21 results on '"Salavati, Mazdak"'
Search Results
2. Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing
- Author
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Salavati, Mazdak, primary, Clark, Richard, additional, Becker, Doreen, additional, Kühn, Christa, additional, Plastow, Graham, additional, Dupont, Sébastien, additional, Moreira, Gabriel Costa Monteiro, additional, Charlier, Carole, additional, and Clark, Emily Louise, additional
- Published
- 2023
- Full Text
- View/download PDF
3. Recent Advances in the Genomic Resources for Sheep
- Author
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Woolley, Shernae A., primary, Salavati, Mazdak, additional, and Clark, Emily L., additional
- Published
- 2023
- Full Text
- View/download PDF
4. Validating genomic prediction for nitrogen efficiency index and its composition traits of Holstein cows in early lactation.
- Author
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Chen, Y., Atashi, H., Mota, R. R., Grelet, C., Vanderick, S., Hu, H., Crowe, Mark, Fahey, Alan, Carter, Fiona, Matthews, Elizabeth, Santoro, Andreia, Byrne, Colin, Rudd, Pauline, O'Flaherty, Roisin, Hallinan, Sinead, Wathes, Claire, Salavati, Mazdak, Cheng, Zhangrui, Fouladi, Ali, and Pollott, Geoff
- Subjects
COWS ,LACTATION in cattle ,LACTATION ,MILK proteins ,DAIRY cattle ,SINGLE nucleotide polymorphisms - Abstract
Nitrogen (N) use efficiency (NUE) is an economically important trait for dairy cows. Recently, we proposed a new N efficiency index (NEI), that simultaneously considers both NUE and N pollution. This study aimed to validate the genomic prediction for NEI and its composition traits and investigate the relationship between SNP effects estimated directly from NEI and indirectly from its composition traits. The NEI composition included genomic estimated breeding value of N intake (NINT), milk true protein N (MTPN) and milk urea N yield. The edited data were 132,899 records on 52,064 cows distributed in 773 herds. The pedigree contained 122,368 animals. Genotypic data of 566,294 SNP was available for 4514 individuals. A total of 4413 cows (including 181 genotyped) and 56 bulls (including 32 genotyped) were selected as the validation populations. The linear regression method was used to validate the genomic prediction of NEI and its composition traits using best linear unbiased prediction (BLUP) and single‐step genomic BLUP (ssGBLUP). The mean theoretical accuracies of validation populations obtained from ssGBLUP were higher than those obtained from BLUP for both NEI and its composition traits, ranging from 0.57 (MTPN) to 0.72 (NINT). The highest mean prediction accuracies for NEI and its composition traits were observed for the genotyped cows estimated under ssGBLUP, ranging from 0.48 (MTPN) to 0.66 (NINT). Furthermore, the SNP effects estimated from NEI composition traits, multiplied by the relative weight were the same as those estimated directly from NEI. This study preliminary showed that genomic prediction can be used for NEI, however, we acknowledge the need for further validation of this result in a larger dataset. Moreover, the SNP effects of NEI can be indirectly calculated using the SNP effects estimated from its composition traits. This study provided a basis for adding genomic information to establish NEI as part of future routine genomic evaluation programs. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
5. Locating a novel autosomal recessive genetic condition using only WGS data from three cases and six controls; a case study of a new variant in the cattle glucokinase gene
- Author
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Pollott, Geoffrey E., Piercy, Richard, Massey, Claire, Salavati, Mazdak, Cheng, Zhangrui, and Wathes, D Claire
- Subjects
glucokinase gene ,cattle ,perinatal mortality ,recessive genetics ,runs of homozigosity ,Irish Moiled ,WGS - Abstract
