Molecular Markers and Their Applications in Cotton Improvement: Recent Advances and Future Prospects | ||
| پژوهش های پنبه ایران | ||
| Volume 13, Issue 1, January 2026, Pages 101-124 PDF (896.48 K) | ||
| Document Type: Review | ||
| DOI: 10.22092/ijcr.2025.371630.1249 | ||
| Authors | ||
| Bahman `Panahi* 1; Rasmieh Hamid2; Zahra Ghorbanzadeh3 | ||
| 1Department of Genomics, Branch for Northwest & West region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran | ||
| 2Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran | ||
| 3Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran. | ||
| Abstract | ||
| Background and Objectives: Cotton (Gossypium spp.), as the most important source of natural fibres and one of the world’s strategic crops, plays a vital role in global economic security and sustainable agricultural systems. Nevertheless, genetic improvement of cotton remains challenging due to the complex inheritance of key quantitative traits such as yield, fibre quality, and resistance to biotic and abiotic stresses. These traits are typically governed by multiple loci, influenced by gene–gene and gene–environment interactions, and further complicated by the polyploid nature of the cotton genome. Consequently, conventional breeding approaches, although effective, are often slow and limited in their capacity to deliver rapid and precise genetic gains. This review aims to synthesise recent advances in molecular marker technologies and their applications in cotton breeding, with particular emphasis on QTL mapping, genome-wide association studies (GWAS), and the integration of multi-omics approaches. Results: The development and application of molecular markers, including simple sequence repeats (SSR), amplified fragment length polymorphisms (AFLP), single nucleotide polymorphisms (SNP), and next-generation sequencing (NGS)-based platforms, have substantially transformed cotton breeding and genomics research. These marker systems have enabled high-density genotyping, accurate assessment of genetic diversity, and the construction of saturated linkage maps, thereby facilitating precise quantitative trait locus (QTL) mapping. GWAS approaches, exploiting diverse germplasm collections and dense SNP datasets, have further expanded the identification of QTLs and candidate genes associated with economically important traits such as fibre length, strength, uniformity, yield components, and tolerance to drought, salinity, and other environmental stresses. Beyond single-layer genomic analyses, the integration of multi-omics data—including transcriptomics, metabolomics, and proteomics—has provided a systems-level understanding of gene regulatory networks and molecular pathways underlying complex traits in cotton. Such integrative strategies have significantly enhanced QTL resolution, improved the identification of functional candidate genes, and facilitated the dissection of polygenic trait architecture. These advances have opened new opportunities for the simultaneous improvement of yield, fibre quality, and stress tolerance through molecular breeding. Despite these achievements, the routine implementation of marker-assisted selection (MAS) and genomic selection (GS) in cotton breeding programmes remains constrained by several challenges. These include the limited availability of allele-specific markers, the presence of homoeologous gene copies in the polyploid genome, environmental instability of QTL effects, and the relatively high costs associated with large-scale genotyping and phenotyping. Addressing these constraints is essential for translating genomic discoveries into practical breeding outcomes. Conclusion: This review provides a comprehensive and systematic overview of the progress, applications, and limitations of molecular markers in cotton breeding. It highlights the transformative potential of combining molecular marker technologies with QTL mapping, GWAS, and multi-omics approaches to accelerate the development of high-yielding, fibre-quality–enhanced, and stress-resilient cotton cultivars. The integration of these advanced genomic tools is expected to bridge the gap between gene discovery and practical breeding, offering a robust framework for precise and targeted cotton improvement. Ultimately, such strategies will contribute to sustainable cotton production and long-term global fibre security. | ||
| Keywords | ||
| Molecular Markers; Cotton Breeding; Marker assisted selection | ||
| References | ||
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