Marker-Assisted Selection in Horticulture: A Comparative Review Across Vegetables, Fruits and Flower Crops

Marker-assisted selection (MAS) has become one of the most reliable and efficient tools in plant breeding for improving complex traits such as disease resistance, fruit quality, shelf-life, and pigment expression, especially in horticultural crops including vegetables, fruits, and flowers. This review focuses on three representative crops - tomato, papaya, and marigold - to understand how MAS has been practically applied at different scales. Tomato exemplifies advanced MAS pipelines, with successful pyramiding of resistance genes such as Ty-2, Ty-3, Ph-3, and I2. Papaya, despite fewer genomic resources, has benefitted from early selection for sex type and PRSV resistance. MAS in floricultural crops like marigold is still emerging, yet efforts in SSR, AFLP, and RAPD marker development are promising. This paper compares marker systems, crop-specific examples, and challenges across these species, highlighting how MAS can transform horticultural breeding through integration with genomic tools.Despite these successes, a critical gap persists between marker discovery and their widespread use in breeding. As emphasized by Foolad & Panthee (2012), many trait-linked markers in tomato remain underutilized due to poor validation across genetic backgrounds and lack of polymorphism in breeding populations, underscoring the importance of developing robust, widely applicable markers for practical MAS deployment.