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Pokharel K, Weldenegodguad M, Dudeck S, Honkatukia M, Lindeberg H, Mazzullo N, Paasivaara A, Peippo J, Soppela P, Stammler F, Kantanen J. Whole-genome sequencing provides novel insights into the evolutionary history and genetic adaptation of reindeer populations in northern Eurasia. Sci Rep 2023; 13:23019. [PMID: 38155192 PMCID: PMC10754820 DOI: 10.1038/s41598-023-50253-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023] Open
Abstract
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.
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Affiliation(s)
- Kisun Pokharel
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
| | - Melak Weldenegodguad
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
| | - Stephan Dudeck
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | | | - Heli Lindeberg
- Natural Resources Institute Finland (Luke), 71750, Maaninka, Finland
| | - Nuccio Mazzullo
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | - Antti Paasivaara
- Natural Resources Institute Finland (Luke), Paavo Havaksentie 3, 90570, Oulu, Finland
| | - Jaana Peippo
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
- NordGen-Nordic Genetic Resource Center, 1432, Ås, Norway
| | - Päivi Soppela
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | | | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland.
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Weldenegodguad M, Pokharel K, Niiranen L, Soppela P, Ammosov I, Honkatukia M, Lindeberg H, Peippo J, Reilas T, Mazzullo N, Mäkelä KA, Nyman T, Tervahauta A, Herzig KH, Stammler F, Kantanen J. Adipose gene expression profiles reveal insights into the adaptation of northern Eurasian semi-domestic reindeer (Rangifer tarandus). Commun Biol 2021; 4:1170. [PMID: 34620965 PMCID: PMC8497613 DOI: 10.1038/s42003-021-02703-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 09/21/2021] [Indexed: 02/08/2023] Open
Abstract
Reindeer (Rangifer tarandus) are semi-domesticated animals adapted to the challenging conditions of northern Eurasia. Adipose tissues play a crucial role in northern animals by altering gene expression in their tissues to regulate energy homoeostasis and thermogenic activity. Here, we perform transcriptome profiling by RNA sequencing of adipose tissues from three different anatomical depots: metacarpal (bone marrow), perirenal, and prescapular fat in Finnish and Even reindeer (in Sakha) during spring and winter. A total of 16,212 genes are expressed in our data. Gene expression profiles in metacarpal tissue are distinct from perirenal and prescapular adipose tissues. Notably, metacarpal adipose tissue appears to have a significant role in the regulation of the energy metabolism of reindeer in spring when their nutritional condition is poor after winter. During spring, genes associated with the immune system are upregulated in the perirenal and prescapular adipose tissue. Blood and tissue parameters reflecting general physiological and metabolic status show less seasonal variation in Even reindeer than in Finnish reindeer. This study identifies candidate genes potentially involved in immune response, fat deposition, and energy metabolism and provides new information on the mechanisms by which reindeer adapt to harsh arctic conditions.
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Affiliation(s)
- Melak Weldenegodguad
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland ,grid.9668.10000 0001 0726 2490Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Kisun Pokharel
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Laura Niiranen
- grid.10858.340000 0001 0941 4873Research Unit of Biomedicine, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Päivi Soppela
- grid.37430.330000 0001 0744 995XArctic Centre, University of Lapland, Rovaniemi, Finland
| | - Innokentyi Ammosov
- grid.495192.2Laboratory of Reindeer Husbandry and Traditional Industries, Yakut Scientific Research Institute of Agriculture, Yakutsk, The Sakha Republic (Yakutia) Russia
| | | | - Heli Lindeberg
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Maaninka, Finland
| | - Jaana Peippo
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland ,NordGen—Nordic Genetic Resource Center, Ås, Norway
| | - Tiina Reilas
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Nuccio Mazzullo
- grid.37430.330000 0001 0744 995XArctic Centre, University of Lapland, Rovaniemi, Finland
| | - Kari A. Mäkelä
- grid.10858.340000 0001 0941 4873Research Unit of Biomedicine, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Tommi Nyman
- grid.454322.60000 0004 4910 9859Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
| | - Arja Tervahauta
- grid.9668.10000 0001 0726 2490Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Karl-Heinz Herzig
