The mechanisms of leukemogenesis induced by bovine leukemia virus (BLV) and the processes underly... more The mechanisms of leukemogenesis induced by bovine leukemia virus (BLV) and the processes underlying the phenomenon of differential host response to BLV infection still remain poorly understood. The aim of the study was to screen the entire cattle genome to identify markers and candidate genes that might be involved in host response to bovine leukemia virus infection. A genome-wide association study was performed using Holstein cows naturally infected by BLV. A data set included 43 cows (BLV positive) and 30 cows (BLV negative) genotyped for 54,609 SNP markers (Illumina Bovine SNP50 BeadChip). The BLV status of cows was determined by serum ELISA, nested-PCR and hematological counts. Linear Regression Analysis with a False Discovery Rate and kinship matrix (computed on the autosomal SNPs) was calculated to find out which SNP markers significantly differentiate BLV-positive and BLV-negative cows. Nine markers reached genome-wide significance. The most significant SNPs were located on chromosomes 23 (rs41583098), 3 (rs109405425, rs110785500) and 8 (rs43564499) in close vicinity of a patatin-like phospholipase domain containing 1 (PNPLA1); adaptor-related protein complex 4, beta 1 subunit (AP4B1); tripartite motif-containing 45 (TRIM45) and cell division cycle associated 2 (CDCA2) genes, respectively. Furthermore, a list of 41 candidate genes was composed based on their proximity to significant markers (within a distance of ca. 1 Mb) and functional involvement in processes potentially underlying BLV-induced pathogenesis. In conclusion, it was demonstrated that host response to BLV infection involves nine sub-regions of the cattle genome (represented by 9 SNP markers), containing many genes which, based on the literature, could be involved to enzootic bovine leukemia progression. New group of promising candidate genes associated with the host response to BLV infection were identified and could therefore be a target for future studies. The functions of candidate genes surrounding significant SNP markers imply that there is no single regulatory process that is solely targeted by BLV infection, but rather the network of interrelated pathways is deregulated, leading to the disruption of the control of B-cell proliferation and programmed cell death.
ContentsThe aim of the study was to screen the entire bull genome to identify markers and candida... more ContentsThe aim of the study was to screen the entire bull genome to identify markers and candidate genes underlying sperm concentration. The analysed data set originates from a population of 877 Polish Holstein‐Friesian bulls. Based on sperm concentration value, two extreme groups of bulls were created: Low (L, n = 126) and High (H, n = 140). Each bull was genotyped using the Illumina BovineSNP50 BeadChip. Genome‐wide association analysis was performed with the use of GoldenHelix SVS7 software. An additive model with a Cohran–Armitage test, Correlation/Trend adjusted by a Bonferroni test, was used to estimate the effect of SNP marker for sperm concentration. Thirteen markers reached genome‐wide significance. The most significant SNPs were located on chromosome 3 (rs109154964 and rs108965556), 14 (rs41621145) and 18 (rs41615539), in the close vicinity of protein arginine methyltransferase 6 (PRMT6), Sel1 repeat containing 1 (SELRC1), triple QxxK/R motif containing (TRIQK) and zinc f...
