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Värv S, Põlluäär T, Sild E, Viinalass H, Kaart T. Genetic Variation and Composition of Two Commercial Estonian Dairy Cattle Breeds Assessed by SNP Data. Animals (Basel) 2024; 14:1101. [PMID: 38612340 PMCID: PMC11010984 DOI: 10.3390/ani14071101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
The aims of this study were to assess the genomic relatedness of Estonian and selected European dairy cattle breeds and to examine the within-breed diversity of two Estonian dairy breeds using genome-wide SNP data. This study was based on a genotyped heifer population of the Estonian Red (ER) and Estonian Holstein (EH) breeds, including about 10% of all female cattle born in 2017-2020 (sample sizes n = 215 and n = 2265, respectively). The within-breed variation study focused on the level of inbreeding using the ROH-based inbreeding coefficient. The genomic relatedness analyses were carried out among two Estonian and nine European breeds from the WIDDE database. Admixture analysis revealed the heterogeneity of ER cattle with a mixed pattern showing several ancestral populations containing a relatively low proportion (1.5-37.0%) of each of the reference populations used. There was a higher FROH in EH (FROH = 0.115) than in ER (FROH = 0.044). Compared to ER, the long ROHs of EH indicated more closely related parents. The paternal origin of the genetic material used in breeding had a low effect on the inbreeding level. However, among EH, the highest genomic inbreeding was estimated in daughters of USA-born sires.
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Affiliation(s)
- Sirje Värv
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 1, 51006 Tartu, Estonia; (T.P.); (E.S.); (H.V.)
| | | | | | | | - Tanel Kaart
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 1, 51006 Tartu, Estonia; (T.P.); (E.S.); (H.V.)
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Hu M, Jiang H, Lai W, Shi L, Yi W, Sun H, Chen C, Yuan B, Yan S, Zhang J. Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array. Animals (Basel) 2023; 13:ani13101717. [PMID: 37238146 DOI: 10.3390/ani13101717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/13/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
Chinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region. However, the population structure and the genetic basis of prominent characteristics of CRS are still unknown. In this study, we systematically describe their population structure, genetic diversity, and selection signature based on genotyping data from 61 CRS individuals with GGP Bovine 100 K chip. The results showed that CRS cattle had low inbreeding levels and had formed a unique genetic structure feature. Using two complementary methods (including comprehensive haplotype score and complex likelihood ratio), we identified 1291 and 1285 potentially selected genes, respectively. There were 141 genes annotated in common 106 overlapping genomic regions covered 5.62 Mb, including PLAG1, PRKG2, DGAT1, PARP10, TONSL, ADCK5, and BMP3, most of which were enriched in pathways related to muscle growth and differentiation, milk production, and lipid metabolism. This study will contribute to understanding the genetic mechanism behind artificial selection and give an extensive reference for subsequent breeding.
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Affiliation(s)
- Mingyue Hu
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Hao Jiang
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Weining Lai
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Lulu Shi
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Wenfeng Yi
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Hao Sun
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Chengzhen Chen
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Bao Yuan
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Shouqing Yan
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Jiabao Zhang
- College of Animal Science, Jilin University, Changchun 130062, China
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Genetic Architecture and Signatures of Selection in the Caqueteño Creole (Colombian Native Cattle). DIVERSITY 2022. [DOI: 10.3390/d14100828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Evolutionary mechanisms have shaped the genomic architecture of Colombian Creole cattle breeds. The mating and selection processes have impacted several traits, promoting differences within and between populations. Studies of population structure and selection signatures in Colombian Creole breeds are scarce, and need more attention to better understand genetic differentiation, gene flow, and genetic distance. This study aimed to analyze the population structure and identify selection imprints in the Criollo Caqueteño (CAQ) population. It used 127 CAQ animals genotyped with Chip HD 777,000 SNPs. The population structure analyses used discriminant principal component analysis (DAPC), integrated haplotype scoring (iHS), and index-fixing (Fst) methodologies to detect selection signals. We can highlight SNP regions on the genes TMPRSS15, PGAM2, and EGFR, identified by the Fst method. Additionally, the iHS regions for cluster 1 identified candidate genes on BTA 3 (CMPK1 and FOXD2), BTA 11 (RCAN1), and BTA 22 (ARPP21). In group 2, we can highlight the genes on BTA 4 (SLC13A4, BRAF), BTA 9 (ULBP), BTA 14 (CSMD3) and BTA 19 (KRTAP9-2). These candidate genes have been associated with fertility traits, precocity, growth, and environmental and disease resistance, indicating a genetic potential in CAQ animals. All this promotes a better understanding of the diversity and genetic structure in the CAQ population. Based on that, our study can significantly assist the sustainable development and conservation of the breed in the Colombian Amazon.
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Guan X, Zhao S, Xiang W, Jin H, Chen N, Lei C, Jia Y, Xu L. Genetic Diversity and Selective Signature in Dabieshan Cattle Revealed by Whole-Genome Resequencing. BIOLOGY 2022; 11:biology11091327. [PMID: 36138806 PMCID: PMC9495734 DOI: 10.3390/biology11091327] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/07/2022] [Accepted: 09/04/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary To protect the genetic resources of Chinese native cattle breeds, we investigated the genetic structure, genetic diversity and genetic signature from artificial or natural selection by sequencing 32 bovine genomes from the breeding farm of the Dabieshan population. We discovered that the ancestral contributions of Dabieshan originated from Chinese indicine and East Asian taurine on the autosomal genome, which had abundant genomic diversity. Some candidate genes associated with fertility, feed efficiency, fat deposition, immune response, heat resistance and the coat color were identified by a selective sweep. The SNPs data were based on genomics, which could establish a foundation for breed amelioration and support conservation for indigenous cattle breeds. Abstract Dabieshan cattle are a typical breed of southern Chinese cattle that have the characteristics of muscularity, excellent meat quality and tolerance to temperature and humidity. Based on 148 whole-genome data, our analysis disclosed the ancestry components of Dabieshan cattle with Chinese indicine (0.857) and East Asian taurine (0.139). The Dabieshan genome demonstrated a higher genomic diversity compared with the other eight populations, supported by the observed nucleotide diversity, linkage disequilibrium decay and runs of homozygosity. The candidate genes were detected by a selective sweep, which might relate to the fertility (GPX5, GPX6), feed efficiency (SLC2A5), immune response (IGLL1, BOLA-DQA2, BOLA-DQB), heat resistance (DnaJC1, DnaJC13, HSPA4), fat deposition (MLLT10) and the coat color (ASIP). We also identified the “East Asian taurine-like” segments in Dabieshan cattle, which might contribute to meat quality traits. The results revealed by the unique and valuable genomic data can build a foundation for the genetic improvement and conservation of genetic resources for indigenous cattle breeds.
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Affiliation(s)
- Xiwen Guan
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Shuanping Zhao
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Weixuan Xiang
- School of Biological Science, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Hai Jin
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Yutang Jia
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Lei Xu
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Correspondence: ; Tel.: +86-153-7547-2704
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Genome-Wide Associative Study of Phenotypic Parameters of the 3D Body Model of Aberdeen Angus Cattle with Multiple Depth Cameras. Animals (Basel) 2022; 12:ani12162128. [PMID: 36009718 PMCID: PMC9405194 DOI: 10.3390/ani12162128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/14/2022] [Accepted: 08/17/2022] [Indexed: 12/21/2022] Open
Abstract
Simple Summary This article aims to develop a new approach to the lifetime evaluation of cattle by 3-D visualization of economic-biological and genetic features. The following indicators were selected as phenotypic features: chest width and chest girth retrieved by 3-D model and meat output on the bones. Correlation analysis showed a reliable positive relationship between chest width and meat output on the bones, which can potentially be used for lifetime evaluation of meat productivity of animals. Genome-wide associations analysis revealed the following potential loci of quantitative traits on cattle chromosomes for chest width, chest girth, and meat output on bones. Abstract In beef cattle breeding, genome-wide association studies (GWAS) using single nucleotide polymorphisms (SNPs) arrays can reveal many loci of various production traits, such as growth, productivity, and meat quality. With the development of genome sequencing technologies, new opportunities are opening up for more accurate identification of areas associated with these traits. This article aims to develop a novel approach to the lifetime evaluation of cattle by 3-D visualization of economic-biological and genetic features. The purpose of this study was to identify significant variants underlying differences in the qualitative characteristics of meat, using imputed data on the sequence of the entire genome. Samples of biomaterial of young Aberdeen-Angus breed cattle (n = 96) were the material for carrying out genome-wide SNP genotyping. Genotyping was performed using a high-density DNA chip Bovine GPU HD BeadChip (Illumina Inc., San Diego, CA, USA), containing ~150 thousand SNPs. The following indicators were selected as phenotypic features: chest width and chest girth retrieved by 3-D model and meat output on the bones. Correlation analysis showed a reliable positive relationship between chest width and meat output on the bones, which can potentially be used for lifetime evaluation of meat productivity of animals.
