1
|
Becker GM, Thorne JW, Burke JM, Lewis RM, Notter DR, Morgan JLM, Schauer CS, Stewart WC, Redden RR, Murdoch BM. Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep. Genet Sel Evol 2024; 56:56. [PMID: 39080565 PMCID: PMC11290166 DOI: 10.1186/s12711-024-00905-7] [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: 07/19/2023] [Accepted: 04/23/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Managing genetic diversity is critically important for maintaining species fitness. Excessive homozygosity caused by the loss of genetic diversity can have detrimental effects on the reproduction and production performance of a breed. Analysis of genetic diversity can facilitate the identification of signatures of selection which may contribute to the specific characteristics regarding the health, production and physical appearance of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, effective population size (Ne), runs of homozygosity (ROH) and Wright's fixation index (FST) outlier approach to identify differential signatures of selection at 36,113 autosomal single nucleotide polymorphisms (SNPs). RESULTS Katahdin sheep had the largest current Ne at the most recent generation estimated with both the GONe and NeEstimator software. The most highly conserved ROH Island was identified in Rambouillet with a signature of selection on chromosome 6 containing 202 SNPs called in an ROH in 50 to 94% of the individuals. This region contained the DCAF16, LCORL and NCAPG genes that have been previously reported to be under selection and have biological roles related to milk production and growth traits. The outlier regions identified through the FST comparisons of Katahdin with Rambouillet and Dorper contained genes with known roles in milk production and mastitis resistance or susceptibility, and the FST comparisons of Rambouillet with Katahdin and Dorper identified genes related to wool growth, suggesting these traits have been under natural or artificial selection pressure in these populations. Genes involved in the cytokine-cytokine receptor interaction pathways were identified in all FST breed comparisons, which indicates the presence of allelic diversity between these breeds in genomic regions controlling cytokine signaling mechanisms. CONCLUSIONS In this paper, we describe signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.
Collapse
Affiliation(s)
- Gabrielle M Becker
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, USA
| | - Jacob W Thorne
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, USA
- Texas A&M AgriLife Extension, Texas A&M University, San Angelo, TX, USA
| | - Joan M Burke
- USDA, ARS, Dale Bumpers Small Farms Research Center, Booneville, AR, USA
| | - Ronald M Lewis
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - David R Notter
- School of Animal Sciences, Virginia Tech, Blacksburg, VA, USA
| | | | - Christopher S Schauer
- Hettinger Research Extension Center, North Dakota State University, Hettinger, ND, USA
| | - Whit C Stewart
- Department of Animal Science, University of Wyoming, Laramie, WY, USA
| | - R R Redden
- Texas A&M AgriLife Extension, Texas A&M University, San Angelo, TX, USA
| | - Brenda M Murdoch
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, USA.
| |
Collapse
|
2
|
Ameri NF, Moradian H, Koshkoiyeh AE, Montazeri M, Madabi ER, Fozi MA. Genetic diversity and positive signatures of selection in indigenous cattle breeds of Iran. Genome 2024; 67:31-42. [PMID: 37962065 DOI: 10.1139/gen-2022-0106] [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] [Indexed: 11/15/2023]
Abstract
Animal domestication, climate changes over time, and artificial selection have played significant roles in shaping the genome structure of various animal species, including cattle. These processes have led to the emergence of several indigenous cattle breeds with distinct genetic characteristics. This study focused on unraveling the genetic diversity and identifying candidate genomic regions in eight indigenous cattle breeds of Iran. The data consisted of ∼777 962 single nucleotide polymorphisms (SNPs) of 89 animals from Iranian indigenous cattle scattered throughout the country. We employed various methods, including integrated haplotype score, FST, and cross-population composite likelihood ratio, to conduct a genome scan for detecting selection signals within and between cattle populations. Average observed heterozygosity across the populations was 0.36, with a range of 0.32-0.40. In addition, negative and low rates of inbreeding (FIS) in the populations were observed. The genome-wide analysis revealed several genomic regions that harbored candidate genes associated with production traits (e.g., MFSD1, TYW5, ADRB2, BLK, and CRTC3), adaptation to local environmental constraints (CACNA2D1, CXCL3, and GRO1), and coat color (DYM). Finally, the study of the reported quantitative trait loci (QTL) regions in the cattle genome demonstrated that the identified regions were associated with QTL related to important traits such as milk composition, body weight, daily gain, feed conversion, and residual feed intake. Overall, this study contributes to a better understanding of the genetic diversity and potential candidate genes underlying important traits in Iranian indigenous cattle breeds, which can inform future breeding and conservation efforts.