Genomic selection programs, besides their practical use, deliver a huge amount of data with singl... more Genomic selection programs, besides their practical use, deliver a huge amount of data with single nucleotide polymorphisms (SNPs) affecting performance traits. Although most SNP effects are small, their distribution along the chromosomes delivers an opportunity to indicate those sub-regions of the genome which may contain causal polymorphisms involved in the genetic variation of the trait (Hayes, Bowman, Chamberlain, & Goddard, 2009). Cole, VanRaden, O'Connell, Tassell, and Sonstegard (2009) analysed the distribution and position of 38,416 SNP effects estimated for the population of 5,285 Holstein bulls and found markers on BTA18 which had a relatively large impact on fertility and conformation traits, longevity and total merit. SNP ss86324977 (rs109478645) mapped in position 57,125,868 was found to be the most significant and is located in the intron of SIGLEC5. protein is located on the cell surface and is involved in binding sialiSIGLEC5 c acid (Angata, Margulies, Green, & Varki, 2004). It is expressed in cells responsible for non-specific immune response (monocytes, granulocytes, macrophages and NK cells) and takes part in adhesion and signalling (Crocker, Paulson, & Varki, 2007; Crocker & Varki, 2001). Foussias, Yousef, and Diamandis (2000) confirmed the expression of SIGLEC5 gene in the uterus and embryo, supporting the hypothesis that the gene might be involved in fertility. Assuming that the SIGLEC5 is a promising candidate gene, it was hypothesized that its effects on performance traits may be caused
The aim of this study was to predict the genomic breeding value (DGV) of production, selected con... more The aim of this study was to predict the genomic breeding value (DGV) of production, selected conformation and reproductive traits, and somatic cell score of dairy cattle in Poland using high-frequency marker haplotypes. The dataset consisted of phenotypic, genotypic, and pedigree data of 1216 Polish Holstein-Friesian bulls. The genotypic data consisted of 54,000 singlenucleotide polymorphisms (SNPs). The data were divided into two subsets: a test dataset (n = 1064) and a validation dataset (n = 152). Genotypic data were selected using three criteria: the percentage of missing genotypes, minor allele frequency, and linkage disequilibrium. The purpose of the data selection was to identify blocks of SNPs that were then used for the construction of haplotypes. Only haplotypes with a frequency higher than 25% were selected. DGV was predicted using four variants of a linear model with random haplotype effects and deregressed breeding values as the response variables. The accuracy of genomic prediction was checked by comparing DGVs with estimated breeding values (EBVs) using two methods: Pearson's correlations and the regression of EBVon DGV. The use of high-frequency haplotypes showed a tendency to underestimate DGVs. None of the models tested was clearly superior with regard to the traits studied. DGVs of production and conformation traits as well as somatic cell score (medium or high heritability traits) were more accurate than those estimated for fertility traits (low heritability traits).
In 2009, a frozen mummy of the steppe bison (SB) (Bison priscus) was discovered between the lower... more In 2009, a frozen mummy of the steppe bison (SB) (Bison priscus) was discovered between the lower Kolyma River and the Alazeya River in northeast Siberia, Russia. The specimen was dated with 14 C and estimated to have lived more than 48,000 14 C years before present (BP). The relationship between SB and the European Bison (EB) (Bison bonasus), also known as wisent or European wood bison, is unresolved and it is unclear whether the SB and EB overlapped in space and time. The aim of our study was to compare genetic variability between the SB specimen and modern EB. We expected higher SB variability due to substantial bottlenecks in the EB approximately one century ago when it became extinct in the wild. The EB (n = 167) and the SB specimen were genotyped with the Illumina BovineHD BeadChip with 777,962 single-nucleotide polymorphism (SNP) markers. Steppe bison DNA was extracted and genotyped six times to account for genotyping errors due to low-quality DNA. We obtained a final set of 7786 SNPs. The mean number of private alleles in EB was 0.027 (± 0.0002) and in SB, it was 0.288 (± 0.0006). This could be explained by factors including differences between species, spatiotemporal divergence, and bottleneck effects. Investigation of historic EB samples could help resolve phylogenetic relationships, the role of the recent bottleneck, and provide information for conservation management to reduce the incidence of disease in the population and maintain its evolutionary potential.
