Flood proofing of Ranjit, a popular variety of North-Eastern India through transfer of Sub1 rice QTL by modified marker-assisted backcross breeding

Abstract

Flooding is one of the major constraints of rice production in the rainfed lowland rice ecosystem. To cope with the frequent flooding in the climate change regime, tolerant cultivars are urgently needed to protect the paddy crop from flash floods. With the help of molecular markers, a major QTL for submergence tolerance “Sub1” was introgressed into a rainfed lowland mega variety Ranjit of N.E. India, by backcrossing followed by two generations of selfing. In this modified marker-assisted backcrossing (MABC), a gene based marker Sub1BC2 and 50051 SNPs were used for foreground and background selection, respectively, in backcrosses between a Sub1 donor, Swarna- Sub1 and the recipient variety, Ranjit. The recombinant selection was skipped and background selection was deferred to BC2F2 generation. The size of the donor fragment was found to be 1.65Mb. The introgression of this small segment was possible due to large population and strict selection in segregating generations for the recurrent parent with the help of 62 DUS characters. Ranjit- Sub1, a selection in BC2F2 generation, showed background recovery of 96.54% and submergence tolerance similar to the tolerant donor parent. Yield, yield-components and grain physico-chemical properties showed successful recovery of these traits in Ranjit-Sub1, with yield potential ranging from 6.5 to 7.0 t/ha, not significantly different from the recurrent parent, Ranjit. Therefore, Ranjit-Sub1 has been recommended for Zone III for submergence stress conditions in India. The study demonstrates a rapid and highly precise strategy adopted to introgress a major QTL by BC2F2 generation into a modern rice variety using a modified MABC.