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Kravitz A, Liao M, Morota G, Tyler R, Cockrum R, Manohar BM, Ronald BSM, Collins MT, Sriranganathan N. Retrospective Single Nucleotide Polymorphism Analysis of Host Resistance and Susceptibility to Ovine Johne's Disease Using Restored FFPE DNA. Int J Mol Sci 2024; 25:7748. [PMID: 39062990 PMCID: PMC11276633 DOI: 10.3390/ijms25147748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024] Open
Abstract
Johne's disease (JD), also known as paratuberculosis, is a chronic, untreatable gastroenteritis of ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP) infection. Evidence for host genetic resistance to disease progression exists, although it is limited due to the extended incubation period (years) and diagnostic challenges. To overcome this, previously restored formalin-fixed paraffin embedded tissue (FFPE) DNA from archived FFPE tissue cassettes was utilized for a novel retrospective case-control genome-wide association study (GWAS) on ovine JD. Samples from known MAP-infected flocks with ante- and postmortem diagnostic data were used. Cases (N = 9) had evidence of tissue infection, compared to controls (N = 25) without evidence of tissue infection despite positive antemortem diagnostics. A genome-wide efficient mixed model analysis (GEMMA) to conduct a GWAS using restored FFPE DNA SNP results from the Illumina Ovine SNP50 Bead Chip, identified 10 SNPs reaching genome-wide significance of p < 1 × 10-6 on chromosomes 1, 3, 4, 24, and 26. Pathway analysis using PANTHER and the Kyoto Encyclopedia of Genes and Genomes (KEGG) was completed on 45 genes found within 1 Mb of significant SNPs. Our work provides a framework for the novel use of archived FFPE tissues for animal genetic studies in complex diseases and further evidence for a genetic association in JD.
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Affiliation(s)
- Amanda Kravitz
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Mingsi Liao
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Ron Tyler
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Rebecca Cockrum
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - B. Murali Manohar
- Department of Veterinary Pathology, Tamilnadu Veterinary and Animal Sciences University, Madhavaram Milk Colony, Chennai 600051, Tamil Nadu India, India
| | - B. Samuel Masilamoni Ronald
- Department of Veterinary Pathology, Tamilnadu Veterinary and Animal Sciences University, Madhavaram Milk Colony, Chennai 600051, Tamil Nadu India, India
| | - Michael T. Collins
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nammalwar Sriranganathan
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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Usai MG, Casu S, Sechi T, Salaris SL, Miari S, Mulas G, Cancedda MG, Ligios C, Carta A. Advances in understanding the genetic architecture of antibody response to paratuberculosis in sheep by heritability estimate and LDLA mapping analyses and investigation of candidate regions using sequence-based data. Genet Sel Evol 2024; 56:5. [PMID: 38200416 PMCID: PMC10777618 DOI: 10.1186/s12711-023-00873-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Paratuberculosis is a contagious and incurable disease that is caused by Mycobacterium avium subsp. paratuberculosis (MAP) with significant negative effects on animal welfare and farm profitability. Based on a large naturally infected flock over 12 years, we analyzed repeated enzyme-linked immunosorbent assay tests (ELISA), OvineSNP50 BeadChip genotypes and whole-genome sequences imputed from 56 influential animals. The main goals were to estimate the genetic parameters of proxy traits for resistance to MAP, identify genomic regions associated with the host's immune response against MAP and search for candidate genes and causative mutations through association and functional annotation analyses of polymorphisms identified by sequencing. RESULTS Two variables were derived from ELISA tests. The first, a binary variable, assessed the infection status of each animal over the entire productive life, while the second considered the level of antibody recorded over time. Very similar results were obtained for both variables. Heritability estimates of about 0.20 were found and a significant region capturing 18% and 13% of the genetic variance was detected on ovine chromosome 20 by linkage disequilibrium and linkage analysis on OvineSNP50 positions. Functional annotation and association analyses on the imputed sequence polymorphisms that were identified in this region were carried out. No significant variants showed a functional effect on the genes that mapped to this region, most of which belong to the major histocompatibility complex class II (MHC II). However, the conditional analysis led to the identification of two significant polymorphisms that can explain the genetic variance associated with the investigated genomic region. CONCLUSIONS Our results confirm the involvement of the host's genetics in susceptibility to MAP in sheep and suggest that selective breeding may be an option to limit the infection. The estimated heritability is moderate with a relevant portion being due to a highly significant region on ovine chromosome 20. The results of the combined use of sequence-based data and functional analyses suggest several genes belonging to the MHC II as the most likely candidates, although no mutations in their coding regions showed a significant association. Nevertheless, information from genotypes of two highly significant polymorphisms in the region can enhance the efficiency of selective breeding programs.
