Genome-Wide Screening Reveals Sex-Specific SNP Markers in Pengba (Osteobrama belangeri)

Osteobrama belangeri , the state fish of Manipur, exhibits sexual dimorphism, with females growing faster than males, making it a promising candidate for monosex culture in aquaculture. To identify sex-associated SNP markers, whole-genome sequencing was performed on 20 individuals (10 males, 10 females) using the Illumina NovaSeq platform. Sequencing generated 40.5 GB of high-quality reads, which were assembled de novo into 5,49,073 scaffolds. SNP discovery revealed a total of 8,41,800 variants, including 9,636 male-specific and 21,045 female-specific SNPs. Among 363 candidate genes analysed, 68 contained 164 genic SNPs (36 exonic and 128 intronic) with a Ts/Tv ratio of 1.22. The exonic SNPs comprised 13 non-synonymous and 23 synonymous substitutions, with a shift in codon preference. Notably, 11 type I SNPs were identified across seven key sex-associated genes. Of these, four were non-synonymous, with three predicted to enhance protein stability in males, while only one such SNP was observed in females. These sex-associated SNPs represent promising markers for monosex culture, early sex determination, and reproductive trait studies. Their further validation could facilitate the development of SNP chips for marker-assisted selection in O. belangeri .