Cotton Genomics and Genetics 2024, Vol.15, No.2, 103-111 http://cropscipublisher.com/index.php/cgg 108 while Chr02 had the fewest (21 markers). The longest chromosome was Chr12 (103.563 cM), and the shortest was Chr02 (28.665 cM). Notably, 15.783% of the markers deviated from the Mendelian ratio, with Chr07 and Chr11 having the most distorted loci. Eight SDRs were identified, with large clusters of segregation distortions on Chr02, Chr06, Chr07, and Chr11, skewed towards heterozygous alleles. This comprehensive mapping provides valuable insights for understanding genetic inheritance and potential regions of interest for further breeding programs. Figure 2 Genetic maps for the 13 chromosomes of the F2interspecific individuals derived between G. thurberi and G. trilobum (Adopted from Li et al., 2018) Image caption: The markers in blue are distorted while markers in red and underlined indicates the distorted regions per chromosomes (Adopted from Li et al., 2018) 5.5 Case study: QTL mapping for fiber quality and yield QTL mapping has been instrumental in improving both fiber quality and yield in cotton. A study on introgression lines derived fromGossypium hirsutumand G. tomentosumidentified 74 QTLs associated with fiber quality and yield traits. These QTLs were distributed across multiple chromosomes, with significant positive additive effects observed for both fiber and yield traits. The identified QTLs and developed introgression lines provide a valuable resource for molecular breeding aimed at enhancing fiber quality and yield in Upland cotton (Keerio et al., 2018). 6 Challenges and Future Directions 6.1 Technical challenges in cytogenetic marker application The application of cytogenetic markers in Gossypiumbreeding programs faces several technical challenges. One significant issue is the complexity of the cotton genome, which includes a high level of repetitive DNA sequences such as tandem repeats (TRs) and satellite DNA (satDNA). These repetitive elements can complicate the identification and mapping of specific markers (Kroupin et al., 2019). Additionally, the presence of cryptic species and species complexes within the Gossypiumgenus can lead to difficulties in establishing common genetic pools, further complicating the use of cytogenetic markers for hybrid identification and breeding. The variability in heterochromatin distribution among different strains and hybrids also poses a challenge, as it can affect the consistency and reliability of marker-based identification (Goes et al., 2020). 6.2 Integration with genomic and bioinformatic tools To overcome these technical challenges, the integration of cytogenetic markers with advanced genomic and bioinformatic tools is essential. Recent advancements in whole-genome sequencing and bioinformatics have enabled the rapid and cost-effective identification of TRs and satDNA, which can be converted into molecular cytogenetic markers. The development of pipelines for high-throughput screening and the use of quantitative PCR (qPCR) for preliminary estimation of TR abundance facilitate the selection of the most abundant and prospective TRs for marker development. Furthermore, the use of fluorescence in situ hybridization (FISH) with probes prepared through PCR amplification of TR units can enhance the accuracy and efficiency of chromosome karyotyping in Gossypiumspecies (Kroupin et al., 2019).
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