Biology subjects

Eriksson, S.

Publications and source records attributed to Eriksson, S..

3 recordsLinked to original sources

bioRxiv2026

Genomic insights into bacterial kidney disease resistance in Arctic charr (Salvelinus alpinus) via a 72k SNP array

Selection for disease resistance forms one of the most highlighted areas of aquaculture breeding. A breeding program for Arctic charr has been operating in Sweden for over 40 years, making it the oldest of its kind worldwide for this species. However, the lack of available genomic resources prevented selection for any disease-resistance traits. A 72k Axiom SNP array was produced in this study and used to assess the potential to select for charr resistant to bacterial kidney disease (BKD), which is currently a major threat to the industry. Following a challenge experiment with Renibacterium salmoninarum, the causative agent of BKD, relevant phenotypic proxies were collected from approximately 2,000 charr. Thereafter, those animals were genotyped with the new 72k SNP array. The magnitude of the estimated variance components suggested potential for breeding for BKD resistance in charr, with relevant heritabilities ranging from 0.05 to 0.56 depending on the resistance proxy used. In addition, GWAS suggested that BKD resistance is a polygenic trait. Furthermore, genomic prediction approaches indicated that BKD-resistant animals can be identified using their SNP genotypes. Accuracies, expressed as Pearson correlation coefficients, when BKD resistance was analysed as a continuous trait, ranged from 0.42 to 0.52. In the scenario where BKD resistance was treated as a binary trait, the efficiency of genomic prediction was assessed using ROC curves, with an area under the curve of 0.72. Finally, no unfavourable correlations were found with growth traits. The developed 72k SNP array has the potential of being a pivotal tool for the Swedish Arctic charr breeding program. Moreover, our data support the use of genomic prediction in breeding BKD-resistant Arctic charr. As a critical next step, further validations in actual industry conditions would be required.

genetics↗

bioRxiv2025

When large-effect damaging alleles enter small populations

Large-effect recessive damaging variants found at relatively high frequencies are common enough in domestic animals that they cause problems in breeding programs. There are several potential reasons. Deleterious variants may rise in frequency because of genetic drift, be driven to intermediate frequency by balancing selection by heterozygote advantage, or be spread by exceptionally influential parents, usually sires, that sometimes occur in animal breeding programs. Further, animal populations are often connected by migration. In this paper, we use a series of population genetic models to address how large-effect damaging alleles establish themselves in small populations, such as domestic animal populations or wild populations of mammals. The results confirm that a lethal allele under directional selection is fairly unlikely to become common, unless there are influential sire events with very large contributions or the population size is very small. On the other hand, a lethal allele under balancing selection can easily become common, especially if there are influential parents. When there is balancing selection, migration between connected populations effectively spreads alleles. The results accord with the many examples of recessive damaging alleles in domestic animals.

genetics↗

bioRxiv2020

A genome-wide scan for candidate lethal variants in Thoroughbred horses.

Recessive lethal variants often segregate at low frequencies in animal populations, such that two randomly selected individuals are unlikely to carry the same mutation. However, the likelihood of an individual inheriting two copies of a recessive lethal mutation is dramatically increased by inbreeding events. Such occurrences are particularly common in domestic animal populations, which are often characterised by high rates of inbreeding and low effective population sizes. To date there have been no published investigations into the presence of specific variants at high frequencies in domestic horse populations. This study aimed to identify potential recessive lethal haplotypes in the Thoroughbred horse breed, a closed population that has been selectively bred for racing performance. In this study, we scanned genotype data from Thoroughbred horses (n = 526) for adjacent single nucleotide polymorphisms (SNPs) at high heterozygote frequencies, but with a complete absence of homozygotes. Two SNPs that matched these criteria were mapped to an intronic region in the LY49B gene, indicating that a closely linked mutation may cause lethality in homozygous state. Despite a complete absence of homozygotes, almost 35% of Thoroughbreds included in these analyses were heterozygous for both SNPs. A similar loss or absence of homozygotes was observed in genotype data from other domestic horse breeds (n = 2030). Variant analysis of whole-genome sequence data (n = 90) identified two SNPs in the 3UTR region of the LY49B gene that may result in loss of function. Analysis of transcriptomic data from equine embryonic tissue revealed that LY49B is expressed in the trophoblast during placentation stage of development. In this study, a region in the LY49B gene was identified as a strong candidate for harbouring a variant causing lethality in homozygous state. These findings suggest that LY49B may have an essential, but as yet unknown function in the implantation stage of equine development. Further investigation of this region may allow for the development of a genetic test to improve fertility rates in horse populations. Identification of other lethal variants could assist in improving natural levels of fertility in horse populations. Author SummaryRecessive lethal mutations may reach high frequencies in livestock populations due to selective breeding practices, resulting in reduced fertility rates. In this study, we characterise recessive lethal mutations at high frequencies in the Thoroughbred horse population, a breed with high rates of inbreeding and low genetic diversity. We identified a haplotype in the LY49B gene that shows strong evidence of being homozygous lethal, despite having high frequencies of heterozygotes in Thoroughbreds and other domestic horse breeds. Two 3UTR variants were identified as most likely to cause loss of function in the LY49B gene, resulting in lethality. This finding provides novel insights into the potential importance of LY49B in equine development. Additionally, this study may assist with breeding strategies to improve fertility rates in the Thoroughbred and other domestic horse breeds.

bioinformatics↗