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Capra E, Lazzari B, Milanesi M, Nogueira GP, Garcia JF, Utsunomiya YT, Ajmone-Marsan P, Stella A. Comparison between indicine and taurine cattle DNA methylation reveals epigenetic variation associated to differences in morphological adaptive traits. Epigenetics 2023; 18:2163363. [PMID: 36600398 PMCID: PMC9980582 DOI: 10.1080/15592294.2022.2163363] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Indicine and taurine subspecies present distinct morphological traits as a consequence of environmental adaptation and artificial selection. Although the two subspecies have been characterized and compared at genome-wide level and at specific loci, their epigenetic diversity has not yet been explored. In this work, Reduced Representation Bisulphite Sequencing (RRBS) profiling of the taurine Angus (A) and indicine Nellore (N) cattle breeds was applied to identify methylation differences between the two subspecies. Genotyping by sequencing (GBS) of the same animals was performed to detect single nucleotide polymorphisms (SNPs) at cytosines in CpG dinucleotides and remove them from the differential methylation analysis. A total of 660,845 methylated cytosines were identified within the CpG context (CpGs) across the 10 animals sequenced (5 N and 5 A). A total of 25,765 of these were differentially methylated (DMCs). Most DMCs clustered in CpG stretches nearby genes involved in cellular and anatomical structure morphogenesis. Also, sequences flanking DMC were enriched in SNPs compared to all other CpGs, either methylated or unmethylated in the two subspecies. Our data suggest a contribution of epigenetics to the regulation and divergence of anatomical morphogenesis in the two subspecies relevant for cattle evolution and sub-species differentiation and adaptation.
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Affiliation(s)
- E Capra
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, Lodi, Italy
| | - B Lazzari
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, Lodi, Italy
| | - M Milanesi
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil.,Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - G P Nogueira
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, Brazil
| | - J F Garcia
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Y T Utsunomiya
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, Brazil
| | - P Ajmone-Marsan
- Department of Animal Science, Food and Nutrition - DIANA, and Nutrigenomics and Proteomics Research Center - PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - A Stella
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, Lodi, Italy
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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,
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3
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Naji MM, Utsunomiya YT, Sölkner J, Rosen BD, Mészáros G. Assessing Bos taurus introgression in the UOA Bos indicus assembly. Genet Sel Evol 2021; 53:96. [PMID: 34922445 PMCID: PMC8684283 DOI: 10.1186/s12711-021-00688-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 11/29/2021] [Indexed: 12/30/2022] Open
Abstract
Background Reference genomes are essential in the analysis of genomic data. As the cost of sequencing decreases, multiple reference genomes are being produced within species to alleviate problems such as low mapping accuracy and reference allele bias in variant calling that can be associated with the alignment of divergent samples to a single reference individual. The latest reference sequence adopted by the scientific community for the analysis of cattle data is ARS_UCD1.2, built from the DNA of a Hereford cow (Bos taurus taurus—B. taurus). A complementary genome assembly, UOA_Brahman_1, was recently built to represent the other cattle subspecies (Bos taurus indicus—B. indicus) from a Brahman cow haplotype to further support analysis of B. indicus data. In this study, we aligned the sequence data of 15 B. taurus and B. indicus breeds to each of these references. Results The alignment of B. taurus individuals against UOA_Brahman_1 detected up to five million more single-nucleotide variants (SNVs) compared to that against ARS_UCD1.2. Similarly, the alignment of B. indicus individuals against ARS_UCD1.2 resulted in one and a half million more SNVs than that against UOA_Brahman_1. The number of SNVs with nearly fixed alternative alleles also increased in the alignments with cross-subspecies. Interestingly, the alignment of B. taurus cattle against UOA_Brahman_1 revealed regions with a smaller than expected number of counts of SNVs with nearly fixed alternative alleles. Since B. taurus introgression represents on average 10% of the genome of Brahman cattle, we suggest that these regions comprise taurine DNA as opposed to indicine DNA in the UOA_Brahman_1 reference genome. Principal component and admixture analyses using genotypes inferred from this region support these taurine-introgressed loci. Overall, the flagged taurine segments represent 13.7% of the UOA_Brahman_1 assembly. The genes located within these segments were previously reported to be under positive selection in Brahman cattle, and include functional candidate genes implicated in feed efficiency, development and immunity. Conclusions We report a list of taurine segments that are in the UOA_Brahman_1 assembly, which will be useful for the interpretation of interesting genomic features (e.g., signatures of selection, runs of homozygosity, increased mutation rate, etc.) that could appear in future re-sequencing analysis of indicine cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00688-1.
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Affiliation(s)
- Maulana M Naji
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Yuri T Utsunomiya
- AgroPartners Consulting, R. Floriano Peixoto, 120 - Sala 43A - Centro, Araçatuba, SP, 16010-220, Brazil.,Department of Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Araçatuba, São Paulo, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, São Paulo, Brazil
| | - Johann Sölkner
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA, ARS, Beltsville, MD, USA.
| | - Gábor Mészáros
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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4
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Utsunomiya YT, Fortunato AAAD, Milanesi M, Trigo BB, Alves NF, Sonstegard TS, Garcia JF. Bos taurus haplotypes segregating in Nellore (Bos indicus) cattle. Anim Genet 2021; 53:58-67. [PMID: 34921423 DOI: 10.1111/age.13164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2021] [Indexed: 11/29/2022]
Abstract
Brazil is the largest exporter of beef in the world, and most of that beef derives from Nellore cattle. Although considered a zebu breed (Bos indicus), the history of Nellore cattle in Brazil is marked by the importation of bulls from India, the use of a Creole taurine (Bos taurus) maternal lineage to quickly expand the herds and backcrossing to Nellore bulls to recover zebu ancestry. As a consequence, the current Brazilian Nellore population carries an average taurine ancestry of approximately 1%. Although that percentage seems small, some taurine variants deviate substantially from that average, with the better-known cases being the PLAG1-Q haplotype involved with body size variation and the Guarani (PG ) polled variant producing hornless animals. Here, we report taurine haplotypes in 9074 Nellore animals genotyped for 539 657 imputed SNP markers. Apart from PLAG1-Q and PG , our analysis further revealed common taurine haplotypes (>3%) spanning genes related to immunity, growth, reproduction and hair and skin phenotypes. Using data from 22 economically important traits, we showed that many of the major QTL previously reported in the breed are at least partially driven by taurine haplotypes. As B. taurus and B. indicus haplotypes are highly divergent, presenting widely different sets of functional variants, our results provide promising targets for future scrutiny in Nellore cattle.
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Affiliation(s)
- Y T Utsunomiya
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,AgroPartners Consulting. R. Floriano Peixoto, 120 - Sala 43A - Centro, Araçatuba, SP, 16010-220, Brazil
| | - A A A D Fortunato
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,Personal-PEC. R. Sebastião Lima, 1336 - Centro, Campo Grande, MS, 79004-600, Brazil
| | - M Milanesi
- AgroPartners Consulting. R. Floriano Peixoto, 120 - Sala 43A - Centro, Araçatuba, SP, 16010-220, Brazil.,Department for Innovation in Biological, Agro-Food and Forest Systems, Università Della Tuscia, Via S. Camillo de Lellis snc, Viterbo, 01100, Italy
| | - B B Trigo
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil
| | - N F Alves
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil
| | | | - J F Garcia
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,AgroPartners Consulting. R. Floriano Peixoto, 120 - Sala 43A - Centro, Araçatuba, SP, 16010-220, Brazil.,Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University, 14884-900 Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, Brazil
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5
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Trigo BB, Utsunomiya ATH, Fortunato AAAD, Milanesi M, Torrecilha RBP, Lamb H, Nguyen L, Ross EM, Hayes B, Padula RCM, Sussai TS, Zavarez LB, Cipriano RS, Caminhas MMT, Lopes FL, Pelle C, Leeb T, Bannasch D, Bickhart D, Smith TPL, Sonstegard TS, Garcia JF, Utsunomiya YT. Variants at the ASIP locus contribute to coat color darkening in Nellore cattle. Genet Sel Evol 2021; 53:40. [PMID: 33910501 PMCID: PMC8082809 DOI: 10.1186/s12711-021-00633-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Nellore cattle (Bos indicus) are well-known for their adaptation to warm and humid environments. Hair length and coat color may impact heat tolerance. The Nellore breed has been strongly selected for white coat, but bulls generally exhibit darker hair ranging from light grey to black on the head, neck, hump, and knees. Given the potential contribution of coat color variation to the adaptation of cattle populations to tropical and sub-tropical environments, our aim was to map positional and functional candidate genetic variants associated with darkness of hair coat (DHC) in Nellore bulls. RESULTS We performed a genome-wide association study (GWAS) for DHC using data from 432 Nellore bulls that were genotyped for more than 777 k single nucleotide polymorphism (SNP) markers. A single major association signal was detected in the vicinity of the agouti signaling protein gene (ASIP). The analysis of whole-genome sequence (WGS) data from 21 bulls revealed functional variants that are associated with DHC, including a structural rearrangement involving ASIP (ASIP-SV1). We further characterized this structural variant using Oxford Nanopore sequencing data from 13 Australian Brahman heifers, which share ancestry with Nellore cattle; we found that this variant originates from a 1155-bp deletion followed by an insertion of a transposable element of more than 150 bp that may impact the recruitment of ASIP non-coding exons. CONCLUSIONS Our results indicate that the variant ASIP sequence causes darker coat pigmentation on specific parts of the body, most likely through a decreased expression of ASIP and consequently an increased production of eumelanin.
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Affiliation(s)
- Beatriz B Trigo
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil
| | - Adam T H Utsunomiya
- International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil
| | - Alvaro A A D Fortunato
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,Personal-PEC, R. Sebastião Lima, 1336-Centro, Campo Grande, MS, 79004-600, Brazil
| | - Marco Milanesi
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil
| | - Rafaela B P Torrecilha
- International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil
| | - Harrison Lamb
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Loan Nguyen
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Elizabeth M Ross
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Ben Hayes
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | | | - Thayla S Sussai
- Centro Universitário Católico Salesiano, Araçatuba, SP, Brazil
| | - Ludmilla B Zavarez
- International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil
| | | | - Maria M T Caminhas
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil
| | - Flavia L Lopes
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil
| | | | - Tosso Leeb
- Institute of Genetics, Vetsuisse-Faculty, University of Bern, Bremgartenstrasse 109A, 3012, Bern, Switzerland.,Dermfocus, University of Bern, Bremgartenstrasse 109A, 3012, Bern, Switzerland
| | - Danika Bannasch
- Institute of Genetics, Vetsuisse-Faculty, University of Bern, Bremgartenstrasse 109A, 3012, Bern, Switzerland.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Derek Bickhart
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA
| | - Timothy P L Smith
- US. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | | | - José F Garcia
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil.,School of Agriculture and Veterinarian Sciences, Jaboticabal, Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (Unesp), Jaboticabal, SP, Brazil
| | - Yuri T Utsunomiya
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil. .,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil. .,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil.
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6
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Abstract
BACKGROUND In evolutionary theory, divergence and speciation can arise from long periods of reproductive isolation, genetic mutation, selection and environmental adaptation. After divergence, alleles can either persist in their initial state (ancestral allele - AA), co-exist or be replaced by a mutated state (derived alleles -DA). In this study, we aligned whole genome sequences of individuals from the Bovinae subfamily to the cattle reference genome (ARS.UCD-1.2) for defining ancestral alleles necessary for selection signatures study. RESULTS Accommodating independent divergent of each lineage from the initial ancestral state, AA were defined based on fixed alleles on at least two groups of yak, bison and gayal-gaur-banteng resulting in ~ 32.4 million variants. Using non-overlapping scanning windows of 10 Kb, we counted the AA observed within taurine and zebu cattle. We focused on the extreme points, regions with top 0. 1% (high count) and regions without any occurrence of AA (null count). High count regions preserved gene functions from ancestral states that are still beneficial in the current condition, while null counts regions were linked to mutated ones. For both cattle, high count regions were associated with basal lipid metabolism, essential for survival of various environmental pressures. Mutated regions were associated to productive traits in taurine, i.e. higher metabolism, cell development and behaviors and in immune response domain for zebu. CONCLUSIONS Our findings suggest that retaining and losing AA in some regions are varied and made it species-specific with possibility of overlapping as it depends on the selective pressure they had to experience.