Collapse
Affiliation(s)
- Nader Forough Ameri
- Department of Animal ScienceFaculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hasan Moradian
- Department of Animal ScienceFaculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - Mahdiyeh Montazeri
- Department of Animal ScienceFaculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Elaheh Rostamzadeh Madabi
- Department of Animal ScienceFaculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Masood Asadi Fozi
- Department of Animal ScienceFaculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| |
Collapse
|
3
|
Díaz Ruiz E, González Ariza A, León Jurado JM, Arando Arbulu A, Bermúdez Oria A, Fernández Prior Á, Delgado Bermejo JV, Navas González FJ. Discriminant Analysis and Data Mining CHAID Decision Tree as Tools to Evaluate the Buffering Effect of Hydroxytyrosol on Reactive Oxygen Species in Rooster Sperm Cryopreservation. Animals (Basel) 2023; 13:3079. [PMID: 37835685 PMCID: PMC10571762 DOI: 10.3390/ani13193079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/28/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
Sperm cryopreservation is effective in safeguarding genetic biodiversity in avian species. However, during this process, spermatozoa are very susceptible to plasma membrane peroxidation in the presence of high concentrations of reactive oxygen species (ROS). To mitigate this effect, the addition of exogenous antioxidants, such as hydroxytyrosol (3,4-dihydroxyphenylethanol; HT), an antioxidant derived from olive oil, to the cryopreservation sperm diluent, could be useful. To verify this, a cryopreservation diluent was supplemented with different concentrations (0 μg/mL, 50 μg/mL, 100 μg/mL, and 150 μg/mL) of HT. For this, semen was collected in 10 replicates from 16 roosters of the Utrerana avian breed, and a pool was prepared with the optimum quality ejaculates in each replicate. After cryopreservation, spermatozoa were thawed and different in vitro semen quality parameters were evaluated. A discriminant canonical analysis (DCA) was carried out and revealed that total motility (TM; Lambda = 0.301, F = 26,173), hypo-osmotic swelling test (HOST; Lambda = 0.338, F = 22,065), and amplitude of lateral head displacement (ALH, Lambda = 0.442; F = 14,180) were the variables with the highest discriminant power. Finally, a chi-squared automatic interaction detection (CHAID) decision tree (DT) was performed excluding fresh semen samples and ROS was found to be the most valuable variable to discriminate between the different established freezing groups. Samples in the absence of HT or with low concentrations of this antioxidant showed less desirable ROS values in cryopreserved rooster semen. The present study could lead to the improvement of cryopreservation techniques for the genetic material of local poultry breeds and optimize the conservation programs of endangered native avian breeds.
Collapse
Affiliation(s)
- Esther Díaz Ruiz
- Department of Genetics, Faculty of Veterinary Medicine, University of Cordoba, 14014 Cordoba, Spain; (E.D.R.); (A.A.A.); (J.V.D.B.); (F.J.N.G.)
| | - Antonio González Ariza
- Department of Genetics, Faculty of Veterinary Medicine, University of Cordoba, 14014 Cordoba, Spain; (E.D.R.); (A.A.A.); (J.V.D.B.); (F.J.N.G.)
