A recent comprehensive genomic analysis based on 50K SNP profiles has shown that the regional Bal... more A recent comprehensive genomic analysis based on 50K SNP profiles has shown that the regional Balkan sheep populations have considerable genetic overlap but are distinctly different from surrounding breeds. All eight Croatian sheep breeds were represented by a small number of individuals per breed. Here, we genotyped 220 individuals representing the native Croatian sheep breeds (Istrian Sheep, Krk Island Sheep, Cres Island Sheep, Rab Island Sheep, Lika Pramenka, Pag Island Sheep, Dalmatian Pramenka, Dubrovnik Sheep) and mouflon using the Ovine Infinium® HD SNP BeadChip (606,006 SNPs). In addition, we included publicly available Balkan Pramenka and other Mediterranean sheep breeds. Our analyses revealed the complex population structure of Croatian sheep breeds and their origin and geographic barriers (island versus mainland). Migration patterns confirmed the historical establishment of breeds and the pathways of gene flow. Inbreeding coefficients (FROH>2 Mb) between sheep populati...
By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population hist... more By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we analyze whole-genome sequences of 386 domestic goats from 75 modern breeds and 7 wild goat species that were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 180 domestic breeds indicate ancient paternal population bottlenecks and expan...
Inferring Prehistorical and Historical Feeding Practices from δ15N and δ13C Isotope Analysis on F... more Inferring Prehistorical and Historical Feeding Practices from δ15N and δ13C Isotope Analysis on Finnish Archaeological Domesticated Ruminant Bones and Teeth
Reindeer (Rangifer tarandus) are semi-domesticated animals adapted to the challenging conditions ... more 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 t...
Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facil... more Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted br...
How animals, particularly livestock, adapt to various climates and environments over short evolut... more How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomi...
Reindeer herding is of great importance for the indigenous people of the Fennoscandia peninsula a... more Reindeer herding is of great importance for the indigenous people of the Fennoscandia peninsula and northern Russia. There are also free-ranging feral populations of reindeer in Finland, Iceland, Norway and Russian Federation. The genus Pestivirus contains several viral species that infect ungulates and often show capacity to transmit between different host species. Sera from 520 Eurasian tundra reindeer (Rangifer tarandus tarandus) from Finland, Sweden, Norway, Iceland and Russian Federation were analysed and the prevalence of pestivirus-specific antibodies was determined. Seropositivity proportion was 48.5% for Sweden and 41.2% for Norway, but only 1.6% for Iceland and 2.5% for Finland. All Russian reindeer investigated were seronegative. Pan-pestivirus RT-PCR of seronegative animals (n = 156) from seropositive herds confirmed their negative status. These results indicate unexpectedly non-uniform circulation of an as yet uncharacterised pestivirus in Eurasian reindeer populations. The high seroprevalence in some regions warrants further studies of pestivirus infection dynamics, effects on reindeer health and population dynamics.
All material supplied via Jukuri is protected by copyright and other intellectual property rights... more All material supplied via Jukuri is protected by copyright and other intellectual property rights. Duplication or sale, in electronic or print form, of any part of the repository collections is prohibited. Making electronic or print copies of the material is permitted only for your own personal use or for educational purposes. For other purposes, this article may be used in accordance with the publisher's terms. There may be differences between this version and the publisher's version. You are advised to cite the publisher's version. This is an electronic reprint of the original article. This reprint may differ from the original in pagination and typographic detail.
