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Manuel More - One of the best experts on this subject based on the ideXlab platform.
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evaluation of snp genotyping in Alpacas using the bovine hd genotyping beadchip
Frontiers in Genetics, 2019Co-Authors: Manuel More, Gustavo Gutierrez, Max F Rothschild, Francesca Bertolini, Abel Ponce F De LeonAbstract:Alpacas are one of four South American Camelid species living in the highlands of the Andes. Production of Alpaca fiber contributes to the economy of the region and the livelihood of many rural families. Fiber quantity and quality are important and in need of a modern breeding program based on genomic selection to accelerate genetic gain. To achieve this is necessary to discover enough molecular markers, single nucleotide polymorphisms (SNPs) in particular, to provide genome coverage and facilitate genome wide association studies (GWAS) to fiber production characteristics. The aim of this study was to discover Alpaca SNPs by genotyping forty Alpaca DNA samples using the BovineHD Genotyping Beadchip. Data analysis was performed with GenomeStudio (Illumina) software. Because different filters and thresholds are reported in the literature we investigated the effects of no-call threshold (≥ 0.05, ≥ 0.15 and ≥ 0.25) and call frequency (≥ 0.9 and = 1.0) in identifying positive SNPs. Average GC Scores, calculated as the average of the 10% and 50% GenCall scores for each SNP (≥ 0.70) and the GenTrain Score ≥ 0.25 parameters were applied to all comparisons. SNPs with Minor Allele Frequency (MAF) ≥ 0.05 or ≥ 0.01 were retained. Since detection of SNPs is based on the stable binding of oligonucleotide probes to the target DNA immediately adjacent to the variant nucleotide, all positive SNP flanking sequences showing perfect alignments between the bovine and Alpaca genomes for the first 21 or 26 nucleotides flanking the variant nucleotide at either side were selected. Only SNPs localized in one scaffold were assumed unique. Unique SNPs identified in both reference genomes were kept and mapped on the Vicugna_pacos 2.0.2 genome. The effects of the no-call threshold ≥ 0.25, call frequency = 1 and average GC ≥ 0.7 were meaningful and identified 6756 SNPs of which 400 were unique and polymorphic (MAF ≥ 0.01). Assignment to Alpaca chromosomes was possible for 292 SNPs. Likewise, 209 SNPs were localized in 202 Alpaca gene loci and 29 of these share the same loci with the dromedary. Interestingly, 69 of 400 Alpaca SNPs have 100% similarity with dromedary.
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Image_1_Evaluation of SNP Genotyping in Alpacas Using the Bovine HD Genotyping Beadchip.pdf
2019Co-Authors: Manuel More, Gustavo Gutierrez, Ma Rothschild, Francesca Ertolini, Abel Ponce F. De LeóAbstract:Alpacas are one of four South American Camelid species living in the highlands of the Andes. Production of Alpaca fiber contributes to the economy of the region and the livelihood of many rural families. Fiber quantity and quality are important and in need of a modern breeding program based on genomic selection to accelerate genetic gain. To achieve this is necessary to discover enough molecular markers, single nucleotide polymorphisms (SNPs) in particular, to provide genome coverage and facilitate genome wide association studies to fiber production characteristics. The aim of this study was to discover Alpaca SNPs by genotyping forty Alpaca DNA samples using the BovineHD Genotyping Beadchip. Data analysis was performed with GenomeStudio (Illumina) software. Because different filters and thresholds are reported in the literature we investigated the effects of no-call threshold (≥0.05, ≥0.15, and ≥0.25) and call frequency (≥0.9 and =1.0) in identifying positive SNPs. Average GC Scores, calculated as the average of the 10% and 50% GenCall scores for each SNP (≥0.70) and the GenTrain score ≥ 0.25 parameters were applied to all comparisons. SNPs with minor allele frequency (MAF) ≥ 0.05 or ≥ 0.01 were retained. Since detection of SNPs is based on the stable binding of oligonucleotide probes to the target DNA immediately adjacent to the variant nucleotide, all positive SNP flanking sequences showing perfect alignments between the bovine and Alpaca genomes for the first 21 or 26 nucleotides flanking the variant nucleotide at either side were selected. Only SNPs localized in one scaffold were assumed unique. Unique SNPs identified in both reference genomes were kept and mapped on the Vicugna_pacos 2.0.2 genome. The effects of the no-call threshold ≥ 0.25, call frequency = 1 and average GC ≥ 0.7 were meaningful and identified 6756 SNPs of which 400 were unique and polymorphic (MAF ≥ 0.01). Assignment to Alpaca chromosomes was possible for 292 SNPs. Likewise, 209 SNPs were localized in 202 Alpaca gene loci and 29 of these share the same loci with the dromedary. Interestingly, 69 of 400 Alpaca SNPs have 100% similarity with dromedary.
