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Plant Science Today (PST)

Review Articles

Vol. 13 No. 3 (2026)

Harnessing haplotypes for genetic improvement in cereal crops

DOI
https://doi.org/10.14719/pst.11934
Submitted
23 September 2025
Published
19-06-2026 — Updated on 12-08-2026
Versions

Abstract

Haplotype-based breeding (HBB) is a transformative approach that utilises genome-assisted breeding (GAB) to enhance the precision and efficiency of crop improvement in cereals. Traditional breeding relies on single gene transfer, poor genetic diversity, time-consuming, less complex traits and linkage drag, whereas HBB utilises advanced breeding tools to capture the haplotypes associated with complex genetic variations. Recent advances in high-density genotyping have enabled the identification of superior haplotypes associated with yield, stress resilience and grain nutritional quality in major cereal crops such as rice, wheat, maize, oats and barley. This facilitates the development of superior varieties through gene introgression breeding methods like marker assisted breeding. The integration of HBB with genome-wide association studies (GWAS) and genomic selection (GS) has further improved the resolution and prediction in breeding programs. Advanced technologies like graph genomes, dynamic haplotype analysis, AI-driven haplotype analysis and CRISPR/Cas-mediated genome editing provides new opportunities to design and deploy haplotypes for climate-resilient and nutrient dense varieties. This review emphasises the importance of haplotype breeding in cereal crops, the approaches involved, existing challenges and its future directions to enhance genetic gains for global food and nutritional security. The persistent enhancement in the identification methods, analytical tools and software will pave the way for crop improvement through next-generation breeding programs.

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