Harmonizing the high throughput techniques for phenomics and genomics is both a challenge and opportunity. There is no replacement of the conventional breeding, but its limitations in terms of speed and accuracy can be overcome by molecular breeding programmes. The conventional phenotyping and breeding approaches are sound, the advantages and opportunities thrown open by automated phenotyping should be availed for faster gains. Since modern genotyping protocols are well developed and high throughput in rice, phenotyping models need more consideration because capturing “right QTL” largely depends upon right phenotyping. In molecular breeding for salinity tolerance, initial success has been made by the discovery of many QTLs and several rice salinity GWAS reports, but still there is a considerable gap between knowledge discovery and actual use of molecular breeding in realization of field oriented salt tolerant rice varieties. Stage-specific and stress-specific QTLs may be identified for need based deployment for which, the screening methodology should be simple and high throughput, reproducible and representative of near-field conditions.