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Affiliation(s)
- Mario Graziano Usai
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
| | - Sara Casu
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy.
| | - Tiziana Sechi
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
| | - Sotero L Salaris
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
| | - Sabrina Miari
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
| | - Giuliana Mulas
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
| | | | - Ciriaco Ligios
- Istituto Zooprofilattico Sperimentale Della Sardegna G. Pegreffi, 07100, Sassari, Italy
| | - Antonello Carta
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
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Kravitz A, Tyler R, Manohar BM, Ronald BSM, Collins MT, Sriranganathan N. Successful restoration of archived ovine formalin fixed paraffin-embedded tissue DNA and single nucleotide polymorphism analysis. Vet Res Commun 2023; 47:131-139. [PMID: 35618986 PMCID: PMC9873697 DOI: 10.1007/s11259-022-09937-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/09/2022] [Indexed: 01/28/2023]
Abstract
Archived formalin fixed paraffin-embedded (FFPE) tissues are powerful tools in medicine, capable of harboring diagnostic and genetic answers to challenging clinical questions. Successful utilization of DNA derived from FFPE samples is dependent upon repairing DNA damage generated from the fixation process. Methods to repair FFPE DNA have been successful in human medicine for a variety of research and clinical applications, yet remain underutilized in veterinary medicine. Despite the available technology, our study is the first to evaluate the repair of FFPE derived DNA from veterinary species for single-nucleotide polymorphism (SNP) analysis using the Illumina OvineSNP50 BeadChip and Illumina FFPE QC and DNA Restore kit. To accomplish this, 48 ovine FFPE samples were run using the Illumina OvineSNP50 BeadChip with and without restoration. Compared to pre-restore data, we found increased sample call rates, SNP call frequency, and assay metrics for all samples post-restoration. Further, we utilized four sheep with available parallel fresh DNA and FFPE DNA to compare assay metrics and genotype calls between the two starting sample types. Although fresh samples generated increased call rates, we found 99% concordance in allele calls between restored FFPE and fresh DNA for all four samples. Our results indicate successful restoration and genotyping of ovine FFPE samples using this technology, with potential for utilization in other veterinary species.
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Affiliation(s)
- Amanda Kravitz
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA USA
| | - Ron Tyler
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA USA
| | - B. Murali Manohar
- Tamilnadu Veterinary and Animal Sciences University, Madhavaram Milk Colony, Chennai, 600051 Tamil Nadu India
| | - B. Samuel Masilamoni Ronald
- Tamilnadu Veterinary and Animal Sciences University, Madhavaram Milk Colony, Chennai, 600051 Tamil Nadu India
| | - Michael T. Collins
- Department of Pathobiological Sciences, University of Wisconsin-Madison School of Veterinary Medicine, Madison, WI USA
| | - Nammalwar Sriranganathan
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA USA
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Kravitz A, Pelzer K, Sriranganathan N. The Paratuberculosis Paradigm Examined: A Review of Host Genetic Resistance and Innate Immune Fitness in Mycobacterium avium subsp. Paratuberculosis Infection. Front Vet Sci 2021; 8:721706. [PMID: 34485444 PMCID: PMC8414637 DOI: 10.3389/fvets.2021.721706] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/23/2021] [Indexed: 11/13/2022] Open
Abstract
Paratuberculosis, or Johne's Disease (JD) is a debilitating chronic enteritis mainly affecting ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP). This organism causes worldwide economic losses to the livestock industry, and is of public health importance due to the potential zoonotic risk between MAP and Crohn's disease (CD) in humans. Without economical treatments, or a vaccine capable of preventing infection without causing cross-reactions with bovine tuberculosis, test-and-cull methods for disease control are imperative. Unfortunately, difficulties in diagnostics and long subclinical stage hinder adequate control and is further complicated by variation in MAP exposure outcome. Interestingly, the majority of infections result in asymptomatic presentation and never progress to clinical disease. One contributing factor is host genetics, where polymorphisms in innate immune genes have been found to influence resistance and susceptibility to disease. Candidate genes identified across studies overlap with those found in CD and tuberculosis including; Solute carrier family 11 member 1 gene (SLC11A1), Nucleotide-binding-oligomerization domain containing gene 2 (NOD2), Major histocompatibility complex type II (MHC-II), and Toll-like receptor (TLR) genes. This review will highlight evidence supporting the vital role of these genes in MAP infection outcome, associated challenges, and implications for the future of JD research.
