Cotton Genomics and Genetics 2024, Vol.15, No.2, 112-126 http://cropscipublisher.com/index.php/cgg 120 NGS has facilitated the discovery of QTLs linked to traits such as fiber quality, yield, and resistance to biotic and abiotic stresses (Le Nguyen et al., 2019; Kushanov et al., 2021). The ability to sequence large populations and perform detailed genetic analyses has accelerated the identification of candidate genes underlying these QTLs, which can then be targeted in marker-assisted selection (MAS) programs to develop improved cotton varieties (Sahu et al., 2020). Figure 4 SNP distribution and phylogenetic relationship inGossypium hirsutum(Adapted from Wang et al., 2022) Image caption: The A illustrates the distribution of SNP markers across the chromosomes of upland cotton (Gossypium hirsutum). The horizontal axis represents the length of each chromosome, with each band corresponding to a specific chromosome. Chromosomes are divided into 1 Mb segments, with color intensity indicating SNP marker density: darker colors represent higher SNP densities, while lighter colors indicate lower densities. SNP markers are densely populated at the chromosome ends, while marker density is lower near the centromeric regions. This distribution pattern aligns with the characteristic that chromosome ends are rich in functional genes, while centromeric regions are dominated by repetitive sequences. This visualization provides insight into the genomic landscape of upland cotton, highlighting regions with significant genetic variation and those with less diversity; The B presents a phylogenetic tree of upland cotton samples constructed based on SNP markers. Each branch represents a sample, with different colors indicating various geographical origins, including samples from inland China, the Yellow River Basin, the Yangtze River Basin, ultra-early maturity cotton regions, Central Asia, and the United States. The figure clearly shows that upland cotton varieties cluster according to their geographical origins, but there is also a certain degree of dispersion within varieties from the same
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