Fig. 6
From: Cotton pan-genome retrieves the lost sequences and genes during domestication and selection
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