Development and validation of SNP markers in three Trachurus species using whole-genome sequencing

Düzgüneş Z. D., Tayhan Y., Çakmak E., Karakuş M., BEKTAŞ Y.

Conservation Genetics Resources, cilt.18, sa.2, 2026 (SCI-Expanded, Scopus) identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 18 Sayı: 2
  • Basım Tarihi: 2026
  • Doi Numarası: 10.1007/s12686-026-01424-x
  • Dergi Adı: Conservation Genetics Resources
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, BIOSIS, Chemical Abstracts Core
  • Anahtar Kelimeler: Population genetics, SNP markers, Stock management, Trachurus mediterraneus, Trachurus picturatus, Trachurus trachurus, Whole-genome sequencing
  • Karadeniz Teknik Üniversitesi Adresli: Evet

Özet

Horse mackerels (Trachurus spp.) of the family Carangidae (Perciformes) are small pelagic migratory fishes widely distributed in temperate to subtropical seas and represent one of Türkiye’s most commercially important groups, contributing about 5.2% of total marine fish production. However, Trachurus trachurus and T. mediterraneus stocks are under intense fishing pressure and face a high risk of depletion, while information on the stock structure of T. picturatus in Turkish waters remains limited. In this study, whole-genome sequencing (WGS) of three species (T. trachurus, T. mediterraneus, and T. picturatus) was conducted using Oxford Nanopore and Illumina NovaSeq platforms to identify single nucleotide polymorphisms (SNPs). For each species ten gene regions were chosen, amplified, and sequenced, resulting in the characterization of 26 bi-allelic polymorphic SNP loci in eight individuals per species. These validated SNPs constitute valuable molecular markers for population structure assessments, stock monitoring, and the development of species-based sustainable management strategies for Trachurus stocks in Turkish and surrounding waters.