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Table_2_Evaluation of SNP Genotyping in Alpacas Using the Bovine HD Genotyping Beadchip.xlsx
2019Co-Authors: Manuel More, Gustavo Gutierrez, Ma Rothschild, Francesca Ertolini, Abel Ponce F. De LeóAbstract:Alpacas are one of four South American Camelid species living in the highlands of the Andes. Production of Alpaca fiber contributes to the economy of the region and the livelihood of many rural families. Fiber quantity and quality are important and in need of a modern breeding program based on genomic selection to accelerate genetic gain. To achieve this is necessary to discover enough molecular markers, single nucleotide polymorphisms (SNPs) in particular, to provide genome coverage and facilitate genome wide association studies to fiber production characteristics. The aim of this study was to discover Alpaca SNPs by genotyping forty Alpaca DNA samples using the BovineHD Genotyping Beadchip. Data analysis was performed with GenomeStudio (Illumina) software. Because different filters and thresholds are reported in the literature we investigated the effects of no-call threshold (≥0.05, ≥0.15, and ≥0.25) and call frequency (≥0.9 and =1.0) in identifying positive SNPs. Average GC Scores, calculated as the average of the 10% and 50% GenCall scores for each SNP (≥0.70) and the GenTrain score ≥ 0.25 parameters were applied to all comparisons. SNPs with minor allele frequency (MAF) ≥ 0.05 or ≥ 0.01 were retained. Since detection of SNPs is based on the stable binding of oligonucleotide probes to the target DNA immediately adjacent to the variant nucleotide, all positive SNP flanking sequences showing perfect alignments between the bovine and Alpaca genomes for the first 21 or 26 nucleotides flanking the variant nucleotide at either side were selected. Only SNPs localized in one scaffold were assumed unique. Unique SNPs identified in both reference genomes were kept and mapped on the Vicugna_pacos 2.0.2 genome. The effects of the no-call threshold ≥ 0.25, call frequency = 1 and average GC ≥ 0.7 were meaningful and identified 6756 SNPs of which 400 were unique and polymorphic (MAF ≥ 0.01). Assignment to Alpaca chromosomes was possible for 292 SNPs. Likewise, 209 SNPs were localized in 202 Alpaca gene loci and 29 of these share the same loci with the dromedary. Interestingly, 69 of 400 Alpaca SNPs have 100% similarity with dromedary.
Abel Ponce F De Leon - One of the best experts on this subject based on the ideXlab platform.
