Cotton Genomics and Genetics 2025, Vol.16, No.5, 210-221 http://cropscipublisher.com/index.php/cgg 216 variations that are particularly crucial for breeding. This is also why pan-genome resources have become an important "supplement package" in trait improvement. Figure 2 An available pan-genome dataset for cotton breeding. a A four-step model of variation during cotton domestication and breeding. b The spectrum of gene allele frequencies at the causal SNP polymorphisms of COL2, CIP1, PRF3, LMI1, GRF, KCS2, and CesA6 in landrace and two geographic groups. c The spectrum of domesticated PAV allele frequ encies of seven genes in landrace and two geographic groups. d An example of functional PAV located on the A08 chromosome. The dashed line in Manhattan plot indicates the threshold for GWAS signals (P < 2.62 × 10- 8; -log P > 7.6). This locus includes four QTLs (lint percentage (LP), fiber weight per boll (FWPB), fiber micronaire (FM), fiber strength (FS)). e Four QTLs were displayed in a panel of multiple accessions. The two dashed lines represent GWAS thresholds for CNV (-log P > 6.45) and SNP (-log P > 4.42), respectively. f The phenotypic difference between presence and absence groups. The numbers below the violin plots show the accession numbers. The significance difference was calculated with a two-sided Wilcoxon rank-sum test (***P < 0.001, **P < 0.01). g Presence frequencies of Ghir_A08G006710 in 182 landrace, 206 GhImpUSO, and 592 GhImpCHN accessions (Adopted from Li et al., 2021)
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