- Agropecuary Provincial Centre, Diputación Provincial de Córdoba, 14071 Cordoba, Spain;
| | | | - Ander Arando Arbulu
- Department of Genetics, Faculty of Veterinary Medicine, University of Cordoba, 14014 Cordoba, Spain; (E.D.R.); (A.A.A.); (J.V.D.B.); (F.J.N.G.)
| | - Alejandra Bermúdez Oria
- Instituto de la Grasa, Consejo Superior de Investigaciones Científicas (CSIC), 41013 Sevilla, Spain; (A.B.O.); (Á.F.P.)
| | - África Fernández Prior
- Instituto de la Grasa, Consejo Superior de Investigaciones Científicas (CSIC), 41013 Sevilla, Spain; (A.B.O.); (Á.F.P.)
| | - Juan Vicente Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Medicine, University of Cordoba, 14014 Cordoba, Spain; (E.D.R.); (A.A.A.); (J.V.D.B.); (F.J.N.G.)
| | - Francisco Javier Navas González
- Department of Genetics, Faculty of Veterinary Medicine, University of Cordoba, 14014 Cordoba, Spain; (E.D.R.); (A.A.A.); (J.V.D.B.); (F.J.N.G.)
| |
Collapse
|
4
|
Naji MM, Jiang Y, Utsunomiya YT, Rosen BD, Sölkner J, Wang C, Jiang L, Zhang Q, Zhang Y, Ding X, Mészáros G. Favored single nucleotide variants identified using whole genome Re-sequencing of Austrian and Chinese cattle breeds. Front Genet 2022; 13:974787. [PMID: 36238155 PMCID: PMC9552183 DOI: 10.3389/fgene.2022.974787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022] Open
Abstract
Cattle have been essential for the development of human civilization since their first domestication few thousand years ago. Since then, they have spread across vast geographic areas following human activities. Throughout generations, the cattle genome has been shaped with detectable signals induced by various evolutionary processes, such as natural and human selection processes and demographic events. Identifying such signals, called selection signatures, is one of the primary goals of population genetics. Previous studies used various selection signature methods and normalized the outputs score using specific windows, in kbp or based on the number of SNPs, to identify the candidate regions. The recent method of iSAFE claimed for high accuracy in pinpointing the candidate SNPs. In this study, we analyzed whole-genome resequencing (WGS) data of ten individuals from Austrian Fleckvieh (Bos taurus) and fifty individuals from 14 Chinese indigenous breeds (Bos taurus, Bos taurus indicus, and admixed). Individual WGS reads were aligned to the cattle reference genome of ARS. UCD1.2 and subsequently undergone single nucleotide variants (SNVs) calling pipeline using GATK. Using these SNVs, we examined the population structure using principal component and admixture analysis. Then we refined selection signature candidates using the iSAFE program and compared it with the classical iHS approach. Additionally, we run Fst population differentiation from these two cattle groups. We found gradual changes of taurine in north China to admixed and indicine to the south. Based on the population structure and the number of individuals, we grouped samples to Fleckvieh, three Chinese taurines (Kazakh, Mongolian, Yanbian), admixed individuals (CHBI_Med), indicine individuals (CHBI_Low), and a combination of admixed and indicine (CHBI) for performing iSAFE and iHS tests. There were more significant SNVs identified using iSAFE than the iHS for the candidate of positive selection and more detectable signals in taurine than in indicine individuals. However, combining admixed and indicine individuals decreased the iSAFE signals. From both within-population tests, significant SNVs are linked to the olfactory receptors, production, reproduction, and temperament traits in taurine cattle, while heat and parasites tolerance in the admixed individuals. Fst test suggests similar patterns of population differentiation between Fleckvieh and three Chinese taurine breeds against CHBI. Nevertheless, there are genes shared only among the Chinese taurine, such as PAX5, affecting coat color, which might drive the differences between these yellowish coated breeds, and those in the greater Far East region.
