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Submergence is one of the major constraints to rice production in many rice growing areas in the world. The Sub1A gene has been demonstrated to dramatically improve submergence tolerance in rice. Here, we report the identification of a novel submergence response ( RS1 ) gene that is specifically induced in the Sub1A -mediated submergence tolerance response. Under submergence, RS1 was upregulated in M202 (Sub1A) but downregulated in M202 in RNA-seq and microarray assays. Expression analyses of various tissues and developmental stages show that RS1 mRNA levels are high in leaves and sheaths, but low in roots, stems, and panicles. Our results also show that RS1 is highly expressed under submergence, drought, and NaCl stresses, but not under cold or dehydration stress. Hormone ABA treatment induces, whereas GA treatment decreases, RS1 expression. The RS1 and Sub1A genes are co-regulated under submergence. Overexpression of RS1 in transgenic Kitaake (without Sub1A ) and M202( Sub1A )×Kitaake do not result in enhanced submergence tolerance. Conversely, down-regulation of RS1 in M202(Sub1A)×Kitaake lead to weaken submergence tolerance. We hypothesize that RS1 may play a role in the Sub1A -mediated submergence tolerance pathway. Key word: Rice ( Oryza sativa L.), submergence, RNA-seq, Sub1A , abiotic stress.

Identification of a novel submergence response gene regulated by the Sub1A gene