Naturally colored cotton offers ecological advantages by eliminating the need for chemical dyeing; however, its limited fiber quality restricts its commercial utilization. The main goal of this study was to evaluate the potential of the SSR marker BNL1604 for marker-assisted selection in naturally colored cotton (G. hirsutum L.) and to assess fiber quality variation among hybrid progenies derived from crosses between colored and elite white-fiber cultivars. As an expected outcome of this approach, we also assessed whether hybridization of naturally colored lines with elite white-fiber cultivars could contribute to the improvement of fiber quality traits in segregating progenies. Five colored lines (brown and green), three elite cultivars, and fifteen derived F₃ progenies were analyzed. Fiber traits, including upper half mean length (UHML), strength, elongation, and micronaire, were measured using HVI. Genotyping was conducted with BNL1604, and in silico mapping localized this marker to chromosome A07, with a homoeologous region on D07. White-fiber cultivars exhibited superior fiber length (33.4–35.4 mm) and strength (>31 g·tex⁻¹) compared with colored lines. Several F₃ hybrids exhibited transgressive segregation (progeny with trait values significantly exceeding those of both parents, as confirmed by frequency distribution and ANOVA analyses). For instance, the F₃ (C-6577 × L-4099) hybrid achieved UHML values of 30.51 mm and strength > 31.93 g·tex⁻¹. Most progenies maintained optimal micronaire (4.0–4.9). It was concluded that the presence of the 107 bp allele of BNL1604 marker was strongly associated with high-quality fiber, specifically improved fiber strength and length. In silico annotation revealed candidate genes near the BNL1604 locus linked to fiber development. These findings highlight the potential of combining hybridization with selection based on the presence of this 107 bp allele to develop high-quality, naturally colored cotton cultivars.

Cotton (Gossypium spp.) is a cornerstone of the global agricultural economy, providing over 35% of the world’s natural fiber and supporting multi-billion-dollar textile and oilseed industries (Zhan...

In the article, the phylogenetic tree of kinship of unique samples created at the Scientific Research Institute of Cotton Selection, Seeding and Cultivation Agrotechnologies and stored in the collection was compiled using molecular markers. 185 primer pairs from TMB, JESPR, GH, NAU, BNL and CIR collections were used, 45 of which turned out to be polymorphic, which allowed to identify 96 polymorphic loci, 20 of which were unique. Phylogenetic analysis of cotton samples based on genotyping using SSR markers divided the samples into 5 different groups. Namangan-34 and Namangan-102 varieties were the most distant from the remaining samples, and these varieties did not differ from each other. Varieties L-175_276 and C-4727 also formed a separate cluster, sample 13 and Sultan variety are related and also form a separate cluster, sample 4 and variety C-7934 also belong. The remaining 29 samples were not significantly different from each other and formed a large cluster, which is called their narrow genetic base.