Collapse
Affiliation(s)
- Maulana M. Naji
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Yifan Jiang
- China Agricultural University, Beijing, China
| | - Yuri T. Utsunomiya
- Department of Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Araçatuba, Brazil
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, USDA‐ARS, Beltsville, MD, United States
| | - Johann Sölkner
- University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Li Jiang
- China Agricultural University, Beijing, China
| | - Qin Zhang
- China Agricultural University, Beijing, China
| | - Yi Zhang
- China Agricultural University, Beijing, China
| | - Xiangdong Ding
- China Agricultural University, Beijing, China
- *Correspondence: Xiangdong Ding, ; Gábor Mészáros,
| | - Gábor Mészáros
- University of Natural Resources and Life Sciences, Vienna, Austria
- *Correspondence: Xiangdong Ding, ; Gábor Mészáros,
| |
Collapse
|
5
|
Izawa K, Fukunaga K, Hirota Y, Orito K. Displacement of center of mass in dogs in response to foot sensory stimulation. Vet Surg 2021; 50:1304-1315. [PMID: 34038003 DOI: 10.1111/vsu.13671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/09/2021] [Accepted: 05/15/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Evaluate center of mass (CoM) displacement values during four-limb and three-limb standing with limb suspension in dogs before and after applying sensory stimulation to a forelimb or hindlimb. STUDY DESIGN Experimental study. ANIMALS Six clinically normal beagles. METHODS A four force-plate apparatus was built to assess static weight distribution. Dogs stood on the device with one limb in contact with each force plate. We created a plastic device to induce sensory stimulation so that lameness could not be detected visually when stimulating the paw. Experimenters confirmed the degree of lameness by walking before and after measurement. Body-weight shifts were induced via suspension of each limb and transient sensory stimulation to the right forelimb or left hindlimb. CoMs of five postures were compared, with and without transient sensory stimulation. RESULTS The four-limb CoM was located cranial to the center of the X- and Y-axis coordinates (X: -0.82 ± 9.12, Y: 61.00 ± 5.82). During three-limb standing with suspension of either forelimb, CoM shifted backward toward the contralateral side compared to four-limb standing. During hindlimb suspension, CoM shifted to the contralateral side. With right forelimb sensory stimulation, there were large CoM changes for both four-limb and three-limb standing (X: -34.53 ± 9.09, Y: 52.21 ± 6.88). CoM changes were small with left hindlimb sensory stimulation (X: 6.47 ± 13.86, Y: 69.41 ± 5.55). CONCLUSION CoMs during four-limb and three-limb standing were influenced by sensory stimulation of a forelimb and, to a lesser extent, of a hindlimb. CLINICAL SIGNIFICANCE Static evaluation of CoM may aid clinicians in the diagnosis and recovery of forelimb lameness.
Collapse
Affiliation(s)
- Kousuke Izawa
- Laboratory of Physiology II, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan.,ONE for Animals, Yokohama, Kanagawa, Japan
| | - Koya Fukunaga
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yuji Hirota
- Laboratory of Basic Education, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Kensuke Orito
- Laboratory of Physiology II, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| |
Collapse
|
6
|
Dall'Olio S, Bovo S, Tinarelli S, Schiavo G, Padalino B, Fontanesi L. Association between candidate gene markers and harness racing traits in Italian trotter horses. Livest Sci 2021. [DOI: 10.1016/j.livsci.2020.104351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
7
|
Di Stasio L, Albera A, Pauciullo A, Cesarani A, Macciotta NPP, Gaspa G. Genetics of Arthrogryposis and Macroglossia in Piemontese Cattle Breed. Animals (Basel) 2020; 10:ani10101732. [PMID: 32987629 PMCID: PMC7598642 DOI: 10.3390/ani10101732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The study was carried out in order to investigate the genetic background of arthrogryposis and macroglossia in the Piemontese cattle breed, for which limited information is available so far. The genotyping of affected and healthy animals with a high-density chip and the subsequent genome-wide association study did not evidence a single strong association with the two pathologies. Therefore, for arthrogryposis, the results do not support the existence of a single-gene model, as reported for other breeds. Rather, 23 significant markers on different chromosomes were found, associated to arthrogryposis, to macroglossia, or to both pathologies, suggesting a more complex genetic mechanism underlying both diseases in the Piemontese breed. The significant single nucleotide polymorphisms (SNPs) allowed the identification of some genes (NTN3, KCNH1, KCNH2, and KANK3) for which a possible role in the pathologies can be hypothesized. The real involvement of these genes needs to be further investigated and validated. Abstract Arthrogryposis and macroglossia are congenital pathologies known in several cattle breeds, including Piemontese. As variations in single genes were identified as responsible for arthrogryposis in some breeds, we decided: (i) to test the hypothesis of a similar genetic determinism for arthrogryposis in the Piemontese breed by genotyping affected and healthy animals with a high-density chip and applying genome-wide association study (GWAS), FST and canonical discriminant analysis (CDA) procedures, and (ii) to investigate with the same approach the genetic background of macroglossia, for which no genetic studies exist so far. The study included 125 animals (63 healthy, 30 with arthrogryposis, and 32 with macroglossia). Differently from what reported for other breeds, the analysis did not evidence a single strong association with the two pathologies. Rather, 23 significant markers on different chromosomes were found (7 associated to arthrogryposis, 11 to macroglossia, and 5 to both pathologies), suggesting a multifactorial genetic mechanism underlying both diseases in the Piemontese breed. In the 100-kb interval surrounding the significant SNPs, 20 and 26 genes were identified for arthrogryposis and macroglossia, respectively, with 12 genes in common to both diseases. For some genes (NTN3, KCNH1, KCNH2, and KANK3), a possible role in the pathologies can be hypothesized, being involved in processes related to muscular or nervous tissue development. The real involvement of these genes needs to be further investigated and validated.
