Zhen Li

Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China
Author    Correspondence author
Cotton Genomics and Genetics, 2025, Vol. 16, No. 6   doi: 10.5376/cgg.2025.16.0030
Received: 20 Nov., 2025    Accepted: 12 Dec., 2025    Published: 25 Dec., 2025

This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Li Z., 2025, Precision breeding of cotton using haplotypes and genome editing tools, Cotton Genomics and Genetics, 16(6): 300-309 (doi: 10.5376/cgg.2025.16.0030)

Cotton, as one of the world's most important fiber crops, requires precision breeding strategies to meet the growing demands for yield, quality, and sustainability. This study focuses on the integration of haplotype-based methods and genome editing tools as innovative approaches to accelerate cotton genetic improvement. First, we discuss the definition, identification, and application of haplotypes in resolving complex traits; second, we outline genome editing systems, particularly CRISPR-Cas technology for modifying specific gene targets in cotton. This study emphasizes the synergistic effect of haplotype information and genome editing as a means to validate candidate gene function and shorten breeding cycles. A case study demonstrating the application potential of these precision tools in improving fiber quality is presented. While exploring challenges such as technological limitations, regulatory hurdles, and data integration, this study predicts that emerging advances in pan-genome analysis, graph-based haplotype analysis, and next-generation editing platforms will establish robust processes for sustainable cotton breeding and genetic innovation.

Cotton breeding; Haplotypes; Genome editing; CRISPR-Cas; Precision agriculture