- grid.10858.340000 0001 0941 4873Research Unit of Biomedicine, Faculty of Medicine, University of Oulu, Oulu, Finland ,grid.10858.340000 0001 0941 4873Medical Research Center, Faculty of Medicine, University of Oulu, Oulu, Finland ,grid.412326.00000 0004 4685 4917Oulu University Hospital, Oulu, Finland ,grid.22254.330000 0001 2205 0971Institute of Pediatrics, Poznań University of Medical Sciences, Poznań, Poland
| | - Florian Stammler
- grid.37430.330000 0001 0744 995XArctic Centre, University of Lapland, Rovaniemi, Finland
| | - Juha Kantanen
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
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Weldenegodguad M, Pokharel K, Ming Y, Honkatukia M, Peippo J, Reilas T, Røed KH, Kantanen J. Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia. Sci Rep 2020; 10:8980. [PMID: 32488117 PMCID: PMC7265531 DOI: 10.1038/s41598-020-65487-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 05/05/2020] [Indexed: 12/24/2022] Open
Abstract
Reindeer are semi-domesticated ruminants that have adapted to the challenging northern Eurasian environment characterized by long winters and marked annual fluctuations in daylight. We explored the genetic makeup behind their unique characteristics by de novo sequencing the genome of a male reindeer and conducted gene family analyses with nine other mammalian species. We performed a population genomics study of 23 additional reindeer representing both domestic and wild populations and several ecotypes from various geographic locations. We assembled 2.66 Gb (N50 scaffold of 5 Mb) of the estimated 2.92 Gb reindeer genome, comprising 27,332 genes. The results from the demographic history analysis suggested marked changes in the effective population size of reindeer during the Pleistocene period. We detected 160 reindeer-specific and expanded genes, of which zinc finger proteins (n = 42) and olfactory receptors (n = 13) were the most abundant. Comparative genome analyses revealed several genes that may have promoted the adaptation of reindeer, such as those involved in recombination and speciation (PRDM9), vitamin D metabolism (TRPV5, TRPV6), retinal development (PRDM1, OPN4B), circadian rhythm (GRIA1), immunity (CXCR1, CXCR2, CXCR4, IFNW1), tolerance to cold-triggered pain (SCN11A) and antler development (SILT2). The majority of these characteristic reindeer genes have been reported for the first time here. Moreover, our population genomics analysis suggested at least two independent reindeer domestication events with genetic lineages originating from different refugial regions after the Last Glacial Maximum. Taken together, our study has provided new insights into the domestication, evolution and adaptation of reindeer and has promoted novel genomic research of reindeer.
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Affiliation(s)
- Melak Weldenegodguad
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-70201, Kuopio, Finland
| | - Kisun Pokharel
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
| | - Yao Ming
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Mervi Honkatukia
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
- Nordic Genetic Resource Centre - NordGen, c/o NMBU - Biovit Box 5003, Ås, NO-1432, Norway
| | - Jaana Peippo
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
| | - Tiina Reilas
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
| | - Knut H Røed
- Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, P.O.Box 369 Centrum, 0102, Oslo, Norway
| | - Juha Kantanen
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland.
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Pokharel K, Peippo J, Weldenegodguad M, Honkatukia M, Li MH, Kantanen J. Gene Expression Profiling of Corpus luteum Reveals Important Insights about Early Pregnancy in Domestic Sheep. Genes (Basel) 2020; 11:genes11040415. [PMID: 32290341 PMCID: PMC7231023 DOI: 10.3390/genes11040415] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 01/10/2023] Open
Abstract
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 non-coding 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).
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Affiliation(s)
- Kisun Pokharel
- Natural Resources, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland; (K.P.); (M.W.)
| | - Jaana Peippo
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland;
| | - Melak Weldenegodguad
- Natural Resources, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland; (K.P.); (M.W.)
| | | | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Correspondence: (M.-H.L.); (J.K.); Tel.: +358-295-326-210 (J.K.)
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland;
- Correspondence: (M.-H.L.); (J.K.); Tel.: +358-295-326-210 (J.K.)