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Affiliation(s)
- Maulana M. Naji
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Yuri T. Utsunomiya
- São Paulo State University (Unesp), School of Veterinary Medicine, Department of Production and Animal Health, Araçatuba, São Paulo Brazil
- International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, São Paulo Brazil
- AgroPartners Consulting. R. Floriano Peixoto, 120-Sala 43A-Centro, Araçatuba, SP 16010-220 Brazil
- Personal-PEC. R. Sebastiao Lima, 1336-Centro, Campo Grande, MS 79004-600 Brazil
| | - Johann Sölkner
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | | | - Gábor Mészáros
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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7
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Batista LFS, Torrecilha RBP, Silva RB, Utsunomiya YT, Silva TBF, Tomokane TY, Pacheco AD, Bosco AM, Paulan SC, Rossi CN, Costa GNO, Marcondes M, Ciarlini PC, Nunes CM, Matta VLR, Laurenti MD. Chromosomal segments may explain the antibody response cooperation for canine leishmaniasis pathogenesis. Vet Parasitol 2020; 288:109276. [PMID: 33152678 DOI: 10.1016/j.vetpar.2020.109276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/22/2022]
Abstract
Visceral leishmaniasis (VL) is marked by hyperactivation of a humoral response secreting high quantity of immunoglobulins (Igs) that are inaccessible to intracellular parasites. Here we investigated the contributions of the antibody response to the canine leishmaniasis pathogenesis. Using correlation and genome-wide association analysis, we investigated the relationship of anti-Leishmania infantum immunoglobulin classes levels with parasite burden, clinical response, renal/hepatic biochemical, and oxidative stress markers in dogs from endemic areas of VL. Immunoglobulin G (IgG) and IgA were positively correlated with parasite burden on lymph node and blood. Increased IgG, IgA and IgE levels were associated with severe canine leishmaniasis (CanL) whereas IgM was elevated in uninfected exposed dogs. Correlations of IgM, IgG and IgA with creatinine, urea, AST and ALT levels in the serum were suggested an involvement of those Igs with renal and hepatic changes. The correlogram of oxidative radicals and antioxidants revealed a likely relationship of IgM, IgG and IgA with oxidative stress and lipid peroxidation in the blood, suggested as mechanisms mediating tissue damage and CanL worsening. The gene mapping on chromosomal segments associated with the quantitative variation of immunoglobulin classes identified genetic signatures involved with reactive oxygen species generation, phagolysosome maturation and rupture, free iron availability, Th1/Th2 differenciation and, immunoglobulin clearance. The findings demonstrated the roles of the antibody response as resistance or susceptibility markers and mediators of CanL pathogenesis. In addition we pinpointed candidate genes as potential targets for the therapy against the damage caused by exacerbated antibody response and parasitism in VL.
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Affiliation(s)
- Luís F S Batista
- Laboratório De Patologia De Doenças Infecciosas, Faculdade De Medicina, Universidade De São Paulo, São Paulo, CEP: 01246903, Brazil.
| | - Rafaela B P Torrecilha
- Departamento De Medicina Veterinária Preventiva e Reprodução Animal, Faculdade De Ciências Agrárias e Veterinárias, Univ Estadual Paulista, Jaboticabal, São Paulo, CEP: 14884-900, Brazil.
| | - Rafaela B Silva
- Escola de Saúde, Universidade Salvador, Salvador, Bahia, CEP: 41720-200, Brazil.
| | - Yuri T Utsunomiya
- Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, Univ Estadual Paulista, Araçatuba, São Paulo, CEP: 16015-050, Brazil.
| | - Thaís B F Silva
- Laboratório De Patologia De Doenças Infecciosas, Faculdade De Medicina, Universidade De São Paulo, São Paulo, CEP: 01246903, Brazil.
| | - Thaíse Y Tomokane
- Laboratório De Patologia De Doenças Infecciosas, Faculdade De Medicina, Universidade De São Paulo, São Paulo, CEP: 01246903, Brazil.
| | - Acácio D Pacheco
- Departamento de Clínica, Cirurgia e Reprodução Animal, Faculdade de Medicina Veterinária, Univ Estadual Paulista, Araçatuba, São Paulo, CEP: 16015-050, Brazil.
| | - Anelise M Bosco
- Departamento de Clínica, Cirurgia e Reprodução Animal, Faculdade de Medicina Veterinária, Univ Estadual Paulista, Araçatuba, São Paulo, CEP: 16015-050, Brazil.
| | - Silvana C Paulan
- Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, Univ Estadual Paulista, Araçatuba, São Paulo, CEP: 16015-050, Brazil.
| | - Claudio N Rossi
- Departamento de Clínica, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, CEP 05508-270, Brazil.
| | - Gustavo N O Costa
- Departamento De Medicina Veterinária Preventiva e Reprodução Animal, Faculdade De Ciências Agrárias e Veterinárias, Univ Estadual Paulista, Jaboticabal, São Paulo, CEP: 14884-900, Brazil.
| | - Mary Marcondes
- Departamento de Clínica, Cirurgia e Reprodução Animal, Faculdade de Medicina Veterinária, Univ Estadual Paulista, Araçatuba, São Paulo, CEP: 16015-050, Brazil.
| | - Paulo C Ciarlini
- Departamento de Clínica, Cirurgia e Reprodução Animal, Faculdade de Medicina Veterinária, Univ Estadual Paulista, Araçatuba, São Paulo, CEP: 16015-050, Brazil.
| | - Cáris M Nunes
- Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, Univ Estadual Paulista, Araçatuba, São Paulo, CEP: 16015-050, Brazil.
| | - Vânia L R Matta
- Laboratório De Patologia De Doenças Infecciosas, Faculdade De Medicina, Universidade De São Paulo, São Paulo, CEP: 01246903, Brazil.
| | - Márcia D Laurenti
- Laboratório De Patologia De Doenças Infecciosas, Faculdade De Medicina, Universidade De São Paulo, São Paulo, CEP: 01246903, Brazil.
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8
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Torrecilha RBP, Milanesi M, Wade CM, Gallana M, Falbo AK, Reichler IM, Hug P, Jagannathan V, Trigo BB, Paulan SC, Bruno DB, Garcia SD, Scaramele NF, Lopes FL, Dolf G, Leeb T, Sölkner J, Garcia JF, Pieńkowska-Schelling A, Schelling C, Utsunomiya YT. Association of missense variants in GDF9 with litter size in Entlebucher Mountain dogs. Anim Genet 2019; 51:78-86. [PMID: 31802524 DOI: 10.1111/age.12882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2019] [Indexed: 12/28/2022]
Abstract
In the past two decades, average litter size (ALS) in Entlebucher Mountain dogs decreased by approximately 0.8 puppies. We conducted a GWAS for ALS using the single-step methodology to take advantage of 1632 pedigree records, 892 phenotypes and 372 genotypes (173 662 markers) for which only 12% of the dogs had both phenotypes and genotypes available. Our analysis revealed associations towards the growth differentiation factor 9 gene (GDF9), which is known to regulate oocyte maturation. The trait heritability was estimated at 43.1%, from which approximately 15% was accountable by the GDF9 locus alone. Therefore, markers flanking GDF9 explained approximately 6.5% of the variance in ALS. Analysis of WGSs revealed two missense substitutions in GDF9, one of which (g.11:21147009G>A) affected a highly conserved nucleotide in vertebrates. The derived allele A was validated in 111 dogs and shown to be associated with decreased ALS (-0.75 ± 0.22 puppies per litter). The variant was further predicted to cause a proline to serine substitution. The affected residue was immediately followed by a six-residue deletion that is fixed in the canine species but absent in non-canids. We further confirmed that the deletion is prevalent in the Canidae family by sequencing three species of wild canids. Since canids uniquely ovulate oocytes at the prophase stage of the first meiotic division, requiring maturation in the oviduct, we conjecture that the amino acid substitution and the six-residue deletion of GDF9 may serve as a model for insights into the dynamics of oocyte maturation in canids.
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Affiliation(s)
- R B P Torrecilha
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agriculture and Veterinarian Sciences, São Paulo State University (Unesp), Via de acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, São Paulo, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - M Milanesi
- International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | | | - M Gallana
- Clinic of Reproductive Medicine, Vetsuisse-Faculty University of Zurich, Eschikon 27, Lindau, 8315, Switzerland
| | - A-K Falbo
- Clinic of Reproductive Medicine, Vetsuisse-Faculty University of Zurich, Eschikon 27, Lindau, 8315, Switzerland
| | - I M Reichler
- Clinic of Reproductive Medicine, Vetsuisse-Faculty University of Zurich, Winterthurerstr. 260, Zürich, 8057, Switzerland
| | - P Hug
- Institute of Genetics, Vetsuisse-Faculty University of Bern, Bremgartenstrasse 109A, Bern, 3012, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse-Faculty University of Bern, Bremgartenstrasse 109A, Bern, 3012, Switzerland
| | - B B Trigo
- International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - S C Paulan
- International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - D B Bruno
- Department of Clinics, Surgery and Animal Reproduction, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793,, 16050-680, Araçatuba, São Paulo, Brazil
| | - S D Garcia
- Department of Clinics, Surgery and Animal Reproduction, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793,, 16050-680, Araçatuba, São Paulo, Brazil
| | - N F Scaramele
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - F L Lopes
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - G Dolf
- Institute of Genetics, Vetsuisse-Faculty University of Bern, Bremgartenstrasse 109A, Bern, 3012, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse-Faculty University of Bern, Bremgartenstrasse 109A, Bern, 3012, Switzerland
| | - J Sölkner
- Division of Livestook Sciences, Department of Sustainable Agriculture System, BOKU - University of Natural Resource and Live Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - J F Garcia
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agriculture and Veterinarian Sciences, São Paulo State University (Unesp), Via de acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, São Paulo, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - A Pieńkowska-Schelling
- Clinic of Reproductive Medicine, Vetsuisse-Faculty University of Zurich, Eschikon 27, Lindau, 8315, Switzerland.,Institute of Genetics, Vetsuisse-Faculty University of Bern, Bremgartenstrasse 109A, Bern, 3012, Switzerland
| | - C Schelling
- Clinic of Reproductive Medicine, Vetsuisse-Faculty University of Zurich, Eschikon 27, Lindau, 8315, Switzerland
| | - Y T Utsunomiya
- International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
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9
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Khayatzadeh N, Mészáros G, Utsunomiya YT, Schmitz-Hsu F, Seefried F, Schnyder U, Ferenčaković M, Garcia JF, Curik I, Sölkner J. Genome-wide mapping of the dominance effects based on breed ancestry for semen traits in admixed Swiss Fleckvieh bulls. J Dairy Sci 2019; 102:11217-11224. [PMID: 31548062 DOI: 10.3168/jds.2019-16899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/01/2019] [Indexed: 11/19/2022]
Abstract
Heterosis is the beneficial deviation of crossbred progeny from the average of parental lines for a particular trait. Heterosis is due to nonadditive genetic effects with dominance and epistatic components. Recent advances in genotyping technology have encouraged researchers to estimate and scan heterosis components for a range of traits in crossbred populations, applying various definitions of such components. In this study, we defined the intralocus (dominance) component of heterosis using local genetic ancestry and performed genome-wide association analysis for admixed Swiss Fleckvieh bulls and their parental populations, Red Holstein Friesian and Swiss Simmental, for semen traits. A linear mixed model for 41,824 SNP, including SNP additive genetic, breed additive, and breed dominance effects on 1,178 bulls (148 Red Holstein Friesian, 213 Swiss Simmental, and 817 Swiss Fleckvieh) with a total of 43,782 measurements was performed. In total, 19 significant regions for breed dominance were identified for volume (2 regions on Bos taurus autosome 10 and 22) and percentage of live spermatozoa (17 regions on Bos taurus autosome 3, 4, 5, 7, 13, 14, and 17), and genes associated with spermatogenesis, sperm motility, and male fertility traits were located there. No significant region for breed dominance was detected for total number of spermatozoa. The signals for breed dominance were relatively wide, most likely due to limited numbers of recombination events in a small number of generations (10-15 generations) of crossbreeding in the recent Swiss Fleckvieh composite.
