Cotton Genomics and Genetics 2025, Vol.16, No.5, 222-231 http://cropscipublisher.com/index.php/cgg 227 Figure 2 Identification of the FL causal gene GbFL2 on chromosome At05. (a) Manhattan plot for FL. The dashed line represents the significance threshold (-log10P = 6). Effect values of genetic markers were tested using F tests and corrected for multiple testing using Bonferroni correction. (b) Local Manhattan plot (top) and LD heatmap (bottom) surrounding the peak on At05. The dashed line represents the significance threshold (-log10P = 5). Red arrows mark the position of the nonsynonymous SNP A05_16286973 in Gbar_A05G017500 (GbFL2). Red dotted lines show the candidate region. (c) Structure of GbFL2. Blue and yellow rectangles mark UTR and CDS respectively. (d) Box plot for FL, based on the haplotypes of the two SNPs. In the box plots, the centre line indicates the median. Box limits are the upper and lower quartiles, and whiskers mark the range of the data; n denotes the number of accessions with the same genotype. We used a two-tailed t-test to perform the significance analysis. (e) Haplotype distribution in diverse geographical regions and subpopulations. The bar chart on the left shows the number of two haplotypes in distinct countries. The map in the middle displays the ratio of two haplotypes in the different provinces of China. The column diagrams below represent the number of two haplotypes in different subpopulations. (f) Expression of GbFL2 in long-fibre accession XH58 (haplotype T) and short-fibre accession Ashi (haplotype G) at the fibre developmental stages (0, 5, 10, 15, 20, 25 DPA), detected by RNA-seq (FPKM value). Data are average values with standard deviation (n = 3 varieties with three technical repeats). Single (*), double (**) and triple (***) asterisks mark statistical significance levels of P < 0.05, 0.01 and 0.001 respectively. (g) qRT-PCR analysis of GbFL2 expression in wild-type (WT), transgenic lines with empty VIGS vector (pCLCrVA) and target gene GbFL2 (pCLCrVA-FL2) of long-fibre (L) accession XH58 and short-fibre (S) accession Ashi. The gene expression level in the long-fibre accession wild type (L_WT) was set to 1. GbUBQ7 is an internal control. (h) Fibre length (mm) of WT, pCLCrVA, (pCLCrVA-FL2 of long-fibre (L) accession XH58 and short-fibre (S) accession Ashi. (i) VIGS phenotypes of GbFL2. (j) The evolutionary origin of GbFL2 (Gbar_A05G017500). We built unrooted trees using the maximum-likelihood method in MEGA7, based on complete CDS sequences. (k) Selection analysis on homologous CDS sequences of GbFL2. Homologous sequence in each cotton species is represented by its genome name on the left side of the circle. The difference value (Ka-Ks) of each group of homologous comparisons is indicated by coloured rectangles according to the colour bar in the upper left corner. While Ka/Ks is generally used as an indicator of selective pressure, the presence of ‘Ks = 0’ here precludes this; therefore, we chose another indicator, that is ‘Ka-Ks’ value. Two types of selection effects, purifying selection (in red) and positive selection (in blue), are shown on the right side of the circle (Adopted from Zhao et al., 2022)
RkJQdWJsaXNoZXIy MjQ4ODYzNA==