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evaluation of snp genotyping in Alpacas using the bovine hd genotyping beadchip
Frontiers in Genetics, 2019Co-Authors: Manuel More, Gustavo Gutierrez, Max F Rothschild, Francesca Bertolini, Abel Ponce F De LeonAbstract:Alpacas are one of four South American Camelid species living in the highlands of the Andes. Production of Alpaca fiber contributes to the economy of the region and the livelihood of many rural families. Fiber quantity and quality are important and in need of a modern breeding program based on genomic selection to accelerate genetic gain. To achieve this is necessary to discover enough molecular markers, single nucleotide polymorphisms (SNPs) in particular, to provide genome coverage and facilitate genome wide association studies (GWAS) to fiber production characteristics. The aim of this study was to discover Alpaca SNPs by genotyping forty Alpaca DNA samples using the BovineHD Genotyping Beadchip. Data analysis was performed with GenomeStudio (Illumina) software. Because different filters and thresholds are reported in the literature we investigated the effects of no-call threshold (≥ 0.05, ≥ 0.15 and ≥ 0.25) and call frequency (≥ 0.9 and = 1.0) in identifying positive SNPs. Average GC Scores, calculated as the average of the 10% and 50% GenCall scores for each SNP (≥ 0.70) and the GenTrain Score ≥ 0.25 parameters were applied to all comparisons. SNPs with Minor Allele Frequency (MAF) ≥ 0.05 or ≥ 0.01 were retained. Since detection of SNPs is based on the stable binding of oligonucleotide probes to the target DNA immediately adjacent to the variant nucleotide, all positive SNP flanking sequences showing perfect alignments between the bovine and Alpaca genomes for the first 21 or 26 nucleotides flanking the variant nucleotide at either side were selected. Only SNPs localized in one scaffold were assumed unique. Unique SNPs identified in both reference genomes were kept and mapped on the Vicugna_pacos 2.0.2 genome. The effects of the no-call threshold ≥ 0.25, call frequency = 1 and average GC ≥ 0.7 were meaningful and identified 6756 SNPs of which 400 were unique and polymorphic (MAF ≥ 0.01). Assignment to Alpaca chromosomes was possible for 292 SNPs. Likewise, 209 SNPs were localized in 202 Alpaca gene loci and 29 of these share the same loci with the dromedary. Interestingly, 69 of 400 Alpaca SNPs have 100% similarity with dromedary.
Gustavo Gutierrez - One of the best experts on this subject based on the ideXlab platform.
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evaluation of snp genotyping in Alpacas using the bovine hd genotyping beadchip
Frontiers in Genetics, 2019Co-Authors: Manuel More, Gustavo Gutierrez, Max F Rothschild, Francesca Bertolini, Abel Ponce F De LeonAbstract:Alpacas are one of four South American Camelid species living in the highlands of the Andes. Production of Alpaca fiber contributes to the economy of the region and the livelihood of many rural families. Fiber quantity and quality are important and in need of a modern breeding program based on genomic selection to accelerate genetic gain. To achieve this is necessary to discover enough molecular markers, single nucleotide polymorphisms (SNPs) in particular, to provide genome coverage and facilitate genome wide association studies (GWAS) to fiber production characteristics. The aim of this study was to discover Alpaca SNPs by genotyping forty Alpaca DNA samples using the BovineHD Genotyping Beadchip. Data analysis was performed with GenomeStudio (Illumina) software. Because different filters and thresholds are reported in the literature we investigated the effects of no-call threshold (≥ 0.05, ≥ 0.15 and ≥ 0.25) and call frequency (≥ 0.9 and = 1.0) in identifying positive SNPs. Average GC Scores, calculated as the average of the 10% and 50% GenCall scores for each SNP (≥ 0.70) and the GenTrain Score ≥ 0.25 parameters were applied to all comparisons. SNPs with Minor Allele Frequency (MAF) ≥ 0.05 or ≥ 0.01 were retained. Since detection of SNPs is based on the stable binding of oligonucleotide probes to the target DNA immediately adjacent to the variant nucleotide, all positive SNP flanking sequences showing perfect alignments between the bovine and Alpaca genomes for the first 21 or 26 nucleotides flanking the variant nucleotide at either side were selected. Only SNPs localized in one scaffold were assumed unique. Unique SNPs identified in both reference genomes were kept and mapped on the Vicugna_pacos 2.0.2 genome. The effects of the no-call threshold ≥ 0.25, call frequency = 1 and average GC ≥ 0.7 were meaningful and identified 6756 SNPs of which 400 were unique and polymorphic (MAF ≥ 0.01). Assignment to Alpaca chromosomes was possible for 292 SNPs. Likewise, 209 SNPs were localized in 202 Alpaca gene loci and 29 of these share the same loci with the dromedary. Interestingly, 69 of 400 Alpaca SNPs have 100% similarity with dromedary.