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Oldenbroek JK, Windig JJ. Opportunities of Genomics for the Use of Semen Cryo-Conserved in Gene Banks. Front Genet 2022; 13:907411. [PMID: 35938018 PMCID: PMC9350965 DOI: 10.3389/fgene.2022.907411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Shortly after the introduction of cryo-conserved semen in the main farm animal species, gene banks were founded. Safeguarding farm animal genetic diversity for future use was and is the main objective. A sampling of sires was based on their pedigree and phenotypic information. Nowadays, DNA information from cryo-conserved sires and from animals in the living populations has become available. The combination of their DNA information can be used to realize three opportunities: 1) to make the gene bank a more complete archive of genetic diversity, 2) to determine the history of the genetic diversity from the living populations, and 3) to improve the performance and genetic diversity of living populations. These three opportunities for the use of gene bank sires in the genomic era are outlined in this study, and relevant recent literature is summarized to illustrate the great value of a gene bank as an archive of genetic diversity.
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Beckman AK, Richey BMS, Rosenthal GG. Behavioral responses of wild animals to anthropogenic change: insights from domestication. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03205-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Hauser M, Signer-Hasler H, Küttel L, Capitan A, Guldbrandtsen B, Hinrichs D, Flury C, Seefried FR, Drögemüller C. Identification of two new recessive MC1R alleles in red-coloured Evolèner cattle and other breeds. Anim Genet 2022; 53:427-435. [PMID: 35451516 PMCID: PMC9373916 DOI: 10.1111/age.13206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/01/2022] [Accepted: 04/09/2022] [Indexed: 11/27/2022]
Abstract
Sequence variations in the melanocortin-1 receptor (MC1R) gene are associated with melanism in different animal species. Six functionally relevant alleles have been described in cattle to date. In a hypothesis-free approach we performed a genome-wide allelic association study with black, red and wild-coloured cattle of three Alpine cattle breeds (Eringer, Evolèner and Valdostana), revealing a single significant association signal close to the MC1R gene. We searched for candidate causative variants by sequencing the entire coding sequence and identified two novel protein-changing variants. We propose designating the mutant alleles at MC1R:c.424C>T as ev1 and at MC1R:c.263G>A as ev2 . Both affect conserved amino acid residues in functionally important transmembrane domains (p.Arg142Cys and p.Ser88Asn). Both alleles segregate predominantly in the Swiss Evolèner breed. They occur in other European cattle breeds such as Abondance and Rotes Höhenvieh as well. We observed almost perfect association between the MC1R genotypes and the coat colour phenotype in a cohort of 513 black, red and wild-coloured cattle. Animals carrying two copies of MC1R loss-of-function alleles or that were compound heterozygous for e, ev1 , or ev2 have a red to dark red (chestnut-like red) coat colour. These findings expand the spectrum of causal MC1R variants causing recessive red in cattle.
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Affiliation(s)
- Miriam Hauser
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Heidi Signer-Hasler
- School of Agricultural, Forest and Food Sciences (HAFL), Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Luzia Küttel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Aurélien Capitan
- ALLICE, Paris, France.,INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Bernt Guldbrandtsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Dirk Hinrichs
- Department of Animal Breeding, Faculty of Organic Agricultural Sciences, University of Kassel, Witzenhausen, Germany
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences (HAFL), Bern University of Applied Sciences, Zollikofen, Switzerland
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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Schiavo G, Bovo S, Ribani A, Moscatelli G, Bonacini M, Prandi M, Mancin E, Mantovani R, Dall'Olio S, Fontanesi L. Comparative analysis of inbreeding parameters and runs of homozygosity islands in 2 Italian autochthonous cattle breeds mainly raised in the Parmigiano-Reggiano cheese production region. J Dairy Sci 2021; 105:2408-2425. [PMID: 34955250 DOI: 10.3168/jds.2021-20915] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/25/2021] [Indexed: 01/19/2023]
Abstract
Reggiana and Modenese are autochthonous cattle breeds, reared in the North of Italy, that can be mainly distinguished for their standard coat color (Reggiana is red, whereas Modenese is white with some pale gray shades). Almost all milk produced by these breeds is transformed into 2 mono-breed branded Parmigiano-Reggiano cheeses, from which farmers receive the economic incomes needed for the sustainable conservation of these animal genetic resources. After the setting up of their herd books in 1960s, these breeds experienced a strong reduction in the population size that was subsequently reverted starting in the 1990s (Reggiana) or more recently (Modenese) reaching at present a total of about 2,800 and 500 registered cows, respectively. Due to the small population size of these breeds, inbreeding is a very important cause of concern for their conservation programs. Inbreeding is traditionally estimated using pedigree data, which are summarized in an inbreeding coefficient calculated at the individual level (FPED). However, incompleteness of pedigree information and registration errors can affect the effectiveness of conservation strategies. High-throughput SNP genotyping platforms allow investigation of inbreeding using genome information that can overcome the limits of pedigree data. Several approaches have been proposed to estimate genomic inbreeding, with the use of runs of homozygosity (ROH) considered to be the more appropriate. In this study, several pedigree and genomic inbreeding parameters, calculated using the whole herd book populations or considering genotyping information (GeneSeek GGP Bovine 150K) from 1,684 Reggiana cattle and 323 Modenese cattle, were compared. Average inbreeding values per year were used to calculate effective population size. Reggiana breed had generally lower genomic inbreeding values than Modenese breed. The low correlation between pedigree-based and genomic-based parameters (ranging from 0.187 to 0.195 and 0.319 to 0.323 in the Reggiana and Modenese breeds, respectively) reflected the common problems of local populations in which pedigree records are not complete. The high proportion of short ROH over the total number of ROH indicates no major recent inbreeding events in both breeds. ROH islands spread over the genome of the 2 breeds (15 in Reggiana and 14 in Modenese) identified several signatures of selection. Some of these included genes affecting milk production traits, stature, body conformation traits (with a main ROH island in both breeds on BTA6 containing the ABCG2, NCAPG, and LCORL genes) and coat color (on BTA13 in Modenese containing the ASIP gene). In conclusion, this work provides an extensive comparative analysis of pedigree and genomic inbreeding parameters and relevant genomic information that will be useful in the conservation strategies of these 2 iconic local cattle breeds.
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Affiliation(s)
- Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Giulia Moscatelli
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Massimo Bonacini
- Associazione Nazionale Allevatori Bovini di Razza Reggiana (ANABORARE), Via Masaccio 11, 42124 Reggio Emilia, Italy
| | - Marco Prandi
- Associazione Nazionale Allevatori Bovini di Razza Reggiana (ANABORARE), Via Masaccio 11, 42124 Reggio Emilia, Italy
| | - Enrico Mancin
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - Stefania Dall'Olio
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy.
