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Sammanfattning

SNP arrays are indispensable tools for integrating genomic information into breeding programs. A SNP array for Nordic Arctic charr (Salvelinus alpinus) containing approximately 600,000 SNPs was developed from variants detected in Swedish, Norwegian and Icelandic farmed populations. In the current study, an in-depth analysis of the genetic diversity status of the Swedish population was conducted using high-quality SNPs. Animals from three non-overlapping year classes were genotyped (n = 382). Following quality control 169,873 SNPs were retained for downstream analysis. A principal components analysis (PCA) did not reveal any underlying genetic structure, in agreement with the background information of this population. A linkage disequilibrium (LD) decay analysis indicated a strong to moderate LD up to a physical distance of 300 kbp. In parallel, the LD estimates were used to estimate the effective population size (Ne), which declined from 260 (15 generations ago) to approximately 20 over the last four generations. Furthermore, runs of homozygosity (ROH) were detected, and inbreeding coefficients were estimated based on them. The median values of the inbreeding coefficients for the three year classes ranged from 14.4 % to 15.9 %. Nevertheless, those inbreeding estimates were primarily based on short ROH (<= 4Mbp), reflecting non-recent shared ancestry. The median inbreeding coefficients based on ROH longer than 4 Mbp, on the other hand, ranged between 8.3 % and 9.7 %. The produced SNP array is expected to be instrumental in the transition of the Nordic Arctic charr industry to the genomic era, allowing, among other things, for a more efficient management of the genetic diversity of captive populations.

Nyckelord

Aquaculture breeding; SNP array; Salmonids; Inbreeding; Runs of homozygosity; Islands of homozygosity

Publicerad i

Aquaculture Reports
2026, volym: 46, artikelnummer: 103369
Utgivare: ELSEVIER

SLU författare

UKÄ forskningsämne

Fisk- och akvakulturforskning

Publikationens identifierare

  • DOI: https://doi.org/10.1016/j.aqrep.2026.103369

Permanent länk till denna sida (URI)

https://res.slu.se/id/publ/146002