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Image_1_Evaluation of SNP Genotyping in Alpacas Using the Bovine HD Genotyping Beadchip.pdf
2019Co-Authors: Manuel More, Gustavo Gutierrez, Ma Rothschild, Francesca Ertolini, Abel Ponce F. De LeóAbstract:Alpacas are one of four South American Camelid species living in the highlands of the Andes. Production of Alpaca fiber contributes to the economy of the region and the livelihood of many rural families. Fiber quantity and quality are important and in need of a modern breeding program based on genomic selection to accelerate genetic gain. To achieve this is necessary to discover enough molecular markers, single nucleotide polymorphisms (SNPs) in particular, to provide genome coverage and facilitate genome wide association studies to fiber production characteristics. The aim of this study was to discover Alpaca SNPs by genotyping forty Alpaca DNA samples using the BovineHD Genotyping Beadchip. Data analysis was performed with GenomeStudio (Illumina) software. Because different filters and thresholds are reported in the literature we investigated the effects of no-call threshold (≥0.05, ≥0.15, and ≥0.25) and call frequency (≥0.9 and =1.0) in identifying positive SNPs. Average GC Scores, calculated as the average of the 10% and 50% GenCall scores for each SNP (≥0.70) and the GenTrain score ≥ 0.25 parameters were applied to all comparisons. SNPs with minor allele frequency (MAF) ≥ 0.05 or ≥ 0.01 were retained. Since detection of SNPs is based on the stable binding of oligonucleotide probes to the target DNA immediately adjacent to the variant nucleotide, all positive SNP flanking sequences showing perfect alignments between the bovine and Alpaca genomes for the first 21 or 26 nucleotides flanking the variant nucleotide at either side were selected. Only SNPs localized in one scaffold were assumed unique. Unique SNPs identified in both reference genomes were kept and mapped on the Vicugna_pacos 2.0.2 genome. The effects of the no-call threshold ≥ 0.25, call frequency = 1 and average GC ≥ 0.7 were meaningful and identified 6756 SNPs of which 400 were unique and polymorphic (MAF ≥ 0.01). Assignment to Alpaca chromosomes was possible for 292 SNPs. Likewise, 209 SNPs were localized in 202 Alpaca gene loci and 29 of these share the same loci with the dromedary. Interestingly, 69 of 400 Alpaca SNPs have 100% similarity with dromedary.
