Abstract

Coilia nasus is a key migratory fish species with significant economic and ecological importance. Its sister species, Coilia brachygnathus , exhibits minimal morphological differentiation but substantial genetic divergence and a markedly lower economic value compared to C. nasus . In this study, we employed whole-genome resequencing to analyze the genetic clustering, principal components, and population structure of both C. nasus and C. brachygnathus . We report the first discovery of natural hybridization between these species in Poyang Lake. Given the difficulty in identifying hybrids based on morphology, we screened for diagnostic genetic markers and identified a short interspersed nucleotide element, T41-2. This element contains a 37-bp InDel region that differs between the C. nasus and C. brachygnathus genomes. The T41-2 InDel marker can be amplified by PCR, visualized via agarose gel electrophoresis, and has been verified as a stable and effective tool for distinguishing C. nasus , C. brachygnathus , and their interspecific hybrids across populations. This represents the first InDel marker enabling rapid discrimination between C. nasus , C. brachygnathus , and their hybrids. This marker is invaluable not only for detecting natural hybrids but also for mitigating artificial hybridization within the Chinese aquaculture industry.