Whole-Genome Resequencing−Based Qualitative Trait Locus Mapping Correlated yellow with the Mutant Color in Honeybees, Apis cerana cerana

TL;DR

This study identifies the yellow gene as responsible for a brown body color mutation in honeybees using genome resequencing and gene expression analysis.

Contribution

The study identifies the yellow gene as the causal locus for a brown body color mutation in honeybees using genome resequencing and RNA interference.

Findings

The yellow gene on chromosome 11 is linked to the brown body color mutation in honeybees.

A 2-base deletion in exon 4 of the yellow gene causes a frameshift mutation.

RNA interference of the yellow gene results in lighter cuticle coloration without affecting survival.

Abstract

This study examined the genetic basis of a mutation in cuticle color in the honeybee Apis cerana cerana using genome resequencing of wild−type and mutant drones produced by a single virgin queen. A candidate locus was identified by calculating the Euclidean distance between mutants and wild types at each SNP, performing Lowess regression to fit a curve to these data, and setting a threshold of the top 0.5% Euclidean distance for candidate region selection. From this, genes with synonymous substitutions became candidate genes. One of these genes, the yellow gene, had a 2 bp deletion causing a frameshift mutation. RT−qPCR of this gene was performed on RNA extracted from mutant and wild−type drones; gene expression was only significantly different between wild types and mutants at the yellow gene. Finally, RNA interference silencing of the yellow gene was used to reduce yellow gene expression in workers and putatively result in a lighter coloration. These results indicate that the yellow gene participated in the body pigmentation, and its defect was responsible for the brown mutation. It promotes the understanding of the molecular basis of body coloration in honeybees, enriching the molecular mechanisms underlying insect pigmentation.

The honeybee, Apis cerana cerana (Ac), is an important pollinator and has adapted to the local ecological environment with relevant coloration. The cuticle coloration of the brown (br) mutant is brown instead of black in wild−type individuals. Therefore, this study aimed to identify and characterize the gene responsible for the br mutation. Genome resequencing with allele segregation measurement using Euclidean distance followed by Lowess regression analysis revealed that the color locus linked to the mutation was located on chromosome 11. A 2−base deletion on exon 4 was identified in the g7628 (yellow) gene after genome assembly and sequence cloning. In addition, the cuticle color of the abdomen of worker bees changed from black to brown when a defect was induced in the yellow gene using short interfering RNA (siRNA); however, the survival rate did not decrease significantly. These results indicate that the yellow gene participated in the body pigmentation, and its defect was responsible for the br mutation. This study promotes the understanding of the molecular basis of body coloration in honeybees, enriching the molecular mechanisms underlying insect pigmentation.

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