Dag Inge Våge

Reindeer and caribou (Rangifer tarandus) play key ecological, cultural, and economical roles across Arctic and Subarctic regions. However, genome-wide patterns of genetic diversity and population structure in semi-domesticated reindeer from Norway remain insufficiently characterized. Here we generated a high-quality chromosome-level genome assembly (GCA_965153185.1) for Norwegian semi-domesticated Eurasian tundra reindeer (Rangifer tarandus tarandus). The genome spans 2.54 Gb, with a scaffold N50 of 75.6 Mb, 96.1% complete Benchmarking Universal Single-Copy Orthologues, and 39,855 predicted protein-coding genes. Using this reference, we performed whole-genome resequencing of 175 individuals from five reindeer populations from Norway and 28 individuals from Iceland, identifying ~19.9 million genetic variants. Genetic differentiation was low among Norwegian populations (FST = 0.005 to 0.011), but substantially higher between Norway and Iceland (FST = 0.140 to 0.161). Populations from Norway exhibited similar levels of nucleotide diversity (π = 1.39 to 1.62 × 10−3), whereas the Icelandic population showed reduced diversity (π = 0.99 × 10−3) and approximately half as many segregating variants. Analyses of runs of homozygosity (ROH) and genome-wide heterozygosity indicated low levels of recent inbreeding across all populations, with long ROHs (>8 Mb) being rare. Despite reduced genetic diversity, the Icelandic population showed limited evidence of recent inbreeding. These patterns are consistent with contrasting demographic histories, with gene flow maintaining diversity among populations from Norway, while founder effects combined with long-term isolation have shaped the Icelandic population.

Trio-binning is a robust method for haplotype-separated assembly, providing the most accurate representation of diploid genomes including complex and haplotype-specific variation. Conventional trio-binning methods depend on parental short-read sequences to differentiate offspring reads originating from the maternal and paternal haplotypes. Here, we present a genotype-based trio-binning pipeline (GT-Trio) which reconstructs parent sequences based on phased parental genotypes and uses this as an alternative source of parental information for haplotype assembly. The GT-Trio pipeline was applied to assemble the maternal and paternal haplotypes of three Norwegian Red cattle individuals, using either imputed sequence variants or SNP array genotypes as input. Haplotypes assembled with GT-Trio using sequence variants as parental input demonstrated high phasing accuracy, similar to that achieved with conventional trio-binning. Using lower-density panels of array SNPs as input resulted in a decrease in phasing accuracy, but still substantially improved haplotype resolution compared to trio-free assembly. We show that the use of high-density parental information from short-reads or sequence variants increases the level of fragmentation in repeat-rich and low heterozygosity regions. Using lower-density parental information from array resolves the contiguity in these regions, but at the expense of phasing accuracy. Overall, GT-Trio provides a robust and scalable framework for haplotype assembly without parental sequencing and is available at https://github.com/theahettasch/GT-Trio .

Norwegian Red (NR) cattle are the main dairy breed in Norway, bred according to a broad breeding goal including health and fertility since the 1970s. Genomic studies on NR cattle have relied on the public Hereford reference, thus increasing the risk of missing or misrepresenting NR breed‐specific variation. Moreover, the Hereford reference is a pseudohaploid assembly, representing homologous chromosomes in a collapsed manner, which results in loss of haplotype‐specific alleles and misrepresentation of complex variants. To develop more refined NR‐specific resources, we utilised long‐read sequencing (PacBio HiFi + ONT) and trio‐binning to construct six new haplotype‐resolved assemblies representing NR genomes. These six NR2025 assemblies show high completeness (BUSCO: 95.82%–98.11%) and contiguity ( N ₅₀ : 73.8–88.5 Mb) and are accurately phased (hamming error rate: 0.46%–2.52%). Most autosomes have been assembled into the acrocentric centromere, and mapping of bovine satellite sequences reveals distinct organisational patterns of different satellite units across this highly repetitive region. The NR2025 assemblies provide a valuable resource for identification of novel variants and haplotypes in the NR population, which will enable more accurate association studies of genotype‐to‐phenotype relations and genomic predictions in NR cattle, ultimately enhancing the efficacy of selection for desirable traits.