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Affiliation(s)
- N Khayatzadeh
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendel-Strasse 33, A-1180 Vienna, Austria.
| | - G Mészáros
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendel-Strasse 33, A-1180 Vienna, Austria
| | - Y T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Cinêcias Agrárias Veterinárias, UNESP-Univ Estadual Paulista, Araçatuba, São Paulo, Brazil 16050-680
| | - F Schmitz-Hsu
- Swissgenetics, Meielenfeldweg 12, Postfach, 3052 Zollikofen, Switzerland
| | - F Seefried
- Qualitas AG, Chamerstrasse 56, Ch-6300, Zug, Switzerland
| | - U Schnyder
- Qualitas AG, Chamerstrasse 56, Ch-6300, Zug, Switzerland
| | - M Ferenčaković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - J F Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Cinêcias Agrárias Veterinárias, UNESP-Univ Estadual Paulista, Araçatuba, São Paulo, Brazil 16050-680; Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP-Univ Estadual Paulista, Araçatuba, São Paulo, Brazil 16050-680
| | - I Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - J Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendel-Strasse 33, A-1180 Vienna, Austria
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10
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Utsunomiya YT, Milanesi M, Fortes MRS, Porto-Neto LR, Utsunomiya ATH, Silva MVGB, Garcia JF, Ajmone-Marsan P. Genomic clues of the evolutionary history of Bos indicus cattle. Anim Genet 2019; 50:557-568. [PMID: 31475748 DOI: 10.1111/age.12836] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2019] [Indexed: 01/08/2023]
Abstract
Together with their sister subspecies Bos taurus, zebu cattle (Bos indicus) have contributed to important socioeconomic changes that have shaped modern civilizations. Zebu cattle were domesticated in the Indus Valley 8000 years before present (YBP). From the domestication site, they expanded to Africa, East Asia, southwestern Asia and Europe between 4000 and 1300 YBP, intercrossing with B. taurus to form clinal variations of zebu ancestry across the landmass of Afro-Eurasia. In the past 150 years, zebu cattle reached the Americas and Oceania, where they have contributed to the prosperity of emerging economies. The zebu genome is characterized by two mitochondrial haplogroups (I1 and I2), one Y chromosome haplogroup (Y3) and three major autosomal ancestral groups (Indian-Pakistani, African and Chinese). Phenotypically, zebu animals are recognized by their hump, large ears and excess skin. They are rustic, resilient to parasites and capable of bearing the hot and humid climates of the tropics. Many resources are available to study the zebu genome, including commercial arrays of SNP, reference assemblies and publicly available genotypes and whole-genome sequences. Nevertheless, many of these resources were initially developed to support research and subsidize industrial applications in B. taurus, and therefore they can produce bias in data analysis. The combination of genomics with precision agriculture holds great promise for the identification of genetic variants affecting economically important traits such as tick resistance and heat tolerance, which were naturally selected for millennia and played a major role in the evolution of B. indicus cattle.
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Affiliation(s)
- Y T Utsunomiya
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M Milanesi
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Chemistry Bld, 68 Cooper Rd, Brisbane, 4072, Qld, Australia
| | - L R Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia QLD, Brisbane, 4067, Qld, Australia
| | - A T H Utsunomiya
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M V G B Silva
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Gado de Leite, Juiz de Fora, MG, 360381330, Brazil
| | - J F Garcia
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900 Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, Brazil
| | - P Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA and BioDNA, Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, Piacenza, 29122, Italy
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11
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Nandolo W, Mészáros G, Banda LJ, Gondwe TN, Lamuno D, Mulindwa HA, Nakimbugwe HN, Wurzinger M, Utsunomiya YT, Woodward-Greene MJ, Liu M, Liu G, Van Tassell CP, Curik I, Rosen BD, Sölkner J. Timing and Extent of Inbreeding in African Goats. Front Genet 2019; 10:537. [PMID: 31214253 PMCID: PMC6558083 DOI: 10.3389/fgene.2019.00537] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 05/17/2019] [Indexed: 11/13/2022] Open
Abstract
Genetic characterization of African goats is one of the current priorities in the improvement of goats in the continent. This study contributes to the characterization effort by determining the levels and number of generations to common ancestors ("age") associated with inbreeding in African goat breeds and identifies regions that contain copy number variation mistyped as being homozygous. Illumina 50k single nucleotide polymorphism genotype data for 608 goats from 31 breeds were used to compute the level and age of inbreeding at both local (marker) and global levels (FG) using a model-based approach based on a hidden Markov model. Runs of homozygosity (ROH) segments detected using the Viterbi algorithm led to ROH-based inbreeding coefficients for all ROH (FROH) and for ROH longer than 2 Mb (FROH > 2Mb). Some of the genomic regions identified as having ROH are likely to be hemizygous regions (copy number deletions) mistyped as homozygous regions. Although the proportion of these miscalled ROH is small and does not substantially affect estimates of levels of inbreeding for individual animals, the inbreeding metrics were adjusted by removing these regions from the ROH. All the inbreeding metrics varied widely across breeds, with overall means of 0.0408, 0.0370, and 0.0691 and medians of 0.0125, 0.0098, and 0.0366 for FROH, FROH > 2Mb, and FG, respectively. Several breeds (including Menabe and Sofia from Madagascar) had high proportions of recent inbreeding, while Small East African, Ethiopian, and most of the West African breeds (including West African Dwarf) had more ancient inbreeding.
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Affiliation(s)
- Wilson Nandolo
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria.,Department of Animal Science, Faculty of Agriculture, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi.,Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States
| | - Gábor Mészáros
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Liveness Jessica Banda
- Department of Animal Science, Faculty of Agriculture, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Timothy N Gondwe
- Department of Animal Science, Faculty of Agriculture, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Doreen Lamuno
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | | | | | - Maria Wurzinger
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Yuri T Utsunomiya
- School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo State University (UNESP), São Paulo, Brazil
| | - M Jennifer Woodward-Greene
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States
| | - Mei Liu
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States
| | - George Liu
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
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12
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Gallana M, Utsunomiya YT, Dolf G, Pintor Torrecilha RB, Falbo AK, Jagannathan V, Leeb T, Reichler I, Sölkner J, Schelling C. Genome-wide association study and heritability estimate for ectopic ureters in Entlebucher mountain dogs. Anim Genet 2018; 49:645-650. [PMID: 30276844 DOI: 10.1111/age.12728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2018] [Indexed: 11/28/2022]
Abstract
An ectopic ureter is a congenital anomaly which may lead to urinary incontinence and without a surgical intervention even to end-stage kidney disease. A genetic component contributes to the development of this anomaly in Entlebucher mountain dogs (EMD); however, its nature remains unclear. Using the Illumina CanineHD bead chip, a case-control genome-wide association study was performed to identify SNPs associated with the trait. Six loci on canine chromosomes 3, 17, 27 and 30 were identified with 16 significantly associated SNPs. There was no single outstanding SNP associated with the phenotype, and the association signals were not close to known genes involved in human congenital anomalies of the kidney or lower urinary tract. Additional research will be necessary to elucidate the potential role of the associated genes in the development of ectopic ureters in the EMD breed.
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Affiliation(s)
- M Gallana
- Clinic for Reproductive Medicine, Vetsuisse-Faculty, University of Zurich, Winterthurerstrasse 260, 8057, Zurich, Switzerland
| | - Y T Utsunomiya
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900, Jaboticabal, São Paulo, Brazil
| | - G Dolf
- Vetsuisse-Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, 3012, Bern, Switzerland
| | - R B Pintor Torrecilha
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900, Jaboticabal, São Paulo, Brazil
| | - A-K Falbo
- Clinic for Reproductive Medicine, Vetsuisse-Faculty, University of Zurich, Winterthurerstrasse 260, 8057, Zurich, Switzerland
| | - V Jagannathan
- Vetsuisse-Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, 3012, Bern, Switzerland
| | - T Leeb
- Vetsuisse-Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, 3012, Bern, Switzerland
| | - I Reichler
- Clinic for Reproductive Medicine, Vetsuisse-Faculty, University of Zurich, Winterthurerstrasse 260, 8057, Zurich, Switzerland
| | - J Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Gregor Mendel Straße 33, 1180, Vienna, Austria
| | - C Schelling
- Vetsuisse-Faculty, Clinic for Reproductive Medicine and Center of Clinical Studies, University of Zurich, Eschikon 27, EHB F 22.1, 8315, Lindau, Switzerland
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13
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Nandolo W, Utsunomiya YT, Mészáros G, Wurzinger M, Khayadzadeh N, Torrecilha RBP, Mulindwa HA, Gondwe TN, Waldmann P, Ferenčaković M, Garcia JF, Rosen BD, Bickhart D, van Tassell CP, Curik I, Sölkner J. Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances. Genet Sel Evol 2018; 50:43. [PMID: 30134820 PMCID: PMC6106898 DOI: 10.1186/s12711-018-0414-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 07/30/2018] [Indexed: 12/22/2022] Open
Abstract
Background Runs of homozygosity (ROH) islands are stretches of homozygous sequence in the genome of a large proportion of individuals in a population. Algorithms for the detection of ROH depend on the similarity of haplotypes. Coverage gaps and copy number variants (CNV) may result in incorrect identification of such similarity, leading to the detection of ROH islands where none exists. Misidentified hemizygous regions will also appear as homozygous based on sequence variation alone. Our aim was to identify ROH islands influenced by marker coverage gaps or CNV, using Illumina BovineHD BeadChip (777 K) single nucleotide polymorphism (SNP) data for Austrian Brown Swiss, Tyrol Grey and Pinzgauer cattle. Methods ROH were detected using clustering, and ROH islands were determined from population inbreeding levels for each marker. CNV were detected using a multivariate copy number analysis method and a hidden Markov model. SNP coverage gaps were defined as genomic regions with intermarker distances on average longer than 9.24 kb. ROH islands that overlapped CNV regions (CNVR) or SNP coverage gaps were considered as potential artefacts. Permutation tests were used to determine if overlaps between CNVR with copy losses and ROH islands were due to chance. Diversity of the haplotypes in the ROH islands was assessed by haplotype analyses. Results In Brown Swiss, Tyrol Grey and Pinzgauer, we identified 13, 22, and 24 ROH islands covering 26.6, 389.0 and 35.8 Mb, respectively, and we detected 30, 50 and 71 CNVR derived from CNV by using both algorithms, respectively. Overlaps between ROH islands, CNVR or coverage gaps occurred for 7, 14 and 16 ROH islands, respectively. About 37, 44 and 52% of the ROH islands coverage in Brown Swiss, Tyrol Grey and Pinzgauer, respectively, were affected by copy loss. Intersections between ROH islands and CNVR were small, but significantly larger compared to ROH islands at random locations across the genome, implying an association between ROH islands and CNVR. Haplotype diversity for reliable ROH islands was lower than for ROH islands that intersected with copy loss CNVR. Conclusions Our findings show that a significant proportion of the ROH islands in the bovine genome are artefacts due to CNV or SNP coverage gaps. Electronic supplementary material The online version of this article (10.1186/s12711-018-0414-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wilson Nandolo
- Division of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Gregor-Mendel Strasse 33, 1180, Vienna, Austria.,Lilongwe University of Agriculture and Natural Resources, P. O. Box 219, Lilongwe, Malawi
| | - Yuri T Utsunomiya
- School of Agricultural and Veterinarian Sciences, Jaboticabal, Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (UNESP), São Paulo, Brazil
| | - Gábor Mészáros
- Division of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Gregor-Mendel Strasse 33, 1180, Vienna, Austria.