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Häfliger IM, Seefried FR, Spengeler M, Drögemüller C. Mining massive genomic data of two Swiss Braunvieh cattle populations reveals six novel candidate variants that impair reproductive success. Genet Sel Evol 2021; 53:95. [PMID: 34915862 PMCID: PMC8675516 DOI: 10.1186/s12711-021-00686-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/26/2021] [Indexed: 11/30/2022] Open
Abstract
Background This study was carried out on the two Braunvieh populations reared in Switzerland, the dairy Brown Swiss (BS) and the dual-purpose Original Braunvieh (OB). We performed a genome-wide analysis of array data of trios (sire, dam, and offspring) from the routine genomic selection to identify candidate regions showing missing homozygosity and phenotypic associations with five fertility, ten birth, and nine growth-related traits. In addition, genome-wide single SNP regression studies based on 114,890 single nucleotide polymorphisms (SNPs) for each of the two populations were performed. Furthermore, whole-genome sequencing data of 430 cattle including 70 putative haplotype carriers were mined to identify potential candidate variants that were validated by genotyping the current population using a custom array. Results Using a trio-based approach, we identified 38 haplotype regions for BS and five for OB that segregated at low to moderate frequencies. For the BS population, we confirmed two known haplotypes, BH1 and BH2. Twenty-four variants that potentially explained the missing homozygosity and associated traits were detected, in addition to the previously reported TUBD1:p.His210Arg variant associated with BH2. For example, for BS we identified a stop-gain variant (p.Arg57*) in the MRPL55 gene in the haplotype region on chromosome 7. This region is associated with the ‘interval between first and last insemination’ trait in our data, and the MRPL55 gene is known to be associated with early pregnancy loss in mice. In addition, we discuss candidate missense variants in the CPT1C, MARS2, and ACSL5 genes for haplotypes mapped in BS. In OB, we highlight a haplotype region on chromosome 19, which is potentially caused by a frameshift variant (p.Lys828fs) in the LIG3 gene, which is reported to be associated with early embryonic lethality in mice. Furthermore, we propose another potential causal missense variant in the TUBGCP5 gene for a haplotype mapped in OB. Conclusions We describe, for the first time, several haplotype regions that segregate at low to moderate frequencies and provide evidence of causality by trait associations in the two populations of Swiss Braunvieh. We propose a list of six protein-changing variants as potentially causing missing homozygosity. These variants need to be functionally validated and incorporated in the breeding program. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00686-3.
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Affiliation(s)
- Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
| | | | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland
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Trujano-Chavez MZ, Sánchez-Ramos R, Pérez-Rodríguez P, Ruíz-Flores A. Genetic Diversity and Population Structure for Resistance and Susceptibility to Mastitis in Braunvieh Cattle. Vet Sci 2021; 8:vetsci8120329. [PMID: 34941856 PMCID: PMC8707377 DOI: 10.3390/vetsci8120329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/05/2021] [Accepted: 12/12/2021] [Indexed: 11/18/2022] Open
Abstract
Mastitis is a disease that causes significant economic losses, since resistance to mastitis is a difficult trait to be improved due to its multifactorial occurrence. Therefore, our objective was to characterize a Mexican Braunvieh cattle population for genetic resistance and susceptibility to mastitis. We used 66 SNP markers for 45 candidate genes in 150 animals. The average heterozygosity was 0.445 ± 0.076, a value higher than those reported for some European breeds. The inbreeding coefficient was slightly negative for resistance to subclinical (−0.058 ± 0.055) and clinical (−0.034 ± 0.076) mastitis, possibly due to low selection for the immunological candidate genes that influence these traits. The genotypic profiles for the candidate loci per K-means group were obtained, as well as the group distribution through the graphics of the principal component analysis. The genotypic profiles showed high genetic diversity among groups. Resistance to clinical mastitis had the lowest presence of the heterozygous genotypes. Although the percentage of highly inbred animals (>50%) is up to 13.3%, there are highly heterozygous groups in terms of the studied traits, a favorable indicator of the presence of genetic diversity. The results of this study constitute evidence of the genetic potential of the Mexican Braunvieh population to improve mastitis-related traits.
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Affiliation(s)
- Mitzilin Zuleica Trujano-Chavez
- Posgrado en Producción Animal, Universidad Autónoma Chapingo, Carretera Federal México-Texcoco Km 38.5, Texcoco 56227, Estado de México, Mexico;
| | - Reyna Sánchez-Ramos
- Recursos Genéticos y Productividad, Colegio de Postgraduados, Carretera Federal México-Texcoco Km 36.5, Texcoco 56230, Estado de México, Mexico;
| | - Paulino Pérez-Rodríguez
- Socio Economía Estadística e Informática-Estadística, Colegio de Postgraduados, Carretera Federal México-Texcoco Km 36.5, Texcoco 56230, Estado de México, Mexico;
| | - Agustín Ruíz-Flores
- Posgrado en Producción Animal, Universidad Autónoma Chapingo, Carretera Federal México-Texcoco Km 38.5, Texcoco 56227, Estado de México, Mexico;
- Correspondence: ; Tel.: +52-595-952-1621
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Häfliger IM, Seefried FR, Drögemüller C. Reverse Genetic Screen for Deleterious Recessive Variants in the Local Simmental Cattle Population of Switzerland. Animals (Basel) 2021; 11:3535. [PMID: 34944310 PMCID: PMC8698008 DOI: 10.3390/ani11123535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/05/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022] Open
Abstract
We herein report the result of a large-scale reverse genetic screen in the Swiss Simmental population, a local dual-purpose cattle breed. We aimed to detect possible recessively inherited variants affecting protein-coding genes, as such deleterious variants can impair fertility and rearing success significantly. We used 115,000 phased SNP data of almost 10 thousand cattle with pedigree data. This revealed evidence for 11 genomic regions of 1.17 Mb on average, with haplotypes (SH1 to SH11) showing a significant depletion in homozygosity and an allele frequency between 3.2 and 10.6%. For the proposed haplotypes, it was unfortunately not possible to evaluate associations with fertility traits as no corresponding data were available. For each haplotype region, possible candidate genes were listed based on their known function in development and disease. Subsequent mining of single-nucleotide variants and short indels in the genomes of 23 sequenced haplotype carriers allowed us to identify three perfectly linked candidate causative protein-changing variants: a SH5-related DIS3:p.Ile678fs loss-of-function variant, a SH8-related CYP2B6:p.Ile313Asn missense variant, and a SH9-related NUBPL:p.Ser143Tyr missense variant. None of these variants occurred in homozygous state in any of more than 5200 sequenced cattle of various breeds. Selection against these alleles in order to reduce reproductive failure and animal loss is recommended.
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Affiliation(s)
- Irene M. Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
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13
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CNGB3 Missense Variant Causes Recessive Achromatopsia in Original Braunvieh Cattle. Int J Mol Sci 2021; 22:ijms222212440. [PMID: 34830323 PMCID: PMC8620519 DOI: 10.3390/ijms222212440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
Sporadic occurrence of inherited eye disorders has been reported in cattle but so far pathogenic variants were found only for rare forms of cataract but not for retinopathies. The aim of this study was to characterize the phenotype and the genetic aetiology of a recessive form of congenital day-blindness observed in several cases of purebred Original Braunvieh cattle. Electroretinography in an affected calf revealed absent cone-mediated function, whereas the rods continue to function normally. Brain areas involved in vision were morphologically normal. When targeting cones by immunofluorescence, a decrease in cone number and an accumulation of beta subunits of cone cyclic-nucleotide gated channel (CNGB3) in the outer plexiform layer of affected animals was obvious. Achromatopsia is a monogenic Mendelian disease characterized by the loss of cone photoreceptor function resulting in day-blindness, total color-blindness, and decreased central visual acuity. After SNP genotyping and subsequent homozygosity mapping with twelve affected cattle, we performed whole-genome sequencing and variant calling of three cases. We identified a single missense variant in the bovine CNGB3 gene situated in a ~2.5 Mb homozygous genome region on chromosome 14 shared between all cases. All affected cattle were homozygous carriers of the p.Asp251Asn mutation that was predicted to be deleterious, affecting an evolutionary conserved residue. In conclusion, we have evidence for the occurrence of a breed-specific novel CNGB3-related form of recessively inherited achromatopsia in Original Braunvieh cattle which we have designated OH1 showing an allele frequency of the deleterious allele of ~8%. The identification of carriers will enable selection against this inherited disorder. The studied cattle might serve as an animal model to further elucidate the function of CNGB3 in mammals.
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14
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Hajihosseinlo A, Nejati-Javaremi A, Miraei-Ashtiani SR. Genetic structure analysis in several populations of cattle using SNP genotypes. Anim Biotechnol 2021; 34:288-300. [PMID: 34591729 DOI: 10.1080/10495398.2021.1960360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Parameters such as effective population size (Ne), runs of homozygosity (ROH), and inbreeding based on ROH (FROH) can give new insight into the level of genetic diversity for the population under selection. This research aimed to measure the extent of linkage disequilibrium (LD), effective population size (Ne), Haplotype Block Structure, and runs of homozygosity (ROHs) in several populations of cattle using SNP genotypes. In this study, that the average r2 decreased with the increasing distance of SNP pairs. A general decrease in Ne can be seen for all four populations, indicating a loss of genetic diversity. The Iranian Holstein had the lowest level of genomic inbreeding at an ROH of 1, 5, 10 Mb, while the French Holstein had the highest. The maximum number of ROH is seen at a distance of less than 1 Mb, and the lowest number of ROH is seen at a distance of 10 Mb. The number of ROH decreases with increasing distance due to the increased recombination rate. This is a concern as an increase in inbreeding leads to a reduction in the effective population size, which was also evident in the study populations.
