Molecular Plant Breeding 2025, Vol.16, No.3, 165-179 http://genbreedpublisher.com/index.php/mpb 168 resistance in upland rice. Recently, Wang et al. (2024) evaluated the drought resistance of 541 rice accessions in the field and identified 25 upland rice varieties, identified 80 key candidate genes, and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Similarly, Wu et al. (2019) characterized ENHANCED DROUGHT TOLERANCE 1 (EDT1), a member of rice’s bZIP transcription factor family, which positively regulates drought tolerance. This gene offers promising targets for breeding drought-resistant rice varieties. Lou et al. (2023) reported that OsSAPK3 is significant in both ABA-dependent and ABA-independent drought stress responses. Furthermore, OsSAPK3 has the potential to enhance rice yield by indirectly regulating tiller number and grain size. These findings offer valuable insights for developing drought-resistant rice varieties. 3.3 Comparative genomics and cross-species analysis Comparative genomics and cross-species analysis have provided insights into the conservation of drought resistance mechanisms across different species. A study on comparative mapping within and across species identified three conserved genomic regions associated with various physiological responses to drought in several grass species, suggesting that these regions have been conserved during genome evolution and could be applied across species for improving drought resistance in cereal crops (Zhang et al., 2001). Another study conducted a comparative transcriptome analysis between drought-tolerant and drought-susceptible rice genotypes, revealing genotype-dependent genes responsible for drought tolerance. This analysis identified specific pathways, such as the α-linolenic acid metabolic pathway, which were significantly up-regulated in drought-tolerant genotypes (Lenka et al., 2011). These findings underscore the potential of leveraging conserved genetic regions and pathways for breeding drought-resistant rice varieties. 4 Functional Mechanisms of Drought Resistance Genes 4.1 Gene regulation and expression under drought stress Drought stress triggers a complex network of gene regulation and expression in rice with DEGs identified under drought conditions through various studies. A meta-analysis of microarray data revealed 643 upregulated and 677 downregulated genes in rice under drought stress. These genes are associated with responses to abiotic stimuli, water deprivation, and ABA signaling (Figure 1) (Gupta et al., 2021; Soltanpour et al., 2022). Figure 1 Workflow of the network-based machine learning framework (Adopted from Gupta et al., 2021)
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