| | - Maria Wurzinger
- Division of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Gregor-Mendel Strasse 33, 1180, Vienna, Austria
| | - Negar Khayadzadeh
- Division of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Gregor-Mendel Strasse 33, 1180, Vienna, Austria
| | - Rafaela B P Torrecilha
- School of Agricultural and Veterinarian Sciences, Jaboticabal, Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (UNESP), São Paulo, Brazil
| | - Henry A Mulindwa
- National Livestock Resources Research Institute, P.O Box 96, Tororo, Uganda
| | - Timothy N Gondwe
- Lilongwe University of Agriculture and Natural Resources, P. O. Box 219, Lilongwe, Malawi
| | - Patrik Waldmann
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
| | - Maja Ferenčaković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - José F Garcia
- School of Agricultural and Veterinarian Sciences, Jaboticabal, Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (UNESP), São Paulo, Brazil.,School of Veterinary Medicine, Araçatuba, Department of Support, Production and Animal Health, São Paulo State University (UNESP), São Paulo, Brazil
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705-2350, USA
| | - Derek Bickhart
- Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705-2350, USA
| | - Curt P van Tassell
- Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705-2350, USA
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - Johann Sölkner
- Division of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Gregor-Mendel Strasse 33, 1180, Vienna, Austria
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14
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Batista LFS, Utsunomiya YT, Silva TBF, Carneiro MM, Paiva JSF, Silva RB, Tomokane TY, Rossi CN, Pacheco AD, Torrecilha RBP, Silveira FT, Marcondes M, Nunes CM, Laurenti MD. Canine leishmaniasis: Genome-wide analysis and antibody response to Lutzomyia longipalpis saliva. PLoS One 2018; 13:e0197215. [PMID: 29742167 PMCID: PMC5942812 DOI: 10.1371/journal.pone.0197215] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/27/2018] [Indexed: 01/22/2023] Open
Abstract
The anti-inflammatory properties of sand fly saliva favor the establishment of the Leishmania infantum infection. In contrast, an antibody response against Lutzomyia longipalpis saliva is often associated with a protective cell-mediated response against canine visceral leishmaniasis. Genetic studies may demonstrate to what extent the ability to secrete anti-saliva antibodies depends on genetic or environmental factors. However, the genetic basis of canine antibody response against sand fly saliva has not been assessed. The aim of this study was to identify chromosomal regions associated with the anti-Lu. longipalpis salivary IgG response in 189 dogs resident in endemic areas in order to provide information for prophylactic strategies. Dogs were classified into five groups based on serological and parasitological diagnosis and clinical evaluation. Anti-salivary gland homogenate (SGH) IgG levels were assessed by Enzyme-Linked Immunosorbent Assay (ELISA). Genomic DNA was isolated from blood samples and genotyped using a SNP chip with 173,662 single nucleotide polymorphism (SNP) markers. The following linear regression model was fitted: IgG level = mean + origin + sex + age + use of a repellent collar, and the residuals were assumed as pseudo-phenotypes for the association test between phenotypes and genotypes (GWA). A component of variance model that takes into account polygenic and sample structure effects (EMMAX) was employed for GWA. Phenotypic findings indicated that anti-SGH IgG levels remained higher in exposed and subclinically infected dogs than in severely diseased dogs even in regression model residuals. Five associated markers were identified on chromosomes 2, 20 and 31. The mapped genes included CD180 (RP105) and MITF related to the rapid activation of B lymphocytes and differentiation into antibody-secreting plasma cells. The findings pointed to chromosomal segments useful for functional confirmation studies and a search for adjuvant molecules of the anti-saliva response.
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Affiliation(s)
- Luís F. S. Batista
- Departamento de Patologia Veterinária, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
- Escola de Saúde, Universidade Salvador, Salvador, Bahia, Brazil
| | - Yuri T. Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Thaís B. F. Silva
- Laboratório de Patologia de Doenças Infecciosas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | - Thaíse Y. Tomokane
- Laboratório de Patologia de Doenças Infecciosas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Claudio N. Rossi
- Departmento de Clínica, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Acácio D. Pacheco
- Departamento de Clínica, Cirurgia e Reprodução Animal, Faculdade de Medicina Veterinária, Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - Rafaela B. P. Torrecilha
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Fernando T. Silveira
- Deparatmento de Parasitologia, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
| | - Mary Marcondes
- Departamento de Clínica, Cirurgia e Reprodução Animal, Faculdade de Medicina Veterinária, Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - Cáris M. Nunes
- Departmento de Saúde Animal e Produção, Faculdade de Medicina Veterinária, Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - Márcia D. Laurenti
- Laboratório de Patologia de Doenças Infecciosas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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15
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Colli L, Milanesi M, Vajana E, Iamartino D, Bomba L, Puglisi F, Del Corvo M, Nicolazzi EL, Ahmed SSE, Herrera JRV, Cruz L, Zhang S, Liang A, Hua G, Yang L, Hao X, Zuo F, Lai SJ, Wang S, Liu R, Gong Y, Mokhber M, Mao Y, Guan F, Vlaic A, Vlaic B, Ramunno L, Cosenza G, Ahmad A, Soysal I, Ünal EÖ, Ketudat-Cairns M, Garcia JF, Utsunomiya YT, Baruselli PS, Amaral MEJ, Parnpai R, Drummond MG, Galbusera P, Burton J, Hoal E, Yusnizar Y, Sumantri C, Moioli B, Valentini A, Stella A, Williams JL, Ajmone-Marsan P. New Insights on Water Buffalo Genomic Diversity and Post-Domestication Migration Routes From Medium Density SNP Chip Data. Front Genet 2018; 9:53. [PMID: 29552025 PMCID: PMC5841121 DOI: 10.3389/fgene.2018.00053] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/02/2018] [Indexed: 01/14/2023] Open
Abstract
The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centers followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species.
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Affiliation(s)
- Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.,Centro di Ricerca sulla Biodiversità e sul DNA Antico (BioDNA), Piacenza, Italy
| | - Marco Milanesi
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, Araçatuba, Brazil.,International Atomic Energy Agency (IAEA), Colaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Elia Vajana
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Daniela Iamartino
- PTP Science Park, Lodi, Italy.,LGS-AIA Associazione Italiana Allevatori, Cremona, Italy
| | - Lorenzo Bomba
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Francesco Puglisi
- Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali, Università degli Studi di Parma, Parma, Italy
| | - Marcello Del Corvo
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | | | - Sahar S E Ahmed
- Cell Biology Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, Giza, Egypt
| | | | | | - Shujun Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Aixin Liang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Guohua Hua
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xingjie Hao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Fuyuan Zuo
- Department of Animal Husbandry, Southwest University, Chongqing, China
| | - Song-Jia Lai
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Shuilian Wang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Ruyu Liu
- College of Animal Science, Guizhou University, Guiyang, China
| | | | - Mahdi Mokhber
- Department of Animal Science, Faculty of Agricultural Science, Urmia University, Urmia, Iran
| | - Yongjiang Mao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Feng Guan
- College of Life Science, China Jiliang University, Hangzhou, China
| | - Augustin Vlaic
- Department of Animal Genetics, Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine, Cluj Napoca, Romania
| | - Bogdan Vlaic
- Department of Animal Genetics, Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine, Cluj Napoca, Romania
| | - Luigi Ramunno
- Department of Agriculture, University of Naples Federico II, Portici, Italy
| | - Gianfranco Cosenza
- Department of Agriculture, University of Naples Federico II, Portici, Italy
| | - Ali Ahmad
- COMSATS Institute of Information Technology, Sahiwal, Pakistan
| | - Ihsan Soysal
- Department of Animal Science, Faculty of Agriculture, Namik Kemal University, Tekirdag, Turkey
| | - Emel Ö Ünal
- Department of Animal Science, Faculty of Agriculture, Namik Kemal University, Tekirdag, Turkey
| | - Mariena Ketudat-Cairns
- School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - José F Garcia
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, Araçatuba, Brazil.,International Atomic Energy Agency (IAEA), Colaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil.,Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp.), São Paulo, Brazil
| | - Yuri T Utsunomiya
- International Atomic Energy Agency (IAEA), Colaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil.,Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp.), São Paulo, Brazil
| | - Pietro S Baruselli
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Maria E J Amaral
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, Brazil
| | - Rangsun Parnpai
- School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | | | - Peter Galbusera
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - James Burton
- IUCN SSC Asian Wild Cattle Specialist Group and Chester Zoo, Upton by Chester, United Kingdom.,Royal (Dick) School of Veterinary Studies & The Roslin Institute, University of Edinburgh, Roslin, United Kingdom
| | - Eileen Hoal
- NRF/DST Centre of Excellence for Biomedical TB Research, MRC Centre for TB Research, and Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
| | - Yulnawati Yusnizar
- Research Centre for Biotechnology, Indonesian Institute of Sciences, Jalan Raya, Indonesia.,Indonesian Buffalo Conservation and Breeding Centre, Ciapus-Bogor, Indonesia
| | - Cece Sumantri
- Department of Animal Production and Technology, Bogor Agricultural University (IPB), Bogor, Indonesia
| | - Bianca Moioli
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Monterotondo, Italy
| | - Alessio Valentini
- Dipartimento per l'Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, DIBAF, Università della Tuscia, Viterbo, Italy
| | | | - John L Williams
- The Davies Research Centre, School of Animal and Veterinary Science, University of Adelaide, Roseworthy, SA, Australia
| | - Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.,Centro di Ricerca sulla Biodiversità e sul DNA Antico (BioDNA), Piacenza, Italy
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16
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Porto-Neto LR, Bickhart DM, Landaeta-Hernandez AJ, Utsunomiya YT, Pagan M, Jimenez E, Hansen PJ, Dikmen S, Schroeder SG, Kim ES, Sun J, Crespo E, Amati N, Cole JB, Null DJ, Garcia JF, Reverter A, Barendse W, Sonstegard TS. Convergent Evolution of Slick Coat in Cattle through Truncation Mutations in the Prolactin Receptor. Front Genet 2018. [PMID: 29527221 PMCID: PMC5829098 DOI: 10.3389/fgene.2018.00057] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Evolutionary adaptations are occasionally convergent solutions to the same problem. A mutation contributing to a heat tolerance adaptation in Senepol cattle, a New World breed of mostly European descent, results in the distinct phenotype known as slick, where an animal has shorter hair and lower follicle density across its coat than wild type animals. The causal variant, located in the 11th exon of prolactin receptor, produces a frameshift that results in a truncated protein. However, this mutation does not explain all cases of slick coats found in criollo breeds. Here, we obtained genome sequences from slick cattle of a geographically distinct criollo breed, namely Limonero, whose ancestors were originally brought to the Americas by the Spanish. These data were used to identify new causal alleles in the 11th exon of the prolactin receptor, two of which also encode shortened proteins that remove a highly conserved tyrosine residue. These new mutations explained almost 90% of investigated cases of animals that had slick coats, but which also did not carry the Senepol slick allele. These results demonstrate convergent evolution at the molecular level in a trait important to the adaptation of an animal to its environment.
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Affiliation(s)
| | - Derek M Bickhart
- US Dairy Forage Research Center, United States Department of Agriculture, Agricultural Research Service, Madison, WI, United States
| | - Antonio J Landaeta-Hernandez
- Unidad de Investigaciones Zootécnicas, Facultad de Ciencias Veterinarias, Universidad del Zulia, Maracaibo, Venezuela
| | - Yuri T Utsunomiya
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University, São Paulo, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Melvin Pagan
- Department of Animal Science, University of Puerto Rico-Mayagüez, Mayagüez, Puerto Rico
| | - Esbal Jimenez
- Department of Animal Science, University of Puerto Rico-Mayagüez, Mayagüez, Puerto Rico
| | - Peter J Hansen
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Serdal Dikmen
- Department of Animal Science, Faculty of Veterinary Medicine, Uludağ University, Bursa, Turkey
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Eui-Soo Kim
- Recombinetics, Inc., Saint Paul, MN, United States
| | - Jiajie Sun
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Edward Crespo
- Unidad de Investigaciones Zootécnicas, Facultad de Ciencias Veterinarias, Universidad del Zulia, Maracaibo, Venezuela
| | - Norman Amati
- Unidad de Investigaciones Zootécnicas, Facultad de Ciencias Veterinarias, Universidad del Zulia, Maracaibo, Venezuela
| | - John B Cole
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Daniel J Null
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Jose F Garcia
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University, São Paulo, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, São Paulo, Brazil
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17
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Khayatzadeh N, Mészáros G, Utsunomiya YT, Schmitz-Hsu F, Seefried F, Schnyder U, Ferenčaković M, Garcia JF, Curik I, Sölkner J. Effects of breed proportion and components of heterosis for semen traits in a composite cattle breed. J Anim Breed Genet 2017; 135:45-53. [PMID: 29164741 DOI: 10.1111/jbg.12304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/22/2017] [Indexed: 11/30/2022]
Abstract
The aim of this study was to estimate the non-additive genetic effects of the dominance component of heterosis as well as epistatic loss on semen traits in admixed Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF) cattle. Heterosis is the additional gain in productivity or fitness of cross-bred progeny over the mid-purebred parental populations. Intralocus gene interaction usually has a positive effect, while epistatic loss generally reduces productivity or fitness due to lack of evolutionarily established interactions of genes from different breeds. Genotypic data on 38,205 SNP of 818 admixed, as well as 148 RHF and 213 SI bulls as the parental breeds were used to predict breed origin of alleles. The genomewide locus-specific breed ancestries of individuals were used to calculate effects of breed difference as well as the dominance component of heterosis, while proxies for two definitions of epistatic loss were derived from 100,000 random pairs of loci. The average Holstein Friesian ancestry in admixed bulls was estimated 0.82. Results of fitting different linear mixed models showed including the dominance component of heterosis considerably improved the model adequacy for three of the four traits. Inclusion of epistatic loss increased the accuracy of the models only for our new definition of the epistatic effect for two traits, while the other definition was so highly correlated with the dominance component that statistical separation was impossible.
