Fig. 4.

pannier is the major elytral colour pattering gene located at the h locus. a Genetic association studies of the h locus. Upper left panel, LOD plot for 4419 RAD tags deduced from genotyping BC1 progeny from the h^C−h^A F0 cross. RAD tags showing segregation patterns of markers located on the X chromosome were excluded from the analysis. The LOD score peaked at RAD tags in Linkage Group 2. RAD tags with complete association with elytral colour patterns corresponded to five genomic scaffolds including the three scaffolds adjacent to the pannier locus (lower bars). Upper right panel, the candidate genomic regions responsible for the major four h alleles. Lower bars, the three genomic scaffolds adjacent to the pannier locus. Grey, genes predicted from RNA-seq. Green, the pannier locus. Contiguity of the scaffolds was predicted based on the truncated genes at the end of scaffolds (Bgb and pnr (pannier)). Arrows indicate the respective candidate genomic regions responsible for each allele. pannier is included in all four relevant regions. The images of ladybird beetles are adapted from Fig. 1b. b Fold changes of gene expression in the presumptive red and black elytral epidermis around the candidate genomic region responsible for h. Grey and red bars on the bottom indicate predicted genes. Red, FDR < 0.01. Only pannier was significantly upregulated in this region at 72 h AP. The samples for RNA-seq were collected as depicted in the right panel in the h^C background. c Gene structures of pannier in H. axyridis. Exon number is indicated above each exon. 1A isoform cDNA was cloned by rapid amplification of cDNA ends (RACE). 2A−4B isoforms were predicted from RNA-seq analysis. pannier has at least four transcription start sites. Coding sequences are located from exon 2 to exon 5 (yellow). There are two alterative exons at exon 3 (3A and 3B), one encoding one of the two zinc finger domains of Pannier (A isoforms), and the other skipping that zinc finger domain (B isoforms)