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Affiliation(s)
- Abbas Hajihosseinlo
- Department of Animal Science, University of Tehran Aras International Campus, Jolfa, Iran
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15
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Upadhyay M, Derks MFL, Andersson G, Medugorac I, Groenen MAM, Crooijmans RPMA. Introgression contributes to distribution of structural variations in cattle. Genomics 2021; 113:3092-3102. [PMID: 34242710 DOI: 10.1016/j.ygeno.2021.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/24/2021] [Accepted: 07/03/2021] [Indexed: 11/19/2022]
Abstract
Structural variations (SVs) are an important source of phenotypic diversity in cattle. Here, 72 whole genome sequences representing taurine and zebu cattle were used to identify SVs. Applying multiple approaches, 16,738 SVs were identified. A comparison against the Database of Genomic Variants archives revealed that 1575 SVs were novel in our data. A novel duplication covering the entire GALNT15 gene, was observed only in N'Dama. A duplication, which was previously reported only in zebu and associated with navel length, was also observed in N'Dama. Investigation of a novel deletion located upstream of CAST13 gene and identified only in Italian cattle and zebu, revealed its introgressed origin in the former. Overall, our data highlights how the SVs distribution in cattle is also shaped by forces such as demographical differences and gene flow. The cattle SVs of this study and its meta-data can be visualized on an interactive genome browser at https://tinyurl.com/svCowArs.
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Affiliation(s)
- Maulik Upadhyay
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden; Population Genomics Group, Department of Veterinary Sciences, Ludwig-Maximilians-University Munich, 80539 Munich, Germany.
| | - Martijn F L Derks
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden.
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, Ludwig-Maximilians-University Munich, 80539 Munich, Germany.
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Richard P M A Crooijmans
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
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16
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Lloret-Villas A, Bhati M, Kadri NK, Fries R, Pausch H. Investigating the impact of reference assembly choice on genomic analyses in a cattle breed. BMC Genomics 2021; 22:363. [PMID: 34011274 PMCID: PMC8132449 DOI: 10.1186/s12864-021-07554-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Reference-guided read alignment and variant genotyping are prone to reference allele bias, particularly for samples that are greatly divergent from the reference genome. A Hereford-based assembly is the widely accepted bovine reference genome. Haplotype-resolved genomes that exceed the current bovine reference genome in quality and continuity have been assembled for different breeds of cattle. Using whole genome sequencing data of 161 Brown Swiss cattle, we compared the accuracy of read mapping and sequence variant genotyping as well as downstream genomic analyses between the bovine reference genome (ARS-UCD1.2) and a highly continuous Angus-based assembly (UOA_Angus_1). RESULTS Read mapping accuracy did not differ notably between the ARS-UCD1.2 and UOA_Angus_1 assemblies. We discovered 22,744,517 and 22,559,675 high-quality variants from ARS-UCD1.2 and UOA_Angus_1, respectively. The concordance between sequence- and array-called genotypes was high and the number of variants deviating from Hardy-Weinberg proportions was low at segregating sites for both assemblies. More artefactual INDELs were genotyped from UOA_Angus_1 than ARS-UCD1.2 alignments. Using the composite likelihood ratio test, we detected 40 and 33 signatures of selection from ARS-UCD1.2 and UOA_Angus_1, respectively, but the overlap between both assemblies was low. Using the 161 sequenced Brown Swiss cattle as a reference panel, we imputed sequence variant genotypes into a mapping cohort of 30,499 cattle that had microarray-derived genotypes using a two-step imputation approach. The accuracy of imputation (Beagle R2) was very high (0.87) for both assemblies. Genome-wide association studies between imputed sequence variant genotypes and six dairy traits as well as stature produced almost identical results from both assemblies. CONCLUSIONS The ARS-UCD1.2 and UOA_Angus_1 assemblies are suitable for reference-guided genome analyses in Brown Swiss cattle. Although differences in read mapping and genotyping accuracy between both assemblies are negligible, the choice of the reference genome has a large impact on detecting signatures of selection that already reached fixation using the composite likelihood ratio test. We developed a workflow that can be adapted and reused to compare the impact of reference genomes on genome analyses in various breeds, populations and species.
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Affiliation(s)
| | - Meenu Bhati
- Animal Genomics, ETH Zürich, Lindau, 8315 Switzerland
| | | | - Ruedi Fries
- Chair of Animal Breeding, TU München, Freising-Weihenstephan, 85354 Germany
| | - Hubert Pausch
- Animal Genomics, ETH Zürich, Lindau, 8315 Switzerland
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17
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Addo S, Klingel S, Thaller G, Hinrichs D. Genetic diversity and the application of runs of homozygosity-based methods for inbreeding estimation in German White-headed Mutton sheep. PLoS One 2021; 16:e0250608. [PMID: 33956807 PMCID: PMC8101715 DOI: 10.1371/journal.pone.0250608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 04/09/2021] [Indexed: 11/19/2022] Open
Abstract
The German White-headed Mutton (GWM) sheep is a monitoring population believed to have been improved through crosses with other breeds, e.g., Texel (TXL) and French Berrichone du Cher (BDC). The primary aim of the study was to analyse genetic diversity and breed composition of GWM sheep. Furthermore, different measures of computing inbreeding from the runs of homozygosity (ROH) were investigated. Data for GWM consisted of pedigree information on 19,000 animals and 40,753 quality filtered SNPs on 46 individuals. Additionally, publicly available genotype data on 209 individuals belonging to nine sheep breeds were included in the analysis. Due to evenness of SNPs spacing and proportionality of the number of SNPs in each autosome to autosome length, a high correlation (rp = 0.99) was found between genomic inbreeding coefficients computed based on the length of ROH (FROH_L) and those computed relative to the number of SNPs in ROH (FROH_N). Total inbreeding was partitioned into values for individual chromosomes revealing the highest levels of inbreeding on chromosomes 1, 2 and 3. Correlations between the ROH-based inbreeding measures and pedigree inbreeding reached 0.82. The observed heterozygosity estimate in GWM was high (0.39), however, the breed suffered low level of effective population size (~50) from a genomic viewpoint. Moreover, effective number of founders (186), and effective number of ancestors (144) implied disequilibrium of founder contribution and a genetic bottleneck in the breed. Multidimensional scaling and network visualisation analyses revealed close connectedness of GWM to BDC and German Texel (GTX). A model-based admixture analysis consistently indicated the flow of genes from other breeds, particularly BDC to GWM. Our analyses highlight the mixed genetic background of GWM sheep and furthermore, suggest a close monitoring of the breed to consolidate its genetic diversity while averting further reduction in the effective population size.
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Affiliation(s)
- Sowah Addo
- Institute of Animal Breeding and Husbandry, Kiel University, Kiel, Germany
- Department of Animal Breeding, University of Kassel, Witzenhausen, Germany
- * E-mail:
| | - Stefanie Klingel
- Arche Warder, Center for Rare and Endangered Domestic Animals, Warder, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Kiel University, Kiel, Germany
| | - Dirk Hinrichs
- Department of Animal Breeding, University of Kassel, Witzenhausen, Germany
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18
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Ben-Jemaa S, Senczuk G, Ciani E, Ciampolini R, Catillo G, Boussaha M, Pilla F, Portolano B, Mastrangelo S. Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle. Front Genet 2021; 12:675569. [PMID: 33995500 PMCID: PMC8113768 DOI: 10.3389/fgene.2021.675569] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/07/2021] [Indexed: 12/31/2022] Open
Abstract
The Maremmana cattle is an ancient Podolian-derived Italian breed raised in semi-wild conditions with distinctive morphological and adaptive traits. The aim of this study was to detect potential selection signatures in Maremmana using medium-density single nucleotide polymorphism array. Putative selection signatures were investigated combining three statistical approaches designed to quantify the excess of haplotype homozygosity either within (integrated haplotype score, iHS) or among pairs of populations (Rsb and XP-EHH), and contrasting the Maremmana with a single reference population composed of a pool of seven Podolian-derived Italian breeds. Overall, the three haplotype-based analyses revealed selection signatures distributed over 19 genomic regions. Of these, six relevant candidate regions were identified by at least two approaches. We found genomic signatures of selective sweeps spanning genes related to mitochondrial function, muscle development, growth, and meat traits (SCIN, THSD7A, ETV1, UCHL1, and MYOD1), which reflects the different breeding schemes between Maremmana (semi-wild conditions) and the other Podolian-derived Italian breeds (semi-extensive). We also identified several genes linked to Maremmana adaptation to the environment of the western-central part of Italy, known to be hyperendemic for malaria and other tick-borne diseases. These include several chemokine (C-C motif) ligand genes crucially involved in both innate and adaptive immune responses to intracellular parasite infections and other genes playing key roles in pulmonary disease (HEATR9, MMP28, and ASIC2) or strongly associated with malaria resistance/susceptibility (AP2B1). Our results provide a glimpse into diverse selection signatures in Maremmana cattle and can be used to enhance our understanding of the genomic basis of environmental adaptation in cattle.
