Molecular Breeding for Enhanced Flooding Tolerance

Molecular elucidation of stress tolerance mechanisms and adaptation greatly facilitates the breeding of elite cultivars, using the available diversity. The SUB1A gene represents an impressive example of the potential of this approach. Some rice cultivars are highly tolerant of prolonged and complete submergence. This ability is linked to a major quantitative trait locus (QTL), SUBMERGENCE TOLERANCE1. It has been molecularly identified and found to carry three genes (SUB1A, SUB1B and SUB1C) (Fig. 5.15) encoding ethylene response factors (Xu et al. 2006).

Fig. 5.15. Structure of the SUB1 locus in rice. SUB1 is a major quantitative trait locus explaining some of the natural variation in submergence tolerance among rice accessions. The SUB1 locus comprises a set of genes encoding ethylene response factors. They activate contrasting submergence survival strategies upon a rise in ethylene concentrations (Fig. 5.14) (Fukao et al. 2009)

While SUB1B and SUB1C are ubiquitously present in rice cultivars, there is variation for SUB1A. First, it is present only in a subset of rice cultivars. Second, two different alleles have been found to be associated with submergence intolerance (SUB1A-2) or submergence tolerance (SUB1A-1). Using marker-assisted breeding, SUB1 has been introgressed into several flooding-sensitive elite rice cultivars. In all cases examined, it was found that varieties can be generated that show substantial increases in flooding tolerance yet retain yield potential and other desired agronomic traits (Xu et al. 2006; Septiningsih et al. 2009) (Fig. 5.16).

Fig. 5.16.Generation of more flooding-tolerant varieties by SUB1 introgression. The SUB1 haplotype from a flooding-tolerant variety (R49830, right) was introduced into an intolerant variety (Swarma, left) by marker-assisted selection, and confers submergence tolerance. In the centre, two individual plants selected from backcrosses that carried the Sub1 haplotype with the least IR49830 background are shown. Fourteen-day-old seedlings were submerged for 14 days and photographed 14 days after de-submergence (Xu et al. 2006)

Variation at the SUB1 locus and the involvement in contrasting strategies (Fig. 5.9) suggest that duplication and divergence of group VII ERFs underlie distinctions in flooding responses in rice, as well as in many other flooding-tolerant species (Bailey-Serres and Voesenek 2010).