Feral cattle residing in Chirikof Island, Alaska, are relatively distinct from breeds used in com... more Feral cattle residing in Chirikof Island, Alaska, are relatively distinct from breeds used in commercial production in North America. However, preliminary evidence suggested that they exhibit substantial genetic relationship with cattle from Yakutian region of Siberia. Thus, our objective was to further elucidate quantify the origins, admixture and divergence of the Chirikof Island cattle relative to cattle from Siberia and USA. Subject animals were genotyped at 15 microsatellite loci. Compared with Turano-Mongolian and North American cattle, Chirikof Island cattle had similar variation, with slightly less observed heterozygosity, fewer alleles per locus and a positive fixation index. Analysis of the genetic distances revealed two primary clusters; one that contained the North American breeds and the Kazakh White head, and a second that contained the Yakutian and Kalmyk breeds, and the Chirikof population. Thus, it is suggested that Chirikof Island cattle may be a composite of British breeds emanating from North America and Turano-Mongolian cattle. A potential founder effect, consistent with historical records of the Russian-American period, may contribute to the adaptation of the Chirikof Island cattle to their harsh high-latitude environment. Further study of adaptive mechanisms manifest by these cattle is warranted.
The major histocompatibility complex (MHC) is a cluster of genes involved with immune responses. ... more The major histocompatibility complex (MHC) is a cluster of genes involved with immune responses. The chicken MHC has been shown to influence resistance to viruses, bacteria, and infections from both internal and external parasites. The highly variable chicken MHC haplotypes were initially identified by the use of haplotype-specific serological reagents. A novel SNP-based panel encompassing 210,000 bp of the MHC-B locus was developed to allow fine scale genetic analyses including rapid identification of novel haplotypes for which serological reagents are not available. The Finnish Landrace breed of chickens traces its origins to almost 1,000 years ago, with multiple lineages maintained as small populations in isolated villages. The breed is well adapted to the cooler Finnish climate and is considered to be an infrequent egg layer. Conservation efforts to protect this endangered breed were initiated by a hobby breeder in the 1960s. An official conservation program was established in 1998 and now 12 different populations are currently maintained by a network of volunteer hobbyist breeders. Variation in the MHC-B region in these populations was examined using a panel of 90 selected SNP. A total of 195 samples from 12 distinct populations (average of 15 individuals sampled per population) were genotyped with the 90 SNP panel specific for the MHC-B region, spanning 210,000 bp. There were 36 haplotypes found, 16 of which are a subset of 78 that had been previously identified in either commercially utilized or heritage breeds from North America with the remaining 20 haplotypes being novel. The average number of MHC-B haplotypes found within each Finnish Landrace population was 5.9, and ranged from one to 13. While haplotypes common to multiple populations were found, populationspecific haplotypes were also identified. This study shows that substantial MHC-B region diversity exists in the Finnish Landrace breed and exemplifies the significance tied to conserving multiple populations of rare breeds.
Drug resistance has emerged as one of the greatest challenges facing malaria control. The recent ... more Drug resistance has emerged as one of the greatest challenges facing malaria control. The recent emergence of resistance to artemisinin (ART) and its partner drugs in ART-based combination therapies (ACT) is threatening the efficacy of this front-line regimen for treating Plasmodium falciparum parasites. Thus, an understanding of the molecular mechanisms that underlie the resistance to ART and the partner drugs has become a high priority for resistance containment and malaria management. Using genome-wide association studies, we investigated the associations of genome-wide single nucleotide polymorphisms with in vitro sensitivities to 10 commonly used antimalarial drugs in 94 P. falciparum isolates from the China-Myanmar border area, a region with the longest history of ART usage. We identified several loci associated with various drugs, including those containing pfcrt and pfdhfr. Of particular interest is a locus on chromosome 10 containing the autophagy-related protein 18 (ATG18)...
SummaryIn the last decades, several endangered breeds of livestock species have been re‐establish... more SummaryIn the last decades, several endangered breeds of livestock species have been re‐established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO‐recommended microsatellites of these landraces and three phenotypically similar Nordic‐type landraces and compared these breeds with central European, Mediterranean and south‐west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south‐west Asian domestication site with a south‐east‐to‐north‐west cline that is clearly steeper than the Mediterranean east‐to‐west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination ...
Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed ... more Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrenc...
