Arabidopsis natural variation as tool for gene function discovery

Abstract

Longer-term partial stagnant flooding, particularly when it occurs following transient complete submergence causes severe damage to modern rice varieties. Progress was made in developing varieties tolerant of complete submergence through transfer of the Submergence-1 (SUB1) gene into popular varieties. However, SUB1 may not be effective under partial stagnant flooding (SF), as the new varieties may not elongate and continue growth when fully or partially submerged because of the SUB1-mediated suppression of elongation. We tested a set of rice genotypes, including a pair of near-isogenic lines (NILs), Swarna and Swarna-Sub1, under either SF or SF following complete submergence of 12 d. Swarna-Sub1 had higher survival and yield than Swarna following 12 d of submergence, but survival and grain yield of all lines decreased substantially when SF of 15–30 cm followed complete submergence, with the sensitive lines experiencing greater reductions in growth and yield. This suggests the importance of combining SUB1 with tolerance of SF in areas where both stresses are expected during the season. Swarna and Swarna-Sub1 are more sensitive to long-term partial SF than IR49830 and IR42 because of their short stature, and Swarna-Sub1 showed slightly higher reduction in tillering than did Swarna when subjected to deeper SF alone, possibly because of further inhibition of elongation by SUB1 if induced in submerged tissue. The results suggest that tolerance of these genotypes to SF depends less on SUB1 introgression and more so on the genetic background of the recipient genotype, with better performance of the genotypes that are inherently taller, such as IR42 and IR49830. The SUB1 donor landrace FR13A and its derivative breeding line IR49830 had better survival and relatively less reduction in grain yield under SF following complete submergence and under longer-term partial SF, indicating that these genotypes may have genes other than SUB1 for submergence and SF tolerance. For better adaptation to prolonged SF, SUB1 should be introgressed into genotypes that tolerate partial SF through better tillering ability and taller shoots, because SUB1 may not be effective in shorter genotypes, as it promotes survival of submerged plants by hindering shoot elongation to conserve energy reserves. Varieties combining tolerance of prolonged SF with SUB1 will have broader adaptation in flood-prone areas and greater impacts on yield stability.