Rapid and high-precision marker assisted backcrossing to introgress the SUB1 QTL into BR11, the rainfed lowland rice mega variety of Bangladesh

Flooding is one of the major hazards of rice production for the rainfed lowland rice ecosystem, and tolerant cultivars are urgently needed to help protect farmers from submergence damage. A quick and efficient strategy was implemented to introgress SUB1, a major QTL for submergence tolerance, into a rainfed lowland mega variety BR11 of Bangladesh by only two backcrosses and one selfing generation. In marker-assisted backcrossing (MABC), one tightly-linked simple sequence repeat (SSR) and two gene-based markers, four flanking SSR and 116 background SSR markers were used for foreground, recombinant and background selection, respectively, in backcrosses between a SUB1 donor IR40931-33-1-3-2 and BR11. BR11-Sub1, identified in a BC2F2 plant, possessed BR11 type SSR alleles on all fragments analyzed except the SUB1 QTL. The introgression size in BR11-Sub1 was 800 Kb indicating approximately 99.8% identity to BR11. BR11-Sub1 along with other introgression lines showed submergence tolerance similar to the tolerant parent. Yield, yield-component parameters and grain physico-chemical properties showed successful recovery of the BR11 traits in BR11-Sub1, with yield potential ranging from 5.2 to 5.6 t/ha, not significantly different from the recurrent parent mega variety BR11. Producing a large number (similar to 1000) of backcross F-1 plants was considered essential to achieve recombination on both sides of the gene, limiting linkage drag with only two backcrosses. A large number of background markers ensured proper recovery of the recurrent parent genome in the BC2F2 generation. The study demonstrates a rapid and highly precise strategy to introgress a major QTL by BC2F2 generation into a modern rice variety using an unadapted donor. The variety can replace BR11 on more than 2 million of ha in Bangladesh and provide major increases in rice production.