Mapping of Growth-Associated SNP Markers in Asian Seabass (Latest calcarifer) Using the Marey Map Approach

The aims of this study were to investigate marker-growth trait associations and construct a SNP-based linkage map for an Asian seabass (KU) population from Thailand. First, we performed GWAS using phenotypes (weight and length) and genotypes (25,647 SNPs) for 1100 390-day-old fish. We selected the top 70 SNPs with allele substitution effects, ranging from 6.84 to 81.91 g for weight and from 0.12 to 1.8 cm for length for further analyses. Cross-validation of 70 SNPs using GBLUP yielded breeding value prediction accuracies 0.65 to 0.70. Second, we utilized previously published genome-wide SNPs and mapping data from multiple populations and the KU data to predict the genetic linkage map for the KU population using the Marey map approach. The KU linkage map consisted of 24 chromosomes spanning 567 Mb, with average marker spacing of 0.07 cM. The number of markers ranged from 598 to 1334, with an average of 1099 markers per chromosome. The predicted local recombination rates varied from 4.76 to 43.40 cM/Mb with an average of 2.35 cM/Mb. Lastly, Kompetitive allele-specific PCR (KASP) markers were developed from 70 SNPs and validated in 200 fish. The KASP assays were successful for all 70 SNPs in 196 fish with SNP call rates of 98.2 to 100%. Fifty-eight SNPs were found to have segregated across the genome, except for chromosomes 23 and 24. The linkage map obtained in this study provides a framework for future QTL mapping of growth-related traits in the KU population.