Genomics-Assisted Plant Breeding in the 21st Century: Technological Advances and Progress

not amenable for automation.Invention of PCR technology and 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 1990s.RAPD, AFLP and SSR markers are the major PCR-based markers that research community has been using in various plant systems.RAPDs were able to simultaneously detect polymorphic loci in various regions of a genome.However, they were anonymous and the level of their reproducibility was very low due to the non-specific binding of short, random primers.Although AFLPs were anonymous too, the level of their reproducibility and sensitivity was v e r y h i g h o w i n g t o t h e l o n g e r + 1 a n d + 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 (Zhang et al., 2011).However, AFLP markers did not find widespread application in molecular genetics and molecular breeding applications, because the detection method was too long, laborious and not amenable to automation.Therefore, it was not surprising that in the beginning of 21 st century SSR markers were declared as "markers of choice" (Powell et al., 1996).SSRs were no longer anonymous; they were highlyreproducible, highly-polymorphic, and amenable to automation.Despite the cost of detection remaining high, SSR markers pervaded all areas of plant molecular genetics and breeding.However, during the last five years, the hegemony of medium-throughput SSRs was eventually broken by SNP markers.First developed for human genome, SNPs have proven universal and are the most abundant forms of genetic variation among individuals within a species (Rafalski, 2002).Although SNPs are less polymorphic than SSR markers because of their bi-allelic nature, they easily compensate this drawback by being abundant, ubiquitous and amenable to high and ultra-high-throughput automation.Since SNPs are currently the most widely used markers in plant molecular genetics and breeding, they are discussed in great detail in the following sections.www.intechopen.com* Based on the information provided by Metzker (2009) and other company web resources 1 Single end read chemistry, 2 paired end read chemistry ф Sequence capacity change with the type of chip used for sequencing. How to referenceIn order to correctly reference this scholarly work, feel free to

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