The aims of this study were to confirm ADAM32 gene expression in selected bovine tissues and iden... more The aims of this study were to confirm ADAM32 gene expression in selected bovine tissues and identify potentially functional polymorphisms within the 5'flanking region. The associations between the polymorphism within ADAM32 and somatic cell count in the Holstein-Friesian cow's milk were examined. Expression studies of ADAM32 in different tissues performed by RT-PCR revealed the presence of the ADAM32 transcript in the liver, mammary and pituitary gland and leukocytes, except for monocytes. Comparative sequencing analysis of 870 bp PCR amplicons obtained from four different Bos taurus breeds and the Bison bonasus fragment of the ADAM32 5' flanking region showed a 21 bp insertion/deletion at position-541 nt to-520 nt and the occurrence of seven SNPs. In silico analysis of the 1180 bp 5' flanking region of ADAM32 indicated that the 21 bp deletion abolished putative binding sites for six transcription factors associated with the immune system. A population of one hundred and two Polish Holstein-Friesian bulls and 241 cows-progeny of 15 heterozygous (InsDel) sires were screened. The frequency of genotypes (for sires) were observed at 0.765, 0.235, 0.0 for DelDel, InsDel and InsIns, respectively, whereas for cows the frequencies are as follows: 0.365, 0.510 and 0.125. The association study performed within the group of daughters of heterozygous sires revealed that cows with the DelDel genotype showed significantly higher somatic cell counts than those with the InsIns genotype (P=0.013). No significant association was found between cows' genotypes and milk production traits.
The aim of this study was to quantify b-casomorphin-7 in raw, hydrolyzed and processed milk in di... more The aim of this study was to quantify b-casomorphin-7 in raw, hydrolyzed and processed milk in different stages of the cow lactation. The obtained results lead to the following conclusion: the highest amount of b-casomorphin-7 released from the hydrolyzed and processed milk is related to the b-casein A1 allele, irrespective of a lactation period. Some traces of b-casomorphin-7 in milk from cows with the b-casein A2 variant are probably a result of the acid hydrolysis of b-casein during its digestion with pepsin. It has been shown that processing of raw milk at high temperatures affects, in a slight degree, the differences between b-casomorphins-7 originating from different b-casein genotypes. The obtained results suggest a possibility to provide a new nutritional factor for milk quality based on the content of b-casomorphin-7 liberated in vivo from milk digested by a mixture of the gastrointestinal enzymes.
Genome-wide association study for posthitis in the free-living population of European bison (Biso... more Genome-wide association study for posthitis in the free-living population of European bison (Bison bonasus)
The aim of the study was to screen the entire bull genome to identify SNP markers and propose can... more The aim of the study was to screen the entire bull genome to identify SNP markers and propose candidate genes potentially involved in the variation of sperm membrane integrity in Holstein-Friesian bulls. Two hundred eighty eight bulls kept in one AI center were included in the study. Each bull was genotyped for 54.001 Single Nucleotide Polymorpisms (SNP) by the Illumina BovineSNP50 BeadChip. Commercial straws of frozen-thawed semen were used for the evaluation of sperm plasma membrane integrity (SYBR-14/PI staining) and sperm mitochondrial function (JC1/PI staining). An additive model for Linear Regression Analysis was applied to estimate the effect of SNP marker for sperm membrane integrity (by the use of GoldenHelix SVS7 software). Five significant markers (encompassing 2,2 MB region located on chromosome 6) for SYBR-14/PI were found. Among them one marker-rs41570391 passed Bonferroni correction test. Within approximately 3 Mb genomic region including significant markers three candidate genes: SGMS2 (Sphingomyelin Synthase 2), TET2 (Methylcytosine dioxygenase 2) and GSTCD genes (Gluthatione S-transferase C terminal domain) were proposed as potentially involved in sperm membrane integrity in frozen-thawed semen of Holstein-Friesian bulls.
Although a large part of the global domestic dog population is free-ranging and free-breeding, kn... more Although a large part of the global domestic dog population is free-ranging and free-breeding, knowledge of genetic diversity in these free-breeding dogs (FBDs) and their ancestry relations to pure-breed dogs is limited, and the indigenous status of FBDs in Asia is still uncertain. We analyse genome-wide SNP variability of FBDs across Eurasia, and show that they display weak genetic structure and are genetically distinct from pure-breed dogs rather than constituting an admixture of breeds. Our results suggest that modern European breeds originated locally from European FBDs. East Asian and Arctic breeds show closest affinity to East Asian FBDs, and they both represent the earliest branching lineages in the phylogeny of extant Eurasian dogs. Our biogeographic reconstruction of ancestral distributions indicates a gradual westward expansion of East Asian indigenous dogs to the Middle East and Europe through Central and West Asia, providing evidence for a major expansion that shaped the patterns of genetic differentiation in modern dogs. This expansion was probably secondary and could have led to the replacement of earlier resident populations in Western Eurasia. This could explain why earlier studies based on modern DNA suggest East Asia as the region of dog origin, while ancient DNA and archaeological data point to Western Eurasia.