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Affiliation(s)
- Slim Ben-Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, University of Carthage, Ariana, Tunisia
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari “Aldo Moro”, Bari, Italy
| | | | - Gennaro Catillo
- Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), Centro di Ricerca Zootecnia e Acquacoltura, Lodi, Italy
| | - Mekki Boussaha
- INRAE, AgroParisTech, University of Paris Saclay, Saint Aubin, France
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy
| | - Baldassare Portolano
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
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Gautason E, Schönherz AA, Sahana G, Guldbrandtsen B. Genomic inbreeding and selection signatures in the local dairy breed Icelandic Cattle. Anim Genet 2021; 52:251-262. [PMID: 33829515 DOI: 10.1111/age.13058] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2021] [Indexed: 12/21/2022]
Abstract
Icelandic Cattle is the only dairy cattle breed native to Iceland. It currently numbers ca. 26 000 breeding females. We used 50k genotypes of over 8000 Icelandic Cattle to estimate genomic and pedigree-based inbreeding and to detect selection signatures using the integrated haplotype score. We used 47 Icelandic bulls genotyped with a 770k SNP chip to estimate LD decay for comparison with other Nordic dairy cattle breeds. We detected ROHs on the autosomes and computed ROH-based autosomal inbreeding coefficients. Average inbreeding coefficients according to pedigree and ROHs were 0.0621 and 0.101. Effective population sizes for the years 2009-2017 according to pedigree, ROHs, genomic relationship matrix, excess of homozygosity and individual increase in inbreeding were 81, 65, 60, 58 and 92 respectively. We identified three regions and six candidate genes that showed a signature of selection according to the integrated haplotype score (P < 0.05) on chromosomes 1, 16 and 23. The LD structure of Icelandic Cattle is shaped by a long period of isolation and a small founder population. The estimate of LD at distances closer than 0.3 Mb is lower in Icelandic Cattle than in Danish Jersey, but is higher than in Danish Holstein and Red Nordic Dairy Cattle breeds. Our findings show that inbreeding rates in Icelandic Cattle currently are sustainable according to FAO guidelines, and our results do not indicate severe historical inbreeding.
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Affiliation(s)
- E Gautason
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark
| | - A A Schönherz
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark.,Department of Animal Science, Aarhus University, Tjele, 8830, Denmark
| | - G Sahana
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark
| | - B Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark.,Department of Animal Sciences, University of Bonn, Endenicher Allee 15, Bonn, 53115, Germany
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20
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Strucken EM, Swaminathan M, Gibson JP. Small SNP panels for breed proportion estimation in Indian crossbred dairy cattle. J Anim Breed Genet 2021; 138:698-707. [PMID: 33687116 PMCID: PMC8519156 DOI: 10.1111/jbg.12544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/26/2021] [Accepted: 02/20/2021] [Indexed: 11/29/2022]
Abstract
Reliably identifying breed proportions in crossbred cattle in smallholder farms is a crucial step to improve mating decisions and optimizing management in these systems. High‐density genotype information is able to estimate higher‐order breed proportions accurately, but, are too expensive for mass application in smallholder systems. We used high‐density genotype information (777 k SNPs) of 623 crossbred cattle from India that had Holstein‐Friesian (HFX) and/or Jersey and indigenous breeds in their ancestry to select a smaller number of SNPs for breed proportion estimation. The accuracy of estimates obtained from panels with 100–500 SNP was compared to estimates based on all SNPs. Panels were selected for highest absolute allele frequency difference between exotic dairy versus indigenous Bos indicus, or between HFX versus Jersey breeds. A step‐wise pruning approach was developed showing that and increased physical distances between markers of 8.5 Mb improved breed proportion estimation compared to a standard 1 Mb distance. A panel of 500 SNPs optimized to estimate HFX versus Jersey versus indicine ancestry was able to estimate indicine breed proportions with r2 = .991, HFX proportions with r2 = .979 and Jersey proportions with r2 = .949. The number of markers was a deciding factor in estimation accuracy, together with the distribution of markers across the genome.
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Affiliation(s)
- Eva M Strucken
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | | | - John P Gibson
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
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21
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Pacheco G, van Grouw H, Shapiro MD, Gilbert MTP, Vieira FG. Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds. Genome Biol Evol 2021; 12:136-150. [PMID: 32053199 PMCID: PMC7144551 DOI: 10.1093/gbe/evaa027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2020] [Indexed: 12/14/2022] Open
Abstract
Through its long history of artificial selection, the rock pigeon (Columba livia Gmelin 1789) was forged into a large number of domestic breeds. The incredible amount of phenotypic diversity exhibited in these breeds has long held the fascination of scholars, particularly those interested in biological inheritance and evolution. However, exploiting them as a model system is challenging, as unlike with many other domestic species, few reliable records exist about the origins of, and relationships between, each of the breeds. Therefore, in order to broaden our understanding of the complex evolutionary relationships among pigeon breeds, we generated genome-wide data by performing the genotyping-by-sequencing (GBS) method on close to 200 domestic individuals representing over 60 breeds. We analyzed these GBS data alongside previously published whole-genome sequencing data, and this combined analysis allowed us to conduct the most extensive phylogenetic analysis of the group, including two feral pigeons and one outgroup. We improve previous phylogenies, find considerable population structure across the different breeds, and identify unreported interbreed admixture events. Despite the reduced number of loci relative to whole-genome sequencing, we demonstrate that GBS data provide sufficient analytical power to investigate intertwined evolutionary relationships, such as those that are characteristic of animal domestic breeds. Thus, we argue that future studies should consider sequencing methods akin to the GBS approach as an optimal cost-effective approach for addressing complex phylogenies.
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Affiliation(s)
- George Pacheco
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Denmark.,The GLOBE Institute, Faculty of Health and Biomedical Sciences, University of Copenhagen, Denmark
| | - Hein van Grouw
- Bird Group, Department of Life Sciences, Natural History Museum, Tring, Hertfordshire, United Kingdom
| | | | - Marcus Thomas P Gilbert
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Denmark.,The GLOBE Institute, Faculty of Health and Biomedical Sciences, University of Copenhagen, Denmark.,NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Filipe Garrett Vieira
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Denmark
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22
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Mei C, Gui L, Hong J, Raza SHA, Aorigele C, Tian W, Garcia M, Xin Y, Yang W, Zhang S, Zan L. Insights into adaption and growth evolution: a comparative genomics study on two distinct cattle breeds from Northern and Southern China. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:959-967. [PMID: 33614243 PMCID: PMC7868925 DOI: 10.1016/j.omtn.2020.12.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/31/2020] [Indexed: 11/29/2022]
Abstract
Mongolian cattle (MG, Bos taurus) and Minnan cattle (MN, Bos indicus) are two different breeds of Chinese indigenous cattle, representing North type and South type, respectively. However, their value and potential have not yet been discovered at the genomic level. In this study, 26 individuals of MN and MG were sequenced for the first time at an average of 13.9- and 12.8-fold, respectively. Large numbers of different variations were identified. In addition, the analyses of phylogenetic and population structure showed that these two cattle breeds are distinct from each other, and results of linkage disequilibrium analysis revealed that these two cattle breeds have undergone various degrees of intense natural or artificial selection. Subsequently, 496 and 306 potential selected genes (PSRs) were obtained in MN and MG, containing 1,096 and 529 potential selected genes (PSGs), respectively. These PSGs, together with the analyzed copy number variation (CNV)-related genes, showed potential relations with their phenotypic characteristics, including environmental adaptability (e.g., DVL2, HSPA4, CDHR4), feed efficiency (e.g., R3HDM1, PLAG1, XKR4), and meat/milk production (e.g., PDHB, LEMD3, APOF). The results of this study help to gain new insights into the genetic characteristics of two distinct cattle breeds and will contribute to future cattle breeding.