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Affiliation(s)
- N Khayatzadeh
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - G Mészáros
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Y T Utsunomiya
- Faculdade de Cinêcias Agrárias Veterinárias, Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP - Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | | | | | | | - M Ferenčaković
- Faculty of Agriculture, Department of Animal Science, University of Zagreb, Zagreb, Croatia
| | - J F Garcia
- Faculdade de Cinêcias Agrárias Veterinárias, Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP - Univ Estadual Paulista, Araçatuba, São Paulo, Brazil.,Faculdade de Medicina Veterinária de Araçatuba, Departamento de Apoio, Saúde e Produção Animal, UNESP - Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - I Curik
- Faculty of Agriculture, Department of Animal Science, University of Zagreb, Zagreb, Croatia
| | - J Sölkner
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
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18
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Utsunomiya ATH, Santos DJA, Boison SA, Utsunomiya YT, Milanesi M, Bickhart DM, Ajmone-Marsan P, Sölkner J, Garcia JF, da Fonseca R, da Silva MVGB. Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan. BMC Genomics 2016; 17:705. [PMID: 27595709 PMCID: PMC5011828 DOI: 10.1186/s12864-016-3049-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/27/2016] [Indexed: 11/21/2022] Open
Abstract
Background Misassembly signatures, created by shuffling the order of sequences while assembling a genome, can be detected by the unexpected behavior of marker linkage disequilibrium (LD) decay. We developed a heuristic process to identify misassembly signatures, applied it to the bovine reference genome assembly (UMDv3.1) and presented the consequences of misassemblies in two case studies. Results We identified 2,906 single nucleotide polymorphism (SNP) markers presenting unexpected LD decay behavior in 626 putative misassembled contigs, which comprised less than 1 % of the whole genome. Although this represents a small fraction of the reference sequence, these poorly assembled segments can lead to severe implications to local genome context. For instance, we showed that one of the misassembled regions mapped to the POLL locus, which affected the annotation of positional candidate genes in a GWAS case study for polledness in Nellore (Bos indicus beef cattle). Additionally, we found that poorly performing markers in imputation mapped to putative misassembled regions, and that correction of marker positions based on LD was capable to recover imputation accuracy. Conclusions This heuristic approach can be useful to cross validate reference assemblies and to filter out markers located at low confidence genomic regions before conducting downstream analyses. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3049-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam T H Utsunomiya
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista - UNESP, Campus de Jaboticabal, São Paulo, Brasil.
| | - Daniel J A Santos
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista - UNESP, Campus de Jaboticabal, São Paulo, Brasil
| | | | - Yuri T Utsunomiya
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista - UNESP, Campus de Jaboticabal, São Paulo, Brasil
| | - Marco Milanesi
- Faculdade de Medicina Veterinária de Araçatuba, Universidade Estadual Paulista - UNESP, Campus de Araçatuba, São Paulo, Brasil
| | - Derek M Bickhart
- Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD, USA
| | - Paolo Ajmone-Marsan
- Institute of Zootechnics and Biodiversity and Ancient DNA Research Center, Università Cattolica del Sacro Cuore, Piacenza, Italy.,Nutrigenomics and Proteomics Research Center - PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Johann Sölkner
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - José F Garcia
- Faculdade de Medicina Veterinária de Araçatuba, Universidade Estadual Paulista - UNESP, Campus de Araçatuba, São Paulo, Brasil.,International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, São Paulo, Brasil
| | - Ricardo da Fonseca
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista - UNESP, Campus de Jaboticabal, São Paulo, Brasil.,Faculdade de Ciências Agrárias e Tecnológicas, Universidade Estadual Paulista - UNESP, Campus de Dracena, São Paulo, Brasil
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19
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Torrecilha RBP, Utsunomiya YT, Bosco AM, Almeida BF, Pereira PP, Narciso LG, Pereira DCM, Baptistiolli L, Calvo-Bado L, Courtenay O, Nunes CM, Ciarlini PC. Correlations between peripheral parasite load and common clinical and laboratory alterations in dogs with visceral leishmaniasis. Prev Vet Med 2016; 132:83-87. [PMID: 27664450 DOI: 10.1016/j.prevetmed.2016.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 10/21/2022]
Abstract
Intensity of peripheral parasite infection has an important role in the transmission of Leishmania spp. from one host to another. As parasite load quantification is still an expensive procedure to be used routinely in epidemiological surveillance, the use of surrogate predictors may be an important asset in the identification of dogs with high transmitting ability. The present study examined whether common clinical and laboratory alterations can serve as predictors of peripheral parasitism in dogs naturally infected with Leishmania spp. Thirty-seven dogs were examined in order to establish correlations between parasite load (PL) in multiple peripheral tissues and common clinical and laboratory findings in canine visceral leishmaniasis (CVL). Quantitative polymerase chain reaction was employed to determine PL in conjunctival swabs, ear skin, peripheral blood and buffy coat. Additionally, a series of hematological, biochemical and oxidative stress markers were quantified. Correlations between net peripheral infection and severity of clinical alterations and variation in laboratory parameters were assessed through a new analytical approach, namely Compressed Parasite Load Data (CPLD), which uses dimension reduction techniques from multivariate statistics to summarize PL across tissues into a single variable. The analysis revealed that elevation in PL is positively correlated with severity of clinical sings commonly observed in CVL, such as skin lesions, ophthalmic alterations, onycogriphosis, popliteal lymphadenomegaly and low body mass. Furthermore, increase in PL was found to be followed by intensification of non-regenerative anemia, neutrophilia, eosinopenia, hepatic injury and oxidative imbalance. These results suggest that routinely used clinical and laboratory exams can be predictive of intensity of peripheral parasite infection, which has an important implication in the identification of dogs with high transmitting ability.
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Affiliation(s)
- R B P Torrecilha
- Departamento de Clínica, Cirurgia e Reprodução Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP-Univ Estadual Paulista, Rua Clóvis Pestana 793, Dona Amélia, Araçatuba, SP, 16050-680, Brazil.
| | - Y T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP- Univ Estadual Paulista, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, 14884-900, Brazil
| | - A M Bosco
- Departamento de Clínica, Cirurgia e Reprodução Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP-Univ Estadual Paulista, Rua Clóvis Pestana 793, Dona Amélia, Araçatuba, SP, 16050-680, Brazil
| | - B F Almeida
- Departamento de Clínica, Cirurgia e Reprodução Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP-Univ Estadual Paulista, Rua Clóvis Pestana 793, Dona Amélia, Araçatuba, SP, 16050-680, Brazil
| | - P P Pereira
- Departamento de Clínica, Cirurgia e Reprodução Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP-Univ Estadual Paulista, Rua Clóvis Pestana 793, Dona Amélia, Araçatuba, SP, 16050-680, Brazil
| | - L G Narciso
- Departamento de Clínica, Cirurgia e Reprodução Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP-Univ Estadual Paulista, Rua Clóvis Pestana 793, Dona Amélia, Araçatuba, SP, 16050-680, Brazil
| | - D C M Pereira
- Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP- Univ Estadual Paulista, Rua Clóvis Pestana 793, Dona Amélia, Araçatuba, SP, 16050-680, Brazil
| | - L Baptistiolli
- Departamento de Clínica, Cirurgia e Reprodução Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP-Univ Estadual Paulista, Rua Clóvis Pestana 793, Dona Amélia, Araçatuba, SP, 16050-680, Brazil
| | - L Calvo-Bado
- School of Life Sciences and Warwick Infectious Disease and Epidemiology Research Group (WIDER), Gibbett Hill Road, CV47AL, Coventry, England, UK
| | - O Courtenay
- School of Life Sciences and Warwick Infectious Disease and Epidemiology Research Group (WIDER), Gibbett Hill Road, CV47AL, Coventry, England, UK
| | - C M Nunes
- Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP- Univ Estadual Paulista, Rua Clóvis Pestana 793, Dona Amélia, Araçatuba, SP, 16050-680, Brazil
| | - P C Ciarlini
- Departamento de Clínica, Cirurgia e Reprodução Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP-Univ Estadual Paulista, Rua Clóvis Pestana 793, Dona Amélia, Araçatuba, SP, 16050-680, Brazil.
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20
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Khayatzadeh N, Mészáros G, Utsunomiya YT, Garcia JF, Schnyder U, Gredler B, Curik I, Sölkner J. Locus-specific ancestry to detect recent response to selection in admixed Swiss Fleckvieh cattle. Anim Genet 2016; 47:637-646. [PMID: 27435758 DOI: 10.1111/age.12470] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2016] [Indexed: 01/08/2023]
Abstract
Identification of selection signatures is one of the current endeavors of evolutionary genetics. Admixed populations may be used to infer post-admixture selection. We calculated local ancestry for Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF), to infer such signals. Illumina Bovine SNP50 BeadChip data for 300 admixed, 88 SI and 97 RHF bulls were used. The average RHF ancestry across the whole genome was 0.70. To identify regions with high deviation from average, we considered two significance thresholds, based on a permutation test and extreme deviation from normal distribution. Regions on chromosomes 13 (46.3-47.3 Mb) and 18 (18.7-25.9 Mb) passed both thresholds in the direction of increased SI. Extended haplotype homozygosity within (iHS) and between (Rsb) populations was calculated to explore additional patterns of pre- and post-admixture selection signals. The Rsb score of admixed and SI was significant in a wide region of chromosome 18 (6.6-24.6 Mb) overlapped with one area of strong local ancestry deviation. FTO, with pleiotropic effect on milk and fertility, NOD2 on dairy and NKD1 and SALL1 on fertility traits are located there. Genetic differentiation of RHF and SI (Fst ), an alternative indicator of pre-admixture selection in pure populations, was calculated. No considerable overlap of peaks of local ancestry deviations and Fst was observed. We found two regions with significant signatures of post-admixture selection in this very young composite, applying comparatively stringent significance thresholds. The signals cover relatively large genomic areas and did not allow pinpointing of the gene(s) responsible for the apparent shift in ancestry proportions.
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Affiliation(s)
- N Khayatzadeh
- Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, A-1180, Vienna, Austria
| | - G Mészáros
- Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, A-1180, Vienna, Austria.
| | - Y T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - J F Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil.,Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - U Schnyder
- Qualitas AG, Chamerstrasse 56, CH-6300, Zug, Switzerland
| | - B Gredler
- Qualitas AG, Chamerstrasse 56, CH-6300, Zug, Switzerland
| | - I Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - J Sölkner
- Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, A-1180, Vienna, Austria
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21
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G. T. Pereira A, Utsunomiya YT, Milanesi M, Torrecilha RBP, Carmo AS, Neves HHR, Carvalheiro R, Ajmone-Marsan P, Sonstegard TS, Sölkner J, Contreras-Castillo CJ, Garcia JF. Pleiotropic Genes Affecting Carcass Traits in Bos indicus (Nellore) Cattle Are Modulators of Growth. PLoS One 2016; 11:e0158165. [PMID: 27410030 PMCID: PMC4943724 DOI: 10.1371/journal.pone.0158165] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 06/10/2016] [Indexed: 12/19/2022] Open
Abstract
Two complementary methods, namely Multi-Trait Meta-Analysis and Versatile Gene-Based Test for Genome-wide Association Studies (VEGAS), were used to identify putative pleiotropic genes affecting carcass traits in Bos indicus (Nellore) cattle. The genotypic data comprised over 777,000 single-nucleotide polymorphism markers scored in 995 bulls, and the phenotypic data included deregressed breeding values (dEBV) for weight measurements at birth, weaning and yearling, as well visual scores taken at weaning and yearling for carcass finishing precocity, conformation and muscling. Both analyses pointed to the pleomorphic adenoma gene 1 (PLAG1) as a major pleiotropic gene. VEGAS analysis revealed 224 additional candidates. From these, 57 participated, together with PLAG1, in a network involved in the modulation of the function and expression of IGF1 (insulin like growth factor 1), IGF2 (insulin like growth factor 2), GH1 (growth hormone 1), IGF1R (insulin like growth factor 1 receptor) and GHR (growth hormone receptor), suggesting that those pleiotropic genes operate as satellite regulators of the growth pathway.
