Rice Genomics and Genetics 2024, Vol.15, No.5, 287-308 http://cropscipublisher.com/index.php/rgg 300 3.2 Mechanisms of anaerobic germination in rice Anaerobic germination in rice involves several genetic and physiological adaptations that allow seeds to germinate and seedlings to grow under low oxygen conditions. Key genes involved in this process include those regulating glycolysis and gluconeogenesis pathways, which are activated to generate energy under anaerobic conditions (Lin et al., 2019). The presence of transcription factors such as ERFs (Ethylene Response Factors) and WRKYs also plays a crucial role in mediating responses to anaerobic stress by regulating the expression of genes involved in energy metabolism and stress responses (Naithani et al., 2023). These mechanisms collectively enable rice seeds to germinate and seedlings to elongate their coleoptiles, facilitating survival in flooded conditions. 3.3 Genetic regulation of root system adaptations to flooding The development of adventitious roots is a critical adaptation for rice plants under flooding conditions. Genetic traits associated with the formation of these roots have been linked to specific quantitative trait loci (QTLs) such as those on chromosomes 1 and 12, which promote the development of aquatic adventitious roots (AAR). These roots exhibit distinct morphological and anatomical traits that enhance their ability to function in submerged environments. For instance, the formation of thicker roots with higher elongation capacity and desiccation tolerance is a key adaptation that allows rice plants to survive prolonged submergence (Lin et al., 2022). Additionally, the regulation of root system architecture by genes such as OsLAZY1 and IL2 is crucial for maintaining root functionality under flooded conditions (Naithani et al., 2023). 3.4 Role of transcription factors and signaling pathways in flood response Transcription factors and signaling pathways play pivotal roles in orchestrating the flood response in rice. A network of 57 transcription factors, including OSH1, OSH15, OSH71, Sub1B, ERFs, WRKYs, NACs, and TCPs, has been identified as key regulators of seed germination, coleoptile elongation, and submergence response (Naithani et al., 2023). These transcription factors interact with each other and with other proteins to regulate the expression of target genes involved in flood tolerance. For example, the ERF66 and ERF67 transcription factors are direct targets of Sub1A-1 and are upregulated in response to submergence, mediating the expression of genes that enhance submergence tolerance (Oe et al., 2021). Additionally, signaling pathways involving ethylene, gibberellins, and abscisic acid are crucial for modulating the plant's growth and stress responses under flooded conditions (Oladosu et al., 2020). The genetic basis of flood tolerance in rice involves a complex interplay of genes, transcription factors, and signaling pathways. Key genes such as those in the SUB1 locus, along with mechanisms for anaerobic germination and root system adaptations, play crucial roles in enabling rice plants to survive and thrive under submergence. Understanding these genetic and molecular mechanisms provides valuable insights for breeding and developing flood-tolerant rice varieties, which is essential for ensuring stable rice production in flood-prone regions (Gonzaga et al., 2017; Barik et al., 2020). 4 Meta-analysis Results 4.1 Distribution and frequency of flood tolerance genes across rice varieties Flood tolerance genes in rice, such as Sub1A, have been widely studied and incorporated into various rice varieties to enhance their resilience to submergence. For instance, the Sub1A gene has been successfully transferred into drought-tolerant japonica rice DT3, resulting in progenies with enhanced submergence stress tolerance (Wu et al., 2021). Additionally, genome-wide association studies (GWAS) have identified significant single nucleotide polymorphisms (SNPs) associated with flood tolerance traits, such as coleoptile length during germination under flooded conditions, across diverse indica rice varieties (Zhang et al., 2017). The distribution of these genes varies significantly among different rice genotypes, with some varieties showing a higher frequency of beneficial alleles for flood tolerance (Thapa et al., 2022). 4.2 Impact of identified genes on agronomic traits such as yield, plant height, and survival rate The incorporation of flood tolerance genes like Sub1A has shown a positive impact on several agronomic traits. For example, rice lines carrying the Sub1A gene exhibited higher survival rates (92%~96%) compared to their
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