A recent comprehensive genomic analysis based on 50K SNP profiles has shown that the regional Bal... more A recent comprehensive genomic analysis based on 50K SNP profiles has shown that the regional Balkan sheep populations have considerable genetic overlap but are distinctly different from surrounding breeds. All eight Croatian sheep breeds were represented by a small number of individuals per breed. Here, we genotyped 220 individuals representing the native Croatian sheep breeds (Istrian Sheep, Krk Island Sheep, Cres Island Sheep, Rab Island Sheep, Lika Pramenka, Pag Island Sheep, Dalmatian Pramenka, Dubrovnik Sheep) and mouflon using the Ovine Infinium® HD SNP BeadChip (606,006 SNPs). In addition, we included publicly available Balkan Pramenka and other Mediterranean sheep breeds. Our analyses revealed the complex population structure of Croatian sheep breeds and their origin and geographic barriers (island versus mainland). Migration patterns confirmed the historical establishment of breeds and the pathways of gene flow. Inbreeding coefficients (FROH>2 Mb) between sheep populati...
By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population hist... more By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we analyze whole-genome sequences of 386 domestic goats from 75 modern breeds and 7 wild goat species that were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 180 domestic breeds indicate ancient paternal population bottlenecks and expan...
Inferring Prehistorical and Historical Feeding Practices from δ15N and δ13C Isotope Analysis on F... more Inferring Prehistorical and Historical Feeding Practices from δ15N and δ13C Isotope Analysis on Finnish Archaeological Domesticated Ruminant Bones and Teeth
Reindeer (Rangifer tarandus) are semi-domesticated animals adapted to the challenging conditions ... more 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 t...
Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facil... more Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted br...
How animals, particularly livestock, adapt to various climates and environments over short evolut... more How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomi...
Reindeer herding is of great importance for the indigenous people of the Fennoscandia peninsula a... more Reindeer herding is of great importance for the indigenous people of the Fennoscandia peninsula and northern Russia. There are also free-ranging feral populations of reindeer in Finland, Iceland, Norway and Russian Federation. The genus Pestivirus contains several viral species that infect ungulates and often show capacity to transmit between different host species. Sera from 520 Eurasian tundra reindeer (Rangifer tarandus tarandus) from Finland, Sweden, Norway, Iceland and Russian Federation were analysed and the prevalence of pestivirus-specific antibodies was determined. Seropositivity proportion was 48.5% for Sweden and 41.2% for Norway, but only 1.6% for Iceland and 2.5% for Finland. All Russian reindeer investigated were seronegative. Pan-pestivirus RT-PCR of seronegative animals (n = 156) from seropositive herds confirmed their negative status. These results indicate unexpectedly non-uniform circulation of an as yet uncharacterised pestivirus in Eurasian reindeer populations. The high seroprevalence in some regions warrants further studies of pestivirus infection dynamics, effects on reindeer health and population dynamics.
All material supplied via Jukuri is protected by copyright and other intellectual property rights... more All material supplied via Jukuri is protected by copyright and other intellectual property rights. Duplication or sale, in electronic or print form, of any part of the repository collections is prohibited. Making electronic or print copies of the material is permitted only for your own personal use or for educational purposes. For other purposes, this article may be used in accordance with the publisher's terms. There may be differences between this version and the publisher's version. You are advised to cite the publisher's version. This is an electronic reprint of the original article. This reprint may differ from the original in pagination and typographic detail.
