Cotton Genomics and Genetics 2024, Vol.15, No.2, 93-102 http://cropscipublisher.com/index.php/cgg 96 transmission genetics and the evolutionary consequences of such genetic exchanges. These introgressions often involve complex interactions between subgenomes, as seen in polyploid species like G. hirsutum, where multilocus interactions predominantly occur within the Dt subgenome (Waghmare et al., 2016). 3.2 Mechanisms facilitating gene flow Several mechanisms facilitate gene flow between Gossypium species, including natural hybridization, human-mediated breeding programs, and the use of chromosome segment introgression lines (CSILs). Natural hybridization can occur in regions where different Gossypium species coexist, leading to spontaneous gene flow. Human-mediated breeding programs often involve controlled crosses and backcrosses to introduce desirable traits from one species into another. For example, the development of CSILs has been used to transfer long staple fiber quality traits fromG. barbadense into the G. hirsutumbackground, utilizing molecular marker-assisted selection to track and select for introgressed segments (Wang et al., 2012). Additionally, the use of synthetic amphiploids has enabled the introgression of genes from diploid species like G. arboreum into tetraploid species like G. hirsutum, despite the challenges posed by species isolation and chromosomal structural variations (Feng et al., 2021). 3.3 Detection and analysis of introgressed genes The detection and analysis of introgressed genes in Gossypiumspecies involve various genomic and bioinformatic techniques. Genome-wide association studies (GWAS) and quantitative trait locus (QTL) mapping are commonly used to identify introgressed loci associated with specific traits. For instance, GWAS and QTL mapping have been employed to detect fiber-micronaire-related haplotype blocks in G. barbadense, one of which was introgressed fromG. hirsutum(Wang et al., 2022). High-density genetic variation maps and specific locus amplified fragment sequencing (SLAF-seq) have also been utilized to identify introgression events and their effects on agronomic traits in both G. hirsutum and G. barbadense (Keerio et al., 2018; Nie et al., 2020). These methods allow researchers to pinpoint the genomic regions involved in introgression and assess their impact on phenotypic traits, thereby providing valuable insights for crop improvement and breeding programs. 4 Interspecific Introgression inGossypiumSpecies 4.1 Historical cases of introgression Interspecific introgression has played a significant role in the evolution and adaptation of Gossypium species. Historical genetic introgression between Gossypium hirsutumand Gossypium barbadense has been documented, with evidence suggesting that these events have contributed to the improvement of agronomic traits in both species. For instance, a study on the genetic variation in cotton varieties developed in Xinjiang, China, identified several interspecific introgression events that were beneficial for fiber quality and yield traits in both G. hirsutum and G. barbadense (Nie et al., 2020). These introgressions have significantly enhanced fiber strength, length, and yield, while also improving the plants’ adaptability to environmental stresses. Specifically, gene introgression events between G. barbadense and G. hirsutumhave played a crucial role in enhancing agronomic traits in cotton (Figure 2). Figure 2 from Nie et al. (2020) illustrates the impact of interspecific introgression, population differentiation, and gene flow between Gossypium barbadense and Gossypium hirsutum. The figure displays the genetic structure of different populations and the genomic distribution of introgression events, revealing how interspecific introgression reshapes the genomic architecture of cotton. The study indicates that these introgression events significantly affect fiber quality and agronomic traits in cotton. By selecting favorable haplotypes, it is possible to enhance cotton's adaptability and performance in various environments. These findings provide a scientific basis for further utilizing genetic diversity to improve cotton. 4.2 Modern examples and case studies Recent studies have further elucidated the role of interspecific introgression in modern cotton breeding. For example, a comprehensive interspecific haplotype map revealed that six introgressions fromG. hirsutum to G. barbadense were significantly associated with phenotypic performance, explaining a substantial portion of the variation in yield and fiber qualities (Fang et al., 2021). Another study focused on the breeding potential of
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