Zhen Li

Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China
Author    Correspondence author
Cotton Genomics and Genetics, 2025, Vol. 16, No. 5   
Received: 01 Jul., 2025    Accepted: 11 Aug., 2025    Published: 01 Sep., 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.

The pan-genome concept has emerged as a powerful framework for understanding genome variability within a species, providing crucial insights into genetic diversity, adaptation, and evolution in plants. In this study, we review the landscape of cotton (Gossypium spp.) genomes through the lens of pan-genomics, with a particular focus on the role of polyploidy and subgenome dynamics. We explore the structural evolution of diploid and polyploid cotton genomes, the composition of core and dispensable genes, and the presence of lineage-specific genes and structural variants across cultivars and wild relatives. Our analysis highlights how pan-genome studies have uncovered key agronomically relevant genes absent in reference genomes and revealed extensive gene presence/absence variation (PAV), SNPs, InDels, and CNVs that contribute to trait diversity. We also examine expression bias and subgenome dominance in allopolyploid cotton, revealing regulatory asymmetries that influence fiber development, stress responses, and reproductive traits. A focused case study on Gossypium hirsutum demonstrates the integration of genomic data from diverse accessions and the discovery of elite trait-associated genes. Finally, we discuss the implications of cotton pan-genomics for molecular breeding, biotechnology, and the development of high-yield, stress-tolerant varieties. This review underscores the transformative potential of pan-genome resources in shaping next-generation cotton improvement strategies.

Cotton pan-genome; Subgenome dominance; Genetic diversity; Polyploidy; Gossypium hirsutum