First High-Density Linkage Map and Quantitative Trait Loci for Disease Resistance in Striped Catfish Pangasianodon hypophthalmus

While striped catfish (<i>Pangasianodon hypophthalmus</i>) is an economically important aquaculture species, its genomic resources remain limited. To date, linkage maps, QTL (quantitative trait loci) analyses, and the identification of candidate genes associated with disease resistance traits are very limited. Therefore, the present study aimed to construct a high-density linkage map and identify candidate genes for this species. Our analysis was conducted on a pedigree population consisting of 560 individuals (490 offspring and 70 parents for 40 families), whose genomes were analyzed using a genotyping-by-sequencing platform. After stringent filtering, 9882 high-quality SNPs were retained for linkage analysis. Linkage analysis placed 8786 markers onto 30 linkage groups (LGs), with an average density of 0.43 SNPs per cM. Recombination rates varied across the 30 linkage groups (LGs), averaging of 3.6 cM/Mb in males, 6.7 cM/Mb in females, and 5.1 cM/Mb when sex-averaged. Using the linkage map, our QTL analysis identified three significant QTLs for disease resistance to <i>Edwardsiella ictaluri</i>, the causative agent of Bacillary Necrosis of Pangasius (BNP). The QTLs were located on LG1, LG9 and LG29, and their peak markers explained 17.03% of the phenotypic variance. An LD-based interval of approximately ±25 kb surrounding the QTL peak was identified as the putative candidate region. However, subsequent genome-wide association analysis did not identify significant SNP effects within these regions, suggesting that the QTLs may represent polygenic or small-effect loci that are detectable only in linkage-based analyses. In summary, this study presents the first high-density SNP-based linkage map for striped catfish and reports significant QTL and associated candidate genes related to disease resistance and growth traits. These findings provide valuable insights into the genetic architecture of economically important traits in <i>P. hypophthalmus</i>. Nevertheless, further validation in independent populations is required before incorporating these markers into selective breeding programs.