Accurate Identification of Native Asian Honey Bee Populations in Jilong (Xizang, China) by Population Genomics and Deep Learning

Zhiyu Liu ¹, Yongqiang Xu ², Wei Sun ¹

⁰State Key Laboratory of Agricultural and Forestry Biosecurity, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agriculture University, Beijing 100193, China.

Insects +

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August 28, 2025

View abstract on PubMed

Summary

Honey bees (Apis cerana) in China's Jilong Valley form a unique genetic group. This discovery aids in conserving these vital pollinators and understanding their distinct lineage.

Area Of Science

Genomics and Population Genetics
Zoology and Entomology
Conservation Biology

Background

The Jilong Valley in Xizang, China, presents unique environmental conditions supporting Apis cerana populations.
Understanding Apis cerana population structure is crucial for conserving germplasm resources and genetic diversity.
Previous research has not fully elucidated the genetic distinctiveness of Apis cerana within the Jilong Valley.

Purpose Of The Study

To investigate the population structure and genetic lineage differentiation of Apis cerana in the Jilong Valley.
To identify genetic markers distinguishing Jilong Apis cerana from other regional populations.
To evaluate the efficacy of machine learning models in identifying honey bee lineages.

Main Methods

Collected Apis cerana specimens from 12 locations across the Jilong Valley.
Integrated publicly available sequencing data from mainland Asian Apis cerana, totaling 296 individuals.
Conducted population structure analysis using SNP data and employed FST screening to identify informative loci.
Trained a convolutional neural network (TraceNet) using identified SNP loci for lineage recognition.

Main Results

Apis cerana in the Jilong Valley represent a genetically distinct population, separate from other regional groups.
Identified specific SNP loci that significantly differentiate Jilong Apis cerana from non-Jilong populations.
The TraceNet model demonstrated high accuracy in recognizing Jilong versus non-Jilong Apis cerana lineages.

Conclusions

The Jilong Valley harbors a unique genetic lineage of Apis cerana, highlighting its ecological significance.
The identified SNP markers and TraceNet model provide effective tools for Apis cerana lineage identification.
Findings support targeted conservation strategies for Apis cerana germplasm resources in the Jilong Valley and similar regions.

Keywords:

Apis cerana lineage identification population genetics population structure

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