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

Abstract

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.

Multiparent-Derived, Marker-Assisted Introgression Lines of the Elite Indian Rice Cultivar, ‘Krishna Hamsa’ Show Resistance against Bacterial Blight and Blast and Tolerance to Drought

“…We targeted four QTLs— qDTY1.1, qDTY2.1, qDTY3.1 and qDTY12.1 —for reproductive-stage drought tolerance. In previous studies, the introgression of these four QTLs in different combination along with Sub1 for submergence tolerance resulted in development and release of drought- and submergence-tolerant versions of mega varieties like Swarna as CR dhan 801 ( qDTY1.1 +qDTY2.1 +qDTY3.1 +Sub1 ) and CR Dhan 802 ( qDTY2.1+qDTY3.1+Sub1 ) and Samba Mahsuri as DRR Dhan 50 ( qDTY2.1+qDTY3.1+Sub1 ) as new cultivars in various rice growing countries of Southern Asia [ 41 , 51 , 52 , 53 ]. In the present study, we identified five ILs viz., IL 19,196 with Xa21+Pi9+qDTY3.1 , ILs 19,174 and 19,193 with xa5+Xa21+qDTY3.1 and ILs 19,246 and 19,247 with qDTY2.1 introgressions and yield advantage of 131 to 346 g/m 2 under reproductive-stage drought stress over Krishna Hamsa, accounting to a percentage yield advantage of 68%–180% along with BB and blast resistance.…”

Salinity tolerance mechanisms and their breeding implications

“…MAB also permits restricting the donor region thereby eluding linkage drag [ 148 ]. Marker-assisted breeding (MAB) was fortunate in the development of salinity tolerance lines in rice [ 148 , 149 , 154 – 158 ]. In rice, marker-assisted breeding has been utilized in pyramiding of QTLs which control tolerance against salinity, submergence, as well as drought [ 6 ].…”

Advances in Developing Multigene Abiotic and Biotic Stress-Tolerant Rice Varieties

“…The identification and introgression of the trait (s)/genomic regions of interest are the well-known approaches for the development of salinity tolerant varieties [93,94]. Marker assisted breeding approaches have been proven successful in developing new improved, high yielding salt tolerance rice varieties [95][96][97][98][99][100].…”