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Table_2_Evaluation of SNP Genotyping in Alpacas Using the Bovine HD Genotyping Beadchip.xlsx
2019Co-Authors: Manuel More, Gustavo Gutierrez, Ma Rothschild, Francesca Ertolini, Abel Ponce F. De LeóAbstract:Alpacas are one of four South American Camelid species living in the highlands of the Andes. Production of Alpaca fiber contributes to the economy of the region and the livelihood of many rural families. Fiber quantity and quality are important and in need of a modern breeding program based on genomic selection to accelerate genetic gain. To achieve this is necessary to discover enough molecular markers, single nucleotide polymorphisms (SNPs) in particular, to provide genome coverage and facilitate genome wide association studies to fiber production characteristics. The aim of this study was to discover Alpaca SNPs by genotyping forty Alpaca DNA samples using the BovineHD Genotyping Beadchip. Data analysis was performed with GenomeStudio (Illumina) software. Because different filters and thresholds are reported in the literature we investigated the effects of no-call threshold (≥0.05, ≥0.15, and ≥0.25) and call frequency (≥0.9 and =1.0) in identifying positive SNPs. Average GC Scores, calculated as the average of the 10% and 50% GenCall scores for each SNP (≥0.70) and the GenTrain score ≥ 0.25 parameters were applied to all comparisons. SNPs with minor allele frequency (MAF) ≥ 0.05 or ≥ 0.01 were retained. Since detection of SNPs is based on the stable binding of oligonucleotide probes to the target DNA immediately adjacent to the variant nucleotide, all positive SNP flanking sequences showing perfect alignments between the bovine and Alpaca genomes for the first 21 or 26 nucleotides flanking the variant nucleotide at either side were selected. Only SNPs localized in one scaffold were assumed unique. Unique SNPs identified in both reference genomes were kept and mapped on the Vicugna_pacos 2.0.2 genome. The effects of the no-call threshold ≥ 0.25, call frequency = 1 and average GC ≥ 0.7 were meaningful and identified 6756 SNPs of which 400 were unique and polymorphic (MAF ≥ 0.01). Assignment to Alpaca chromosomes was possible for 292 SNPs. Likewise, 209 SNPs were localized in 202 Alpaca gene loci and 29 of these share the same loci with the dromedary. Interestingly, 69 of 400 Alpaca SNPs have 100% similarity with dromedary.
Joh M. Chasto - One of the best experts on this subject based on the ideXlab platform.
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Image_8_Bacterial Communities in the Alpaca Gastrointestinal Tract Vary With Diet and Body Site.JPEG
2019Co-Authors: Courtney Carroll, Kyle D. Olse, Natha J. Ricks, Kimberly A. Dill-mcfarland, Garre Sue, Todd F. Robinso, Joh M. ChastoAbstract:Gut -associated microbes (‘gut microbiota’) impact the nutrition of their hosts, especially in ruminants and pseudoruminants that consume high-cellulose diets. Examples include the pseudoruminant Alpaca. To better understand how body site and diet influence the Alpaca microbiota, we performed three 16S rRNA gene surveys. First, we surveyed the compartment 1 (C1), duodenum, jejunum, ileum, cecum, and large intestine (LI) of Alpacas fed a grass hay (GH; tall fescue) or alfalfa hay (AH) diet for 30 days. Second, we performed a C1 survey of Alpacas fed a series of 2-week mixed grass hay (MGH) diets supplemented with ∼25% dry weight barley, quinoa, amaranth, or soybean meal. Third, we examined the microbial differences of Alpacas with normal versus poor body condition. Samples from GH- and AH-fed Alpacas grouped by diet and body site but none of the four supplements significantly altered C1 microbiota composition, relative to each other, and none of the OTUs were differentially abundant between Alpacas with normal versus poor body conditions. Taken together, the findings of a diet- and body-site specific Alpaca microbiota are consistent with previous findings in ruminants and other mammals, but we provide no evidence to link changes in Alpaca body condition with variation in microbiota relative abundance or identity.
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Data_Sheet_3_Bacterial Communities in the Alpaca Gastrointestinal Tract Vary With Diet and Body Site.xlsx
2019Co-Authors: Courtney Carroll, Kyle D. Olse, Natha J. Ricks, Kimberly A. Dill-mcfarland, Garre Sue, Todd F. Robinso, Joh M. ChastoAbstract:Gut -associated microbes (‘gut microbiota’) impact the nutrition of their hosts, especially in ruminants and pseudoruminants that consume high-cellulose diets. Examples include the pseudoruminant Alpaca. To better understand how body site and diet influence the Alpaca microbiota, we performed three 16S rRNA gene surveys. First, we surveyed the compartment 1 (C1), duodenum, jejunum, ileum, cecum, and large intestine (LI) of Alpacas fed a grass hay (GH; tall fescue) or alfalfa hay (AH) diet for 30 days. Second, we performed a C1 survey of Alpacas fed a series of 2-week mixed grass hay (MGH) diets supplemented with ∼25% dry weight barley, quinoa, amaranth, or soybean meal. Third, we examined the microbial differences of Alpacas with normal versus poor body condition. Samples from GH- and AH-fed Alpacas grouped by diet and body site but none of the four supplements significantly altered C1 microbiota composition, relative to each other, and none of the OTUs were differentially abundant between Alpacas with normal versus poor body conditions. Taken together, the findings of a diet- and body-site specific Alpaca microbiota are consistent with previous findings in ruminants and other mammals, but we provide no evidence to link changes in Alpaca body condition with variation in microbiota relative abundance or identity.
