Development of InDel-Based Identification Methods for Wild and Domesticated Populations: A Case Study of Larimichthys...

Area of Science:

• Aquaculture Genetics
• Population Genomics
• Molecular Ecology

Background:

• Sustainable aquaculture relies on managing genetic resources from wild populations.
• Differentiating recently domesticated fish from wild stocks is challenging due to low genetic differentiation.

Purpose of the Study:

• To develop insertion/deletion (InDel)-based molecular markers for distinguishing wild and domesticated large yellow croaker (Larimichthys crocea).
• To establish a practical method for identifying population origins in aquaculture.

Main Methods:

• Whole-genome resequencing data was used to identify InDels with significant allele frequency differences between wild and domesticated populations.
• Two marker panels were developed: one with large-fragment InDels and another with coding-region InDels.
• Multi-locus scoring models and Receiver Operating Characteristic (ROC) analysis were employed to assess discriminatory power.

Main Results:

• Principal Component Analysis (PCA) showed partial separation between wild and domesticated groups.
• The developed InDel marker panels demonstrated high discriminatory performance, with Area Under the Curve (AUC) values of 0.9608 and 0.9771.
• Classification agreement rates reached 90.0% and 91.7%, indicating reliable identification of population status.

Conclusions:

• Targeted InDel markers offer a practical, PCR-based approach for distinguishing wild and domesticated large yellow croaker populations, even with limited genetic differentiation.
• This workflow provides a valuable reference for developing similar identification methods in other recently domesticated species.
• Further validation in independent populations is recommended for broader applicability.