Phylogenetic Relationships of Tetraploid Cotton Species (Gossypium L.) and Their Genetic Potential for Breeding Programs

Background Gossypium mustelinum Miers ex Watt is a rare, wild tetraploid cotton species native to northeastern Brazil, yet its phylogenetic relationships with cultivated cottons ( G. hirsutum and G. barbadense ) and its genetic potential for breeding remain largely unexplored. This study aimed to investigate the cross-compatibility and molecular phylogenetic relationships between G. mustelinum and several accessions of G. hirsutum , G. barbadense , and G. darwinii to assess its utility as a genetic resource for cotton improvement. Results Interspecific hybridizations resulted in 22 distinct F ₁ combinations, showing varied cross-compatibility and reciprocal differences suggesting cytoplasmic or unilateral incompatibility. Notably, the G. hirsutum subsp. glabrum var. marie-galante × G. mustelinum cross exhibited the highest complete seed set (87.2%), despite a low boll set. F ₁ and F ₂ hybrids demonstrated significant potential for improved fiber traits. For instance, the 'Beshqahramon' variety ( G. hirsutum ) × G. mustelinum F ₁ hybrid showed a high positive heterosis for fiber length (hp = 33.00), and its F ₂ population had a mean fiber length of 36.2 mm with 0.62 heritability. Similarly, the 'Beshqahramon' variety × G. mustelinum F ₂ combination yielded the highest mean fiber yield at 41.2% with 0.61 heritability. Molecular phylogenetic analysis using 47 polymorphic simple sequence repeat (SSR) markers revealed a close relationship between G. mustelinum and G. hirsutum subsp. paniculatum (genetic distance = 0.13), and G. hirsutum subsp. glabrum var. marie-galante (genetic distance = 0.17). G. barbadense accessions and G. darwinii formed a separate cluster. Conclusions Our findings confirm the distinct phylogenetic position of G. mustelinum and highlight its significant potential as a genetic resource for cotton breeding, particularly for introgression of valuable traits like enhanced fiber length and yield into G. hirsutum . The identification of promising transgressive segregants with fiber lengths of 41.0–43.0 mm and fiber yields of 40.0–51.0% provides valuable germplasm for developing new long and medium-staple cotton varieties. Further genomic studies are warranted to fully characterize its genetic potential and overcome interspecific hybridization barriers.