Collapse
Affiliation(s)
- Liliana Di Stasio
- Department of Agricultural, Forest and Food Sciences, University of Torino, Largo Baccini 2, 10095 Grugliasco (TO), Italy; (A.P.); (G.G.)
- Correspondence:
| | - Andrea Albera
- Associazione Nazionale Allevatori Bovini di Razza Piemontese, strada provinciale Trinita’ 31/A, 12061 Carrù (CN), Italy;
| | - Alfredo Pauciullo
- Department of Agricultural, Forest and Food Sciences, University of Torino, Largo Baccini 2, 10095 Grugliasco (TO), Italy; (A.P.); (G.G.)
| | - Alberto Cesarani
- Department of Agriculture, University of Sassari, Via De Nicola 9, 07100 Sassari, Italy; (A.C.); (N.P.P.M.)
| | - Nicolò P. P. Macciotta
- Department of Agriculture, University of Sassari, Via De Nicola 9, 07100 Sassari, Italy; (A.C.); (N.P.P.M.)
| | - Giustino Gaspa
- Department of Agricultural, Forest and Food Sciences, University of Torino, Largo Baccini 2, 10095 Grugliasco (TO), Italy; (A.P.); (G.G.)
| |
Collapse
|
8
|
Senczuk G, Guerra L, Mastrangelo S, Campobasso C, Zoubeyda K, Imane M, Marletta D, Kusza S, Karsli T, Gaouar SBS, Pilla F, Ciani E. Fifteen Shades of Grey: Combined Analysis of Genome-Wide SNP Data in Steppe and Mediterranean Grey Cattle Sheds New Light on the Molecular Basis of Coat Color. Genes (Basel) 2020; 11:genes11080932. [PMID: 32823527 PMCID: PMC7464420 DOI: 10.3390/genes11080932] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 12/20/2022] Open
Abstract
Coat color is among the most distinctive phenotypes in cattle. Worldwide, several breeds share peculiar coat color features such as the presence of a fawn pigmentation of the calf at birth, turning over time to grey, and sexual dichromatism. The aim of this study was to search for polymorphisms under differential selection by contrasting grey cattle breeds displaying the above phenotype with non-grey cattle breeds, and to identify the underlying genes. Using medium-density SNP array genotype data, a multi-cohort FST-outlier approach was adopted for a total of 60 pair-wise comparisons of the 15 grey with 4 non-grey cattle breeds (Angus, Limousin, Charolais, and Holstein), with the latter selected as representative of solid and piebald phenotypes, respectively. Overall, more than 50 candidate genes were detected; almost all were either directly or indirectly involved in pigmentation, and some of them were already known for their role in phenotypes related with hair graying in mammals. Notably, 17 relevant genes, including SDR16C5, MOS, SDCBP, and NSMAF, were located in a signal on BTA14 convergently observed in all the four considered scenarios. Overall, the key stages of pigmentation (melanocyte development, melanogenesis, and pigment trafficking/transfer) were all represented among the pleiotropic functions of the candidate genes, suggesting the complex nature of the grey phenotype in cattle.
Collapse
Affiliation(s)
- Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy; (G.S.); (F.P.)
| | - Lorenzo Guerra
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari, 70125 Bari, Italy; (L.G.); (C.C.)