New Mendelian genetic conditions, which adversely affect livestock, arise all the time. To manage them effectively, some methods need to be devised that are quick and accurate. Until recently, finding the causal genomic site of a new autosomal recessive genetic disease has required a two-stage approach using single-nucleotide polymorphism (SNP) chip genotyping to locate the region containing the new variant. This region is then explored using fine-mapping methods to locate the actual site of the new variant. This study explores bioinformatic methods that can be used to identify the causative variants of recessive genetic disorders with full penetrance with just nine whole genome-sequenced animals to simplify and expedite the process to a one-step procedure. Using whole genome sequencing of only three cases and six carriers, the site of a novel variant causing perinatal mortality in Irish moiled calves was located. Four methods were used to interrogate the variant call format (VCF) data file of these nine animals, they are genotype criteria (GCR), autozygosity-by-difference (ABD), variant prediction scoring, and registered SNP information. From more than nine million variants in the VCF file, only one site was identified by all four methods (Chr4: g.77173487A>T (ARS-UCD1.2 (GCF_002263795.1)). This site was a splice acceptor variant located in the glucokinase gene ( GCK). It was verified on an independent sample of animals from the breed using genotyping by polymerase chain reaction at the candidate site and autozygosity-by-difference using SNP-chips. Both methods confirmed the candidate site. Investigation of the GCR method found that sites meeting the GCR were not evenly spread across the genome but concentrated in regions of long runs of homozygosity. Locating GCR sites was best performed using two carriers to every case, and the carriers should be distantly related to the cases, within the breed concerned. Fewer than 20 animals need to be sequenced when using the GCR and ABD methods together. The genomic site of novel autosomal recessive Mendelian genetic diseases can be located using fewer than 20 animals combined with two bioinformatic methods, autozygosity-by-difference, and genotype criteria. In many instances it may also be confirmed with variant prediction scoring. This should speed-up and simplify the management of new genetic diseases to a single-step process.
- Published
- 2022
6. 378 Characterizing Functional Genetic Regulatory Elements in Sheep Reference Genome
- Author
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Murdoch, Brenda M, primary, Davenport, Kimberly M, additional, Xie, Shangqian, additional, Salavati, Mazdak, additional, Clark, Emily, additional, Archibald, Alan, additional, White, Stephen N, additional, Mousel, Michelle R, additional, Worley, Kim, additional, Bhattarai, Suraj, additional, McKay, Stephanie D, additional, Caulton, Alex, additional, Clarke, Shannon, additional, Brauning, Rudiger, additional, Hadfield, Tracy, additional, Rosen, Benjamin D, additional, Smith, Timothy P L, additional, and Cockett, Noelle, additional
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- 2022
- Full Text
- View/download PDF
7. Locating a novel autosomal recessive genetic variant in the cattle glucokinase gene using only WGS data from three cases and six carriers
- Author
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Pollott, Geoffrey E., primary, Piercy, Richard J., additional, Massey, Claire, additional, Salavati, Mazdak, additional, Cheng, Zhangrui, additional, and Wathes, D. Claire, additional
- Published
- 2022
- Full Text
- View/download PDF
8. Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions
- Author
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Salavati, Mazdak, Woolley, Shernae A., Cortés Araya, Yennifer, Halstead, Michelle M., Stenhouse, Claire, Johnsson, Martin, Ashworth, Cheryl J., Archibald, Alan L., Donadeu, Francesc X., Hassan, Musa A., and Clark, Emily L.
- Subjects
Genetics and Breeding - Abstract
There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the "Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)" to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs.
- Published
- 2022
9. Proportion of Concentrate in the Diet of Early Lactation Dairy Cows Has Contrasting Effects on Circulating Leukocyte Global Transcriptomic Profiles, Health and Fertility According to Parity.
