| dc.description.abstract | Atlantic cod (Gadus morhua) and Atlantic halibut (Hippoglossus hippoglossus) are economically important fish species farmed in Norway. Loss of genetic diversity due to intense directional selection and early maturation of sex has been a bottleneck affecting their production. This study investigated inbreeding, population structure, and analysis and validation of gender probes in Atlantic cod and Atlantic halibut from 50K SNP genotyping data. Inbreeding was estimated using different statistics in Plink v1.9, namely inbreeding coefficient, linkage disequilibrium (LD), and runs of homozygosity (ROH). The true number of populations (K) was estimated using STRUCTURE 2.3.4 and STRUCTURE HARVESTER, while the gender probes were analysed and validated through QIAGEN CLC Genomics Workbench. The results showed a presence of inbreeding in both Atlantic cod and Atlantic halibut individuals with positive inbreeding coefficient values (>0 to <1). LD decay was observed with increase in distance between SNPs, but still with high average r² value > 0.2 and the number of individuals as well as the chromosomes having high LD (r² > 0.2) were detected. The ROH were characterized based on length, short (0 - 4 Mb) and long segments (≥ 4 Mb), and its distribution on chromosomes and individuals were analysed. In Atlantic cod and Atlantic halibut, ROH was identified in 304 and 28 individuals out of 378 individuals, while 48 and 7 individuals fell into a ROH class with longer segments (>16 Mb), respectively. Also, in Atlantic cod 13 out of 844 ROH and in Atlantic halibut 14 out of 68 ROH are found to have long ROH segments ≥ 10 Mb, indicating recent inbreeding. Population structure analysis determined the true number of populations (K) in Atlantic cod to be eight (i.e., K = 8) and two for Atlantic halibut (i.e., K = 2). Furthermore, gender probes analyses validated 30 probes in Atlantic cod and 67 probes in Atlantic halibut with clear signal intensities in male as compared to female and neo males. Blast searches with these probes as queries, along with use of the “Find binding sites and create Fragments” function in CLC Genomic Workbench against their respective genome assemblies confirmed that the 30 cod probes bind to chromosome 11 or LG 11 (GenBank sequence CM021420.1) and the 67 halibut probes bind to chromosome 13 or LG 13 (GenBank sequence CM020201.1) showing their exact binding coordinates. Thus, the information on inbreeding estimation could suggest the optimal breeding strategies for cod and halibut producers, while the validation of sex probes in their respective linkage groups have a great potential to be exploited in cod and halibut farming.
Keywords: Atlantic cod; Gadus morhua; Atlantic halibut; Hippoglossus hippoglossus; SNP; inbreeding coefficient; gender probes; runs of homozygosity; linkage disequilibrium | |