Feral cattle residing in Chirikof Island, Alaska, are relatively distinct from breeds used in com... more Feral cattle residing in Chirikof Island, Alaska, are relatively distinct from breeds used in commercial production in North America. However, preliminary evidence suggested that they exhibit substantial genetic relationship with cattle from Yakutian region of Siberia. Thus, our objective was to further elucidate quantify the origins, admixture and divergence of the Chirikof Island cattle relative to cattle from Siberia and USA. Subject animals were genotyped at 15 microsatellite loci. Compared with Turano-Mongolian and North American cattle, Chirikof Island cattle had similar variation, with slightly less observed heterozygosity, fewer alleles per locus and a positive fixation index. Analysis of the genetic distances revealed two primary clusters; one that contained the North American breeds and the Kazakh White head, and a second that contained the Yakutian and Kalmyk breeds, and the Chirikof population. Thus, it is suggested that Chirikof Island cattle may be a composite of British breeds emanating from North America and Turano-Mongolian cattle. A potential founder effect, consistent with historical records of the Russian-American period, may contribute to the adaptation of the Chirikof Island cattle to their harsh high-latitude environment. Further study of adaptive mechanisms manifest by these cattle is warranted.
The major histocompatibility complex (MHC) is a cluster of genes involved with immune responses. ... more The major histocompatibility complex (MHC) is a cluster of genes involved with immune responses. The chicken MHC has been shown to influence resistance to viruses, bacteria, and infections from both internal and external parasites. The highly variable chicken MHC haplotypes were initially identified by the use of haplotype-specific serological reagents. A novel SNP-based panel encompassing 210,000 bp of the MHC-B locus was developed to allow fine scale genetic analyses including rapid identification of novel haplotypes for which serological reagents are not available. The Finnish Landrace breed of chickens traces its origins to almost 1,000 years ago, with multiple lineages maintained as small populations in isolated villages. The breed is well adapted to the cooler Finnish climate and is considered to be an infrequent egg layer. Conservation efforts to protect this endangered breed were initiated by a hobby breeder in the 1960s. An official conservation program was established in 1998 and now 12 different populations are currently maintained by a network of volunteer hobbyist breeders. Variation in the MHC-B region in these populations was examined using a panel of 90 selected SNP. A total of 195 samples from 12 distinct populations (average of 15 individuals sampled per population) were genotyped with the 90 SNP panel specific for the MHC-B region, spanning 210,000 bp. There were 36 haplotypes found, 16 of which are a subset of 78 that had been previously identified in either commercially utilized or heritage breeds from North America with the remaining 20 haplotypes being novel. The average number of MHC-B haplotypes found within each Finnish Landrace population was 5.9, and ranged from one to 13. While haplotypes common to multiple populations were found, populationspecific haplotypes were also identified. This study shows that substantial MHC-B region diversity exists in the Finnish Landrace breed and exemplifies the significance tied to conserving multiple populations of rare breeds.
Drug resistance has emerged as one of the greatest challenges facing malaria control. The recent ... more Drug resistance has emerged as one of the greatest challenges facing malaria control. The recent emergence of resistance to artemisinin (ART) and its partner drugs in ART-based combination therapies (ACT) is threatening the efficacy of this front-line regimen for treating Plasmodium falciparum parasites. Thus, an understanding of the molecular mechanisms that underlie the resistance to ART and the partner drugs has become a high priority for resistance containment and malaria management. Using genome-wide association studies, we investigated the associations of genome-wide single nucleotide polymorphisms with in vitro sensitivities to 10 commonly used antimalarial drugs in 94 P. falciparum isolates from the China-Myanmar border area, a region with the longest history of ART usage. We identified several loci associated with various drugs, including those containing pfcrt and pfdhfr. Of particular interest is a locus on chromosome 10 containing the autophagy-related protein 18 (ATG18)...
SummaryIn the last decades, several endangered breeds of livestock species have been re‐establish... more SummaryIn the last decades, several endangered breeds of livestock species have been re‐established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO‐recommended microsatellites of these landraces and three phenotypically similar Nordic‐type landraces and compared these breeds with central European, Mediterranean and south‐west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south‐west Asian domestication site with a south‐east‐to‐north‐west cline that is clearly steeper than the Mediterranean east‐to‐west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination ...
Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed ... more Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrenc...
Uploads
Papers by Juha Kantanen