1, surface rooting QTL qSOR1, deep rooting gene DRO1, and numerous transporters for their respective nutrients and stress-responsive factors have been identified and validated under different circumstances. Identifying the desired QTLs and transporters underlying these traits and then designing an ideal root architecture can help in developing a suitable DSR cultivar and aid in further advancement in this direction.

Rice is an ideal crop for improvement of nitrogen use efficiency (NUE), especially with urea, its predominant fertilizer. There is a paucity of studies on rice genotypes contrasting for NUE. We compared low urea-responsive transcriptomes of contrasting rice genotypes, namely Nidhi (low NUE) and Panvel1 (high NUE). Transcriptomes of whole plants grown with media containing normal (15 mM) and low urea (1.5 mM) revealed 1497 and 2819 differentially expressed genes (DEGs) in Nidhi and Panvel1, respectively, of which 271 were common. Though 1226 DEGs were genotype-specific in Nidhi and 2548 in Panvel1, there was far higher commonality in underlying processes. High NUE is associated with the urea-responsive regulation of other nutrient transporters, miRNAs, transcription factors (TFs) and better photosynthesis, water use efficiency and post-translational modifications. Many of their genes co-localized to NUE-QTLs on chromosomes 1, 3 and 9. A field evaluation under different doses of urea revealed better agronomic performance including grain yield, transport/uptake efficiencies and NUE of Panvel1. Comparison of our urea-based transcriptomes with our previous nitrate-based transcriptomes revealed many common processes despite large differences in their expression profiles. Our model proposes that differential involvement of transporters and TFs, among others, contributes to better urea uptake, translocation, utilization, flower development and yield for high NUE.

Direct-seeded rice (DSR) production is the primary focus of this study, which explores the diversity of rice genotypes concerning their ability to withstand anaerobic germination conditions. Using advanced statistical analysis, a total of 250 rice cultivars were assessed for several anaerobic germination attributes. Significant variability was observed among genotypes for key traits including germination % (ARC14855, AG 387), shoot length and seedling dry weight, indicating potential donors for anaerobic germination tolerance. Trait association analysis, variability analysis, principal component analysis and cluster analysis were employed to uncover the genetic and phenotypic factors influencing anaerobic germination tolerance. The genotypes of cluster III could be used as donors for anaerobic germination studies, as the genotypes have revealed high average values for all the traits. The findings underscore the importance of genetic variability and heritability in breeding resilient rice varieties suited for DSR cultivation, offering valuable insights for enhancing rice cultivation practices in the face of challenges such as water scarcity and labour shortages. To improve the sustainability and productivity of paddy production systems, this research advances rice breeding procedures that aim to create varieties tolerant to anaerobic conditions.

Speed breeding (SB) has emerged as a technology that helps in developing new, improved crop varieties by dramatically shortening the time period taken for their generation. This is achieved by optimizing environmental parameters such as photoperiod, temperature and soil moisture. This process enables the development of multiple generations per year, thereby speeding up the development of homozygous lines and elite cultivars. Integration with modern molecular tools, including marker-assisted selection (MAS) and genomic selection (GS) with SB, enhances the precision and efficiency of trait selection, leading to faster genetic gain. Despite these advantages, adoption of this technique faces challenges such as infrastructure demands, shortage of skilled personnel, energy requirements and regional disparities in technology access. Addressing these bottlenecks through targeted investment, capacity building and policy support is required to harness SB technique for global food security. This review elucidates the principles, applications and limitations of SB and highlights its pivotal role in modern plant breeding and sustainable agriculture.