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy;
| | - Claudia Campobasso
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari, 70125 Bari, Italy; (L.G.); (C.C.)
| | - Kaouadji Zoubeyda
- Department of Biology, University Abou Bekr Bélkaid, Tlemcen 13000, Algeria; (K.Z.); (M.I.); (S.B.S.G.)
| | - Meghelli Imane
- Department of Biology, University Abou Bekr Bélkaid, Tlemcen 13000, Algeria; (K.Z.); (M.I.); (S.B.S.G.)
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, 95123 Catania, Italy;
| | - Szilvia Kusza
- Animal Genetics Laboratory, University of Debrecen, 4032 Debrecen, Hungary;
| | - Taki Karsli
- Department of Animal Science, Akdeniz University, 07070 Antalya, Turkey;
| | | | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy; (G.S.); (F.P.)
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari, 70125 Bari, Italy; (L.G.); (C.C.)
- Correspondence:
| | | |
Collapse
|
9
|
Manca E, Cesarani A, Gaspa G, Sorbolini S, Macciotta NP, Dimauro C. Use of the Multivariate Discriminant Analysis for Genome-Wide Association Studies in Cattle. Animals (Basel) 2020; 10:ani10081300. [PMID: 32751408 PMCID: PMC7460480 DOI: 10.3390/ani10081300] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary In the traditional single marker regression approach for genome-wide association studies, if the number of involved individuals is small and the number of single nucleotide polymorphisms (SNPs) to be tested is very large, the probability of getting a significant association simply due to chance becomes enormous. Other techniques, such as the Bayesian methods, require several a priori assumptions, as an a priori posterior inclusion probability threshold, that can limit their effectiveness. In the present study, a multivariate algorithm able to partially overcome this problem was proposed. On simulated data, with 3000 individuals, only 13 and 3 quantitative trait loci (QTLs) were obtained with the single marker regression and the Bayesian approaches, respectively. On the other hand, the multivariate algorithm detected 65 QTLs in the same scenario. The gap between the single marker regression and the multivariate methods slowly decreased as the number of animals increased. This figure was also confirmed on real data. Abstract Genome-wide association studies (GWAS) are traditionally carried out by using the single marker regression model that, if a small number of individuals is involved, often lead to very few associations. The Bayesian methods, such as BayesR, have obtained encouraging results when they are applied to the GWAS. However, these approaches, require that an a priori posterior inclusion probability threshold be fixed, thus arbitrarily affecting the obtained associations. To partially overcome these problems, a multivariate statistical algorithm was proposed. The basic idea was that animals with different phenotypic values of a specific trait share different allelic combinations for genes involved in its determinism. Three multivariate techniques were used to highlight the differences between the individuals assembled in high and low phenotype groups: the canonical discriminant analysis, the discriminant analysis and the stepwise discriminant analysis. The multivariate method was tested both on simulated and on real data. The results from the simulation study highlighted that the multivariate GWAS detected a greater number of true associated single nucleotide polymorphisms (SNPs) and Quantitative trait loci (QTLs) than the single marker model and the Bayesian approach. For example, with 3000 animals, the traditional GWAS highlighted only 29 significantly associated markers and 13 QTLs, whereas the multivariate method found 127 associated SNPs and 65 QTLs. The gap between the two approaches slowly decreased as the number of animals increased. The Bayesian method gave worse results than the other two. On average, with the real data, the multivariate GWAS found 108 associated markers for each trait under study and among them, around 63% SNPs were also found in the single marker approach. Among the top 118 associated markers, 76 SNPs harbored putative candidate genes.
Collapse
Affiliation(s)
- Elisabetta Manca
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy; (E.M.); (A.C.); (S.S.); (N.P.P.M.)
| | - Alberto Cesarani
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy; (E.M.); (A.C.); (S.S.); (N.P.P.M.)
| | - Giustino Gaspa
- Dipartimento di Scienze Agrarie, Forestali e Ambientali, Università degli studi di Torino, 10095 Grugliasco, Italy;
| | - Silvia Sorbolini
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy; (E.M.); (A.C.); (S.S.); (N.P.P.M.)
| | - Nicolò P.P. Macciotta
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy; (E.M.); (A.C.); (S.S.); (N.P.P.M.)
| | - Corrado Dimauro
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy; (E.M.); (A.C.); (S.S.); (N.P.P.M.)