Domesticated species are often composed of distinct populations differing in the character and st... more Domesticated species are often composed of distinct populations differing in the character and strength of artificial and natural selection pressures, providing a valuable model to study adaptation. In contrast to pure-breed dogs that constitute artificially maintained inbred lines, free-ranging dogs are typically free-breeding, i.e. unrestrained in mate choice. Many traits in free-breeding dogs (FBDs) may be under similar natural and sexual selection conditions to wild canids, while relaxation of sexual selection is expected in pure-breed dogs. We used a Bayesian approach with strict false-positive control criteria to identify FST-outlier SNPs between FBDs and either European or East Asian breeds, based on 167,989 autosomal SNPs. By identifying outlier SNPs located within coding genes, we found four candidate genes under diversifying selection shared by these two comparisons. Three of them are associated with the Hedgehog (HH) signalling pathway regulating vertebrate morphogenesis. A comparison between FBDs and East Asian breeds also revealed diversifying selection on BBS6 gene, which was earlier shown to cause snout shortening and dental crowding via disrupted HH signalling. Our results suggest that relaxation of natural and sexual selection in pure-breed dogs as opposed to FBDs could have led to mild changes in regulation of the HH signalling pathway. HH inhibits adhesion and migration of neural crest cells from neural tube, and minor deficits of these cells during embryonic development have been proposed as the underlying cause of "domestication syndrome". This suggests that the process of breed formation involved the same genetic and developmental pathways as the process of domestication.
The mechanisms of leukemogenesis induced by bovine leukemia virus (BLV) and the processes underly... more The mechanisms of leukemogenesis induced by bovine leukemia virus (BLV) and the processes underlying the phenomenon of differential host response to BLV infection still remain poorly understood. The aim of the study was to screen the entire cattle genome to identify markers and candidate genes that might be involved in host response to bovine leukemia virus infection. A genome-wide association study was performed using Holstein cows naturally infected by BLV. A data set included 43 cows (BLV positive) and 30 cows (BLV negative) genotyped for 54,609 SNP markers (Illumina Bovine SNP50 BeadChip). The BLV status of cows was determined by serum ELISA, nested-PCR and hematological counts. Linear Regression Analysis with a False Discovery Rate and kinship matrix (computed on the autosomal SNPs) was calculated to find out which SNP markers significantly differentiate BLV-positive and BLV-negative cows. Nine markers reached genome-wide significance. The most significant SNPs were located on chromosomes 23 (rs41583098), 3 (rs109405425, rs110785500) and 8 (rs43564499) in close vicinity of a patatin-like phospholipase domain containing 1 (PNPLA1); adaptor-related protein complex 4, beta 1 subunit (AP4B1); tripartite motif-containing 45 (TRIM45) and cell division cycle associated 2 (CDCA2) genes, respectively. Furthermore, a list of 41 candidate genes was composed based on their proximity to significant markers (within a distance of ca. 1 Mb) and functional involvement in processes potentially underlying BLV-induced pathogenesis. In conclusion, it was demonstrated that host response to BLV infection involves nine sub-regions of the cattle genome (represented by 9 SNP markers), containing many genes which, based on the literature, could be involved to enzootic bovine leukemia progression. New group of promising candidate genes associated with the host response to BLV infection were identified and could therefore be a target for future studies. The functions of candidate genes surrounding significant SNP markers imply that there is no single regulatory process that is solely targeted by BLV infection, but rather the network of interrelated pathways is deregulated, leading to the disruption of the control of B-cell proliferation and programmed cell death.