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Affiliation(s)
- Chugang Mei
- Northwest A&F University, Yangling 712100, Shaanxi, China.,National Beef Cattle Improvement Center, Yangling 712100, China
| | - Linsheng Gui
- Northwest A&F University, Yangling 712100, Shaanxi, China.,Qinghai University, Xining 810008, China
| | - Jieyun Hong
- Northwest A&F University, Yangling 712100, Shaanxi, China.,Yunnan Agricultural University, Kunming 650031, China
| | | | - Chen Aorigele
- Inner Mongolia Agricultural University, Hohhot 010000, China
| | - Wanqiang Tian
- Yangling Vocational & Technical College, Yangling 712100, China
| | | | - Yaping Xin
- Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wucai Yang
- Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Song Zhang
- Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Linsen Zan
- Northwest A&F University, Yangling 712100, Shaanxi, China.,National Beef Cattle Improvement Center, Yangling 712100, China
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23
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Abstract
Runs of homozygosity (ROH) are chromosomal stretches that in a diploid genome appear in a homozygous state and display identical alleles at multiple contiguous loci. This study aimed to systematically compare the genomic distribution of the ROH islands among five populations of wild vs commercial chickens of both layer and broiler type. To this end, we analyzed whole genome sequences of 115 birds including white layer (WL, n = 25), brown layer (BL, n = 25), broiler line A (BRA, n = 20), broiler line B (BRB, n = 20) and Red Junglefowl (RJF, n = 25). The ROH segments varied in size markedly among populations, ranging from 0.3 to 21.83 Mb reflecting their past genealogy. White layers contained the largest portion of the genome in homozygous state with an average ROH length of 432.1 Mb (±18.7) per bird, despite carrying it in short segments (0.3-1 Mb). Population-wise inbreeding measures based on Wright's (Fis) and genomic (FROH) metrics revealed highly inbred genome of layer lines relative to the broilers and Red Junglefowl. We further revealed the ROH islands, among commercial lines overlapped with QTL related to limb development (GREM1, MEOX2), body weight (Meis2a.1, uc_338), eggshell color (GLCCI1, ICA1, UMAD1), antibody response to Newcastle virus (ROBO2), and feather pecking. Comparison of ROH landscape in sequencing resolution demonstrated that a sizable portion of genome of commercial lines segregates in homozygote state, reflecting many generations of assortative mating and intensive selection in their recent history. In contrary, wild birds carry shorter ROH segments, likely suggestive of older evolutionary events.
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Moscarelli A, Sardina MT, Cassandro M, Ciani E, Pilla F, Senczuk G, Portolano B, Mastrangelo S. Genome-wide assessment of diversity and differentiation between original and modern Brown cattle populations. Anim Genet 2020; 52:21-31. [PMID: 33174276 DOI: 10.1111/age.13019] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2020] [Indexed: 02/06/2023]
Abstract
Identifying genomic regions involved in the differences between breeds can provide information on genes that are under the influence of both artificial and natural selection. The aim of this study was to assess the genetic diversity and differentiation among four different Brown cattle populations (two original vs. two modern populations) and to characterize the distribution of runs of homozygosity (ROH) islands using the Illumina Bovine SNP50 BeadChip genotyping data. After quality control, 34 735 SNPs and 106 animals were retained for the analyses. Larger heterogeneity was highlighted for the original populations. Patterns of genetic differentiation, multidimensional scaling, and the neighboring joining tree distinguished the modern from the original populations. The FST -outlier identified several genes putatively involved in the genetic differentiation between the two groups, such as stature and growth, behavior, and adaptability to local environments. The ROH islands within both the original and the modern populations overlapped with QTL associated with relevant traits. In modern Brown (Brown Swiss and Italian Brown), ROH islands harbored candidate genes associated with milk production traits, in evident agreement with the artificial selection conducted to improve this trait in these populations. In original Brown (Original Braunvieh and Braunvieh), we identified candidate genes related with fat deposition, confirming that breeding strategies for the original Brown populations aimed to produce dual-purpose animals. Our study highlighted the presence of several genomic regions that vary between Brown populations, in line with their different breeding histories.
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Affiliation(s)
- A Moscarelli
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, 90128, Italy
| | - M T Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, 90128, Italy
| | - M Cassandro
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, Legnaro, 35020, Italy
| | - E Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari, Bari, 70124, Italy
| | - F Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, 86100, Italy
| | - G Senczuk
- Dipartimento Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, 86100, Italy
| | - B Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, 90128, Italy
| | - S Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, 90128, Italy
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Teissier M, Larroque H, Brito LF, Rupp R, Schenkel FS, Robert-Granié C. Genomic predictions based on haplotypes fitted as pseudo-SNP for milk production and udder type traits and SCS in French dairy goats. J Dairy Sci 2020; 103:11559-11573. [PMID: 33041034 DOI: 10.3168/jds.2020-18662] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/27/2020] [Indexed: 12/18/2022]
Abstract
The development of statistical methods aiming to improve the accuracy of genomic predictions is of utmost value for dairy goat breeding programs. In this context, the use of haplotypes, instead of individual SNP, could improve the accuracy of genomic predictions by better capturing the effect of causal variants, instead of relying solely on linkage disequilibrium with individual SNP. Haplotypes can be included in genomic evaluation models in various ways, such as fitting them as pseudo-SNP (i.e., haplotypes converted into biallelic SNP format). This can be easily incorporated in the software already available for single-step genomic predictions (ssGBLUP). Therefore, the aim of this study was to compare the predictive performances of ssGBLUP and weighted ssGBLUP (WssGBLUP) based on individual SNP or on haplotypes fitted as pseudo-SNP. Performance was compared in terms of accuracy, bias, and weights for SNP versus pseudo-SNP. Genomic predictions were performed on 5 milk production traits, 5 udder type traits, and somatic cell score (SCS). The training population was formed by 307 Alpine and 247 Saanen progeny-tested bucks, genotyped using the Illumina Goat SNP50 BeadChip (Illumina, San Diego, CA). The validation population included 205 Alpine and 146 Saanen young bucks. The accuracy of genomic predictions was evaluated in the validation population as the Pearson correlation between genomic estimated breeding values (GEBV), predicted based on various methods, and daughter deviation (DD) based on the official genetic evaluation of January 2016. Haplotype-based models were shown to improve the performance of genomic predictions for some traits. Gains in accuracy of up to +19% (0.310 to 0.368 for fat yield) in Alpine and up to +3% (0.361 to 0.373 for udder shape) in Saanen were observed with ssGBLUP. The ssGBLUP accuracies averaged across all traits and methods were equal to 0.467 (SNP) versus 0.471 (pseudo-SNP) in Alpine and 0.528 (SNP) versus 0.523 (pseudo-SNP) in Saanen. With WssGBLUP, gains in accuracy of up to 24% (0.298 to 0.370 for fat yield) in Alpine and 14% (0.431 to 0.490 for SCS) in Saanen were observed with WssGBLUP. Accuracies of WssGBLUP averaged across all traits and methods were equal to 0.455 (SNP and pseudo-SNP) in Alpine and 0.542 (SNP) versus 0.528 (pseudo-SNP) in Saanen. The average (±SD) slope of the regression of DD on GEBV for the validation animals, across all breeds, traits and scenarios, were equal to 0.82 ± 0.20 (SNP) and 0.83 ± 0.18 (pseudo-SNP) for ssGBLUP and 0.67 ± 0.16 (SNP) and 0.65 ± 0.16 (pseudo-SNP) for WssGBLUP, which suggest that haplotype-based models and ssGBLUPSNP were similarly biased. However, WssGBLUP was more biased than ssGBLUP, and its gains in accuracies were limited to milk production traits. Despite the fact that genomic predictions based on haplotypes require additional steps and time, the observed gains in GEBV predictive performance indicate that haplotype-based methods could be recommended for some traits.