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Pokharel K, Weldenegodguad M, Popov R, Honkatukia M, Huuki H, Lindeberg H, Peippo J, Reilas T, Zarovnyaev S, Kantanen J. Whole blood transcriptome analysis reveals footprints of cattle adaptation to sub-arctic conditions. Anim Genet 2019; 50:217-227. [PMID: 30957254 PMCID: PMC6593690 DOI: 10.1111/age.12783] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2019] [Indexed: 12/17/2022]
Abstract
Indigenous cattle breeds in northern Eurasia have adapted to harsh climate conditions. The local breeds are important genetic resources with cultural and historical heritages, and therefore, their preservation and genetic characterization are important. In this study, we profiled the whole‐blood transcriptome of two native breeds (Northern Finncattle and Yakutian cattle) and one commercial breed (Holstein) using high‐throughput RNA sequencing. More than 15 000 genes were identified, of which two, 89 and 162 genes were significantly upregulated exclusively in Northern Finncattle, Yakutian cattle and Holstein cattle respectively. The functional classification of these significantly differentially expressed genes identified several biological processes and pathways related to signalling mechanisms, cell differentiation and host–pathogen interactions that, in general, point towards immunity and disease resistance mechanisms. The gene expression pattern observed in Northern Finncattle was more similar to that of Yakutian cattle, despite sharing similar living conditions with the Holstein cattle included in our study. In conclusion, our study identified unique biological processes in these breeds that may have helped them to adapt and survive in northern and sub‐arctic environments.
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Affiliation(s)
- K Pokharel
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland
| | - M Weldenegodguad
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, Kuopio, FI-70311, Finland
| | - R Popov
- Yakutian Research Institute of Agriculture (FGBNU Yakutskij NIISH), ul. Bestyzhevo-Marlinskogo 23/1, Yakutsk, 67001, The Sakha Republic (Yakutia), Russia
| | - M Honkatukia
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland.,The Nordic Genetic Resources Center (Nordgen), P.O. Box 115, Ås, NO-1431, Norway
| | - H Huuki
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland
| | - H Lindeberg
- Production Systems, Natural Resources Institute Finland (Luke), Halolantie 31A, Maaninka, FI-71750, Finland
| | - J Peippo
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland
| | - T Reilas
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland
| | - S Zarovnyaev
- GBU Saha Agroplem, ul. Ordzhonkidze 20/204, Yakutsk, 67700, The Sakha Republic (Yakutia), Russia
| | - J Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland
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Weldenegodguad M, Popov R, Pokharel K, Ammosov I, Ming Y, Ivanova Z, Kantanen J. Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions. Front Genet 2019; 9:728. [PMID: 30687392 PMCID: PMC6336893 DOI: 10.3389/fgene.2018.00728] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 12/22/2018] [Indexed: 12/30/2022] Open
Abstract
Northern Fennoscandia and the Sakha Republic in the Russian Federation represent the northernmost regions on Earth where cattle farming has been traditionally practiced. In this study, we performed whole-genome sequencing to genetically characterize three rare native breeds Eastern Finncattle, Western Finncattle and Yakutian cattle adapted to these northern Eurasian regions. We examined the demographic history, genetic diversity and unfolded loci under natural or artificial selection. On average, we achieved 13.01-fold genome coverage after mapping the sequencing reads on the bovine reference genome (UMD 3.1) and detected a total of 17.45 million single nucleotide polymorphisms (SNPs) and 1.95 million insertions-deletions (indels). We observed that the ancestral species (Bos primigenius) of Eurasian taurine cattle experienced two notable prehistorical declines in effective population size associated with dramatic climate changes. The modern Yakutian cattle exhibited a higher level of within-population variation in terms of number of SNPs and nucleotide diversity than the contemporary European taurine breeds. This result is in contrast to the results of marker-based cattle breed diversity studies, indicating assortment bias in previous analyses. Our results suggest that the effective population size of the ancestral Asiatic taurine cattle may have been higher than that of the European cattle. Alternatively, our findings could indicate the hybrid origins of the Yakutian cattle ancestries and possibly the lack of intensive artificial selection. We identified a number of genomic regions under selection that may have contributed to the adaptation to the northern and subarctic environments, including genes involved in disease resistance, sensory perception, cold adaptation and growth. By characterizing the native breeds, we were able to obtain new information on cattle genomes and on the value of the adapted breeds for the conservation of cattle genetic resources.
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Affiliation(s)
- Melak Weldenegodguad
- Department of Production Systems, Natural Resources Institute Finland (Luke), Helsinki, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ruslan Popov
- Yakutian Research Institute of Agriculture (FGBNU Yakutskij NIISH), Yakutsk, Russia
| | - Kisun Pokharel
- Department of Production Systems, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Innokentyi Ammosov
- Board of Agricultural Office of Eveno-Bytantaj Region, Batagay-Alyta, Russia
| | - Yao Ming
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | - Zoya Ivanova
- Yakutian Research Institute of Agriculture (FGBNU Yakutskij NIISH), Yakutsk, Russia
| | - Juha Kantanen
- Department of Production Systems, Natural Resources Institute Finland (Luke), Helsinki, Finland
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