ContentsThe aim of the study was to screen the entire bull genome to identify markers and candida... more ContentsThe aim of the study was to screen the entire bull genome to identify markers and candidate genes underlying sperm concentration. The analysed data set originates from a population of 877 Polish Holstein‐Friesian bulls. Based on sperm concentration value, two extreme groups of bulls were created: Low (L, n = 126) and High (H, n = 140). Each bull was genotyped using the Illumina BovineSNP50 BeadChip. Genome‐wide association analysis was performed with the use of GoldenHelix SVS7 software. An additive model with a Cohran–Armitage test, Correlation/Trend adjusted by a Bonferroni test, was used to estimate the effect of SNP marker for sperm concentration. Thirteen markers reached genome‐wide significance. The most significant SNPs were located on chromosome 3 (rs109154964 and rs108965556), 14 (rs41621145) and 18 (rs41615539), in the close vicinity of protein arginine methyltransferase 6 (PRMT6), Sel1 repeat containing 1 (SELRC1), triple QxxK/R motif containing (TRIQK) and zinc f...
Genomic selection programs, besides their practical use, deliver a huge amount of data with singl... more Genomic selection programs, besides their practical use, deliver a huge amount of data with single nucleotide polymorphisms (SNPs) affecting performance traits. Although most SNP effects are small, their distribution along the chromosomes delivers an opportunity to indicate those sub-regions of the genome which may contain causal polymorphisms involved in the genetic variation of the trait (Hayes, Bowman, Chamberlain, & Goddard, 2009). Cole, VanRaden, O'Connell, Tassell, and Sonstegard (2009) analysed the distribution and position of 38,416 SNP effects estimated for the population of 5,285 Holstein bulls and found markers on BTA18 which had a relatively large impact on fertility and conformation traits, longevity and total merit. SNP ss86324977 (rs109478645) mapped in position 57,125,868 was found to be the most significant and is located in the intron of SIGLEC5. protein is located on the cell surface and is involved in binding sialiSIGLEC5 c acid (Angata, Margulies, Green, & Varki, 2004). It is expressed in cells responsible for non-specific immune response (monocytes, granulocytes, macrophages and NK cells) and takes part in adhesion and signalling (Crocker, Paulson, & Varki, 2007; Crocker & Varki, 2001). Foussias, Yousef, and Diamandis (2000) confirmed the expression of SIGLEC5 gene in the uterus and embryo, supporting the hypothesis that the gene might be involved in fertility. Assuming that the SIGLEC5 is a promising candidate gene, it was hypothesized that its effects on performance traits may be caused
The aim of this study was to predict the genomic breeding value (DGV) of production, selected con... more The aim of this study was to predict the genomic breeding value (DGV) of production, selected conformation and reproductive traits, and somatic cell score of dairy cattle in Poland using high-frequency marker haplotypes. The dataset consisted of phenotypic, genotypic, and pedigree data of 1216 Polish Holstein-Friesian bulls. The genotypic data consisted of 54,000 singlenucleotide polymorphisms (SNPs). The data were divided into two subsets: a test dataset (n = 1064) and a validation dataset (n = 152). Genotypic data were selected using three criteria: the percentage of missing genotypes, minor allele frequency, and linkage disequilibrium. The purpose of the data selection was to identify blocks of SNPs that were then used for the construction of haplotypes. Only haplotypes with a frequency higher than 25% were selected. DGV was predicted using four variants of a linear model with random haplotype effects and deregressed breeding values as the response variables. The accuracy of genomic prediction was checked by comparing DGVs with estimated breeding values (EBVs) using two methods: Pearson's correlations and the regression of EBVon DGV. The use of high-frequency haplotypes showed a tendency to underestimate DGVs. None of the models tested was clearly superior with regard to the traits studied. DGVs of production and conformation traits as well as somatic cell score (medium or high heritability traits) were more accurate than those estimated for fertility traits (low heritability traits).
