**1. Introduction**

*Oryza sativa* is an essential food crop contributing 30% of calories for at least 62.8% of the world population. Presently, rice was cultivated over 167.13 m ha within 114 countries with annual production of 486.62 mt (on milled basis) [1]. Majority of population in Asian consumed rice as a basic staple crop with over than 90% of rice were produced in Asia [2]. Revolution in Green technology played an important role in adoption of major increasing in rice production over last four decades. Approximately 450 million tons to 650 million tons of world rice consumption is projected to surge by 2011 and 2050, respectively [3].

Scientist and plant breeder are facing a new challenge in crop improvement due to climate change issue including limitation of water and cultivated land, new emerging pathogen and pest resulted serious yield losses. Among the major constraints, blast disease, bacterial blight, sheath blight, tungro viruses, brown spot and a number of grain discoloration diseases [4] accounted for serious rice losses.

Several amendments can be implemented to overcome these limitations such as breeding high yielding varieties, durable resistance to diseases and tolerance to abiotic stresses [5]. Rice yield potential can be enhanced by using numerous approaches such as conventional hybridization, ideotype breeding, heterosis breeding, wide hybridization and molecular breeding [6]. In molecular rice breeding, there are two main strategies can be used by applying the biotechnology concept which are MAS and Genetically Engineering. MAS like genetic engineering is a technique used to introgress targeted gene however its offers tools for specific selection for further breeding in existing plant material. The field of plant genetics and breeding has irreversibly changed with the development of DNA (or molecular markers) [7].

Since past two decade, revolutionized in molecular marker to enhance the effectiveness in breeding and to significantly shorten the development time of varieties bring about the concept of molecular marker assisted selection (MAS) as an efficient plant selection [8–10]. A genetic marker is any noticeable character or otherwise assayable phenotype, for which alleles at individual loci segregate in a Mendelian manner. The genetic markers covered include (1) morphological markers (2) biochemical markers (alloenzymes and other protein markers) and (3) molecular markers (based on DNA-DNA hybridization) [11, 12]. In this chapter, we present the latest DNA-based markers in a few studies related to abiotic and biotic stress genes using the MAS application in rice breeding programs. These markers have proven significantly useful from different findings published in screening, fine mapping and gene pyramiding approaches.