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Affiliation(s)
- Amanda Kravitz
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Kevin Pelzer
- Department of Large Animal Clinical Sciences, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Nammalwar Sriranganathan
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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Jang J, Kim K, Lee YH, Kim H. Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids. BMC Genomics 2021; 22:531. [PMID: 34253178 PMCID: PMC8276479 DOI: 10.1186/s12864-021-07808-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/10/2021] [Indexed: 01/10/2023] Open
Abstract
Background CNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV. Results Here, autosome-wide CNVs were called by read depth of NGS alignment result and copy number variation regions (CNVRs) defined from 102 Eurasian taurine (EAT) of 14 breeds, 28 Asian indicine (ASI) of 6 breeds, 22 African taurine (AFT) of 2 breeds, and 184 African humped cattle (AFH) of 17 breeds. The copy number of every CNVRs were compared between populations and CNVRs with population differentiated copy numbers were sorted out using the pairwise statistics VST and Kruskal-Wallis test. Three hundred sixty-two of CNVRs were significantly differentiated in both statistics and 313 genes were located on the population differentiated CNVRs. Conclusion For some of these genes, the averages of copy numbers were also different between populations and these may be candidate genes under selection. These include olfactory receptors, pathogen-resistance, parasite-resistance, heat tolerance and productivity related genes. Furthermore, breed- and individual-level comparison was performed using the presence or copy number of the autosomal CNVRs. Our findings were based on identification of CNVs from short Illumina reads of 336 individuals and 39 breeds, which to our knowledge is the largest dataset for this type of analysis and revealed important CNVs that may play a role in cattle adaption to various environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07808-7.
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Affiliation(s)
- Jisung Jang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Kwondo Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Young Ho Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea. .,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea. .,eGnome, Inc, Seoul, South Korea.
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Yaman Y, Aymaz R, Keleş M, Bay V, Hatipoğlu E, Kaptan C, Başkurt A, Yilmaz O, Heaton MP. Evaluation of CD109, PCP4 and SEMA3D genes for their association with Ovine Johne's disease in Turkish sheep. Anim Biotechnol 2021; 32:519-525. [PMID: 33612073 DOI: 10.1080/10495398.2021.1887880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Johne's disease is a chronic, contagious, zoonotic disease that affects numerous species including livestock and sometimes humans. The disease is globally distributed in sheep populations and caused by Mycobacterium avium Subsp. paratuberculosis (MAP). A previous genome-wide association study identified single nucleotide polymorphism (SNP) markers associated with OJD serostatus in CD109, PCP4, and SEMA3D genes. Our aim was to evaluate the same markers for association with OJD seroprevalence in Turkish sheep in a retrospective matched case-control study. The serological status for OJD in 1801 sheep was determined for four native and four composite breeds from three research flocks. One hundred eleven matched case-control pairs were constructed according to breed type and age from 1750 comingled ewes reared in the same environment. A Single Nucleotide Primer Extension (SNuPE) assay was designed to genotype PCP4-Intron 1, PCP4-3'UTR, SEMA3D, CD109-intron 2 and CD109-intron 8 markers and a McNemar's test was performed on the matched pairs. An association with these five markers was not detected with the OJD serostatus in Turkish sheep (power of detection, 0.95; odds ratio >3; McNemar's p < .05). Thus, a wider search may be needed to identify any major underlying genetic risk factors for OJD in Turkish sheep.
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Affiliation(s)
- Yalçın Yaman
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, Bandirma, Balikesir, Turkey
| | - Ramazan Aymaz
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, Bandirma, Balikesir, Turkey
| | - Murat Keleş
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, Bandirma, Balikesir, Turkey
| | - Veysel Bay
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, Bandirma, Balikesir, Turkey
| | - Ecem Hatipoğlu
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, Bandirma, Balikesir, Turkey
| | - Cüneyt Kaptan
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, Bandirma, Balikesir, Turkey
| | - Atilla Başkurt
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, Bandirma, Balikesir, Turkey
| | - Onur Yilmaz
- Department of Animal Science, Faculty of Agriculture, Aydın Adnan Menderes University, Aydın, Turkey
| | - Michael P Heaton
- Department of Genetics, U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
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Ghoreishifar SM, Eriksson S, Johansson AM, Khansefid M, Moghaddaszadeh-Ahrabi S, Parna N, Davoudi P, Javanmard A. Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds. Genet Sel Evol 2020; 52:52. [PMID: 32887549 PMCID: PMC7487911 DOI: 10.1186/s12711-020-00571-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/21/2020] [Indexed: 02/01/2023] Open
Abstract
Background Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions. Results Five statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p-values were adjusted for multiple testing (FDR < 5%), and significant genomic regions were identified. Annotation of genes in these regions revealed various verified and novel candidate genes that are associated with a diverse range of traits, including e.g. high altitude adaptation and response to hypoxia (DCAF8, PPP1R12A, SLC16A3, UCP2, UCP3, TIGAR), cold acclimation (AQP3, AQP7, HSPB8), body size and stature (PLAG1, KCNA6, NDUFA9, AKAP3, C5H12orf4, RAD51AP1, FGF6, TIGAR, CCND2, CSMD3), resistance to disease and bacterial infection (CHI3L2, GBP6, PPFIBP1, REP15, CYP4F2, TIGD2, PYURF, SLC10A2, FCHSD2, ARHGEF17, RELT, PRDM2, KDM5B), reproduction (PPP1R12A, ZFP36L2, CSPP1), milk yield and components (NPC1L1, NUDCD3, ACSS1, FCHSD2), growth and feed efficiency (TMEM68, TGS1, LYN, XKR4, FOXA2, GBP2, GBP5, FGD6), and polled phenotype (URB1, EVA1C). Conclusions We identified genomic regions that may provide background knowledge to understand the mechanisms that are involved in economic traits and adaptation to cold climate in cattle. Incorporating p-values of different statistics in a single DCMS framework may help select and prioritize candidate genes for further analyses.
