Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions

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Gene Expression Profiling of Corpus luteum Reveals Important Insights about Early Pregnancy in Domestic Sheep

The majority of pregnancy loss in ruminants occurs during the preimplantation stage, which is thus the most critical period determining reproductive success. Here, we performed a comparative transcriptome study by sequencing total mRNA from corpus luteum (CL) collected during the preimplantation stage of pregnancy in Finnsheep, Texel and F1 crosses. A total of 21,287 genes were expressed in our data. Highly expressed autosomal genes in the CL were associated with biological processes such as progesterone formation (STAR, CYP11A1, and HSD3B1) and embryo implantation (e.g., TIMP1, TIMP2 and TCTP). Among the list of differentially expressed genes, sialic acid-binding immunoglobulin (Ig)-like lectins (SIGLEC3, SIGLEC14, SIGLEC8), ribosomal proteins (RPL17, RPL34, RPS3A, MRPS33) and chemokines (CCL5, CCL24, CXCL13, CXCL9) were upregulated in Finnsheep, while four multidrug resistance-associated proteins (MRPs) were upregulated in Texel ewes. A total of 17 known genes and two uncharacterized noncoding RNAs (ncRNAs) were differentially expressed in breed-wise comparisons owing to the flushing diet effect. The significantly upregulated TXNL1 gene indicated potential for embryonic diapause in Finnsheep and F1. Moreover, we report, for the first time in any species, several genes that are active in the CL during early pregnancy (including TXNL1, SIGLEC14, SIGLEC8, MRP4, and CA5A).202

Differences in Adipose Gene Expression Profiles between Male and Female Even Reindeer (Rangifer tarandus) in Sakha (Yakutia)

Reindeer are native to harsh northern Eurasian environments which are characterized by long and cold winters, short summers, and limited pasture vegetation. Adipose tissues play a significant role in these animals by modulating energy metabolism, immunity, and reproduction. Here, we have investigated the transcriptome profiles of metacarpal, perirenal, and prescapular adipose tissues in Even reindeer and searched for genes that were differentially expressed in male and female individuals. A total of 15,551 genes were expressed, where the transcriptome profile of metacarpal adipose tissue was found to be distinct from that of perirenal and prescapular adipose tissues. Interestingly, 10 genes, including PRDM9, which is known to have an important role in adaptation and speciation in reindeer, were always upregulated in all three tissues of male reindeer

EquCab_Finn: A new reference genome assembly for the domestic horse, Finnhorse

Finnhorse is Finland's native and national horse breed and it has genetic affinities to northern European and Asian horses. It has historical importance for agriculture, forest work and transport and as a war horse. Finnhorse has four breeding sections in the studbook and is under conservation and characterisation efforts. We sequenced and annotated the genome of a Finnhorse mare from the working horse section using PacBio and Omni-C data. This genome can complement the existing Thoroughbred reference genome (EquCab 3.0) and facilitate genetic studies of horses from northern Eurasia. We assembled 2.4 Gb of the genome with an N50 scaffold length of 83.8 Mb and the genome annotation resulted in a total of 19 748 protein coding genes of which 1200 were Finnhorse specific. The assembly has high quality and synteny with the current horse reference genome. We manually curated five genes of interest and deposited the final assembly in the European Nucleotide Archive under the accession no. PRJEB71364

Pure wild forest reindeer (Rangifer tarandus fennicus) or hybrids? A whole-genome sequencing approach to solve the taxonomical status

In Finland, the geographic distribution of domestic reindeer (Rangifer tarandus tarandus) and Finnish wild forest reindeer (Rangifer tarandus fennicus) partly overlap in the vicinity of the southern border of the reindeer herding area. Additionally, domestic reindeer are occasionally kept as pets within the distribution range of the wild forest reindeer. Hybridisation of these two subspecies is one of the major threats for the wild forest reindeer population. Concerns about potential hybridisation served as the catalyst also for this study, which we aimed to clarify the taxonomic status of presumed wild forest reindeer individuals intended as founder individuals for a reintroduction project. To do this, we resequenced genomes of four Rangifer tarandus individuals with unknown taxonomical status and investigated their ancestries by comparing the genomic data with the existing resequenced data of the Finnish domestic reindeer and Finnish wild forest reindeer. The genetic relationship investigations indicated that all individuals we analysed were pure wild forest reindeer, making them suitable as founder individuals for the reintroduction project. Thus, our study provided critical knowledge for practical conservation action, where it was essential to recognise each individual’s origin. In the future, it will also offer novel insights into the spread of native wild forest reindeer to new geographic regions in Finland. For subsequent studies, additional resequenced genomic data of Rangifer individuals will be needed to develop an ancestry information marker panel of single nucleotide polymorphisms for rapid and cost-effective identification of hybrid individuals of these subspecies

Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies

Reindeer, called caribou in North America, has a circumpolar distribution and all extant populations belong to the same species (Rangifer tarandus). It has survived the Holocene thanks to its immense adaptability and successful coexistence with humans in different forms of hunting and herding cultures. Here, we examine the paternal and maternal history of Rangifer based on robust Y-chromosomal and mitochondrial DNA (mtDNA) trees representing Eurasian tundra reindeer, Finnish forest reindeer, Svalbard reindeer, Alaska tundra caribou, and woodland caribou. We first assembled Y-chromosomal contigs, representing 1.3 Mb of single-copy Y regions. Based on 545 Y-chromosomal and 458 mtDNA SNPs defined in 55 males, maximum parsimony trees were created. We observed two well separated clades in both phylogenies: the “EuroBeringian clade” formed by animals from Arctic Islands, Eurasia, and a few from North America and the “North American clade” formed only by caribou from North America. The time calibrated Y tree revealed an expansion and dispersal of lineages across continents after the Last Glacial Maximum. We show for the first time unique paternal lineages in Svalbard reindeer and Finnish forest reindeer and reveal a circumscribed Y haplogroup in Fennoscandian tundra reindeer. The Y chromosome in domesticated reindeer is markedly diverse indicating that several male lineages have undergone domestication and less intensive selection on males. This study places R. tarandus onto the list of species with resolved Y and mtDNA phylogenies and builds the basis for studies of the distribution and origin of paternal and maternal lineages in the future

Whole-genome sequencing provides novel insights into the evolutionary history and genetic adaptation of reindeer populations in northern Eurasia

Domestic reindeer (Rangifer tarandus) play a vital role in the culture and livelihoods of indigenous people across northern Eurasia. These animals are well adapted to harsh environmental conditions, such as extreme cold, limited feed availability and long migration distances. Therefore, understanding the genomics of reindeer is crucial for improving their management, conservation and utilisation. In this study, we have generated a new genome assembly for the Fennoscandian domestic reindeer with high contiguity, making it the most complete reference genome for reindeer to date. The new genome assembly was utilised to explore genetic diversity, population structure and selective sweeps in Eurasian Rangifer tarandus populations which was based on the largest population genomic dataset for reindeer, encompassing 58 individuals from diverse populations. Phylogenetic analyses revealed distinct genetic clusters, with the Finnish wild forest reindeer (Rangifer tarandus fennicus) standing out as a unique subspecies. Divergence time estimates suggested a separation of ~ 52 thousand years ago (Kya) between the northern European Rangifer tarandus fennicus and Rangifer tarandus tarandus. Our study identified four main genetic clusters: Fennoscandian, the eastern/northern Russian and Alaskan group, the Finnish forest reindeer, and the Svalbard reindeer. Furthermore, two independent reindeer domestication processes were inferred, suggesting separate origins for the domestic Fennoscandian and eastern/northern Russian reindeer. Notably, shared genes under selection, including retroviral genes, point towards molecular domestication processes that aided adaptation of this species to diverse environments

Adipose gene expression profiles in Northern Finncattle, Mirandesa cattle, Yakutian cattle and commercial Holstein cattle

The drastic change in global climate has led to in-depth studies of the geneticresources of native cattle adapted to challenging environments. Native cattle breeds may harbor unique genetic mechanisms that have enabled them adapt to their given environmental conditions. Adipose tissues are key factors in the regulation of metabolism and energy balance and are crucial for the molecular switches needed to adapt to rapid environmental and nutritional changes. The transcriptome landscape of four adipose tissues was used in this study to investigate the differential gene expression profiles in three local breeds, Yakutian cattle (Sakha Republic), Northern Finncattle (Finland), Mirandesa cattle (Portugal) and commercial Holstein cattle. A total of 26 animals (12 cows, 14 bulls) yielded 81 samples of perirenal adipose tissue (n = 26), metacarpal adipose tissue (n = 26), tailhead adipose tissue (n = 26) and prescapular adipose tissue (n = 3). More than 17,000 genes were expressed in our dataset. Principal component analysis of the normalized expression profiles revealed a differential expression profile of the metacarpal adipose tissue. We found that the genes upregulated in the metacarpal adipose tissue of Yakutian cattle, such as NR4A3, TEKT3, and FGGY, were associated with energy metabolism and response to cold temperatures. In Mirandesa cattle, the upregulated genes in perirenal adipose tissue were related to immune response and inflammation (AVPR2, CCN1, and IL6), while in Northern Finncattle, the upregulated genes appeared to be involved in various physiological processes, including energy metabolism (IGFBP2). According to the sex-based comparisons, the most interesting result was the upregulation of the TPRG1 gene in three tissues of Yakutian cattle females, suggesting that adaptation is related to feed efficiency. The highest number of differentially expressed genes was found between Yakutian cattle and Holstein, several of which were associated with immunity in Yakutian cattle, indicating potential differences in disease resistance and immunity between the two breeds. This study highlights the vast difference in gene expression profiles in adipose tissues among breeds from different climatic environments, most likely highlighting selective pressure and the potential significance of the uniquely important regulatory functions of metacarpal adipose tissue

Genomic characterization of northern Eurasian cattle (Bos taurus) and reindeer (Rangifer tarandus)

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