Cotton Genomics and Genetics 2025, Vol.16, No.1, 39-47 http://cropscipublisher.com/index.php/cgg 42 upland cotton (Gossypium hirsutum) and sea island cotton (Gossypium barbadense) (Hu et al., 2019). Positively selected genes (PSGs) related to fiber improvement are mainly concentrated in the A subgenome, while genes related to stress resistance are mostly found in the D subgenome (Zhang et al., 2015). During fiber development, some genes show similar expression changes and form co-expression networks, indicating that selection and domestication have affected regulatory pathways (Chen et al., 2020). These marks left by domestication are very valuable targets for future breeding programs that want to improve fiber quality and stress resistance. 4.3 Introgression and hybridization Gene introgression and hybridization are also critical to the evolution and breeding of cotton. By constructing gene introgression populations, such as introducing useful chromosome segments from G. barbadense into G. hirsutum, researchers can more easily find quantitative trait loci (QTLs) related to high-quality fibers (Wang et al., 2018a). Some wild cotton relatives also provide many useful genes that can cope with environmental problems. Their genes can be introgressed into cultivated cotton, not only breaking through the recombination barrier, but also bringing new favorable alleles (Peng et al., 2022). These processes can increase the genetic diversity of cotton and improve its ability to adapt to the environment, which will help to continuously breed better cotton varieties. 5 Case Study: Comparative Genomics of G. hirsutumandG. barbadense 5.1 Background of the study region and cultivar focus Upland cotton (Gossypium hirsutum) and sea island cotton (Gossypium barbadense) are the two most widely planted allotetraploid cotton varieties. These two cottons are widely used because of their natural fiber yield. Upland cotton has high yield and strong adaptability, and can be grown in various environments; while sea island cotton is particularly popular because of its very good fiber quality (Figure2) (Hu et al., 2019). In recent years, scientists have successfully completed the assembly of high-quality reference genomes of these two varieties, TM-1 (upland cotton) and 3-79 (sea island cotton). These achievements provide an important basis for subsequent genetic comparison and breeding research. 5.2 Key comparative findings Comparative analysis of the genomes of upland cotton and sea island cotton revealed many structural differences. For example, large-scale inversions close to centromeres appeared on multiple chromosomes, and there were obvious differences in the centromere region (Meng et al., 2023). The two cottons differ in the expression of some genes, the number of gene families, and gene structure, and these differences are the key to their respective evolution and differentiation (Chang et al., 2023). In particular, the location and sequence changes of centromeres played an important role in the formation of species. In addition, comparison of mitochondrial genomes showed that there were also obvious differences in the number of genes and repeat sequences between the two (Tang et al., 2015). Through the analysis of QTLs and gene families such as R2R3-MYB, researchers found common and unique gene loci related to fiber quality, yield, and stress resistance of the two cottons (Said et al., 2015). 5.3 Outcomes and breeding implications These high-quality genome and comparative research results have greatly accelerated the discovery of quantitative trait loci (QTLs) and key genes related to fiber quality and yield in cotton (Wang et al., 2019). Researchers used gene introgression lines to introduce some high-quality chromosome fragments of sea island cotton into upland cotton, which can more accurately locate QTLs that control high-quality fiber traits, and also found some stable sites that improve fiber quality and yield at the same time (Wang et al., 2018a). Now, scientists are also using whole-genome introgression analysis and kmer genotyping methods to further identify useful alleles and fragments that are helpful for multiple traits, which will provide great help for future marker-assisted selection and target trait combinations (Li et al., 2022a). These technological advances provide new methods for combining the high-yield advantages of upland cotton with the high-quality fibers of sea island cotton, and are also expected to improve the economic benefits and agricultural value of cotton.
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