Cotton Genomics and Genetics 2024, Vol.15, No.2, 81-92 http://cropscipublisher.com/index.php/cgg 87 The upper panel shows the phylogenetic tree based on whole-genome SNPs, and the lower panel shows the population structure analysis based on different cluster numbers (K=2 and K=3). The branch colors are consistent with Figure 2a. The phylogenetic tree shows that A1 andA2 genomes cluster into two independent branches, validating their independent evolution and providing evidence for understanding the independent evolution of A1 andA2 genomes (Adapted from Huang et al., 2020) 5.5 Evolutionary dynamics and genome variation The evolutionary dynamics and genome variation within Gossypium species pose significant challenges to taxonomy. The activity of genome-specific repetitive sequences, such as the ICRd motif in the D genome, contributes to genome variation and complicates the understanding of evolutionary relationships (Lu et al., 2020). The structural variations and gene expression changes observed in allotetraploid cotton species highlight the ongoing evolutionary processes that influence genome architecture and species differentiation (Hu et al., 2019). These dynamic evolutionary changes necessitate continuous updates to taxonomic classifications to reflect the current understanding of Gossypiumgenomics. 6 Applications of GossypiumTaxonomy in Breeding and Conservation 6.1 Implications for cotton breeding programs The taxonomic classification of Gossypium has profound implications for cotton breeding programs. Understanding the genetic diversity and evolutionary history of Gossypiumspecies allows breeders to identify and utilize favorable traits from wild and domesticated species. For instance, the reference genome sequences of Gossypium hirsutumand Gossypium barbadense have facilitated the identification of quantitative trait loci (QTLs) associated with superior fiber quality, which can be introgressed into breeding lines to improve cotton varieties (Hu et al., 2019; Wang et al., 2019). Additionally, the genetic analysis of mutagenesis in wild cotton species has identified candidate genes related to flowering traits, which can be used in marker-assisted selection to develop early-flowering and high-yielding cotton varieties (Kushanov et al., 2022). 6.2 Conservation strategies for wildGossypiumspecies Conservation of wild Gossypium species is crucial for maintaining genetic diversity, which is essential for the long-term sustainability of cotton breeding programs. The genetic diversity of Gossypium populations in Amazonian native communities highlights the importance of preserving these genetic resources (Morales-Aranibar et al., 2023). Conservation strategies should focus on protecting natural habitats and promoting in situ conservation of wild species. Additionally, ex situ conservation methods, such as seed banks and botanical gardens, can be employed to safeguard genetic material for future use in breeding programs (Peng et al., 2022; Morales-Aranibar et al., 2023). 6.3 Utilization of genetic diversity The genetic diversity within the Gossypium genus provides a valuable resource for improving cotton crops. Comparative genomics and phylogenetic studies have revealed extensive structural variations and gene family expansions that contribute to the adaptation and resilience of different Gossypiumspecies (Wu et al., 2018; Hu et al., 2019). By leveraging this genetic diversity, breeders can introduce traits such as disease resistance, drought tolerance, and improved fiber quality into cultivated cotton varieties. The identification of divergence hotspot regions and site-specific selection in chloroplast genomes further aids in understanding the evolutionary relationships and potential for genetic improvement (Wu et al., 2018). 6.4 Case studies in breeding and conservation Several case studies illustrate the successful application of Gossypium taxonomy in breeding and conservation efforts. For example, the introgression of favorable chromosome segments from Gossypium barbadense into Gossypium hirsutumhas led to the development of cotton lines with enhanced fiber quality (Wang et al., 2019). Wang et al. (2019) conducted a detailed analysis of the reference genome sequences of two cultivated cotton species, Gossypium hirsutum and Gossypium barbadense. The study employed single-molecule real-time sequencing, optical mapping, and high-throughput chromosome conformation capture techniques to construct high-quality genome assemblies for both species. Comparative genomic analysis revealed multiple structural variations. Additionally, a backcross population incorporating the superior fiber traits of G. barbadense was
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