SNP markers and their impact on plant breeding

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.

Figure 1

Segregation patterns of simple, hemi-, and homoeo-SNPs assayed using KASPar chemistry across tetraploid cotton species [G. hirsutum (AD₁) and G. barbadense (AD₂)] and their diploid progenitors [G. arboreum, G. herbaceum (A subgenome), and G. raimondii (D-subgenome)]. (a) Simple, or true SNP detects allelic variation between homologous loci of A subgenome of G. hirsutum (AD₁) and G. barbadense (AD₂). (b) Hemi-SNPs detect allelic variation in homozygous state in G. barbadense (AD₂) and heterozygous state in G. hirsutum (AD₁). (c) Homoeo-SNP detects homoelogous and/or paralogous loci both in A and D subgenomes, which are monomorphic between G. barbadense (AD₂) and G. hirsutum (AD₁). Allele calls depicted in blue, red, green, pink, and black represent alleles A, B, and AB, no amplification or missing locus, and no template control (NTC), respectively.