- Correspondence: ; Tel.: +39079229298
| |
Collapse
|
10
|
Whole genome detection of recent selection signatures in Sarabi cattle: a unique Iranian taurine breed. Genes Genomics 2019; 42:203-215. [DOI: 10.1007/s13258-019-00888-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/12/2019] [Indexed: 12/13/2022]
|
11
|
Early diagnosis using canonical discriminant analysis of innate immune receptor gene expression profiles in a murine infectious or sterile systemic inflammation model. J Trauma Acute Care Surg 2017; 84:583-589. [PMID: 29287057 DOI: 10.1097/ta.0000000000001789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Infection in patients with systemic inflammation is difficult to diagnose with a single biomarker. We aimed to clarify the time course of change in the gene expression profile of innate immune receptors in infectious or sterile inflammation and to establish an early diagnostic method using canonical discriminant analysis (CDA) of the gene expression profile. METHODS To compare infectious and sterile inflammation, we used cecal ligation and puncture (CLP) and 20% full-thickness burn injury (Burn) models. C57BL/6 mice underwent sham treatment (n = 9 × three groups), CLP (n = 12 × three groups), or Burn (n = 12 × three groups) injury. Mice were killed at 6, 12, and 24 hours after injury, and total RNA was extracted from whole blood. We used quantitative real-time polymerase chain reaction to investigate gene expression of innate immune receptors Toll-like receptor 2 (TLR2), TLR4, TLR9, NLRP3 (nucleotide-binding oligomerization domain-like receptor family pyrin domain containing 3), and retinoic acid-inducible gene I. To evaluate all gene expression together as patterns, each value was standardized, and CDA was performed at each time point. RESULTS Gene expression of TLR2 and TLR4 was already significantly increased in both CLP and Burn compared with sham mice at 6 hours after injury (p < 0.05). Gene expression of TLR9 was significantly decreased in CLP compared with sham and Burn mice at 12 hours and 24 hours after injury (p < 0.05) but not at 6 hours. Gene expression of NLRP3 was significantly increased in CLP and Burn compared with sham mice at 6 hours and 24 hours after injury (p < 0.05). In the CDA, each group showed distinctive gene expression patterns at only 6 hours after injury. Each group was clearly classified, and the classification error rates were 0% at all of the time points. CONCLUSIONS Canonical discriminant analysis of the gene expression profile of innate immune receptors could be a novel approach for diagnosing the pathophysiology of complicated systemic inflammation from the early stage of injury.
Collapse
|
12
|
Species composition and environmental adaptation of indigenous Chinese cattle. Sci Rep 2017; 7:16196. [PMID: 29170422 PMCID: PMC5700937 DOI: 10.1038/s41598-017-16438-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/13/2017] [Indexed: 12/13/2022] Open
Abstract
Indigenous Chinese cattle combine taurine and indicine origins and occupy a broad range of different environments. By 50 K SNP genotyping we found a discontinuous distribution of taurine and indicine cattle ancestries with extremes of less than 10% indicine cattle in the north and more than 90% in the far south and southwest China. Model-based clustering and f4-statistics indicate introgression of both banteng and gayal into southern Chinese cattle while the sporadic yak influence in cattle in or near Tibetan area validate earlier findings of mitochondrial DNA analysis. Geographic patterns of taurine and indicine mitochondrial and Y-chromosomal DNA diversity largely agree with the autosomal cline. The geographic distribution of the genomic admixture of different bovine species is proposed to be the combined effect of prehistoric immigrations, gene flow, major rivers acting as genetic barriers, local breeding objectives and environmental adaptation. Whole-genome scan for genetic differentiation and association analyses with both environmental and morphological covariables are remarkably consistent with previous studies and identify a number of genes implicated in adaptation, which include TNFRSF19, RFX4, SP4 and several coat color genes. We propose indigenous Chinese cattle as a unique and informative resource for gene-level studies of climate adaptation in mammals.
Collapse
|