Cotton (Gossypium spp.) is the most important natural fiber source in the world. The genetic potential of cotton can be successfully and efficiently exploited by identifying and solving the complex fundamental problems of systematics, evolution, and phylogeny, based on interspecific hybridization of cotton. This study describes the results of interspecific hybridization of G. herbaceum L. (A₁-genome) and G. mustelinum Miers ex Watt (AD₄-genome) species, obtaining fertile hybrids through synthetic polyploidization of otherwise sterile triploid forms with colchicine (C₂₂H₂₅NO₆) treatment. The fertile F₁C hybrids were produced from five different cross combinations: (1) G. herbaceum subsp. frutescens × G. mustelinum; (2) G. herbaceum subsp. pseudoarboreum × G. mustelinum; (3) G. herbaceum subsp. pseudoarboreum f. harga × G. mustelinum; (4) G. herbaceum subsp. africanum × G. mustelinum; (5) G. herbaceum subsp. euherbaceum (variety A-833) × G. mustelinum. Cytogenetic analysis discovered normal conjugation of bivalent chromosomes in addition to univalent, open, and closed ring-shaped quadrivalent chromosomes at the stage of metaphase I in the F₁C and F₂C hybrids. The setting of hybrid bolls obtained as a result of these crosses ranged from 13.8–92.2%, the fertility of seeds in hybrid bolls from 9.7–16.3%, and the pollen viability rates from 36.6–63.8%. Two transgressive plants with long fiber of 35.1–37.0 mm and one plant with extra-long fiber of 39.1–41.0 mm were identified in the F₂C progeny of G. herbaceum subsp. frutescens × G. mustelinum cross. Phylogenetic analysis with 72 SSR markers that detect genomic changes showed that tetraploid hybrids derived from the G. herbaceum × G. mustelinum were closer to the species G. mustelinum. The G. herbaceum subsp. frutescens was closer to the cultivated form, and its subsp. africanum was closer to the wild form. New knowledge of the interspecific hybridization and synthetic polyploidization was developed for understanding the genetic mechanisms of the evolution of tetraploid cotton during speciation. The synthetic polyploids of cotton obtained in this study would provide beneficial genes for developing new cotton varieties of the G. hirsutum species, with high-quality cotton fiber and strong tolerance to biotic or abiotic stress. In particular, the introduction of these polyploids to conventional and molecular breeding can serve as a bridge of transferring valuable genes related to high-quality fiber and stress tolerance from different cotton species to the new cultivars.

Expanding genetic variability of cultivated cotton (Gossypium hirsutum) is essential for improving fiber quality and pest resistance. This study synthesized allotetraploids through interspecific hybridization between G. herbaceum (A₁) and G. nelsonii (G₃). Upon chromosome doubling using 0.2% colchicine, fertile F₁C allotetraploids (A₁A₁G₃G₃) were developed. Cytogenetic analysis confirmed chromosome stability of synthetic allotetraploids, and 74 polymorphic SSR markers verified hybridity and parental contributions. The F₁C hybrids exhibited enhanced resistance to cotton aphids (Aphis gossypii) and whiteflies (Aleyrodidae), with respective infestation rates of 5.2–5.6% and 5.4–5.8%, lower than those of G. hirsutum cv. Ravnak-1 (22.1% and 23.9%). Superior fiber length (25.0–26.0 mm) was observed in complex hybrids and backcross progeny, confirming the potential for trait introgression into elite cultivars. Phylogenetic analysis based on SSR data clearly differentiated G. herbaceum from Australian wild species, demonstrating successful bridging of divergent genomes. The F₁C hybrids consistently expressed dominant G. nelsonii-derived traits regardless of the hybridization direction and clustered phylogenetically closer to the wild parent. These synthetic allotetraploids could broaden the genetic base of G. hirsutum, addressing cultivation constraints through improved biotic stress resilience and fiber quality traits. The study establishes a robust framework for utilizing wild Gossypium species to overcome genetic bottlenecks in conventional cotton breeding programs.