In 2009, a frozen mummy of the steppe bison (SB) (Bison priscus) was discovered between the lower... more In 2009, a frozen mummy of the steppe bison (SB) (Bison priscus) was discovered between the lower Kolyma River and the Alazeya River in northeast Siberia, Russia. The specimen was dated with 14 C and estimated to have lived more than 48,000 14 C years before present (BP). The relationship between SB and the European Bison (EB) (Bison bonasus), also known as wisent or European wood bison, is unresolved and it is unclear whether the SB and EB overlapped in space and time. The aim of our study was to compare genetic variability between the SB specimen and modern EB. We expected higher SB variability due to substantial bottlenecks in the EB approximately one century ago when it became extinct in the wild. The EB (n = 167) and the SB specimen were genotyped with the Illumina BovineHD BeadChip with 777,962 single-nucleotide polymorphism (SNP) markers. Steppe bison DNA was extracted and genotyped six times to account for genotyping errors due to low-quality DNA. We obtained a final set of 7786 SNPs. The mean number of private alleles in EB was 0.027 (± 0.0002) and in SB, it was 0.288 (± 0.0006). This could be explained by factors including differences between species, spatiotemporal divergence, and bottleneck effects. Investigation of historic EB samples could help resolve phylogenetic relationships, the role of the recent bottleneck, and provide information for conservation management to reduce the incidence of disease in the population and maintain its evolutionary potential.
The aims of this study were to confirm ADAM32 gene expression in selected bovine tissues and iden... more The aims of this study were to confirm ADAM32 gene expression in selected bovine tissues and identify potentially functional polymorphisms within the 5'flanking region. The associations between the polymorphism within ADAM32 and somatic cell count in the Holstein-Friesian cow's milk were examined. Expression studies of ADAM32 in different tissues performed by RT-PCR revealed the presence of the ADAM32 transcript in the liver, mammary and pituitary gland and leukocytes, except for monocytes. Comparative sequencing analysis of 870 bp PCR amplicons obtained from four different Bos taurus breeds and the Bison bonasus fragment of the ADAM32 5' flanking region showed a 21 bp insertion/deletion at position-541 nt to-520 nt and the occurrence of seven SNPs. In silico analysis of the 1180 bp 5' flanking region of ADAM32 indicated that the 21 bp deletion abolished putative binding sites for six transcription factors associated with the immune system. A population of one hundred and two Polish Holstein-Friesian bulls and 241 cows-progeny of 15 heterozygous (InsDel) sires were screened. The frequency of genotypes (for sires) were observed at 0.765, 0.235, 0.0 for DelDel, InsDel and InsIns, respectively, whereas for cows the frequencies are as follows: 0.365, 0.510 and 0.125. The association study performed within the group of daughters of heterozygous sires revealed that cows with the DelDel genotype showed significantly higher somatic cell counts than those with the InsIns genotype (P=0.013). No significant association was found between cows' genotypes and milk production traits.
The aim of this study was to quantify b-casomorphin-7 in raw, hydrolyzed and processed milk in di... more The aim of this study was to quantify b-casomorphin-7 in raw, hydrolyzed and processed milk in different stages of the cow lactation. The obtained results lead to the following conclusion: the highest amount of b-casomorphin-7 released from the hydrolyzed and processed milk is related to the b-casein A1 allele, irrespective of a lactation period. Some traces of b-casomorphin-7 in milk from cows with the b-casein A2 variant are probably a result of the acid hydrolysis of b-casein during its digestion with pepsin. It has been shown that processing of raw milk at high temperatures affects, in a slight degree, the differences between b-casomorphins-7 originating from different b-casein genotypes. The obtained results suggest a possibility to provide a new nutritional factor for milk quality based on the content of b-casomorphin-7 liberated in vivo from milk digested by a mixture of the gastrointestinal enzymes.