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Affiliation(s)
- Anirene G. T. Pereira
- Departamento de Agroindústria, Alimentos e Nutrição, Escola Superior de Agricultura “Luiz de Queiroz”, USP, Piracicaba, Brazil
- International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, São Paulo, Brazil
| | - Yuri T. Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP–Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
- International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, São Paulo, Brazil
| | - Marco Milanesi
- Departamento de Apoio, Produção e Saúde Animal, UNESP—Univ Estadual Paulista, Faculdade de Medicina Veterinária de Araçatuba, Araçatuba, São Paulo, Brazil
- International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, São Paulo, Brazil
| | - Rafaela B. P. Torrecilha
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP–Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
- International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, São Paulo, Brazil
| | - Adriana S. Carmo
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP–Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
- International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, São Paulo, Brazil
| | | | - Roberto Carvalheiro
- Departamento de Zootecnia, UNESP—Univ. Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | | | | | - Johann Sölkner
- BOKU—University of Natural Resources and Life Sciences, Department of Sustainable Agricultural Systems, Division of Livestock Sciences, Vienna, Austria
| | - Carmen J. Contreras-Castillo
- Departamento de Agroindústria, Alimentos e Nutrição, Escola Superior de Agricultura “Luiz de Queiroz”, USP, Piracicaba, Brazil
| | - José F. Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP–Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
- Departamento de Apoio, Produção e Saúde Animal, UNESP—Univ Estadual Paulista, Faculdade de Medicina Veterinária de Araçatuba, Araçatuba, São Paulo, Brazil
- International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, São Paulo, Brazil
- * E-mail:
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22
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Utsunomiya YT, Milanesi M, Utsunomiya ATH, Ajmone-Marsan P, Garcia JF. GHap: an R package for genome-wide haplotyping. Bioinformatics 2016; 32:2861-2. [DOI: 10.1093/bioinformatics/btw356] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/31/2016] [Indexed: 11/13/2022] Open
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23
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Zhou Y, Utsunomiya YT, Xu L, Hay EHA, Bickhart DM, Alexandre PA, Rosen BD, Schroeder SG, Carvalheiro R, de Rezende Neves HH, Sonstegard TS, Van Tassell CP, Ferraz JBS, Fukumasu H, Garcia JF, Liu GE. Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus. BMC Genomics 2016; 17:419. [PMID: 27245577 PMCID: PMC4888316 DOI: 10.1186/s12864-016-2461-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/11/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Apart from single nucleotide polymorphism (SNP), copy number variation (CNV) is another important type of genetic variation, which may affect growth traits and play key roles for the production of beef cattle. To date, no genome-wide association study (GWAS) for CNV and body traits in beef cattle has been reported, so the present study aimed to investigate this type of association in one of the most important cattle subspecies: Bos indicus (Nellore breed). RESULTS We have used intensity data from over 700,000 SNP probes across the bovine genome to detect common CNVs in a sample of 2230 Nellore cattle, and performed GWAS between the detected CNVs and nine growth traits. After filtering for frequency and length, a total of 231 CNVs ranging from 894 bp to 4,855,088 bp were kept and tested as predictors for each growth trait using linear regression analysis with principal components correction. There were 49 significant associations identified among 17 CNVs and seven body traits after false discovery rate correction (P < 0.05). Among the 17 CNVs, three were significant or marginally significant for all the traits. We have compared the locations of associated CNVs with quantitative trait locus and the RefGene database, and found two sets of 9 CNVs overlapping with either known QTLs or genes, respectively. The gene overlapping with CNV100, KCNJ12, is a functional candidate for muscle development and plays critical roles in muscling traits. CONCLUSION This study presents the first CNV-based GWAS of growth traits using high density SNP microarray data in cattle. We detected 17 CNVs significantly associated with seven growth traits and one of them (CNV100) may be involved in growth traits through KCNJ12.
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Affiliation(s)
- Yang Zhou
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.,College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi, 712100, China
| | - Yuri T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil
| | - Lingyang Xu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.,Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - El Hamidi Abdel Hay
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA
| | - Derek M Bickhart
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA
| | - Pamela Almeida Alexandre
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635, Brazil
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA
| | - Roberto Carvalheiro
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil
| | - Haroldo Henrique de Rezende Neves
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.,Present address: Recombinetics, Inc., St Paul, MN, 55104, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635, Brazil
| | - Jose Fernando Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil. .,Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista, Araçatuba, São Paulo, 16050-680, Brazil. .,International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.
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24
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Utsunomiya YT, Ribeiro ÉS, Quintal APN, Sangalli JR, Gazola VR, Paula HB, Trinconi CM, Lima VMF, Perri SHV, Taylor JF, Schnabel RD, Sonstegard TS, Garcia JF, Nunes CM. Genome-Wide Scan for Visceral Leishmaniasis in Mixed-Breed Dogs Identifies Candidate Genes Involved in T Helper Cells and Macrophage Signaling. PLoS One 2015; 10:e0136749. [PMID: 26348501 PMCID: PMC4562658 DOI: 10.1371/journal.pone.0136749] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 08/07/2015] [Indexed: 12/20/2022] Open
Abstract
We conducted a genome-wide scan for visceral leishmaniasis in mixed-breed dogs from a highly endemic area in Brazil using 149,648 single nucleotide polymorphism (SNP) markers genotyped in 20 cases and 28 controls. Using a mixed model approach, we found two candidate loci on canine autosomes 1 and 2. The positional association on chromosome 2 mapped to a predicted DNAse sensitive site in CD14+ monocytes that serve as a cis-regulatory element for the expression of interleukin alpha receptors 2 (IL2RA) and 15 (IL15RA). Both interleukins were previously found to lead to protective T helper 1 cell (Th1) response against Leishmania spp. in humans and mice. The associated marker on chromosome 1 was located between two predicted transcription factor binding sites regulating the expression of the transducin-like enhancer of split 1 gene (TLE1), an important player in Notch signaling. This pathway is critical for macrophage activity and CD4+ T cell differentiation into Th1 and T helper 2. Together, these findings suggest that the human and mouse model for protective response against Leishmania spp., which involves Th1 and macrophage modulation by interleukins 2, 15, gamma interferon and Notch signaling, may also hold for the canine model.
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Affiliation(s)
- Yuri T. Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Érica S. Ribeiro
- Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP—Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - Amanda P. N. Quintal
- Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP—Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - Juliano R. Sangalli
- Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP—Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - Valquiria R. Gazola
- Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP—Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - Henrique B. Paula
- Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP—Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - Cristiana M. Trinconi
- Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP—Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - Valéria M. F. Lima
- Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP—Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - Silvia H. V. Perri
- Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP—Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - Jeremy F. Taylor
- Division of Animal Sciences, University of Missouri, Columbia, 65211, United States of America
| | - Robert D. Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, 65211, United States of America
| | - Tad S. Sonstegard
- Animal Genomics and Improvement Laboratory, ARS-USDA—Agricultural Research Service—United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - José F. Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil
- Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP—Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - Cáris M. Nunes
- Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP—Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
- * E-mail:
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25
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Santana MHA, Ventura RV, Utsunomiya YT, Neves HHR, Alexandre PA, Oliveira Junior GA, Gomes RC, Bonin MN, Coutinho LL, Garcia JF, Silva SL, Fukumasu H, Leme PR, Ferraz JBS. A genomewide association mapping study using ultrasound-scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle. J Anim Breed Genet 2015; 132:420-7. [PMID: 26016521 DOI: 10.1111/jbg.12167] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/11/2015] [Indexed: 01/02/2023]
Abstract
The aim of this study was to identify candidate genes and genomic regions associated with ultrasound-derived measurements of the rib-eye area (REA), backfat thickness (BFT) and rumpfat thickness (RFT) in Nellore cattle. Data from 640 Nellore steers and young bulls with genotypes for 290 863 single nucleotide polymorphisms (SNPs) were used for genomewide association mapping. Significant SNP associations were explored to find possible candidate genes related to physiological processes. Several of the significant markers detected were mapped onto functional candidate genes including ARFGAP3, CLSTN2 and DPYD for REA; OSBPL3 and SUDS3 for BFT; and RARRES1 and VEPH1 for RFT. The physiological pathway related to lipid metabolism (CLSTN2, OSBPL3, RARRES1 and VEPH1) was identified. The significant markers within previously reported QTLs reinforce the importance of the genomic regions, and the other loci offer candidate genes that have not been related to carcass traits in previous investigations.
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Affiliation(s)
- M H A Santana
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Pirassununga, Brazil
| | - R V Ventura
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Pirassununga, Brazil.,Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada.,Beef Improvement Opportunties (BIO), Guelph, ON, Canada
| | - Y T Utsunomiya
- Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, Brazil
| | - H H R Neves
- Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, Brazil.,GenSys Consultores Associados S/C Ltda, Porto Alegre, Brazil
| | - P A Alexandre
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Pirassununga, Brazil
| | - G A Oliveira Junior
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Pirassununga, Brazil
| | - R C Gomes
- Empresa Brasileira de Pesquisa Agropecuária, CNPGC/EMBRAPA, Campo Grande, Brazil
| | - M N Bonin
- Empresa Brasileira de Pesquisa Agropecuária, CNPGC/EMBRAPA, Campo Grande, Brazil
| | - L L Coutinho
- Escola Superior de Agricultura Luiz de Queiroz, USP, Piracicaba, Brazil
| | - J F Garcia
- Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, Brazil
| | - S L Silva
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Pirassununga, Brazil
| | - H Fukumasu
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Pirassununga, Brazil
| | - P R Leme
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Pirassununga, Brazil
| | - J B S Ferraz
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Pirassununga, Brazil
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26
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Santana MHA, Gomes RC, Utsunomiya YT, Neves HHR, Novais FJ, Bonin MN, Fukumasu H, Garcia JF, Alexandre PA, Oliveira Junior GA, Coutinho LL, Ferraz JBS. Genome-wide association with residual body weight gain in Bos indicus cattle. Genet Mol Res 2015; 14:5229-33. [PMID: 26125717 DOI: 10.4238/2015.may.18.14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Weight gain is a key performance trait for beef cat-tle; however, attention should be given to the production costs for better profitability. Therefore, a feed efficiency trait based on per-formance can be an interesting approach to improve performance without increasing food costs. To identify candidate genes and ge-nomic regions associated with residual body weight gain (RWG), we conducted a genome-wide association study (GWAS) with 720 Nellore cattle using the GRAMMAR-Gamma association test. We identified 30 significant single nucleotide polymorphisms (SNPs), especially on chromosomes 2, 8, 12, and 17. Several genes and quantitative train loci (QTLs) present in the regions identified were appointed; we highlight DMRT2 (doublesex and mab-3 related tran-scription factor 2), IFFO2 (intermediate filament family orphan 2), LNX2 (ligand of numb-protein X 2), MTIF3 (mitochondrial transla-tional initiation factor 3), and TRNAG-CCC (transfer RNA glycine anticodon CCC). The metabolic pathways that can explain part of the phenotypic variation in RWG are related to oxidative stress and muscle control.
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Affiliation(s)
- M H A Santana
- Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP, Brasil
| | - R C Gomes
- Empresa Brasileira de Pesquisa Agropecuária, Campo Grande, MS, Brasil
| | - Y T Utsunomiya
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - H H R Neves
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - F J Novais
- Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP, Brasil
| | - M N Bonin
- Empresa Brasileira de Pesquisa Agropecuária, Campo Grande, MS, Brasil
| | - H Fukumasu
- Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP, Brasil
| | - J F Garcia
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - P A Alexandre
- Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP, Brasil
| | | | - L L Coutinho
- Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brasil
| | - J B S Ferraz
- Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP, Brasil
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Mészáros G, Boison SA, Pérez O'Brien AM, Ferenčaković M, Curik I, Da Silva MVB, Utsunomiya YT, Garcia JF, Sölkner J. Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle. Front Genet 2015; 6:173. [PMID: 26074948 PMCID: PMC4443735 DOI: 10.3389/fgene.2015.00173] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 04/20/2015] [Indexed: 11/30/2022] Open
Abstract
Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (FROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated NeROH was 125 (NeROH>16 Mb), 186 (NeROH>8 Mb) and 370 (NeROH>4 Mb) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in NeLD, to 780, 120, and 80 for 100, 10, and 5 generations ago, respectively. Genomic selection was developed for and is working well in large breeds. The same methodology was applied in Tyrol Grey cattle, using different reference populations. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13–0.91 and 0.12–0.63, when estimated breeding values and deregressed breeding values were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being a consequence of low reliabilities of pseudo-phenotypes in the validation set, thus being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds, even if its primary usage differs from that of large breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations.
