As a term, “next generation plant breeding” is increasingly becoming popular in crop breeding programmes, conferences, scientific fora and social media (Schnable, 2013). Being a frontier area of crop science and business, it is gaining considerable interest among scientific community and policymakers and funds flow from entrepreneurs and research funding agencies. Plant breeding is a continuous attempt to alter genetic architecture of crop plants for efficient utilization as food, fodder, fiber, fuel or other end uses. Although the scientific concepts in plant breeding originated about 100 years ago, domestication and selection of desirable plants from prehistoric periods have contributed tremendously to ensure human food security (Gepts, 2004). During the past few decades, well supported crop improvement programmes for major crops started reaping benefits from cutting edge technologies of biological sciences, particularly in the form of molecular markers and transgenic crop development, which in combination with conventional phenotype based selection, defines the current generation plant breeding practices. Different types of molecular markers have been developed and extensively used during the last three decades for identifying linkage between genes and markers, discovering quantitative trait loci (QTLs), pyramiding desired genes and performing marker assisted foreground and background selections for introgression of desired traits (Varshney and Tuberosa, 2007). However, these markers are based mostly on electrophoretic separation of DNA fragments, which limits detection of genetic polymorphism. In large plant breeding populations, genotyping may take up several months depending on marker system, adding more cost to genotyping. The next generation plant breeding would thus demand more efficient technologies to develop low cost, high-throughput genotyping for screening large populations within a smaller time frame.