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Affiliation(s)
- Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden.
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Majid Khansefid
- AgriBio Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, 3083, Australia
| | - Sima Moghaddaszadeh-Ahrabi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Islamic Azad University, Tabriz Branch, Tabriz, Iran
| | - Nahid Parna
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, B2N5E3, Canada
| | - Arash Javanmard
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
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Usai MG, Casu S, Sechi T, Salaris SL, Miari S, Sechi S, Carta P, Carta A. Mapping genomic regions affecting milk traits in Sarda sheep by using the OvineSNP50 Beadchip and principal components to perform combined linkage and linkage disequilibrium analysis. Genet Sel Evol 2019; 51:65. [PMID: 31744455 PMCID: PMC6862840 DOI: 10.1186/s12711-019-0508-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 11/05/2019] [Indexed: 02/01/2023] Open
Abstract
Background The detection of regions that affect quantitative traits (QTL), to implement selection assisted by molecular information, remains of particular interest in dairy sheep for which genetic gain is constrained by the high costs of large-scale phenotype and pedigree recording. QTL detection based on the combination of linkage disequilibrium and linkage analysis (LDLA) is the most suitable approach in family-structured populations. The main issue in performing LDLA mapping is the handling of the identity-by-descent (IBD) probability matrix. Here, we propose the use of principal component analysis (PCA) to perform LDLA mapping for milk traits in Sarda dairy sheep. Methods A resource population of 3731 ewes belonging to 161 sire families and genotyped with the OvineSNP50 Beadchip was used to map genomic regions that affect five milk traits. The paternally and maternally inherited gametes of genotyped individuals were reconstructed and IBD probabilities between them were defined both at each SNP position and at the genome level. A QTL detection model fitting fixed effects of principal components that summarize IBD probabilities was tested at each SNP position. Genome-wide (GW) significance thresholds were determined by within-trait permutations. Results PCA resulted in substantial dimensionality reduction, in fact 137 and 32 (on average) principal components were able to capture 99% of the IBD variation at the locus and genome levels, respectively. Overall, 2563 positions exceeded the 0.05 GW significance threshold for at least one trait, which clustered into 75 QTL regions most of which affected more than one trait. The strongest signal was obtained for protein content on Ovis aries (OAR) chromosome 6 and overlapped with the region that harbours the casein gene cluster. Additional interesting positions were identified on OAR4 for fat content and on OAR11 for the three yield traits. Conclusions PCA is a good strategy to summarize IBD probabilities. A large number of regions associated to milk traits were identified. The outputs provided by the proposed method are useful for the selection of candidate genes, which need to be further investigated to identify causative mutations or markers in strong LD with them for application in selection programs assisted by molecular information.
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Affiliation(s)
- Mario Graziano Usai
- Genetics and Biotechnology-Agris Sardegna, Loc. Bonassai S.S. 291 Sassari-Fertilia - Km. 18.600, 07100, Sassari, Italy
| | - Sara Casu
- Genetics and Biotechnology-Agris Sardegna, Loc. Bonassai S.S. 291 Sassari-Fertilia - Km. 18.600, 07100, Sassari, Italy.
