The use of molecular markers has revolutionized the pace and precision of plant genetic analysis which in turn facilitated the implementation of molecular breeding of crops. The last three decades have seen tremendous advances in the evolution of marker systems and the respective detection platforms. Markers based on single nucleotide polymorphisms (SNPs) have rapidly gained the center stage of molecular genetics during the recent years due to their abundance in the genomes and their amenability for high-throughput detection formats and platforms. Computational approaches dominate SNP discovery methods due to the ever-increasing sequence information in public databases; however, complex genomes pose special challenges in the identification of informative SNPs warranting alternative strategies in those crops. Many genotyping platforms and chemistries have become available making the use of SNPs even more attractive and efficient. This paper provides a review of historical and current efforts in the development, validation, and application of SNP markers in QTL/gene discovery and plant breeding by discussing key experimental strategies and cases exemplifying their impact. 1. Introduction Allelic variations within a genome of the same species can be classified into three major groups that include differences in the number of tandem repeats at a particular locus [microsatellites, or simple sequence repeats (SSRs)] [1], segmental insertions/deletions (InDels) [2], and single nucleotide polymorphisms (SNPs) [3]. In order to detect and track these variations in the individuals of a progeny at DNA level, researchers have been developing and using genetic tools called molecular markers [4]. Although SSRs, InDels, and SNPs are the three major allelic variations discovered so far, a plethora of molecular markers were developed to detect the polymorphisms that resulted from these three types of variation [5]. Evolution of molecular markers has been primarily driven by the throughput and cost of detection method and the level of reproducibility [6]. Depending on detection method and throughput, all molecular markers can be divided into three major groups: (1) low-throughput, hybridization-based markers such as restriction fragment length polymorphisms (RFLPs) [4]; (2) medium-throughput, PCR-based markers that include random amplification of polymorphic DNA (RAPD) [7], amplified fragment length polymorphism (AFLP) [8], SSRs [9]; (3) high-throughput (HTP) sequence-based markers: SNPs [3]. In late eighties, RFLPs were the most popular molecular markers that were widely
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