Molecular Strategies in Contemporary Plant Breeding: A Comparative Analysis of Marker-Assisted Selection and Genomic Selection

Abstract

Molecular breeding has become an integral component of contemporary crop improvement because it enables selection decisions to be supported by genome-level information. This review compares marker-assisted selection (MAS) and genomic selection (GS) as two major molecular strategies used in plant breeding. MAS uses molecular markers linked to major genes or quantitative trait loci and is most effective when target traits are controlled by one or a few loci with stable, relatively large effects. It has been applied to the introgression and pyramiding of disease resistance, stress tolerance and quality-related traits in crops such as rice, wheat, groundnut and chickpea. However, its efficiency declines for complex traits that are governed by many small-effect loci and are strongly influenced by environmental variation. GS addresses this limitation by using genome-wide marker information to estimate genomic breeding values without requiring prior identification of significant marker-trait associations. This approach is therefore suitable for polygenic traits, including yield, drought tolerance, heat adaptation and complex quality attributes. The review discusses the evolution of molecular marker systems, the principles and applications of MAS, statistical models used in GS and the genotyping and phenotyping technologies that support these approaches. It also considers the integration of MAS and GS with speed breeding, genome editing, high-throughput phenotyping, artificial intelligence, pangenomic resources and enviromics. Overall, MAS and GS are complementary rather than competing approaches. Their appropriate use depends on trait architecture, breeding objectives, available resources, training population design, data-management capacity, phenotyping reliability and the stage of the breeding pipeline. The review emphasises their coordinated use within practical, evidence-informed crop improvement programmes.