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

The rapid expansion of aquaculture breeding has increased the need to identify wild genetic resources for germplasm management and sustainable breeding. However, distinguishing wild from domesticated populations remains challenging in species with recent domestication histories and low genetic differentiation. In this study, we used the large yellow croaker (Larimichthys crocea) as a case study species to develop specific insertion/deletion (InDels)-based identification methods for wild and domesticated populations based on whole-genome resequencing data. Four large-fragment InDels with significant allelic frequency differences between populations were selected as one marker panel. In addition, four coding-region InDels predicted to alter amino acid sequences were selected as another marker panel based on allele-frequency differences, coding-region annotation, and supporting SNP-based Fst or nucleotide-diversity signals. Principal component analysis (PCA) based on these selected InDel loci showed partial separation with some overlap between wild and domesticated samples. Therefore, multi-locus scoring models were established by assigning scores to wild-predominant alleles. Receiver operating characteristic (ROC) analysis showed strong discriminatory performance for both panels, with area under the ROC curve (AUC) values of 0.9608 and 0.9771 and classification agreement rates with known sample status of 90.0% and 91.7%, respectively. These results indicate that targeted InDel markers can provide a practical PCR-based approach for distinguishing wild and domesticated large yellow croaker populations with limited genetic differentiation. This workflow may provide a reference for marker development in other recently domesticated species, although further validation in independent populations and target species is needed.