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Bacterial Communities in the Alpaca Gastrointestinal Tract Vary With Diet and Body Site
Frontiers Media S.A., 2019Co-Authors: Courtney Carroll, Kyle D. Olse, Natha J. Ricks, Kimberly A. Dill-mcfarland, Garre Sue, Todd F. Robinso, Joh M. ChastoAbstract:Gut -associated microbes (‘gut microbiota’) impact the nutrition of their hosts, especially in ruminants and pseudoruminants that consume high-cellulose diets. Examples include the pseudoruminant Alpaca. To better understand how body site and diet influence the Alpaca microbiota, we performed three 16S rRNA gene surveys. First, we surveyed the compartment 1 (C1), duodenum, jejunum, ileum, cecum, and large intestine (LI) of Alpacas fed a grass hay (GH; tall fescue) or alfalfa hay (AH) diet for 30 days. Second, we performed a C1 survey of Alpacas fed a series of 2-week mixed grass hay (MGH) diets supplemented with ∼25% dry weight barley, quinoa, amaranth, or soybean meal. Third, we examined the microbial differences of Alpacas with normal versus poor body condition. Samples from GH- and AH-fed Alpacas grouped by diet and body site but none of the four supplements significantly altered C1 microbiota composition, relative to each other, and none of the OTUs were differentially abundant between Alpacas with normal versus poor body conditions. Taken together, the findings of a diet- and body-site specific Alpaca microbiota are consistent with previous findings in ruminants and other mammals, but we provide no evidence to link changes in Alpaca body condition with variation in microbiota relative abundance or identity
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Table_1_Bacterial Communities in the Alpaca Gastrointestinal Tract Vary With Diet and Body Site.XLSX
2019Co-Authors: Courtney Carroll, Kyle D. Olse, Natha J. Ricks, Kimberly A. Dill-mcfarland, Garre Sue, Todd F. Robinso, Joh M. ChastoAbstract:Gut -associated microbes (‘gut microbiota’) impact the nutrition of their hosts, especially in ruminants and pseudoruminants that consume high-cellulose diets. Examples include the pseudoruminant Alpaca. To better understand how body site and diet influence the Alpaca microbiota, we performed three 16S rRNA gene surveys. First, we surveyed the compartment 1 (C1), duodenum, jejunum, ileum, cecum, and large intestine (LI) of Alpacas fed a grass hay (GH; tall fescue) or alfalfa hay (AH) diet for 30 days. Second, we performed a C1 survey of Alpacas fed a series of 2-week mixed grass hay (MGH) diets supplemented with ∼25% dry weight barley, quinoa, amaranth, or soybean meal. Third, we examined the microbial differences of Alpacas with normal versus poor body condition. Samples from GH- and AH-fed Alpacas grouped by diet and body site but none of the four supplements significantly altered C1 microbiota composition, relative to each other, and none of the OTUs were differentially abundant between Alpacas with normal versus poor body conditions. Taken together, the findings of a diet- and body-site specific Alpaca microbiota are consistent with previous findings in ruminants and other mammals, but we provide no evidence to link changes in Alpaca body condition with variation in microbiota relative abundance or identity.
Su Xiaohui - One of the best experts on this subject based on the ideXlab platform.
