ABSTRACT
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 used in plant molecular genetics because they were reproducible and codominant [10]. However, the detection of RFLPs was an expensive, labor-and time-consuming process, which made these markers eventually obsolete. Moreover, RFLP markers were not amenable to automation. Invention of PCR technology and the application of this method for the rapid detection of polymorphisms overthrew low-throughput RFLP markers, and new generation of PCR-based markers emerged in the beginning of nineties. RAPD, AFLP, and SSR markers are the major PCR-based markers that research community has been using in various plant systems. RAPDs are able to simultaneously detect polymorphic loci in various regions of a genome [11]. However, they are anonymous and the level of their reproducibility is very low due to the non-specific binding of short, random primers. Although AFLPs are anonymous too, the level of their reproducibility and sensitivity is very high owing to the longer +1 and +3 selective primers and the presence of discriminatory nucleotides at 3′ end of each primer. That is why AFLP markers are still popular in molecular genetics research in crops with little to zero reference genome sequence available [12]. However, AFLP markers did not find widespread application in molecular breeding owing to the lengthy and laborious detection method, which was not amenable to automation either. Therefore, it was not surprising that soon after the discovery of SSR markers in the genome of a plant, they were declared as “markers of choice” [13], because SSRs were able to eliminate all drawbacks of the above-mentioned DNA marker technologies. SSRs were no longer anonymous; they were highly reproducible, highly polymorphic, and amenable to automation. Despite the cost of detection remaining high, SSR markers had pervaded all areas of plant molecular genetics and breeding in late 90s and the beginning of 21st century. However, during the last five years, the hegemony of medium-throughput SSRs was eventually broken by SNP
markers. First discovered in human genome, SNPs proved to be universal as well as the most abundant forms of genetic variation among individuals of the same species [14]. Although SNPs are less polymorphic than SSR markers because of their biallelic nature, they easily compensate this drawback by being abundant, ubiquitous, and amenable to high-and ultrahigh-throughput automation. However, despite these obvious advantages, there were only a limited number of examples of application of SNP markers in plant breeding by 2009 [15]. In this paper, we tried to summarize the recent progress in the utility of SNP markers in plant breeding.