| | - Tiziana Sechi
- Genetics and Biotechnology-Agris Sardegna, Loc. Bonassai S.S. 291 Sassari-Fertilia - Km. 18.600, 07100, Sassari, Italy
| | - Sotero L Salaris
- Genetics and Biotechnology-Agris Sardegna, Loc. Bonassai S.S. 291 Sassari-Fertilia - Km. 18.600, 07100, Sassari, Italy
| | - Sabrina Miari
- Genetics and Biotechnology-Agris Sardegna, Loc. Bonassai S.S. 291 Sassari-Fertilia - Km. 18.600, 07100, Sassari, Italy
| | - Stefania Sechi
- Genetics and Biotechnology-Agris Sardegna, Loc. Bonassai S.S. 291 Sassari-Fertilia - Km. 18.600, 07100, Sassari, Italy
| | - Patrizia Carta
- Genetics and Biotechnology-Agris Sardegna, Loc. Bonassai S.S. 291 Sassari-Fertilia - Km. 18.600, 07100, Sassari, Italy
| | - Antonello Carta
- Genetics and Biotechnology-Agris Sardegna, Loc. Bonassai S.S. 291 Sassari-Fertilia - Km. 18.600, 07100, Sassari, Italy
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Cecchi F, Russo C, Fratini F, Turchi B, Preziuso G, Cantile C. Preliminary association analysis of microsatellites and Mycobacterium avium subspecies paratuberculosis infection in the native Garfagnina goats. JOURNAL OF APPLIED ANIMAL RESEARCH 2017. [DOI: 10.1080/09712119.2017.1417129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Francesca Cecchi
- Department of Veterinary Science, University of Pisa, Pisa, Italy
| | - Claudia Russo
- Department of Veterinary Science, University of Pisa, Pisa, Italy
| | - Filippo Fratini
- Department of Veterinary Science, University of Pisa, Pisa, Italy
| | - Barbara Turchi
- Department of Veterinary Science, University of Pisa, Pisa, Italy
| | | | - Carlo Cantile
- Department of Veterinary Science, University of Pisa, Pisa, Italy
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Identification of candidate genes for paratuberculosis resistance in the native Italian Garfagnina goat breed. Trop Anim Health Prod 2017; 49:1135-1142. [DOI: 10.1007/s11250-017-1306-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 04/26/2017] [Indexed: 01/10/2023]
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Seroussi E, Rosov A, Shirak A, Lam A, Gootwine E. Unveiling genomic regions that underlie differences between Afec-Assaf sheep and its parental Awassi breed. Genet Sel Evol 2017; 49:19. [PMID: 28187715 PMCID: PMC5301402 DOI: 10.1186/s12711-017-0296-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 02/06/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Sheep production in Israel has improved by crossing the fat-tailed local Awassi breed with the East Friesian and later, with the Booroola Merino breed, which led to the formation of the highly prolific Afec-Assaf strain. This strain differs from its parental Awassi breed in morphological traits such as tail and horn size, coat pigmentation and wool characteristics, as well as in production, reproductive and health traits. To identify major genes associated with the formation of the Afec-Assaf strain, we genotyped 41 Awassi and 141 Afec-Assaf sheep using the Illumina Ovine SNP50 BeadChip array, and analyzed the results with PLINK and EMMAX software. The detected variable genomic regions that differed between Awassi and Afec-Assaf sheep (variable genomic regions; VGR) were compared to selection signatures that were reported in 48 published genome-wide association studies in sheep. Because the Afec-Assaf strain, but not the Awassi breed, carries the Booroola mutation, association analysis of BMPR1B used as the test gene was performed to evaluate the ability of this study to identify a VGR that includes such a major gene. RESULTS Of the 20 detected VGR, 12 were novel to this study. A ~7-Mb VGR was identified on Ovies aries chromosome OAR6 where the Booroola mutation is located. Similar to other studies, the most significant VGR was detected on OAR10, in a region that contains candidate genes affecting horn type (RXFP2), climate adaptation (ALOX5AP), fiber diameter (KATNAl1), coat pigmentation (FRY) and genes associated with fat distribution. The VGR on OAR2 included BNC2, which is also involved in controlling coat pigmentation in sheep. Six other VGR contained genes that were shown to be involved in coat pigmentation by analyzing their mammalian orthologues. Genes associated with fat distribution in humans, including GRB14 and COBLL1, were located in additional VGR. Sequencing DNA from Awassi and Afec-Assaf individuals revealed non-synonymous mutations in some of these candidate genes. CONCLUSIONS Our results highlight VGR that differentiate the Awassi breed from the Afec-Assaf strain, some of which may include genes that confer an advantage to Afec-Assaf and Assaf over Awassi sheep with respect to intensive sheep production under Mediterranean conditions.
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Affiliation(s)
- Eyal Seroussi
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Alexander Rosov
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Andrey Shirak
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Alon Lam
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Elisha Gootwine
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
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