- Author
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Cheng, Zhangrui, McLaughlin, Danielle L., Little, Mark W., Ferris, Conrad, Salavati, Mazdak, Ingvartsen, Klaus L., Crowe, Mark A., and Wathes, D. Claire
- Subjects
LACTATION in cattle ,DAIRY cattle ,CONTRAST effect ,LACTATION ,HOLSTEIN-Friesian cattle ,DIET - Abstract
The functionality of circulating leukocytes in dairy cows is suppressed after calving, with negative energy balance as a risk factor. Leukocyte transcriptomic profiles were compared separately in 44 multiparous (MP) and 18 primiparous (PP) Holstein–Friesian cows receiving diets differing in concentrate proportion to test whether immune dysfunction could be mitigated by appropriate nutrition. After calving, cows were offered either (1) low concentrate (LC); (2) medium concentrate (MC) or (3) high concentrate (HC) diets with proportions of concentrate to grass silage of 30%:70%, 50%:50% and 70%:30%, respectively. Cow phenotype data collected included circulating metabolites, milk yield and health and fertility records. RNA sequencing of circulating leukocytes at 14 days in milk was performed. The HC diet improved energy balance in both age groups. There were more differentially expressed genes in PP than MP cows (460 vs. 173, HC vs. LC comparison) with few overlaps. The MP cows on the LC diet showed upregulation of the complement and coagulation cascade and innate immune defence mechanisms against pathogens and had a trend of more cases of mastitis and poorer fertility. In contrast, the PP cows on the HC diet showed greater immune responses based on both gene expression and phenotypic data and longer interval of calving to conception. The leukocytes of MP and PP cows therefore responded differentially to the diets between age, nutrient supply and immunity affecting their health and subsequent fertility. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
10. Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions
- Author
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Consortium, Vargoats, primary, Nijman, Isaäc, additional, Rosen, Benjamin, additional, Bardou, Philippe, additional, Faraut, Thomas, additional, Cumer, Tristan, additional, Daly, Kevin, additional, Zheng, Zhuqing, additional, Cai, Yudong, additional, Asadollahpour, Hojjat, additional, Cinar-Kul, Bengi, additional, Zhang, Wei-Yi, additional, e, guangxin, additional, Ayin, A, additional, Baird, Hayley, additional, Bakhtin, Meirat, additional, Balteanu, Valentin, additional, Barfield, Diana, additional, Berger, Beate, additional, Blichfeldt, Thor, additional, Boink, Geert, additional, Bugiwati, Sri Rachma, additional, Cai, Zexi, additional, Carolan, Sean, additional, Clark, Emily, additional, Curik, Vladka Cubrić, additional, Dagong, Muhammad, additional, Dorji, Tashi, additional, Drew, Louise, additional, Guo, Jiazhong, additional, Hallsson, Jón, additional, Horvat, Simon, additional, Kantanen, Juha, additional, Kawaguchi, Fuki, additional, Kazymbet, Polat, additional, khayatzadeh, Negar, additional, Kim, Namshin, additional, Shah, Manoj Kumar, additional, Liao, Yuying, additional, Martinez, Amparo, additional, Masangkay, Joseph, additional, Masaoka, Maho, additional, Mazza, Raffaele, additional, McEwan, John, additional, Milanesi, Marco, additional, Faruque, Md Omar, additional, Nomura, Yuto, additional, Ouchene-Khelifi, Nadjet-Amina, additional, Pereira, Filipe, additional, Sahana, Goutam, additional, Salavati, Mazdak, additional, Sasazaki, Shinji, additional, SILVA, Anne DA, additional, Simčič, Mojca, additional, Soelkner, Johann, additional, Sutherland, Alison, additional, Tigchelaar, Johannes, additional, Zhang, Hongping, additional, Consortium, Econogene, additional, Marsan, Paolo Ajmone, additional, Bradley, Daniel, additional, Colli, Licia, additional, Drögemüller, Cord, additional, Jiang, Yu, additional, Lei, chuzhao, additional, Mannen, H, additional, Pompanon, Francois, additional, TOSSER-KLOPP, GWENOLA, additional, and Lenstra, Johannes A., additional