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Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and Alpaca
'Springer Science and Business Media LLC', 2020Co-Authors: Fa Ruiwe, Gu Zhongru, Guang Xuanmi, Marín, Jua Carlos, Varas Valeria, González, Benito A., Wheeler, Jane C., Hu Yafei, Li Erli, Su XiaohuiAbstract:Abstract Background: Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and Alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published Alpaca genome, and resequence seven individuals of all four species to better understand domestication and introgression between the llama and Alpaca. Results: Phylogenomic analysis confirms that the llama was domesticated from the guanaco and the Alpaca from the vicuña. Introgression was much higher in the Alpaca genome (36%) than the llama (5%) and could be dated close to the time of the Spanish conquest, approximately 500 years ago. Introgression patterns are at their most variable on the X-chromosome of the Alpaca, featuring 53 genes known to have deleterious X-linked phenotypes in humans. Strong genome-wide introgression signatures include olfactory receptor complexes into both species, hypertension resistance into Alpaca, and fleece/fiber traits into llama. Genomic signatures of domestication in the llama include male reproductive traits, while in Alpaca feature fleece characteristics, olfaction-related and hypoxia adaptation traits. Expression analysis of the introgressed region that is syntenic to human HSA4q21, a gene cluster previously associated with hypertension in humans under hypoxic conditions, shows a previously undocumented role for PRDM8 downregulation as a potential transcriptional regulation mechanism, analogous to that previously reported at high altitude for hypoxia-inducible factor 1α. Conclusions: The unprecedented introgression signatures within both domestic camelid genomes may reflect post-conquest changes in agriculture and the breakdown of traditional management practices
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Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and Alpaca
'Springer Science and Business Media LLC', 2020Co-Authors: Fa Ruiwe, Gu Zhongru, Guang Xuanmi, Marín, Jua Carlos, Varas Valeria, Wheeler, Jane C., Hu Yafei, González Pérez Enito, Li Elri, Su XiaohuiAbstract:Background Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and Alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuna (their putative wild progenitors), compare these with the published Alpaca genome, and resequence seven individuals of all four species to better understand domestication and introgression between the llama and Alpaca. Results Phylogenomic analysis confirms that the llama was domesticated from the guanaco and the Alpaca from the vicuna. Introgression was much higher in the Alpaca genome (36%) than the llama (5%) and could be dated close to the time of the Spanish conquest, approximately 500 years ago. Introgression patterns are at their most variable on the X-chromosome of the Alpaca, featuring 53 genes known to have deleterious X-linked phenotypes in humans. Strong genome-wide introgression signatures include olfactory receptor complexes into both species, hypertension resistance into Alpaca, and fleece/fiber traits into llama. Genomic signatures of domestication in the llama include male reproductive traits, while in Alpaca feature fleece characteristics, olfaction-related and hypoxia adaptation traits. Expression analysis of the introgressed region that is syntenic to human HSA4q21, a gene cluster previously associated with hypertension in humans under hypoxic conditions, shows a previously undocumented role for PRDM8 downregulation as a potential transcriptional regulation mechanism, analogous to that previously reported at high altitude for hypoxia-inducible factor 1 alpha. Conclusions The unprecedented introgression signatures within both domestic camelid genomes may reflect post-conquest changes in agriculture and the breakdown of traditional management practices.Agro-Scientific Research in the Public Interest of China 201303119 Strategic Priority Program of the Chinese Academy of Sciences XDB31000000 National Natural Science Foundation of China (NSFC) 31821001 Cardiff University Chinese Academy of Sciences President's International Fellowship Initiative Young Sanjin Scholars Distinguished Professor program in Shanxi Agricultural University CXTD201201 Aid Program for Innovation Research Team in Shanxi Agricultural University CXTD201201 FONDECYT grant CONICYT of Chile 1140785 Science and Technology Department of Qinghai Province Major Project "Sanjiangyaun National Park Animal Genome Program" Second Tibetan Plateau Scientific Expedition and Research Program (STEP) 2019QZKK050
