Rice Genomics and Genetics 2024, Vol.15, No.5, 287-308 http://cropscipublisher.com/index.php/rgg 299 Figure 1 Statistical analysis and candidate region estimation of seq-rs2699 and seq-rs2701 (Adopted from Zhang et al., 2017) Image caption: (A) Haplotypes consist of the two significant SNPs, Numbers indicates the amounts of corresponding accessions; (B) Phenotypic effect of each haplotype; (C) Local manhattan plots and LD heatmap around the peak on chromosome 6, the candidate region estimated usingr2>0.6 (Adopted from Zhang et al., 2017) 3 Genetic Basis of Flood Tolerance in Rice 3.1 Overview of genes associated with submergence tolerance Submergence tolerance in rice is primarily governed by the SUB1 locus, which includes the genes Sub1A, Sub1B, and Sub1C. These genes have been extensively studied for their role in enabling rice plants to survive prolonged periods of submergence. The Sub1A-1 allele, in particular, has been identified as a key player in conferring submergence tolerance, as seen in the variety FR13A (Oe et al., 2021). The SUB1 locus operates by limiting elongation growth during submergence, thereby conserving energy and enhancing survival rates (Oladosu et al., 2020). Additionally, allelic variations in these genes among different rice cultivars have been linked to varying levels of submergence tolerance, although no consistent association has been found due to low minor allele frequencies and exceptions in the genotype panel (Figure 2) (Singh et al., 2020). Figure 2 Regeneration of rice cultivars afer two weeks of complete submergence in a concrete pond at NDUAT, Ayodhya in 2012 (Adopted from Singh et al., 2020) Image caption: Diferential response of the cultivars (planted in single rows) is clearly visible two weeks afer de-submergence (Adopted from Singh et al., 2020)
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