Fig. 6
From: Mapping intron retention events contributing to complex traits using splice quantitative trait locus
The IR event in GhGC1 (GH_D03G1277) and its association with cotton lint percentage (LP). a Manhattan plots for LP based on GWAS [51] and sQTL mapping (bottom). Each dot represents a single SNP. The GWAS plot shows a signal on chromosome D03 that is associated with lint percentage, and the cis-sQTL plot shows a signal in GhGC1 (D03:43241915:43241985:clu_81849). b Local Manhattan plot [51] and LD heat map (bottom) for the sSNP (D03:43244243). The arrowhead indicates the SNP in the candidate gene. The horizontal dashed line indicates the significance threshold (p-value < 1 × 10−5). Red box shows the sSNP locus, the orange box shows the pSNP locus, the blue box shows the GhGC1. c Visualization of GhGC1 transcript structure and genotype-specific splicing (TT, TC, and CC). The IGV screenshot [51] shows the total read numbers for each junction among individuals of different haplotypes. The structural schematic (bottom) shows the impact of IR on the GhGC1 protein. Retention of the 1st intron alters the predicted protein sequence and produces a premature stop codon (PTC). The red dotted box shows the IR locus. d Boxplot showing the difference of PSI explained by the haplotype (TT, TC, and CC) of sSNP D03:43244243. Boxes in box plots span from the first to third quartiles, and center lines indicate the second quartile (median). p-values were calculated by two-sided Student’s t-test. e Boxplot showing the difference in lint percentage (%) explained by the haplotype (TT, TC, and CC) of sSNP D03:43244243. Boxes in box plots span from the first to third quartiles, and center lines indicate the second quartile (median). p-values were calculated by two-sided Student’s t-test. f Transcriptomic level of GhGC1 in different tissues, including R (root), S (stem), and L (leaf), during ovule and fiber development, based on the FPKM values from a single experiment