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- 2022
- Full Text
- View/download PDF
11. KLB dysregulation mediates disrupted muscle development in intrauterine growth restriction
- Author
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Cortes‐Araya, Yennifer, primary, Stenhouse, Claire, additional, Salavati, Mazdak, additional, Dan‐Jumbo, Susan O., additional, Ho, William, additional, Ashworth, Cheryl J., additional, Clark, Emily, additional, Esteves, Cristina L., additional, and Donadeu, F. Xavier, additional
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- 2022
- Full Text
- View/download PDF
12. An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome
- Author
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Davenport, Kimberly M, primary, Bickhart, Derek M, additional, Worley, Kim, additional, Murali, Shwetha C, additional, Salavati, Mazdak, additional, Clark, Emily L, additional, Cockett, Noelle E, additional, Heaton, Michael P, additional, Smith, Timothy P L, additional, Murdoch, Brenda M, additional, and Rosen, Benjamin D, additional
- Published
- 2022
- Full Text
- View/download PDF
13. Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions
- Author
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Salavati, Mazdak, primary, Woolley, Shernae A, additional, Cortés Araya, Yennifer, additional, Halstead, Michelle M, additional, Stenhouse, Claire, additional, Johnsson, Martin, additional, Ashworth, Cheryl J, additional, Archibald, Alan L, additional, Donadeu, Francesc X, additional, Hassan, Musa A, additional, and Clark, Emily L, additional
- Published
- 2021
- Full Text
- View/download PDF
14. An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
- Author
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Yuan, Can, Tang, Lijing, Lopdell, Thomas, Petrov, Vyacheslav A., Oget-Ebrad, Claire, Moreira, Gabriel Costa Monteiro, Gualdrón Duarte, José Luis, Sartelet, Arnaud, Cheng, Zhangrui, Salavati, Mazdak, Wathes, D. Claire, Crowe, Mark A., Coppieters, Wouter, Littlejohn, Mathew, Charlier, Carole, Druet, Tom, Georges, Michel, and Takeda, Haruko
- Abstract
We report the generation of an organism-wide catalog of 976,813 cis-acting regulatory elements for the bovine detected by the assay for transposase accessible chromatin using sequencing (ATAC-seq). We regroup these regulatory elements in 16 components by nonnegative matrix factorization. Correlation between the genome-wide density of peaks and transcription start sites, correlation between peak accessibility and expression of neighboring genes, and enrichment in transcription factor binding motifs support their regulatory potential. Using a previously established catalog of 12,736,643 variants, we show that the proportion of single-nucleotide polymorphisms mapping to ATAC-seq peaks is higher than expected and that this is owing to an approximately 1.3-fold higher mutation rate within peaks. Their site frequency spectrum indicates that variants in ATAC-seq peaks are subject to purifying selection. We generate eQTL data sets for liver and blood and show that variants that drive eQTL fall into liver- and blood-specific ATAC-seq peaks more often than expected by chance. We combine ATAC-seq and eQTL data to estimate that the proportion of regulatory variants mapping to ATAC-seq peaks is approximately one in three and that the proportion of variants mapping to ATAC-seq peaks that are regulatory is approximately one in 25. We discuss the implication of these findings on the utility of ATAC-seq information to improve the accuracy of genomic selection.
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- 2023
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15. Transcriptomic Analysis of Circulating Leukocytes Obtained during the Recovery from Clinical Mastitis Caused by Escherichia coli in Holstein Dairy Cows.
