Cotton Genomics and Genetics 2024, Vol.15, No.2, 93-102 http://cropscipublisher.com/index.php/cgg 99 and yield traits (Keerio et al., 2018). Additionally, genome-wide association studies (GWAS) have been employed to detect introgression events and selective sweep loci, providing insights into the genetic basis of agronomic traits in Gossypium hirsutumand Gossypium barbadense (Nie et al., 2020). Chromosome segment introgression lines (CSILs) have also been developed using molecular marker-assisted selection, allowing for the detailed analysis of introgressed segments and their effects on fiber quality traits (Wang et al., 2012). 6.2 Key genes and pathways involved Introgression events have been shown to introduce key genes and pathways that contribute to the adaptation and improvement of Gossypiumspecies. For instance, the introgression of haplotype blocks fromG. hirsutumto G. barbadense has been linked to significant improvements in fiber micronaire and other agronomic traits (Wang et al., 2022). In G. barbadense, specific introgressed loci have been associated with enhanced fiber yield and quality, highlighting the role of these genetic elements in the species' adaptation to different environments (Nie et al., 2020). Furthermore, genes involved in stress response, digestive absorption, and secondary metabolite synthesis have been identified as having significant introgression signals, suggesting their importance in environmental adaptation and biocomponent metabolism (Jiang et al., 2022). 6.3 Functional genomics and transcriptomics Functional genomics and transcriptomics approaches have provided deeper insights into the molecular mechanisms underlying introgression and its effects on Gossypium species. The use of high-density genetic variation maps has revealed the correlation between asymmetric interspecific introgressions and the improvement of agronomic traits in both G. hirsutum and G. barbadense (Nie et al., 2020). Transcriptomic analyses have identified key genes with pleiotropic effects that control multiple traits, such as growth period, plant architecture, and vegetative growth habit, further elucidating the complex genetic interactions resulting from introgression (Wang et al., 2022). Additionally, the integration of metabolomic data with genomic analyses has highlighted the role of specific genes, such as CYP512U6, in the biosynthesis of important secondary metabolites, demonstrating the functional impact of introgressed genes on the metabolic pathways of Gossypiumspecies (Jiang et al., 2022). 7 Challenges and Controversies 7.1 Barriers to introgression Despite the potential benefits, several barriers to successful introgression exist. One major challenge is the genetic incompatibility between species, which can hinder the transfer of desirable traits. For example, while interspecific introgression has been shown to improve certain traits in G. barbadense, it often comes with trade-offs, such as decreased fiber quality when yield is increased, and vice versa (Fang et al., 2021). Additionally, the narrow genetic base of G. hirsutum poses a significant barrier, limiting the effectiveness of introgression from G. barbadense (Zhang et al., 2016). 7.2 Potential negative consequences The process of introgression is not without its potential drawbacks. One concern is the possibility of introducing deleterious alleles along with beneficial ones, which can negatively impact the overall fitness of the recipient species. For instance, while introgression has been shown to improve fiber yield in G. barbadense, it can also lead to a decrease in fiber quality (Nie et al., 2020; Fang et al., 2021). Moreover, the introduction of foreign genetic material can disrupt existing gene networks, leading to unforeseen phenotypic consequences. 7.3 Ethical and ecological considerations The ethical and ecological implications of interspecific introgression must also be carefully considered. From an ethical standpoint, the manipulation of genetic material between species raises questions about the long-term impacts on biodiversity and the natural evolutionary processes. Ecologically, the introduction of new genetic material can have unpredictable effects on local ecosystems, potentially leading to the displacement of native species or the disruption of existing ecological balances (Hamilton and Miller, 2016). Conservation practitioners have traditionally been wary of hybridization due to these potential risks, although some argue that adaptive introgression could be a valuable tool for enhancing the evolutionary potential of species in the face of climate change (Hamilton and Miller, 2016).
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