A Critical Review of Submergence Tolerance Breeding beyond Sub 1 Gene to Mega Varieties in the Context of Climate Change

Abstract

Flash flood, stagnant flooding and anaerobic germination are various forms of submergence that occurs at different stages of rice growth causing significant damage to crop production for more than 15 millions poor farmers in the rainfed lowland region of South and Southeast. Before the discovery of Sub 1 gene farmers had to rely on low yielding, submergence-intolerant varieties that incurred yield drastic reduction to complete failure of the crop every year. With the discovery of major quantitative trait loci (QTL) submergence 1 (Sub 1) which is responsible for this trait, submergence tolerance breeding has achieved its milestone to overcome the burning issue. Cloning and isolation of SUB1 locus in popular submergence tolerance parent FR13A that led to the identification of ethylene-responsive factor (ERF) gene SUB1A-1 that is responsible for submergence tolerance. The Sub 1 QTL is a single gene that has the LOD score of 36 which explained phenotypic variance of 69% conferring tolerance to complete submergence of two weeks. The submergence -1 (Sub-1) locus representing a cluster of three ethylene responsive factor (ERF) genes: sub1A, sub1B and sub1C. Identification of the SUB1 gene was the entry point for enabled marker assisted selection
(MAS) for submergence tolerance. Popular varieties also are known as mega varieties which possessed high yielding and good grain quality was used as the recurrent parent in marker assisted backcrossing (MABC). Beyond the Sub 1 varieties, the present day rice breeders paid attention to tolerance to stagnant flooding and tolerance to anaerobic germination under deep water and flash flood during seedling germination respectively. Quantitative Trait Loci (QTLs) have been identified for anaerobic germination also referred to as AG (AG1 and AG2) and stagnant flooding for deepwater rice (SNORKEL1 and SNORKEL2). Furthermore, the combination of both traits conferring tolerance to stagnant flooding with Sub 1 or Sub 1 with anaerobic germination (AG) is the future direction of rice breeding through gene pyramiding approach to develop the rice varieties tolerant to multiple stresses to enhance yield and quality to combat the future challenge of food and nutritional insecurity.