Novel genetic mapping tools in plants: SNPs and LD-based approaches

Use of DNA-based genetic markers [1] has forever changed the practice of genetics. In the 20 years since that discovery, many different types of DNA-based genetic markers have been used for the construction of genetic maps, for the analysis of genetic diversity, trait mapping, as well as for applied diagnostic purposes. A bewildering array of acronyms, such as RFLP, SSR, AFLP, RAPD, AP-PCR, DAF, SAMPL, and many others describes these methodologies [2]. AFLPs and SSRs have become especially popular due to the former's high multiplex ratio and the latter's high degree of informativeness [3]. Also, arbitrary primer-based methods, such as RAPD, found their applications because of their simplicity. All of these methods constitute indirect approaches towards assessing DNA sequence differences: single nucleotide polymorphisms (SNPs, [4]) and insertions/deletions (indels). A direct analysis of sequence difference between many individuals at a large number of loci has now become practical. Dramatic advances in sequencing technology have resulted in the determination of complete DNA sequences of many organisms including most notably human, and, from a plant scientists' perspective, Arabidopsis [5]. The next important objective is to determine sequence diversity of genic and regulatory regions in these and other species. This would allow the understanding of the relationship between phenotypic diversity and genetic diversity. We discuss here the development and applications of SNP genetic markers in corn and other crop plants, and the contribution of these studies towards the understanding of the organization of genetic diversity in plants. We also discuss linkage disequilibrium-based trait mapping approaches.