Applying Genomics Tools for Breeding Submergence Tolerance in Rice - Translational Genomics for Crop Breeding: Abiotic Stress, Yield and Quality - page 9

Chapter 2

Applying Genomics Tools for Breeding
Submergence Tolerance inRice

EndangM.Septiningsih,BertrandC.Y.Collard,SigridHeuer,JuliaBailey-Serres,
AbdelbagiM.Ismail,and DavidJ.Mackill

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.

More than 20 million ha of rain-fed lowlands
are flood prone, with conditions ranging from
flash flood to deepwater, which can be up to
several meters and last for months (Mackill
et al. 2010). Over thousands of years, rice has
developed adaptive mechanisms to grow well in

Introduction

Flooding stress is a widespread problem that
adversely affects farmers in rice-growing areas,
especially in the flood-prone, rain-fed lowlands
of South and Southeast Asia and West Africa.