Advances in Horticultural Crop Breeding: from Conventional Selection to Genomic and Genome-Editing Technologies
Yogesh V. Wayal
Department of Genetics and Plant Breeding, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram 695522, Kerala, India.
Harshavardhan Mohan Totawar
Department of Vegetable Science, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram - 695522, Kerala, India.
Jagmal P. Khatana
Department of Agronomy, Chimanbhai Patel College of Agriculture, Sardarkrushinagar Dantiwada Agricultural University, Dantiwada - 385506, Gujarat, India.
M. V. Keerthana
Department of vegetable science, College of Agriculture, Vellanikkara, Kerala Agricultural University, Thrissur - 680656, Kerala, India.
Choudhari Balaji Keshavrao
Department of Agronomy, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram - 695522, Kerala, India.
G. Athira
Department of vegetable science, College of Agriculture, Vellanikkara, Kerala Agricultural University, Thrissur - 680656, Kerala, India.
Purushottam Kumar Nandu
Department of Floriculture and Landscaping, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram - 695522, Kerala, India.
Kavya Suresh
Department of vegetable science, College of Agriculture, Vellanikkara, Kerala Agricultural University, Thrissur - 680656, Kerala, India.
P. S. Laxmi
Department of Postharvest Management, College of Agriculture, Vellanikkara, Kerala Agricultural University, Thrissur - 680656, Kerala, India.
Khushal B. Muradi
*
Department of vegetable science, College of Agriculture, Vellanikkara, Kerala Agricultural University, Thrissur - 680656, Kerala, India.
*Author to whom correspondence should be addressed.
Abstract
Horticultural crops-including fruits, vegetables, ornamentals, spices, and plantation crops-are essential to global food security, human nutrition, and agricultural economies. However, their genetic improvement has long been constrained by biological complexities such as polyploidy, extended juvenile phases, vegetative propagation, and narrow elite germplasm pools. This review synthesizes breeding strategies across major horticultural crops, tracing the progression from classical phenotypic selection to molecular marker-assisted approaches and advanced genome editing technologies. Conventional breeding established the genetic foundation for crop improvement through hybridization, backcrossing, mutation breeding, and heterosis exploitation. The integration of molecular markers (RFLPs, SSRs, SNPs) with marker-assisted selection (MAS), quantitative trait locus (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS) significantly enhanced breeding precision and efficiency. Advances in whole-genome sequencing, transcriptomics, metabolomics, and pan-genomics have further strengthened genomic resources for trait discovery and predictive breeding. More recently, CRISPR/Cas9 systems, including base editing and prime editing, have enabled precise targeted trait modification, demonstrated in applications such as extended shelf-life tomato, waxy-starch potato, Fusarium-resistant banana, and canker-resistant citrus. Despite these advances, challenges remain, including regulatory heterogeneity, transformation recalcitrance in elite genotypes, polyploid genome complexity, and public acceptance concerns. This review highlights critical research gaps and proposes an integrated breeding framework that combines classical genetics, genomic prediction, and precision genome editing to accelerate the development of climate-resilient, nutritionally enhanced, and commercially competitive horticultural crops.
Keywords: Conventional breeding, marker-assisted selection, QTL mapping, CRISPR/Cas9, omics-assisted breeding