The recent advances in genomics particularly mapping of QTLs and genome-wide association studies offers great potential to identify functional genes through candidate gene analysis for the stress-related complex trait like cold tolerance. Rapid advances in sequencing technology have enabled to detect functional SNP for the candidate genes. Use of a large set of polymorphic SNPs for recipient parent’s genome recovery together with the functional SNPs in the breeding program could expedite the improvement of cold tolerance in the breeding programs involving indica-japonica crosses avoiding undesirable linkage drag of unwanted traits from japonica donors. However, marker-assisted selection (MAS), as it was expected to reshape the breeding program and expedite gain from selection (Stuber et al. 1982, Tanksely et al. 1989), has failed to significantly improve polygenic traits (Bernardo 2008, Xu and Crouch 2008). Although MAS has been effective for the manipulation of large effect alleles with known association to a marker (Xu et al. 2006, Zhong et al. 2006, Neeraja et al. 2007), it has been at an impasse when many alleles of small effects govern the traits. Genomic selection (GS) approach offers a great scope for rapid improvement without detailed study for individual loci. Since, GS relies on the prediction of genomic estimated breeding values (GEBVs) for individual lines in a phenotyped and genotyped training population, a breeding population with enhanced frequencies for all possible favorable alleles of traits of interest can be developed from the selected individuals and bred over multiple generations without the need for further time consuming and laborious phenotyping (Meuwissen et al. 2001). GS application in cattle breeding program has been already successfully for increasing meat production (Hayes et al. 2009). In wheat and maize breeding, GS approaches are being regularly used for crop improvement of yield and quality traits (Heffner et al. 2010, Jannik et al. 2010). In rice breeding program, it is still maiden approach. Only a few reports are available. Spindel et al. (2015) reported the first GS application in rice for yield and yield-related traits. Since cold tolerance is a polygenic trait and is controlled by several genes with an additive effect, GS application in the breeding program could expedite genetic gain from selection under low-temperature stress in rice.