- Author
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Cheng, Zhangrui, Palma-Vera, Sergio, Buggiotti, Laura, Salavati, Mazdak, Becker, Frank, Werling, Dirk, and Wathes, D. Claire
- Subjects
BOVINE mastitis ,MASTITIS ,ERYTHROCYTES ,DAIRY cattle ,GTPASE-activating protein ,ESCHERICHIA coli ,LEUCOCYTES - Abstract
Simple Summary: Escherichia coli is a bacterium which infects cow udders causing clinical mastitis, a potentially severe disease with welfare and economic consequences. During an infection, white blood cells (leukocytes) enter the udder to provide immune defence and assist tissue repair. We sequenced RNA derived from circulating leukocytes to investigate which genes are up- or down-regulated in dairy cows with naturally occurring cases of clinical mastitis in comparison with healthy control cows from the same farm. We also looked for genetic variations between infected and healthy cows. Blood samples were taken either EARLY (around 10 days) or LATE (after 4 weeks) during the recovery phase after diagnosis. Many genes (1090) with immune and inflammatory functions were up-regulated during the EARLY phase. By the LATE phase only 29 genes were up-regulated including six haemoglobin subunits, possibly important for the production of new red blood corpuscles. Twelve genetic variations which were associated with an increased or decreased expression of some important immune genes were identified between the infected and control cows. These results show that the initial inflammatory response to E. coli continued for at least 10 days despite the cows having received prompt veterinary treatment, but they had largely recovered within 4 weeks. Genetic differences between cows may predispose some animals to infection. The risk and severity of clinical infection with Escherichia coli as a causative pathogen for bovine mastitis is influenced by the hosts' phenotypic and genotypic variables. We used RNA-Seq analysis of circulating leukocytes to investigate global transcriptomic profiles and genetic variants from Holstein cows with naturally occurring cases of clinical mastitis, diagnosed using clinical symptoms and milk microbiology. Healthy lactation-matched cows served as controls (CONT, n = 6). Blood samples were collected at two time periods during the recovery phase post diagnosis: EARLY (10.3 ± 1.8 days, n = 6) and LATE (46.7 ± 11 days, n = 3). Differentially expressed genes (DEGs) between the groups were identified using CLC Genomics Workbench V21 and subjected to enrichment analysis. Variant calling was performed following GATKv3.8 best practice. The comparison of E. coli(+) EARLY and CONT cows found the up-regulation of 1090 DEGs, mainly with immune and inflammatory functions. The key signalling pathways involved NOD-like and interleukin-1 receptors and chemokines. Many up-regulated DEGs encoded antimicrobial peptides including cathelicidins, beta-defensins, S100 calcium binding proteins, haptoglobin and lactoferrin. Inflammation had largely resolved in the E. coli(+) LATE group, with only 29 up-regulated DEGs. Both EARLY and LATE cows had up-regulated DEGs encoding ATP binding cassette (ABC) transporters and haemoglobin subunits were also up-regulated in LATE cows. Twelve candidate genetic variants were identified in DEGs between the infected and CONT cows. Three were in contiguous genes WIPI1, ARSG and SLC16A6 on BTA19. Two others (RAC2 and ARHGAP26) encode a Rho-family GTPase and Rho GTPase-activating protein 26. These results show that the initial inflammatory response to E. coli continued for at least 10 days despite prompt treatment and provide preliminary evidence for genetic differences between cows that may predispose them to infection. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
16. VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity.
- Author
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Denoyelle, Laure, Talouarn, Estelle, Bardou, Philippe, Colli, Licia, Alberti, Adriana, Danchin, Coralie, Del Corvo, Marcello, Engelen, Stéfan, Orvain, Céline, Palhière, Isabelle, Rupp, Rachel, Sarry, Julien, Salavati, Mazdak, Amills, Marcel, Clark, Emily, Crepaldi, Paola, Faraut, Thomas, Masiga, Clet Wandui, Pompanon, François, and Rosen, Benjamin D.
- Subjects
GOATS ,GENOME-wide association studies ,GOAT breeds ,GENETIC variation ,GENETIC distance ,SINGLE nucleotide polymorphisms - Abstract
Background: Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra. Findings: A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin. Conclusions: We report on an unprecedented international effort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal effects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
17. Comparison of the transcriptome in circulating leukocytes in early lactation between primiparous and multiparous cows provides evidence for age-related changes.
