Single-backcross approach to transfer submergence tolerance from IR64-Sub1 to related rice varieties

Sub1, a gene conferring tolerance to 1-2 wk flooding, was successfully transferred to 6 rice mega varieties (Swarna, Sambha Mahsuri, IR64, BR11, TDK1 and CR 1009) in 2-3 backcrosses using marker-assisted backcrossing. This breeding approach could be further shortened to 1 backcross using the improved Sub1 lines and related popular varieties as parents. Two Southeast Asian varieties, Ciherang from Indonesia and PSB Rc18 from the Philippines, were good candidates for the single-backcross approach because they are related to IR64 by descent. Polymorphism survey with IR64-Sub1 using 285 single sequence repeat (SSR) markers across the 12 rice chromosome showed percent polymorphism with Ciherang at around 24% and with PSB Rc18, around 41%. A total of 520 BC1F1 plants from the Ciherang/IR64-Sub1 population were subjected to target screening, and 216 plants heterozygous for Sub1 were subjected to background screening using 28 evenly-spaced SSR markers from the polymorphic regions of the genome. The procedure was repeated in 1395 BC1F2 plants from 2 best BC1F1 plants, in which 303 of them with Sub1 were screened using the remaining heterozygous markers. One plan obtained the Ciherang genotype in all the SSR markers used except for the Sub1 region in Chromosome 9. Seed increase of this line is ongoing. The same scheme was used in the PSB Rc18/IR64-Sub1 population, starting with target screening in 862 BC1F1 plants, followed by background screening in 443 individuals using 38 SSR markers. Target screening was done in 395 BC1F2 plants from 3 best BC1F1 plants, followed with background screening in 108 plants. Two plants, with 1-3 heterozygous alleles left will be further purified in the BC1F3 generation. Results from these two populations show the importance of having large BC1F2 population (around 1,000 plants) to transfer Sub1 in one backcross.