Understanding how genetic drift and inbreeding can shape phenotypic traits and the expression of rare genetic variants can be important for conservation management in small and isolated populations. Following the recolonization of the grey wolf (Canis lupus) on the Scandinavian peninsula, the population has remained small and semi-isolated. The population traces back to seven founders, only and is highly inbred. Inbreeding depression has been demonstrated including effects on reproductive output and several congenital deformities. Some wolves also show anomalous coat color, characterized by hypopigmentation displayed as white tail tips, or even larger areas of white fur. In this study, we utilized four decades of monitoring data, dating back to the recolonization of the Scandinavian peninsula in 1983, to examine the occurrence of expressed anomalous coat color investigating its origin and inheritance, genetic architecture, and the effect of inbreeding. SNP genotyping revealed a distinct haplotype linked to the Melanocyte-inducing transcription factor (MITF) gene that co-segregated with anomalous coat color, suggesting a direct causal effect of this variant. The MITF gene regulates mammal melanocyte development, which in turn affects pigmentation. Our findings demonstrate that the identified gene variant is recessive, which in the homozygous state likely causes the disruption of normal melanocyte development, leading to unpigmented or hypopigmented areas. The origin of this haplotype was traced back to a third founder, reproducing for the first time in 1991. Indeed, the genetic constraints and subsequent inbreeding shaped by few founders, small population size, and semi-isolation over several decades point towards the importance of genetic diversity and facilitated gene flow between populations, but also how such vital immigration can bring about unforeseen side effects if inbreeding continues within the immigrant lineages.

Norwegian Red (NR) cattle are the main dairy breed in Norway, bred according to a broad breeding goal including health and fertility since the 1970s. Genomic studies on NR cattle have relied on the public Hereford reference, thus increasing the risk of missing or misrepresenting NR breed-specific variation. Moreover, the Hereford reference is a pseudohaploid assembly, representing homologous chromosomes in a collapsed manner, which results in loss of haplotype-specific alleles and misrepresentation of complex variants. To develop more refined NR specific resources, we utilised long-read sequencing (PacBio HiFi + ONT) and trio-binning to construct six new haplotype-resolved assemblies representing NR genomes. These six NR2025 assemblies show high completeness (BUSCO: 95.82-98.11%) and contiguity (N50: 73.8-88.5 Mb) and are accurately phased (hamming error rate: 0.46-2.52%). Most autosomes have been assembled into the acrocentric centromere, and mapping of bovine satellite sequences reveal distinct organisational patterns of different satellite units across this highly repetitive region. The NR2025 assemblies provide a valuable resource for identification of novel variants and haplotypes in the NR population, which will enable more accurate association studies of genotype-to-phenotype relations and genomic predictions in NR cattle, ultimately enhancing the efficacy of selection for desirable traits.