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Affiliation(s)
- Marc Teissier
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet-Tolosan, France.
| | - Hélène Larroque
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet-Tolosan, France
| | - Luiz F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Rachel Rupp
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet-Tolosan, France
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
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Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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Alam MZ, Lee YM, Son HJ, Hanna LH, Riley DG, Mannen H, Sasazaki S, Park SP, Kim JJ. Genetic characteristics of Korean Jeju Black cattle with high density single nucleotide polymorphisms. Anim Biosci 2020; 34:789-800. [PMID: 32882779 PMCID: PMC8100474 DOI: 10.5713/ajas.19.0888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 06/29/2020] [Indexed: 11/27/2022] Open
Abstract
Objective Conservation and genetic improvement of cattle breeds require information about genetic diversity and population structure of the cattle. In this study, we investigated the genetic diversity and population structure of the three cattle breeds in the Korean peninsula. Methods Jeju Black, Hanwoo, Holstein cattle in Korea, together with six foreign breeds were examined. Genetic diversity within the cattle breeds was analyzed with minor allele frequency (MAF), observed and expected heterozygosity (HO and HE), inbreeding coefficient (FIS) and past effective population size. Molecular variance and population structure between the nine breeds were analyzed using a model-based clustering method. Genetic distances between breeds were evaluated with Nei’s genetic distance and Weir and Cockerham’s FST. Results Our results revealed that Jeju Black cattle had lowest level of heterozygosity (HE = 0.21) among the studied taurine breeds, and an average MAF of 0.16. The level of inbreeding was −0.076 for Jeju Black, while −0.018 to −0.118 for the other breeds. Principle component analysis and neighbor-joining tree showed a clear separation of Jeju Black cattle from other local (Hanwoo and Japanese cattle) and taurine/indicine cattle breeds in evolutionary process, and a distinct pattern of admixture of Jeju Black cattle having no clustering with other studied populations. The FST value between Jeju Black cattle and Hanwoo was 0.106, which was lowest across the pair of breeds ranging from 0.161 to 0.274, indicating some degree of genetic closeness of Jeju Black cattle with Hanwoo. The past effective population size of Jeju Black cattle was very small, i.e. 38 in 13 generation ago, whereas 209 for Hanwoo. Conclusion This study indicates genetic uniqueness of Jeju Black cattle. However, a small effective population size of Jeju Black cattle indicates the requirement for an implementation of a sustainable breeding policy to increase the population for genetic improvement and future conservation.
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Affiliation(s)
- M Zahangir Alam
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea.,Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Yun-Mi Lee
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
| | - Hyo-Jung Son
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
| | - Lauren H Hanna
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58105, USA
| | - David G Riley
- Department of Animal Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Hideyuki Mannen
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Shinji Sasazaki
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Se Pill Park
- Faculty of Biotechnology, Jeju National University, Jeju 13557, Korea
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
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Cesarani A, Gaspa G, Pauciullo A, Degano L, Vicario D, Macciotta NPP. Genome-wide analysis of homozygosity regions in european simmental bulls. J Anim Breed Genet 2020; 138:69-79. [PMID: 33263211 DOI: 10.1111/jbg.12502] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/08/2020] [Accepted: 07/18/2020] [Indexed: 01/15/2023]
Abstract
The study of Runs of Homozygosity (ROH) is a useful approach for the characterization of the genome of livestock populations. Due to their high relationship with autozygosity, ROH allow to make inference about population genetic history, to estimate the level of inbreeding, to assess within breed heterogeneity and to detect the footprints of selection on livestock genomes. Aim of this study was to investigate the distribution of runs of homozygosity in bulls belonging to five European Simmental populations and to assess the relationship between three production traits (milk yield, fat and protein contents) and autozygosity. ROH count, distribution and ROH-based coefficient of inbreeding (FROH ) were calculated for 3,845 Simmental bulls of five different European countries: Austria (AT), Switzerland (CH), Czech Republic (CZ), Germany (DE) and Italy (IT). Average values of ROH number per animal, and total genome length covered by ROH were 77.8 ± 20.7 and 205 ± 74.4 Mb, respectively. Bulls from AT, DE and IT exhibited similar ROH characteristics. Swiss animals showed the highest (12.6%), while CZ the lowest (4.6%) FROH coefficient. The relationship between ROH occurrence and milk production traits was investigated through a genome-wide ROH-traits association analysis (GWRA). A total of 34 regions previously associated with milk traits (yield and/or composition) were identified by GWRA. Results of the present research highlight a mixed genetic background in the 5 European Simmental populations, with the possible presence of three subgroups. Moreover, a strong relationship between autozygosity and production traits has been detected.
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Affiliation(s)
- Alberto Cesarani
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy.,Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), Udine, Italy
| | - Giustino Gaspa
- Department of Agricultural, Forestry and Alimentary Sciences, University of Torino, Grugliasco, Italy
| | - Alfredo Pauciullo
- Department of Agricultural, Forestry and Alimentary Sciences, University of Torino, Grugliasco, Italy
| | - Lorenzo Degano
- Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), Udine, Italy
| | - Daniele Vicario
- Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), Udine, Italy
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Crysnanto D, Pausch H. Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery. Genome Biol 2020; 21:184. [PMID: 32718320 PMCID: PMC7385871 DOI: 10.1186/s13059-020-02105-0%0a%0a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/14/2020] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND The current bovine genomic reference sequence was assembled from a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation, a drawback of linear references that causes reference allele bias. High nucleotide diversity and the separation of individuals by hundreds of breeds make cattle ideally suited to investigate the optimal composition of variation-aware references. RESULTS We augment the bovine linear reference sequence (ARS-UCD1.2) with variants filtered for allele frequency in dairy (Brown Swiss, Holstein) and dual-purpose (Fleckvieh, Original Braunvieh) cattle breeds to construct either breed-specific or pan-genome reference graphs using the vg toolkit. We find that read mapping is more accurate to variation-aware than linear references if pre-selected variants are used to construct the genome graphs. Graphs that contain random variants do not improve read mapping over the linear reference sequence. Breed-specific augmented and pan-genome graphs enable almost similar mapping accuracy improvements over the linear reference. We construct a whole-genome graph that contains the Hereford-based reference sequence and 14 million alleles that have alternate allele frequency greater than 0.03 in the Brown Swiss cattle breed. Our novel variation-aware reference facilitates accurate read mapping and unbiased sequence variant genotyping for SNPs and Indels. CONCLUSIONS We develop the first variation-aware reference graph for an agricultural animal ( https://doi.org/10.5281/zenodo.3759712 ). Our novel reference structure improves sequence read mapping and variant genotyping over the linear reference. Our work is a first step towards the transition from linear to variation-aware reference structures in species with high genetic diversity and many sub-populations.
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Crysnanto D, Pausch H. Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery. Genome Biol 2020; 21:184. [PMID: 32718320 PMCID: PMC7385871 DOI: 10.1186/s13059-020-02105-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The current bovine genomic reference sequence was assembled from a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation, a drawback of linear references that causes reference allele bias. High nucleotide diversity and the separation of individuals by hundreds of breeds make cattle ideally suited to investigate the optimal composition of variation-aware references. RESULTS We augment the bovine linear reference sequence (ARS-UCD1.2) with variants filtered for allele frequency in dairy (Brown Swiss, Holstein) and dual-purpose (Fleckvieh, Original Braunvieh) cattle breeds to construct either breed-specific or pan-genome reference graphs using the vg toolkit. We find that read mapping is more accurate to variation-aware than linear references if pre-selected variants are used to construct the genome graphs. Graphs that contain random variants do not improve read mapping over the linear reference sequence. Breed-specific augmented and pan-genome graphs enable almost similar mapping accuracy improvements over the linear reference. We construct a whole-genome graph that contains the Hereford-based reference sequence and 14 million alleles that have alternate allele frequency greater than 0.03 in the Brown Swiss cattle breed. Our novel variation-aware reference facilitates accurate read mapping and unbiased sequence variant genotyping for SNPs and Indels. CONCLUSIONS We develop the first variation-aware reference graph for an agricultural animal ( https://doi.org/10.5281/zenodo.3759712 ). Our novel reference structure improves sequence read mapping and variant genotyping over the linear reference. Our work is a first step towards the transition from linear to variation-aware reference structures in species with high genetic diversity and many sub-populations.