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Affiliation(s)
- Gábor Mészáros
- Division of Livestock Sciences, University of Natural Resources and Life Sciences Vienna, Austria
| | - Solomon A Boison
- Division of Livestock Sciences, University of Natural Resources and Life Sciences Vienna, Austria
| | - Ana M Pérez O'Brien
- Division of Livestock Sciences, University of Natural Resources and Life Sciences Vienna, Austria
| | | | - Ino Curik
- Department of Animal Science, University of Zagreb Zagreb, Croatia
| | | | | | - Jose F Garcia
- UNESP-Universidade Estadual Paulista Jaboticabal, Brazil
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences Vienna, Austria
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O'Brien AMP, Höller D, Boison SA, Milanesi M, Bomba L, Utsunomiya YT, Carvalheiro R, Neves HHR, da Silva MVB, VanTassell CP, Sonstegard TS, Mészáros G, Ajmone-Marsan P, Garcia F, Sölkner J. Low levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations. Genet Sel Evol 2015; 47:31. [PMID: 25928250 PMCID: PMC4404172 DOI: 10.1186/s12711-015-0109-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 02/27/2015] [Indexed: 11/10/2022] Open
Abstract
Background Nelore and Gir are the two most important indicine cattle breeds for production of beef and milk in Brazil. Historical records state that these breeds were introduced in Brazil from the Indian subcontinent, crossed to local taurine cattle in order to quickly increase the population size, and then backcrossed to the original breeds to recover indicine adaptive and productive traits. Previous investigations based on sparse DNA markers detected taurine admixture in these breeds. High-density genome-wide analyses can provide high-resolution information on the genetic composition of current Nelore and Gir populations, estimate more precisely the levels and nature of taurine introgression, and shed light on their history and the strategies that were used to expand these breeds. Results We used the high-density Illumina BovineHD BeadChip with more than 777 K single nucleotide polymorphisms (SNPs) that were reduced to 697 115 after quality control filtering to investigate the structure of Nelore and Gir populations and seven other worldwide populations for comparison. Multidimensional scaling and model-based ancestry estimation clearly separated the indicine, European taurine and African taurine ancestries. The average level of taurine introgression in the autosomal genome of Nelore and Gir breeds was less than 1% but was 9% for the Brahman breed. Analyses based on the mitochondrial SNPs present in the Illumina BovineHD BeadChip did not clearly differentiate taurine and indicine haplotype groupings. Conclusions The low level of taurine ancestry observed for both Nelore and Gir breeds confirms the historical records of crossbreeding and supports a strong directional selection against taurine haplotypes via backcrossing. Random sampling in production herds across the country and subsequent genotyping would be useful for a more complete view of the admixture levels in the commercial Nelore and Gir populations. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0109-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana M Perez O'Brien
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
| | - Daniela Höller
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
| | - Solomon A Boison
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
| | - Marco Milanesi
- Università Cattolica del Sacro Cuore di Piacenza, Institute of Zootechnica and Biodiversity and Ancient DNA Research Center - BioDNA, Piacenza, Italy.
| | - Lorenzo Bomba
- Università Cattolica del Sacro Cuore di Piacenza, Institute of Zootechnica and Biodiversity and Ancient DNA Research Center - BioDNA, Piacenza, Italy.
| | - Yuri T Utsunomiya
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrária e Veterinárias, Jaboticabal, SP, Brazil.
| | - Roberto Carvalheiro
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrária e Veterinárias, Jaboticabal, SP, Brazil.
| | - Haroldo H R Neves
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrária e Veterinárias, Jaboticabal, SP, Brazil.
| | - Marcos V B da Silva
- Empresa Brasileira de Pesquisa Agropecuária - Embrapa Gado de Leite, Juiz de Fora, MG, Brazil.
| | - Curtis P VanTassell
- United States Department of Agriculture - Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, MD, USA.
| | - Tad S Sonstegard
- United States Department of Agriculture - Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, MD, USA.
| | - Gábor Mészáros
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
| | - Paolo Ajmone-Marsan
- Università Cattolica del Sacro Cuore di Piacenza, Institute of Zootechnica and Biodiversity and Ancient DNA Research Center - BioDNA, Piacenza, Italy.
| | - Fernando Garcia
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrária e Veterinárias, Jaboticabal, SP, Brazil. .,Universidade Estadual Paulista (UNESP) - Faculdade de Medicina Veterinária de Araçatuba, Araçatuba, SP, Brazil.
| | - Johann Sölkner
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
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29
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Utsunomiya YT, Pérez O'Brien AM, Sonstegard TS, Sölkner J, Garcia JF. Genomic data as the "hitchhiker's guide" to cattle adaptation: tracking the milestones of past selection in the bovine genome. Front Genet 2015; 6:36. [PMID: 25713583 PMCID: PMC4322753 DOI: 10.3389/fgene.2015.00036] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/26/2015] [Indexed: 11/13/2022] Open
Abstract
The bovine species have witnessed and played a major role in the drastic socio-economical changes that shaped our culture over the last 10,000 years. During this journey, cattle "hitchhiked" on human development and colonized the world, facing strong selective pressures such as dramatic environmental changes and disease challenge. Consequently, hundreds of specialized cattle breeds emerged and spread around the globe, making up a rich spectrum of genomic resources. Their DNA still carry the scars left from adapting to this wide range of conditions, and we are now empowered with data and analytical tools to track the milestones of past selection in their genomes. In this review paper, we provide a summary of the reconstructed demographic events that shaped cattle diversity, offer a critical synthesis of popular methodologies applied to the search for signatures of selection (SS) in genomic data, and give examples of recent SS studies in cattle. Then, we outline the potential and challenges of the application of SS analysis in cattle, and discuss the future directions in this field.
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Affiliation(s)
- Yuri T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP) Jaboticabal, São Paulo, Brazil
| | - Ana M Pérez O'Brien
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture Beltsville, MA, USA
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU) Vienna, Austria
| | - José F Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP) Jaboticabal, São Paulo, Brazil ; Laboratório de Bioquímica e Biologia Molecular Animal, Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, Universidade Estadual Paulista (UNESP) Araçatuba, São Paulo, Brazil
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Zavarez LB, Utsunomiya YT, Carmo AS, Neves HHR, Carvalheiro R, Ferenčaković M, Pérez O'Brien AM, Curik I, Cole JB, Van Tassell CP, da Silva MVGB, Sonstegard TS, Sölkner J, Garcia JF. Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes. Front Genet 2015; 6:5. [PMID: 25688258 PMCID: PMC4310349 DOI: 10.3389/fgene.2015.00005] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/07/2015] [Indexed: 11/18/2022] Open
Abstract
The use of relatively low numbers of sires in cattle breeding programs, particularly on those for carcass and weight traits in Nellore beef cattle (Bos indicus) in Brazil, has always raised concerns about inbreeding, which affects conservation of genetic resources and sustainability of this breed. Here, we investigated the distribution of autozygosity levels based on runs of homozygosity (ROH) in a sample of 1,278 Nellore cows, genotyped for over 777,000 SNPs. We found ROH segments larger than 10 Mb in over 70% of the samples, representing signatures most likely related to the recent massive use of few sires. However, the average genome coverage by ROH (>1 Mb) was lower than previously reported for other cattle breeds (4.58%). In spite of 99.98% of the SNPs being included within a ROH in at least one individual, only 19.37% of the markers were encompassed by common ROH, suggesting that the ongoing selection for weight, carcass and reproductive traits in this population is too recent to have produced selection signatures in the form of ROH. Three short-range highly prevalent ROH autosomal hotspots (occurring in over 50% of the samples) were observed, indicating candidate regions most likely under selection since before the foundation of Brazilian Nellore cattle. The putative signatures of selection on chromosomes 4, 7, and 12 may be involved in resistance to infectious diseases and fertility, and should be subject of future investigation.
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Affiliation(s)
- Ludmilla B Zavarez
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Yuri T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Adriana S Carmo
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Haroldo H R Neves
- GenSys Consultores Associados Porto Alegre, Rio Grande do Sul, Brazil ; Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Roberto Carvalheiro
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Maja Ferenčaković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb Zagreb, Croatia
| | - Ana M Pérez O'Brien
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU - University of Natural Resources and Life Sciences Vienna, Austria
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb Zagreb, Croatia
| | - John B Cole
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Marcos V G B da Silva
- Bioinformatics and Animal Genomics Laboratory, Embrapa Dairy Cattle Juiz de Fora, Minas Gerais, Brazil
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU - University of Natural Resources and Life Sciences Vienna, Austria
| | - José F Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil ; Laboratório de Bioquímica e Biologia Molecular Animal, Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista Araçatuba, São Paulo, Brazil
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31
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Carvalheiro R, Boison SA, Neves HHR, Sargolzaei M, Schenkel FS, Utsunomiya YT, O'Brien AMP, Sölkner J, McEwan JC, Van Tassell CP, Sonstegard TS, Garcia JF. Accuracy of genotype imputation in Nelore cattle. Genet Sel Evol 2014; 46:69. [PMID: 25927950 PMCID: PMC4192291 DOI: 10.1186/s12711-014-0069-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 09/19/2014] [Indexed: 01/09/2023] Open
Abstract
Background Genotype imputation from low-density (LD) to high-density single nucleotide polymorphism (SNP) chips is an important step before applying genomic selection, since denser chips tend to provide more reliable genomic predictions. Imputation methods rely partially on linkage disequilibrium between markers to infer unobserved genotypes. Bos indicus cattle (e.g. Nelore breed) are characterized, in general, by lower levels of linkage disequilibrium between genetic markers at short distances, compared to taurine breeds. Thus, it is important to evaluate the accuracy of imputation to better define which imputation method and chip are most appropriate for genomic applications in indicine breeds. Methods Accuracy of genotype imputation in Nelore cattle was evaluated using different LD chips, imputation software and sets of animals. Twelve commercial and customized LD chips with densities ranging from 7 K to 75 K were tested. Customized LD chips were virtually designed taking into account minor allele frequency, linkage disequilibrium and distance between markers. Software programs FImpute and BEAGLE were applied to impute genotypes. From 995 bulls and 1247 cows that were genotyped with the Illumina® BovineHD chip (HD), 793 sires composed the reference set, and the remaining 202 younger sires and all the cows composed two separate validation sets for which genotypes were masked except for the SNPs of the LD chip that were to be tested. Results Imputation accuracy increased with the SNP density of the LD chip. However, the gain in accuracy with LD chips with more than 15 K SNPs was relatively small because accuracy was already high at this density. Commercial and customized LD chips with equivalent densities presented similar results. FImpute outperformed BEAGLE for all LD chips and validation sets. Regardless of the imputation software used, accuracy tended to increase as the relatedness between imputed and reference animals increased, especially for the 7 K chip. Conclusions If the Illumina® BovineHD is considered as the target chip for genomic applications in the Nelore breed, cost-effectiveness can be improved by genotyping part of the animals with a chip containing around 15 K useful SNPs and imputing their high-density missing genotypes with FImpute. Electronic supplementary material The online version of this article (doi:10.1186/s12711-014-0069-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roberto Carvalheiro
- UNESP, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, 14884-900, Brazil.
| | - Solomon A Boison
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems BOKU, University of Natural Resources and Life Sciences, Vienna, A-1180, Austria.
| | - Haroldo H R Neves
- UNESP, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, 14884-900, Brazil. .,GenSys Consultores Associados S/C Ltda, Porto Alegre, 90680-000, Brasil.
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G2W1, Canada. .,The Semex Alliance, Guelph, Ontario, Canada.
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G2W1, Canada.
| | - Yuri T Utsunomiya
- UNESP, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, 14884-900, Brazil.
| | - Ana Maria Pérez O'Brien
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems BOKU, University of Natural Resources and Life Sciences, Vienna, A-1180, Austria.
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems BOKU, University of Natural Resources and Life Sciences, Vienna, A-1180, Austria.
| | - John C McEwan
- Centre for Reproduction and Genomics, AgResearch, Invermay, Mosgiel, New Zealand.
| | - Curtis P Van Tassell
- United States Department of Agriculture, Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, MD, 20705, USA.
| | - Tad S Sonstegard
- United States Department of Agriculture, Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, MD, 20705, USA.
| | - José Fernando Garcia
- UNESP, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, 14884-900, Brazil. .,UNESP, Universidad Estadual Paulista, Faculdade de Medicina Veterinária de Araçatuba, Araçatuba, São Paulo, 16050-680, Brazil.