Several genes have variants that impact fecundity in mammals. We sequenced parts of some genes with internationally known high-fecundity variants in sheep from the northern Faroese islands. No known variant was found. Other variants were found, but none could be linked to twin/multiple births. This was further investigated using 362 ewes from four flocks and a genotyping array containing 51,646 ovine SNPs. We previously used these data to show that the genetic distance among the animals were clearly related to geography (as islands). When analysing genetic variations against fertility (measured as present and historical single or multiple births), only a single SNP showed statistical significance, and this was located outside any known coding region. When the four flocks were individually analysed, a few SNPs showed statistical significance in one flock, but not in other flocks. This strongly indicated that the hits were random and not functionally linked to high fertility. Thus, we were not able to find any gene or genome region that could be linked to high fertility or fecundity in Faroese sheep. Úrtak Fleiri ílegur hava avbrigdir, ið hava ávirkan á fruktabærið hjá súgdjórum. Vit sekvenseraðu nakrar ílegur, sum í øðrum londum eru kendar fyri at hava avbrigdir, ið kunnu setast í samband við høgt fruktabæri, fyri at vita, um tær eisini vóru í seyði í norðara parti av Føroyum. Ongar av hesum frukta-bærisavbrigdum vórðu funnar í føroyska seyðinum. Onnur avbrigdir vóru tó funnin, men eingi av teimum kundu knýtast at fleirlembum. Vit kannaðu eisini 362 ær úr fýra høgum í Føroyum, har vit nýttu eitt íleguúrval (genotyping array) við 51.646 seyðavbrigdum (Single Nucleotide Polymorphisms, SNPs). Vit hava áður brúkt hesar dátur til at vísa, at arvafrøðiliga fjarstøðan ímillum seyðin er týðiliga knýttur at, hvørjari oyggj seyðurin kemur úr. Tá arvaligi munurin varð samanborin við fruktabæri (núverandi og søguligar ein- og fleirlembur), var tað bert eitt avbrigdi, sum var hagfrøðiliga týðandi, men hetta avbrigdið var uttan fyri nakað kent proteinkotandi øki. Tá ærnar í hvørjum av teimum fýra høgunum vórðu samanbornar sínámillum, vóru tað nøkur fá avbrigdi, sum vóru hagfrøðiliga týðandi í einum haga, men sum ikki vóru tað í hinum høgunum. Hetta er ein sterk ábending um, at hesin munurin er tilvildarligur, og hevur ikki veruligt samband við fruktbærið hjá føroyska seyðinum. Sostatt funnu vit onga ílegu ella íleguøki, sum kann setast í samband høgt fruktabæri ella lambatal hjá føroyskum seyði.

Hyperactive sperm motility is important for successful fertilization. In the present study, a proteome profiling approach was performed to identify the differences between Landrace boars with different levels of hyperactive sperm motility in liquid extended semen. Two contrasts were studied: (i) high versus low levels of sperm hyperactivity at semen collection day and (ii) high versus low change in levels of sperm hyperactivity after 96 h semen storage. Testicular samples were analyzed on a Q Exactive mass spectrometer and more than 6000 proteins were identified in the 13 samples. The most significant differentially expressed proteins were mediator complex subunit 28 (MED28), cell division cycle 37 like 1 (CDC37L1), ubiquitin specific peptidase 10 (USP10), zinc finger FYVE-type containing 26 (ZFYVE26), protein kinase C delta (PRKCD), actinin alpha 4 (ACTN4), N(alpha)-acetyltransferase 30 (NAA30), C1q domain-containing (LOC110258309) and uncharacterized LOC100512926. Of the differentially expressed proteins, 11 have previously been identified as differentially expressed at the corresponding mRNA transcript level using the same samples and contrasts. These include sphingosine kinase 1 isoform 2 (SPHK1), serine and arginine rich splicing factor 1 (SRSF1), and tubulin gamma-1 (TUBG1) which are involved in the acrosome reaction and sperm motility. A mass spectrometry approach was applied to investigate the protein profiles of boars with different levels of hyperactive sperm motility. This study identified several proteins previously shown to be involved in sperm motility and quality, but also proteins with no known function for sperm motility. Candidates that are differentially expressed on both mRNA and protein levels are especially relevant as biological markers of semen quality.

Background: The accumulation of carotenoids in adipose tissue leading to yellow fat is, in sheep, a heritable recessive trait that can be attributed to a nonsense mutation in the beta-carotene oxygenase 2 (BCO2) gene. However, not all sheep breeds suffering from yellow fat have this nonsense mutation, meaning that other functional mechanisms must exist. We investigated one such breed, the Norwegian spælsau. Results: In spælsau we detected an aberration in BCO2 mRNA. Nanopore sequencing of genomic DNA revealed the insertion of a 7.9 kb endogenous Jaagsiekte Sheep Retrovirus (enJSRV) sequence in the first intron of the BCO2 gene. Close examination of its cDNA revealed that the BCO2 genes first exon was spliced together with enJSRV-sequence immediately downstream of a potential -AG splice acceptor site at enJSRV position 415. The hybrid protein product consists of 29 amino acids coded by the BCO2 exon 1, one amino acid coded by the junction sequence, followed by 28 amino acids arbitrary coded for by the enJSRV-sequence, before a translation stop codon is reached. Conclusions: Considering that the functional BCO2 protein consists of 575 amino acids, it is unlikely that the 58 amino acid BCO2/enJSRV hybrid protein can display any enzymatic function. The existence of this novel BCO2 allele represents an alternative functional mechanism accounting for BCO2 inactivation and is a perfect example of the potential benefits for searching for structural variants using long-read sequencing data.