Background/Objectives: The classification and phylogenetic relationships of Gossypium hirsutum L. landraces, despite their proximity to southern Mexico, remain unresolved. This study aimed to clarify these relationships using SSR markers and hybridization methods, focusing on subspecies and race differentiation within G. hirsutum L. Methods: Seventy polymorphic SSR markers (out of 177 tested) were used to analyze 141 alleles and calculate genetic distances among accessions. Phylogenetic relationships were determined using MEGA software (version 11.0.13) and visualized in a phylogenetic tree. ANOVA in NCSS 12 was used for statistical analysis. Over 1000 inter-race crosses were conducted to assess boll-setting rates. Results: Distinct phylogenetic patterns were identified between G. hirsutum subspecies and races, correlating with boll-setting rates. Latifolium, richmondii, and morilli showed no significant increase in boll-setting rates in reciprocal crosses. Cultivars Omad and Bakht, as paternal parents, yielded higher boll-setting rates. Religiosum and yucatanense displayed high boll- and seed-setting rates as maternal parents but low rates as paternal parents. Additionally, phylogenetic analysis revealed a close relationship between cultivars ‘Omad’ and ‘Bakht’ with G. hirsutum race richmondii, indicating their close evolutionary relationship. Conclusions: Reciprocal differentiation characteristics of G. hirsutum subspecies and races, particularly religiosum and yucatanense, should be considered during hybridization for genetic and breeding studies. Understanding the phylogenetic relationships among G. hirsutum taxa is crucial for exploring the genetic diversity of this economically important species.

Cotton is a globally important crop, with fiber quality traits governed by complex quantitative trait loci (QTL). However, the utility of QTL data is often limited due to inconsistencies across studies. This study conducted a comprehensive Meta-QTL (MQTL) analysis by integrating 2864 QTLs from 50 independent studies published between 2000 and 2024. Of these, 2162 high-confidence QTLs were projected onto a consensus genetic map using BioMercator V4.2.3, resulting in the identification of 75 MQTLs across the cotton genome. These MQTLs exhibited significantly reduced confidence intervals and enhanced statistical support, with 14 MQTLs reported for the first time. Several MQTLs, including MQTLchr7-1, MQTLchr14-1, and MQTLchr24-1, were identified as stable clusters harboring key fiber quality and stress tolerance traits. Candidate gene analysis within select MQTL regions revealed 75 genes, 38 of which were annotated with significant gene ontology terms related to lignin catabolism, flavin binding, and stress responses. Notably, GhLAC-4, GhCTL2, and UDP-glycosyltransferase 92A1 were highlighted for their potential roles in fiber development and abiotic stress tolerance. These findings provide a refined genomic framework for cotton improvement and offer valuable resources for marker-assisted selection (MAS) and functional genomics aimed at enhancing fiber quality, yield, and stress resilience in cotton breeding programs.

The restricted genetic diversity of current cotton varieties (Gossypium hirsutum L.) considerably limits breeding opportunities aimed at enhancing fiber quality and resistance to environmental factors. Wild types of allotetraploid cottons are valuable sources of genetic variation, and their breeding potential has not yet been fully utilized. In this study, the inheritance and variability of important agronomic traits were analyzed in F₁ and F₂ hybrid generations obtained from intra- and interspecific crosses involving G. hirsutum, G. barbadense, and G. darwinii. The phylogenetic relationships of allotetraploid species were analyzed using molecular-genetic and cytogenetic methods, and their breeding potential was evaluated. Cytogenetic analysis of the F₁ hybrids revealed the occurrence of univalents at metaphase I of meiosis, while bivalent numbers reached 25.9 in some hybrid combinations. Based on molecular marker analysis, significant genetic differences and polymorphism were identified between var. gambia and var. m. palmerii. There were reciprocal translocations, shown as multivalents, during ecotypic differentiation in other cross combinations. Positive transgressive segregation for the enhancement of fiber length was identified in F₂ populations. Notably, in certain hybrid combinations, fiber length extended to 40.9 mm. Furthermore, molecular analysis identified 113 unique alleles across the genotypes examined. These findings affirm that wild and exotic allotetraploid cotton forms constitute a significant source of genetic diversity for breeding programs.