Discovery of Natural Hybridization and Development of an Efficient Identification Marker Between Coilia Nasus and Coilia Brachygnathus

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.