Favorable alleles: Gh = G. hirsutum ; Gb = G. barbadense ; Gt = G. tomentosum ; Gm = G. mustelinum[90,114–116].

The QTL detection in reciprocal backcross populations of G. hirsutum x G. barbadense crosses [117] using BC4F1 and BC4F2 populations under three environmental conditions by SNP genotyping showed a small effect QTL made up 87% and 100% of QTL in G. hirsutum and G. barbadense, respectively; favorable alleles masked by unfavorable alleles, and there was higher potential forG. hirsutum improvement than G. barbadense. Three stable QTLs—two for fiber micronaire and fiber elongation in G. hirsutum and one for upper half mean length in G. barbadense —were observed, while four QTLs related to fiber quality exhibited opposite effects in reciprocal crosses, indicating the epistasis effects there [117]. Chandnani et al. (2017) studied the backcross population (BC3F1) of G. hirsutum × G. mustelinum using 216SR markers on 3202 plants, revealing allelic interactions, constraints on fixation, selection of donor alleles, and challenges in the retention of introgressed chromatin for crop improvement [118]. Waghmare et al. (2016) analyzed the introgression pattern/heredity into G. hirsutum from its sister G. tomentosum and found there were similar rates of introgression into two subgenomes of G. hirsutum(AtDt) and one unusual region for preferential introgression, and suggested genetic background profoundly preferential introgression, while the complex heredity of wild genetic material introgression imposed challenges to utilizing exotic genetic material crop improvements there. However, Wang et al. (2017) performed QTL mapping for fiber length in advanced backcross generations (BC₃F₂, BC₃F_2:3 and BC₃F_2:4) of G. hirsutum xG. mustelinum and found the same complexity in exotic introgression transmission but found the co-localization of many QRLs for upper half-mean length and the uniformity index of short fiber contents, indicating the co-selection potential of these QTLs for improvements [119]. The QTL mapping using the same population for fiber strength and fineness using SSR markers identified QTLs for fiber strength and 27 for micronaire and found that alleles from G. mustelinum increased fiber strength for 8 of the 15 QTLs and reduced micronaire length for 15 of 27 of the identified QTLs [120], supporting the notion that the fiber quality can be improved by utilizing genetic introgression from G. mustelinum. Transcriptome analysis for fiber strength in G. hirsutum line IL9 having introgression from G. mustelinum revealed there were 52 differentially expressed genes (DEGs) contributing to fiber strength relating to introgression from G. mustelinum, and two genes with known functions were identified within the fiber-strength quantitative trait loci (QTL) regions [121]. Wang et al. reported 15 stable QTLs for fiber quality and later used transcriptome analysis using same population; the integration of DEGs and QTL identified 31 genes in 9 QTLs, of which 25 probably related to fibers, suggesting candidate genes for fiber quality improvements [122]. Using a chromosome segment substitution line, Lu et al. (2021) identified six QTLs associated with fiber length and two QTLs associated with fiber strength, and through integrating transcriptome and qPCR data, they identified four promising candidate genes for fiber length associated with those QTLs [123]. A SLAF-Seq-based approach to construct high-density genetic map for Identifying fiber quality related QTL using RILs of with introgression from G. barbadense identified 104 QTLs, comprising 67 for fiber quality and 37 for yield-related traits, and identified six putative candidate genes for stable QTL, including GhPEL6, GhCSLC6,and GhTBL5 for fiber length QTLs and GhCOBL4, GhMYB4 , andGhMYB85 for lint percentage QTLs [124].

The number of QTLs found for each fiber quality trait, their distributions in the genome, and the sources of favorable alleles from the respective polyploid progenitors have revealed a number of interesting findings about the genetic control of cotton fiber properties and the potential benefit of interspecific introgression. Introgressed alleles can improve Upland cotton fiber length, strength, elongation, and fineness; however, this also includes alleles from non-domesticated species with poor fiber quality as donor parents (Table 3). Nearly half of the QTLs were found in a small number of genomic regions known as ‘fiber QTL hotspots’, and the majority of the loci have predominantly additive gene action, confirming the long-held belief that polyploid Gossypium species are a source of valuable alleles for improving Upland cotton fiber quality. The high number of loci with minor effects, low level of consistency across loci discovered in various populations with the same pedigree, and absence of homoeologous linkage, however, underscore the overall difficulty of modifying these quantitatively inherited fiber properties. These findings show that lint fiber formation may be mediated by a complex gene network and that the evolution of spinnable fiber may have been mediated by coordinated changes in the expression of functionally different cotton genes. According to the enormous number of QTLs linked to the Dt-subgenome, which comes from an ancestor that does not generate spinnable fiber, it plays a substantial role in the genetic regulation of fiber growth and development. Despite the challenges of controlling alien alleles during introgressive breeding, a number of QTLs for fiber strength and length have now been successfully introgressed into Upland cotton, and their authenticity and improvement value has been confirmed using molecular markers: these QTLs are promising candidates for breeding using markers. Scientists from Nanjing Agricultural University in China, for example, have discovered a large fiber strength QTL (QTLFS1) on chromosome 24 in the germplasm line ‘Suyuan 7235,’ which is assumed to have been introgressed from the diploid species G. anomalum [115]. F2, F2: 3, backcross, and recombinant inbred mapping populations resulting from the cross of line ‘Suyuan 7235’ ‘TM-1’ were used to find this QTL [115,116]. QTLFS1 was shown to be stable in four test locations in China and the United States over two growing seasons [125], indicating that it might be a promising option for increasing Upland cotton germplasm fiber strength. Kumar et al. [109] tested this idea by introgressing this QTL region into two upland genotypes from the United States (‘Sealand 542’ and ‘Sealand 883’) with varied fiber strengths and found that segregating progenies bearing this QTL had enhanced fiber strength. This locus has now been independently demonstrated to possess at least three QTL clusters, with the allele from ‘Suyuan 7235’ imparting higher fiber strength, by utilizing a high marker density bordering the 10 cm gap inside the QTL region [109,126]. Shen et al. verified a fiber length QTL on Chromosome 1 (qFL-chr1) that was originally introgressed from G. barbadense using an inbred backcross technique [125]. The impacts of qFL-chr1 were identified in all three populations when planted in Nanjing, China, and Georgia in the United States over two years. The genetic effects of qFL-chr1 and QTLFS1 are small, with the donor alleles increasing fiber length and strength by just 1.45 mm [109] and 22.8 kN m kg^–1[125], respectively. However, the acquired genetic resources and DNA marker toolkits represent two substantial contributions to Upland cotton fiber quality enhancement. First, QTL-carrying near-isogenic lines provide a novel genetic source for enhancing fiber length and strength in Upland germplasm. As previously stated, Upland cotton has a limited gene pool as a result of its evolutionary history, domestication, and current plant breeding procedures. Because farmed germplasm is so closely related, many beneficial genes, particularly those linked to production and fiber quality, may have become fixed in the top gene pool. While some transgressive segregation in fiber properties will continue to be discovered through crossing among elite parents, the use of interspecific gene combinations such as these QTLs provides an important source of new genetic variation to ensure continued genetic gain in Upland cotton fiber improvement.