Genomics-assisted backcross breeding for infusing climate resilience in high-yielding green revolution varieties of rice.

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.