- Author
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Buggiotti, Laura, Cheng, Zhangrui, Salavati, Mazdak, Wathes, Claire D., the Genotype plus Environment Consortium, Fahey, Alan, Crisà, Alessandra, Fouladi, Ali, Wylie, Alistair, Vanlierde, Amelie, Fogh, Anders, Santoro, Andreia, Cromie, Andrew, Van Laere, Anne-Sophie, Pearn, Armin, Evertson, Arnold, Laine, Aurelie, Bernardo, Beatriz Sanz, Moioli, Bianca, and Vanranst, Bonny
- Subjects
LACTATION ,TRANSCRIPTOMES ,COWS ,LACTATION in cattle ,LEUCOCYTES ,DNA replication ,ZINC-finger proteins - Abstract
Background: Previous studies have identified many immune pathways which are consistently altered in humans and model organisms as they age. Dairy cows are often culled at quite young ages due to an inability to cope adequately with metabolic and infectious diseases, resulting in reduced milk production and infertility. Improved longevity is therefore a desirable trait which would benefit both farmers and their cows. This study analysed the transcriptome derived from RNA-seq data of leukocytes obtained from Holstein cows in early lactation with respect to lactation number. Results: Samples were divided into three lactation groups for analysis: i) primiparous (PP, n = 53), ii) multiparous in lactations 2–3 (MP 2–3, n = 121), and iii) MP in lactations 4–7 (MP > 3, n = 55). Leukocyte expression was compared between PP vs MP > 3 cows with MP 2–3 as background using DESeq2 followed by weighted gene co-expression network analysis (WGCNA). Seven modules were significantly correlated (r ≥ 0.25) to the trait lactation number. Genes from the modules which were more highly expressed in either the PP or MP > 3 cows were pooled, and the gene lists subjected to David functional annotation cluster analysis. The top three clusters from modules more highly expressed in the PP cows all involved regulation of gene transcription, particularly zinc fingers. Another cluster included genes encoding enzymes in the mitochondrial beta-oxidation pathway. Top clusters up-regulated in MP > 3 cows included the terms Glycolysis/Gluconeogenesis, C-type lectin, and Immunity. Differentially expressed candidate genes for ageing previously identified in the human blood transcriptome up-regulated in PP cows were mainly associated with T-cell function (CCR7, CD27, IL7R, CAMK4, CD28), mitochondrial ribosomal proteins (MRPS27, MRPS9, MRPS31), and DNA replication and repair (WRN). Those up-regulated in MP > 3 cows encoded immune defence proteins (LYZ, CTSZ, SREBF1, GRN, ANXA5, ADARB1). Conclusions: Genes and pathways associated with lactation number in cows were identified for the first time to date, and we found that many were comparable to those known to be associated with ageing in humans and model organisms. We also detected changes in energy utilization and immune responses in leukocytes from older cows. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
18. Characterizing Functional Genetic Regulatory Elements in Sheep Reference Genome.
- Author
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Murdoch, Brenda M., Davenport, Kimberly M., Xie, Shangqian, Salavati, Mazdak, Clark, Emily, Archibald, Alan, White, Stephen N., Mousel, Michelle R., Worley, Kim, Bhattarai, Suraj, McKay, Stephanie D., Caulton, Alex, Clarke, Shannon, Brauning, Rudiger, Hadfield, Tracy, Rosen, Benjamin D., Smith, Timothy P. L., and Cockett, Noelle
- Subjects
WHOLE genome sequencing ,SHEEP ,GENOMES ,PHENOTYPES ,ANIMAL health ,HISTONES ,MOBILE genetic elements - Abstract
Characterizing the locations of genetic regulatory elements is critical for understanding the regulatory mechanisms of complex phenotypic traits related to production traits and health in livestock species. The Ovine Functional Annotation of Animal Genomes (FAANG) Project aims to characterize transcriptional regulatory elements across the sheep genome to facilitate a better understanding of the biological mechanisms influencing phenotypic traits in sheep. Assays including sequencing of messenger RNA (mRNA-seq), cap analysis of gene expression (CAGE), chromatin immunoprecipitation of histones (ChIP-seq), assay for transposase-accessible chromatin (ATAC-seq), whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) were performed on tissues collected from the Rambouillet ewe used to assemble the reference genome ARS-UI_ Ramb_v2.0. Histone modifications were used to define nine chromatin states for tissues across the genome depicting promoters and enhancers (active, poised, and repressed) using ChromHMM. Chromatin states were overlayed with RNA-seq, ATAC-seq and DNA methylation. These data suggest that active promoter and enhancer states reside in open chromatin regions with a greater transcriptional activity and hypomethylated regions than other states. Further, poised and repressed enhancers did not primarily reside in open chromatin and had less transcriptional activity and more hypermethylated sites compared with active states. Collectively these data define transcriptional regulatory regions throughout the ovine genome which provides a valuable resource to better understand regulatory regions in the genome and how these influence economically important traits in sheep and other livestock species. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
19. Proportion of Concentrate in the Diet of Early Lactation Dairy Cows Has Contrasting Effects on Circulating Leukocyte Global Transcriptomic Profiles, Health and Fertility According to Parity.