Background: One objective of this study was to identify putative quantitative trait loci (QTL) that affect indicator phenotypes for growth, nitrogen, and carbon metabolism in muscle, liver, and adipose tissue, and for feed efficiency. Another objective was to perform an RNAseq analysis (184 fish from all families), to identify genes that are associated with carbon and nitrogen metabolism in the liver. The material consisted of a family experiment that was performed in freshwater and included 2281 individuals from 23 full-sib families. During the 12-day feed conversion test, families were randomly allocated to family tanks (50 fish per tank and 2 tanks per family) and fed a fishmeal-based diet labeled with the stable isotopes ¹⁵ N and ¹³ C at inclusion levels of 2 and 1%, respectively. Results: Using a linear mixed-model algorithm, a QTL for pre-smolt growth was identified on chromosome 9 and a QTL for carbon metabolism in the liver was identified on chromosome 12 that was closely related to feed conversion ratio on a tank level. For the indicators of feed efficiency traits that were derived from the stable isotope ratios ( ¹⁵ N and ¹³ C) of muscle tissue and growth, no convincing QTL was detected, which suggests that these traits are polygenic. The transcriptomic analysis showed that high carbon and nitrogen metabolism was associated with individuals that convert protein from the feed more efficiently, primarily due to higher expression of the proteasome, lipid, and carbon metabolic pathways in liver. In addition, we identified seven transcription factors that were associated with carbon and nitrogen metabolism and located in the identified QTL regions. Conclusions: Analyses revealed one QTL associated with pre-smolt growth and one QTL for carbon metabolism in the liver. Both of these traits are associated with feed efficiency. However, more accurate mapping of the putative QTL will require a more diverse family material. In this experiment, fish that have a high carbon and nitrogen metabolism in the liver converted protein from the feed more efficiently, potentially because of a higher expression of the proteasome, lipid, and carbon metabolic pathways in liver. Within the QTL regions, we detected seven transcription factors that were associated with carbon and nitrogen metabolism.

Background: The accumulation of carotenoids in adipose tissue leading to yellow fat is, in sheep, a heritable recessive trait that can be attributed to a nonsense mutation in the beta-carotene oxygenase 2 (BCO2) gene. However, not all sheep breeds suffering from yellow fat have this nonsense mutation, meaning that other functional mechanisms must exist. We investigated one such breed, the Norwegian spælsau. Results: In spælsau we detected an aberration in BCO2 mRNA. Nanopore sequencing of genomic DNA revealed the insertion of a 7.9 kb endogenous Jaagsiekte Sheep Retrovirus (enJSRV) sequence in the first intron of the BCO2 gene. Close examination of its cDNA revealed that the BCO2 genes first exon was spliced together with enJSRV-sequence immediately downstream of a potential - AG splice acceptor site at enJSRV position 415. The hybrid protein product consists of 29 amino acids coded by the BCO2 exon 1, followed by 29 amino acids arbitrary coded for by the enJSRV-sequence, before a translation stop codon is reached. Conclusions: Considering that the functional BCO2 protein consists of 575 amino acids, it is unlikely that the 58 amino acid BCO2/enJSRV hybrid protein can display any enzymatic function. The existence of this novel BCO2 allele represents an alternative functional mechanism accounting for BCO2 inactivation and is a perfect example of the potential benefits for searching for structural variants using long-read sequencing data.