Applying genomics tools for breeding submergence tolerance in rice

Abstract

Flooding stress is one of the most important abiotic stresses constraining rice production, especially in rain-fed lowland areas. The effect of this stress has intensified in past decades and is predicted to increase in the years to come as a result of global climate change. At the International Rice Research Institute (IRRI), breeding for tolerance to submergence imposed by flash flooding during the vegetative stage has been one of the institute’s priority objectives for more than three decades. Several tolerant breeding lines have been developed through conventional breeding; however none of those early varieties has been widely accepted by farmers. An important breakthrough was the identification of the major quantitative trait locus (QTL) SUB1 in the mid-1990s, which led to the identification of three ethylene responsive factors (ERFs), of which SUB1A is the primary contributor for tolerance. These findings and the available molecular marker technology have enabled breeders to develop submergence-tolerant varieties through a fast-track marker-assisted backcrossing (MABC) strategy to introgress SUB1 using mega varieties as recurrent parents. Currently eight Sub1 varieties have been developed in IRRI, six of which have been released in several countries. The success of Sub1 varieties has inspired the development of new breeding products for other stresses using a similar strategy, such as tolerance to anaerobic conditions during germination and stagnant flooding. Recent advances in genomics have tremendously increased the efficiency of marker-assisted breeding, bringing us to the point where rice varieties resilient to multiple stresses can be developed to meet future challenges facing rice production, most of which have intensified with global climate changes.