- Author
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Cheng Z, McLaughlin DL, Little MW, Ferris C, Salavati M, Ingvartsen KL, Crowe MA, Wathes DC, and The GplusE Consortium
- Subjects
- Pregnancy, Female, Cattle, Animals, Parity, Diet veterinary, Milk metabolism, Fertility, Leukocytes, Transcriptome, Lactation physiology
- Abstract
The functionality of circulating leukocytes in dairy cows is suppressed after calving, with negative energy balance as a risk factor. Leukocyte transcriptomic profiles were compared separately in 44 multiparous (MP) and 18 primiparous (PP) Holstein-Friesian cows receiving diets differing in concentrate proportion to test whether immune dysfunction could be mitigated by appropriate nutrition. After calving, cows were offered either (1) low concentrate (LC); (2) medium concentrate (MC) or (3) high concentrate (HC) diets with proportions of concentrate to grass silage of 30%:70%, 50%:50% and 70%:30%, respectively. Cow phenotype data collected included circulating metabolites, milk yield and health and fertility records. RNA sequencing of circulating leukocytes at 14 days in milk was performed. The HC diet improved energy balance in both age groups. There were more differentially expressed genes in PP than MP cows (460 vs. 173, HC vs. LC comparison) with few overlaps. The MP cows on the LC diet showed upregulation of the complement and coagulation cascade and innate immune defence mechanisms against pathogens and had a trend of more cases of mastitis and poorer fertility. In contrast, the PP cows on the HC diet showed greater immune responses based on both gene expression and phenotypic data and longer interval of calving to conception. The leukocytes of MP and PP cows therefore responded differentially to the diets between age, nutrient supply and immunity affecting their health and subsequent fertility.
- Published
- 2022
- Full Text
- View/download PDF
20. Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions.
- Author
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Nijman IJ, Rosen BD, Bardou P, Faraut T, Cumer T, Daly KG, Zheng Z, Cai Y, Asadollahpour H, Kul BÇ, Zhang WY, E G, Ayin A, Baird H, Bakhtin M, Bâlteanu VA, Barfield D, Berger B, Blichfeldt T, Boink G, Bugiwati SRA, Cai Z, Carolan S, Clark E, Cubric-Curik V, Dagong MIA, Dorji T, Drew L, Guo J, Hallsson J, Horvat S, Kantanen J, Kawaguchi F, Kazymbet P, Khayatzadeh N, Kim N, Shah MK, Liao Y, Martínez A, Masangkay JS, Masaoka M, Mazza R, McEwan J, Milanesi M, Omar FM, Nomura Y, Ouchene-Khelifi NA, Pereira F, Sahana G, Salavati M, Sasazaki S, Da Silva A, Simčič M, Sölkner J, Sutherland A, Tigchelaar J, Zhang H, Ajmone-Marsan P, Bradley DG, Colli L, Drögemüller C, Jiang Y, Lei C, Mannen H, Pompanon F, Tosser-Klopp G, and Lenstra JA
- Subjects
- Animals, Goats genetics, Haplotypes genetics, Phylogeny, Y Chromosome genetics, DNA, Mitochondrial genetics, Genetic Variation
- Abstract
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 and DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which 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 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographical range., (© 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)
- Published
- 2022
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21. Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions.
- Author
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Salavati M, Woolley SA, Cortés Araya Y, Halstead MM, Stenhouse C, Johnsson M, Ashworth CJ, Archibald AL, Donadeu FX, Hassan MA, and Clark EL
- Subjects
- Animals, Chromatin Immunoprecipitation Sequencing, Female, Male, Muscles, Pregnancy, Sus scrofa genetics, Swine genetics, Chromatin genetics, Regulatory Sequences, Nucleic Acid
- Abstract
There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the "Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)" to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs., (© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.)
- Published
- 2022
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