Genetic Markers, Trait Mapping and Marker-Assisted Selection in Plant Breeding

Abstract

Genetic markers have long been used for characterization of plant genetic diversity and exploitation in crop improvement. The advent of DNA marker technology (during 1980s) has revolutionized crop breeding research as it has enabled the breeding of elite cultivars with targeted selection of desirable gene or gene combinations in breeding programmes. DNA markers are considered better over traditional morphology and protein-based markers because they are abundant, neutral, reliable, convenient to automate and cost-effective. Over the years, DNA marker technology has matured from restriction based to PCR based to sequence based and to eventually the sequence itself with the emergence of novel genome sequencing technologies. Trait mapping has been the foremost application of molecular markers in plant breeding. Genomic locations of numerous genes or quantitative trait loci (QTLs) associated with agronomically important traits have been determined in several crop plants using linkage or association mapping approaches. Plant breeders always look for an easy, rapid and reliable method of selection of desirable plants in breeding populations. Conventionally, desirable plants are selected based on phenotypic observations. The phenotypic selection for complex agronomic traits is difficult, unpredictable and challenging. Once the marker-trait association is correctly established, the gene- or QTL-linked markers can be used to select plants carrying desirable traits, the process called marker-assisted selection (MAS). Marker-assisted backcrossing (MABC) has been widely used for transferring single major gene or combination of major genes into the background of elite cultivar; the process refers to gene pyramiding. Marker-assisted recurrent selection (MARS) and genome-wide association analysis (GWA) are considered potential MAS strategies for improvement of complex traits but still remain as theoretical possibilities in plant breeding. Though molecular markers and MAS have promises for improved plant breeding process, the marker-trait associations or QTLs are statistical associations, which are influenced by several factors such as trait heritability, phenotyping methods, marker density, population type and other experimental conditions that might lead to false positives. Therefore, a cautiously optimistic approach is necessary to consider MAS in crop breeding programmes. In this chapter, the potentials of genetic markers in plant breeding are described.