Doubled Haploid Technologies in the Era of Gene Editing: Advances, Integration, and Prospects for Accelerated Crop Improvement
Raji Vasudevan Namboodiri *
Genetics and Plant Breeding, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala, Postcode / ZIP: 680656, India.
*Author to whom correspondence should be addressed.
Abstract
Doubled haploid (DH) technology has long been valued in plant breeding for its capacity to generate completely homozygous lines within a single generation, compressing the timescale required for cultivar development by several years relative to conventional selfing programmes. The recent emergence of transformative gene editing platforms—most notably CRISPR-Cas9 and its diverse derivatives—has created new paradigms for precision crop improvement, and the intersection of DH technology with targeted genomic modification now represents one of the most dynamic frontiers in applied plant genetics. Despite the advances, practical integration of DH and gene editing technologies faces substantive obstacles. This review presents a comprehensive narrative synthesis of the current state of DH technologies in the context of contemporary gene editing, examining the mechanistic foundations of haploid induction, the principal methods of DH production, including anther culture, isolated microspore culture, wide hybridisation, in vivo haploid inducer systems and centromere-mediated genome elimination, and the evolution of gene editing tools from site-specific nucleases through base editors to prime editors. The integration of these two technological domains is critically reviewed, with particular focus on the use of microspores and isolated haploid cells as substrates for CRISPR-mediated editing, the haploid inducer-mediated editing (HI-Edit) approach developed in maize, and the engineering of centromeric histone variants for bespoke haploid induction. Applications across major cereal crops, horticultural species and emerging crops are discussed, together with the regulatory frameworks governing the deployment of genome-edited DH lines and the ethical considerations associated with equitable access. Key challenges, including genotype-dependent recalcitrance, reduced editing efficiency in gametophytic cells, chimerism, off-target mutation management and chromosomal instability during genome doubling, are identified and evaluated. A synthesis of the evidence suggests that the convergence of DH and gene editing technologies holds substantial promise for delivering improved cultivars with enhanced yield, stress resilience and nutritional quality within compressed breeding timescales, and future directions, including integration with speed breeding, single-cell genomics and artificial intelligence-assisted breeding design, are considered.
Keywords: Doubled haploids, CRISPR-Cas9, plant breeding, genome editing, HI-edit, centromere engineering