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Pérez O'Brien AM, Utsunomiya YT, Mészáros G, Bickhart DM, Liu GE, Van Tassell CP, Sonstegard TS, Da Silva MVB, Garcia JF, Sölkner J. Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle. Genet Sel Evol 2014; 46:19. [PMID: 24592996 PMCID: PMC4014805 DOI: 10.1186/1297-9686-46-19] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 01/09/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium (LD) patterns. METHODS By comparing the differences in regional LD variation between dairy and beef cattle types, and between indicine and taurine subspecies, we aim at finding signatures of selection for production and adaptation in cattle breeds. The VarLD method was applied to compare the LD variation in the autosomal genome between breeds, including Angus and Brown Swiss, representing taurine breeds, and Nelore and Gir, representing indicine breeds. Genomic regions containing the top 0.01 and 0.1 percentile of signals were characterized using the UMD3.1 Bos taurus genome assembly to identify genes in those regions and compared with previously reported selection signatures and regions with copy number variation. RESULTS For all comparisons, the top 0.01 and 0.1 percentile included 26 and 165 signals and 17 and 125 genes, respectively, including TECRL, BT.23182 or FPPS, CAST, MYOM1, UVRAG and DNAJA1. CONCLUSIONS The VarLD method is a powerful tool to identify differences in linkage disequilibrium between cattle populations and putative signatures of selection with potential adaptive and productive importance.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Johann Sölkner
- University of Natural Resources and Life Sciences, Vienna, Austria.
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Neves HHR, Carvalheiro R, O'Brien AMP, Utsunomiya YT, do Carmo AS, Schenkel FS, Sölkner J, McEwan JC, Van Tassell CP, Cole JB, da Silva MVGB, Queiroz SA, Sonstegard TS, Garcia JF. Accuracy of genomic predictions in Bos indicus (Nellore) cattle. Genet Sel Evol 2014; 46:17. [PMID: 24575732 PMCID: PMC4014866 DOI: 10.1186/1297-9686-46-17] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 02/18/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Nellore cattle play an important role in beef production in tropical systems and there is great interest in determining if genomic selection can contribute to accelerate genetic improvement of production and fertility in this breed. We present the first results of the implementation of genomic prediction in a Bos indicus (Nellore) population. METHODS Influential bulls were genotyped with the Illumina Bovine HD chip in order to assess genomic predictive ability for weight and carcass traits, gestation length, scrotal circumference and two selection indices. 685 samples and 320 238 single nucleotide polymorphisms (SNPs) were used in the analyses. A forward-prediction scheme was adopted to predict the genomic breeding values (DGV). In the training step, the estimated breeding values (EBV) of bulls were deregressed (dEBV) and used as pseudo-phenotypes to estimate marker effects using four methods: genomic BLUP with or without a residual polygenic effect (GBLUP20 and GBLUP0, respectively), a mixture model (Bayes C) and Bayesian LASSO (BLASSO). Empirical accuracies of the resulting genomic predictions were assessed based on the correlation between DGV and dEBV for the testing group. RESULTS Accuracies of genomic predictions ranged from 0.17 (navel at weaning) to 0.74 (finishing precocity). Across traits, Bayesian regression models (Bayes C and BLASSO) were more accurate than GBLUP. The average empirical accuracies were 0.39 (GBLUP0), 0.40 (GBLUP20) and 0.44 (Bayes C and BLASSO). Bayes C and BLASSO tended to produce deflated predictions (i.e. slope of the regression of dEBV on DGV greater than 1). Further analyses suggested that higher-than-expected accuracies were observed for traits for which EBV means differed significantly between two breeding subgroups that were identified in a principal component analysis based on genomic relationships. CONCLUSIONS Bayesian regression models are of interest for future applications of genomic selection in this population, but further improvements are needed to reduce deflation of their predictions. Recurrent updates of the training population would be required to enable accurate prediction of the genetic merit of young animals. The technical feasibility of applying genomic prediction in a Bos indicus (Nellore) population was demonstrated. Further research is needed to permit cost-effective selection decisions using genomic information.
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Affiliation(s)
- Haroldo H R Neves
- UNESP, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900, Brazil.
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Santana MHA, Utsunomiya YT, Neves HHR, Gomes RC, Garcia JF, Fukumasu H, Silva SL, Leme PR, Coutinho LL, Eler JP, Ferraz JBS. Genome-wide association study for feedlot average daily gain in Nellore cattle (Bos indicus). J Anim Breed Genet 2014; 131:210-6. [PMID: 24906027 DOI: 10.1111/jbg.12084] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 01/23/2014] [Indexed: 02/05/2023]
Abstract
The genome-wide association study (GWAS) results are presented for average daily gain (ADG) in Nellore cattle. Phenotype of 720 male Bos indicus animals with information of ADG in feedlots and 354,147 single-nucleotide polymorphisms (SNPs) obtained from a database added by information from Illumina Bovine HD (777,962 SNPs) and Illumina BovineSNP50 (54,609) by imputation were used. After quality control and imputation, 290,620 SNPs remained in the association analysis, using R package Genome-wide Rapid Association using Mixed Model and Regression method GRAMMAR-Gamma. A genomic region with six significant SNPs, at Bonferroni-corrected significance, was found on chromosome 3. The most significant SNP (rs42518459, BTA3: 85849977, p = 9.49 × 10(-8)) explained 5.62% of the phenotypic variance and had the allele substitution effect of -0.269 kg/day. Important genes such as PDE4B, LEPR, CYP2J2 and FGGY are located near this region, which is overlapped by 12 quantitative trait locus (QTLs) described for several production traits. Other regions with markers with suggestive effects were identified in BTA6 and BTA10. This study showed regions with major effects on ADG in Bos indicus in feedlots. This information may be useful to increase the efficiency of selecting this trait and to understand the physiological processes involved in its regulation.
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Affiliation(s)
- M H A Santana
- Faculdade de Zootecnia e Engenharia de Alimentos, USP - Univ. de São Paulo, Pirassununga, Brazil
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Santana MHA, Utsunomiya YT, Neves HHR, Gomes RC, Garcia JF, Fukumasu H, Silva SL, Oliveira Junior GA, Alexandre PA, Leme PR, Brassaloti RA, Coutinho LL, Lopes TG, Meirelles FV, Eler JP, Ferraz JBS. Genome-wide association analysis of feed intake and residual feed intake in Nellore cattle. BMC Genet 2014; 15:21. [PMID: 24517472 PMCID: PMC3925773 DOI: 10.1186/1471-2156-15-21] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 02/04/2014] [Indexed: 11/30/2022] Open
Abstract
Background Feed intake plays an important economic role in beef cattle, and is related with feed efficiency, weight gain and carcass traits. However, the phenotypes collected for dry matter intake and feed efficiency are scarce when compared with other measures such as weight gain and carcass traits. The use of genomic information can improve the power of inference of studies on these measures, identifying genomic regions that affect these phenotypes. This work performed the genome-wide association study (GWAS) for dry matter intake (DMI) and residual feed intake (RFI) of 720 Nellore cattle (Bos taurus indicus). Results In general, no genomic region extremely associated with both phenotypic traits was observed, as expected for the variables that have their regulation controlled by many genes. Three SNPs surpassed the threshold for the Bonferroni multiple test for DMI and two SNPs for RFI. These markers are located on chromosomes 4, 8, 14 and 21 in regions near genes regulating appetite and ion transport and close to important QTL as previously reported to RFI and DMI, thus corroborating the literature that points these two processes as important in the physiological regulation of intake and feed efficiency. Conclusions This study showed the first GWAS of DMI to identify genomic regions associated with feed intake and efficiency in Nellore cattle. Some genes and QTLs previously described for DMI and RFI, in other subspecies (Bos taurus taurus), that influences these phenotypes are confirmed in this study.
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Affiliation(s)
- Miguel H A Santana
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Av, Duque de Caxias Norte, 225, 13635-900 Pirassununga, São Paulo, Brazil.
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Porto-Neto LR, Sonstegard TS, Liu GE, Bickhart DM, Da Silva MVB, Machado MA, Utsunomiya YT, Garcia JF, Gondro C, Van Tassell CP. Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping. BMC Genomics 2013; 14:876. [PMID: 24330634 PMCID: PMC4046821 DOI: 10.1186/1471-2164-14-876] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 12/05/2013] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Natural selection has molded evolution across all taxa. At an arguable date of around 330,000 years ago there were already at least two different types of cattle that became ancestors of nearly all modern cattle, the Bos taurus taurus more adapted to temperate climates and the tropically adapted Bos taurus indicus. After domestication, human selection exponentially intensified these differences. To better understand the genetic differences between these subspecies and detect genomic regions potentially under divergent selection, animals from the International Bovine HapMap Experiment were genotyped for over 770,000 SNP across the genome and compared using smoothed F(ST). The taurine sample was represented by ten breeds and the contrasting zebu cohort by three breeds. RESULTS Each cattle group evidenced similar numbers of polymorphic markers well distributed across the genome. Principal components analyses and unsupervised clustering confirmed the well-characterized main division of domestic cattle. The top 1% smoothed F(ST), potentially associated to positive selection, contained 48 genomic regions across 17 chromosomes. Nearly half of the top F(ST) signals (n = 22) were previously detected using a lower density SNP assay. Amongst the strongest signals were the BTA7:~50 Mb and BTA14:~25 Mb; both regions harboring candidate genes and different patterns of linkage disequilibrium that potentially represent intrinsic differences between cattle types. The bottom 1% of the smoothed F(ST) values, potentially associated to balancing selection, included 24 regions across 13 chromosomes. These regions often overlap with copy number variants, including the highly variable region at BTA23:~24 Mb that harbors a large number of MHC genes. Under these regions, 318 unique Ensembl genes are annotated with a significant overrepresentation of immune related pathways. CONCLUSIONS Genomic regions that are potentially linked to purifying or balancing selection processes in domestic cattle were identified. These regions are of particular interest to understand the natural and human selective pressures to which these subspecies were exposed to and how the genetic background of these populations evolved in response to environmental challenges and human manipulation.
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Affiliation(s)
- Laercio R Porto-Neto
- Animal Genetics Laboratory, The University of Queensland, School of Veterinary Science, Gatton, QLD 4343, Australia.
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Utsunomiya YT, do Carmo AS, Carvalheiro R, Neves HHR, Matos MC, Zavarez LB, Pérez O'Brien AM, Sölkner J, McEwan JC, Cole JB, Van Tassell CP, Schenkel FS, da Silva MVGB, Porto Neto LR, Sonstegard TS, Garcia JF. Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height. BMC Genet 2013; 14:52. [PMID: 23758625 PMCID: PMC3683327 DOI: 10.1186/1471-2156-14-52] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 06/05/2013] [Indexed: 12/30/2022] Open
Abstract
Background Birth weight (BW) is an economically important trait in beef cattle, and is associated with growth- and stature-related traits and calving difficulty. One region of the cattle genome, located on Bos primigenius taurus chromosome 14 (BTA14), has been previously shown to be associated with stature by multiple independent studies, and contains orthologous genes affecting human height. A genome-wide association study (GWAS) for BW in Brazilian Nellore cattle (Bos primigenius indicus) was performed using estimated breeding values (EBVs) of 654 progeny-tested bulls genotyped for over 777,000 single nucleotide polymorphisms (SNPs). Results The most significant SNP (rs133012258, PGC = 1.34 × 10-9), located at BTA14:25376827, explained 4.62% of the variance in BW EBVs. The surrounding 1 Mb region presented high identity with human, pig and mouse autosomes 8, 4 and 4, respectively, and contains the orthologous height genes PLAG1, CHCHD7, MOS, RPS20, LYN, RDHE2 (SDR16C5) and PENK. The region also overlapped 28 quantitative trait loci (QTLs) previously reported in literature by linkage mapping studies in cattle, including QTLs for birth weight, mature height, carcass weight, stature, pre-weaning average daily gain, calving ease, and gestation length. Conclusions This study presents the first GWAS applying a high-density SNP panel to identify putative chromosome regions affecting birth weight in Nellore cattle. These results suggest that the QTLs on BTA14 associated with body size in taurine cattle (Bos primigenius taurus) also affect birth weight and size in zebu cattle (Bos primigenius indicus).
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Affiliation(s)
- Yuri T Utsunomiya
- Faculdade de Medicina Veterinária de Araçatuba, Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
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Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Câmara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FSL, Lau LPL, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CTA, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JGR, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJM, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL, Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo ARR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IKFDM, de Oliveira CJF, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JCM, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, Moré DD, Muntean CT, Nandakumar HP, Nogueira MFG, Olsaker I, Pant SD, Panzitta F, Pastor RCP, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BPVL, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH, White SN, Wilming LG, Wunderlich KR, Yang J, Zhao FQ. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 2009; 324:522-8. [PMID: 19390049 DOI: 10.1126/science.1169588] [Citation(s) in RCA: 806] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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