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Rice is the most important food crop both in value and volume for the Asian population. Frequent drought, flood and salinity stresses exacerbated by global climate change adversely affect rice production in more than fifty percent of the rice growing areas. Green revolution high yielding varieties carrying sd1 dwarfing gene have almost fully replaced the traditional climate resilient landraces and varieties of rice. However, these were bred primarily for yield under high input conditions and therefore are sensitive to adverse climatic conditions. Hence, there is urgent need to combine the high productivity with climate resilience. Knowledge of rice genome and genes for tolerance to different abiotic stresses provided us an opportunity to transfer favorable alleles of these genes into high yielding varieties through genomics-assisted backcross breeding through multi-institutional networks. Six consistent genomic regions (QTLs) for grain yield under drought; namely qDTY1.1, qDTY2.1, qDTY2.2, qDTY3.1, qDTY3.2 and qDTY12.1 have been transferred to flood tolerant versions of mega varieties of rice, Swarna, Samba Mahsuri and IR 64. To address the problem of flash flooding qSUB1 QTL has been transferred to nine popular rice varieties, namely ADT 46, Bahadur, Ranjit, HUR 105, Sarjoo 52, Pooja, Pratikshya MTU 1075 and Rajendra Mahsuri. Further, qSALTOL1 QTL for seedling stage salt tolerance and qSSISFH8.1 for reproductive stage salt tolerance have been transferred to six popular rice varieties, ADT 45, Gayatri, MTU 1010, PR 114, Pusa 44 and Sarjoo 52. We used foreground selection markers for the presence of desired gene/QTL and recombinant selection markers for reduction of linkage drag around these genes. Genotypic background selection was done after BC3F3 stage using a 50K SNP chip on a set of 20 advance lines obtained by phenotypic selection for closeness to the recipient parents. Near-isogenic lines (NILs) with more than 95% similarity to the recipient parent genome have been released and notified for commercial cultivation and are gaining fast popularity. These climate smart rice varieties will provide production stability in the adverse ecologies and support farmer’s income and livelihood.

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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 Sub1BC 2 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 BC 2 F 2 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 BC 2 F 2 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 BC 2 F 2 generation into a modern rice variety using a modified MABC.