Abstract
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.
Highlights
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]
SNP markers have become extremely popular in plant molecular genetics due to their genome-wide abundance and amenability for high- to ultra-high-throughput detection platforms
The use of SNP markers in marker-assisted breeding (MAB) programs has been growing at a faster pace and so is the development of technologies and platforms for the discovery and HTP screening of SNPs in many crops
Summary
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]. 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]. SNPs are less polymorphic than SSR markers because of their biallelic nature, they compensate this drawback by being abundant, ubiquitous, and amenable to high- and ultra-high-throughput automation. Despite these obvious advantages, there were only a limited number of examples of application of SNP markers in plant breeding by 2009 [15]. We tried to summarize the recent progress in the utility of SNP markers in plant breeding
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