Genome-wide association study for posthitis in the free-living population of European bison (Biso... more Genome-wide association study for posthitis in the free-living population of European bison (Bison bonasus)
The aim of the study was to screen the entire bull genome to identify SNP markers and propose can... more The aim of the study was to screen the entire bull genome to identify SNP markers and propose candidate genes potentially involved in the variation of sperm membrane integrity in Holstein-Friesian bulls. Two hundred eighty eight bulls kept in one AI center were included in the study. Each bull was genotyped for 54.001 Single Nucleotide Polymorpisms (SNP) by the Illumina BovineSNP50 BeadChip. Commercial straws of frozen-thawed semen were used for the evaluation of sperm plasma membrane integrity (SYBR-14/PI staining) and sperm mitochondrial function (JC1/PI staining). An additive model for Linear Regression Analysis was applied to estimate the effect of SNP marker for sperm membrane integrity (by the use of GoldenHelix SVS7 software). Five significant markers (encompassing 2,2 MB region located on chromosome 6) for SYBR-14/PI were found. Among them one marker-rs41570391 passed Bonferroni correction test. Within approximately 3 Mb genomic region including significant markers three candidate genes: SGMS2 (Sphingomyelin Synthase 2), TET2 (Methylcytosine dioxygenase 2) and GSTCD genes (Gluthatione S-transferase C terminal domain) were proposed as potentially involved in sperm membrane integrity in frozen-thawed semen of Holstein-Friesian bulls.
Although a large part of the global domestic dog population is free-ranging and free-breeding, kn... more Although a large part of the global domestic dog population is free-ranging and free-breeding, knowledge of genetic diversity in these free-breeding dogs (FBDs) and their ancestry relations to pure-breed dogs is limited, and the indigenous status of FBDs in Asia is still uncertain. We analyse genome-wide SNP variability of FBDs across Eurasia, and show that they display weak genetic structure and are genetically distinct from pure-breed dogs rather than constituting an admixture of breeds. Our results suggest that modern European breeds originated locally from European FBDs. East Asian and Arctic breeds show closest affinity to East Asian FBDs, and they both represent the earliest branching lineages in the phylogeny of extant Eurasian dogs. Our biogeographic reconstruction of ancestral distributions indicates a gradual westward expansion of East Asian indigenous dogs to the Middle East and Europe through Central and West Asia, providing evidence for a major expansion that shaped the patterns of genetic differentiation in modern dogs. This expansion was probably secondary and could have led to the replacement of earlier resident populations in Western Eurasia. This could explain why earlier studies based on modern DNA suggest East Asia as the region of dog origin, while ancient DNA and archaeological data point to Western Eurasia.
Domesticated species are often composed of distinct populations differing in the character and st... more Domesticated species are often composed of distinct populations differing in the character and strength of artificial and natural selection pressures, providing a valuable model to study adaptation. In contrast to pure-breed dogs that constitute artificially maintained inbred lines, free-ranging dogs are typically free-breeding, i.e. unrestrained in mate choice. Many traits in free-breeding dogs (FBDs) may be under similar natural and sexual selection conditions to wild canids, while relaxation of sexual selection is expected in pure-breed dogs. We used a Bayesian approach with strict false-positive control criteria to identify FST-outlier SNPs between FBDs and either European or East Asian breeds, based on 167,989 autosomal SNPs. By identifying outlier SNPs located within coding genes, we found four candidate genes under diversifying selection shared by these two comparisons. Three of them are associated with the Hedgehog (HH) signalling pathway regulating vertebrate morphogenesis. A comparison between FBDs and East Asian breeds also revealed diversifying selection on BBS6 gene, which was earlier shown to cause snout shortening and dental crowding via disrupted HH signalling. Our results suggest that relaxation of natural and sexual selection in pure-breed dogs as opposed to FBDs could have led to mild changes in regulation of the HH signalling pathway. HH inhibits adhesion and migration of neural crest cells from neural tube, and minor deficits of these cells during embryonic development have been proposed as the underlying cause of "domestication syndrome". This suggests that the process of breed formation involved the same genetic and developmental pathways as the process of domestication.
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