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Senczuk G, Mastrangelo S, Ciani E, Battaglini L, Cendron F, Ciampolini R, Crepaldi P, Mantovani R, Bongioni G, Pagnacco G, Portolano B, Rossoni A, Pilla F, Cassandro M. The genetic heritage of Alpine local cattle breeds using genomic SNP data. Genet Sel Evol 2020; 52:40. [PMID: 32664855 PMCID: PMC7362560 DOI: 10.1186/s12711-020-00559-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/09/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Assessment of genetic diversity and population structure provides important control metrics to avoid genetic erosion, inbreeding depression and crossbreeding between exotic and locally-adapted cattle breeds since these events can have deleterious consequences and eventually lead to extinction. Historically, the Alpine Arc represents an important pocket of cattle biodiversity with a large number of autochthonous breeds that provide a fundamental source of income for the entire regional economy. By using genotype data from medium-density single nucleotide polymorphism (SNP) arrays, we performed a genome-wide comparative study of 23 cattle populations from the Alpine Arc and three cosmopolitan breeds. RESULTS After filtering, we obtained a final genotyping dataset consisting of 30,176 SNPs for 711 individuals. The local breeds showed high or intermediate values of genetic diversity compared to the highly selected cosmopolitan breeds. Patterns of genetic differentiation, multidimensional scaling, admixture analysis and the constructed phylogenetic tree showed convergence, which indicates the presence of gene flow among the breeds according to both geographic origin and historical background. Among the most differentiated breeds, we identified the modern Brown cattle. In spite of admixture events, several local breeds have preserved distinctive characteristics, which is probably due to differences in genetic origin and geographic location. CONCLUSIONS This study represents one of the most comprehensive genome-wide analysis of the Alpine cattle breeds to date. Using such a large dataset that includes the majority of the local breeds found in this region, allowed us to expand knowledge on the evaluation and status of Alpine cattle biodiversity. Our results indicate that although many of the analyzed local breeds are listed as endangered, they still harbor a large amount of genetic diversity, even when compared to some cosmopolitan breeds. This finding, together with the reconstruction of the phylogeny and the relationships between these Alpine Arc cattle breeds, provide crucial insights not only into the improvement of genetic stocks but also into the implementation of future conservation strategies.
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Affiliation(s)
- Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of Bari, 70124 Bari, Italy
| | - Luca Battaglini
- Dipartimento di Scienze Agrarie Forestali e Alimentari, University of Torino, 10095 Grugliasco, Italy
| | - Filippo Cendron
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, 35020 Legnaro, Italy
| | - Roberta Ciampolini
- Dipartimento di Scienze Veterinarie, University of Pisa, 56100 Pisa, Italy
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie ed Ambientali - Produzione, Territorio, Agroenergia, University of Milano, 20133 Milan, Italy
| | - Roberto Mantovani
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, 35020 Legnaro, Italy
| | - Graziella Bongioni
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Loc. La Quercia, 26027 Rivolta d’Adda, CR Italy
| | - Giulio Pagnacco
- Istituto di Biologia e Biotecnologia Agraria (IBBA), CNR, 20133 Milan, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Attilio Rossoni
- Italian Brown Cattle Breeders’ Association, Loc. Ferlina 204, 37012 Bussolengo, VR Italy
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy
| | - Martino Cassandro
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, 35020 Legnaro, Italy
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Cardoso DF, Fernandes Júnior GA, Scalez DCB, Alves AAC, Magalhães AFB, Bresolin T, Ventura RV, Li C, de Sena Oliveira MC, Porto-Neto LR, Carvalheiro R, de Oliveira HN, Tonhati H, Albuquerque LG. Uncovering Sub-Structure and Genomic Profiles in Across-Countries Subpopulations of Angus Cattle. Sci Rep 2020; 10:8770. [PMID: 32471998 PMCID: PMC7260210 DOI: 10.1038/s41598-020-65565-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 05/04/2020] [Indexed: 11/09/2022] Open
Abstract
Highlighting genomic profiles for geographically distinct subpopulations of the same breed may provide insights into adaptation mechanisms to different environments, reveal genomic regions divergently selected, and offer initial guidance to joint genomic analysis. Here, we characterized similarities and differences between the genomic patterns of Angus subpopulations, born and raised in Canada (N = 382) and Brazil (N = 566). Furthermore, we systematically scanned for selection signatures based on the detection of autozygosity islands common between the two subpopulations, and signals of divergent selection, via FST and varLD tests. The principal component analysis revealed a sub-structure with a close connection between the two subpopulations. The averages of genomic relationships, inbreeding coefficients, and linkage disequilibrium at varying genomic distances were rather similar across them, suggesting non-accentuated differences in overall genomic diversity. Autozygosity islands revealed selection signatures common to both subpopulations at chromosomes 13 (63.77-65.25 Mb) and 14 (22.81-23.57 Mb), which are notably known regions affecting growth traits. Nevertheless, further autozygosity islands along with FST and varLD tests unravel particular sites with accentuated population subdivision at BTAs 7 and 18 overlapping with known QTL and candidate genes of reproductive performance, thermoregulation, and resistance to infectious diseases. Our findings indicate overall genomic similarity between Angus subpopulations, with noticeable signals of divergent selection in genomic regions associated with the adaptation in different environments.
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Affiliation(s)
- Diercles Francisco Cardoso
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil.
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada.
| | - Gerardo Alves Fernandes Júnior
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Daiane Cristina Becker Scalez
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Anderson Antonio Carvalho Alves
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Ana Fabrícia Braga Magalhães
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Tiago Bresolin
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Ricardo Vieira Ventura
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science (FMVZ), University of Sao Paulo (USP), Pirassununga, SP, Brazil
| | - Changxi Li
- Department of Agricultural Food and Nutritional Science, Faculty of Agricultural, Life & Environmental Sciences, University of Alberta, Edmonton, AB, Canada
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | | | | | - Roberto Carvalheiro
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
- National Council for Science and Technological Development, Brasília, Distrito Federal, Brazil
| | - Henrique Nunes de Oliveira
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
- National Council for Science and Technological Development, Brasília, Distrito Federal, Brazil
| | - Humberto Tonhati
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
- National Council for Science and Technological Development, Brasília, Distrito Federal, Brazil
| | - Lucia Galvão Albuquerque
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil.
- National Council for Science and Technological Development, Brasília, Distrito Federal, Brazil.
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Hiltpold M, Niu G, Kadri NK, Crysnanto D, Fang ZH, Spengeler M, Schmitz-Hsu F, Fuerst C, Schwarzenbacher H, Seefried FR, Seehusen F, Witschi U, Schnieke A, Fries R, Bollwein H, Flisikowski K, Pausch H. Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility. PLoS Genet 2020; 16:e1008804. [PMID: 32407316 PMCID: PMC7252675 DOI: 10.1371/journal.pgen.1008804] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 05/27/2020] [Accepted: 04/28/2020] [Indexed: 12/30/2022] Open
Abstract
Cattle are ideally suited to investigate the genetics of male reproduction, because semen quality and fertility are recorded for all ejaculates of artificial insemination bulls. We analysed 26,090 ejaculates of 794 Brown Swiss bulls to assess ejaculate volume, sperm concentration, sperm motility, sperm head and tail anomalies and insemination success. The heritability of the six semen traits was between 0 and 0.26. Genome-wide association testing on 607,511 SNPs revealed a QTL on bovine chromosome 6 that was associated with sperm motility (P = 2.5 x 10−27), head (P = 2.0 x 10−44) and tail anomalies (P = 7.2 x 10−49) and insemination success (P = 9.9 x 10−13). The QTL harbors a recessive allele that compromises semen quality and male fertility. We replicated the effect of the QTL on fertility (P = 7.1 x 10−32) in an independent cohort of 2481 Brown Swiss bulls. The analysis of whole-genome sequencing data revealed that a synonymous variant (BTA6:58373887C>T, rs474302732) in WDR19 encoding WD repeat-containing protein 19 was in linkage disequilibrium with the fertility-associated haplotype. WD repeat-containing protein 19 is a constituent of the intraflagellar transport complex that is essential for the physiological function of motile cilia and flagella. Bioinformatic and transcription analyses revealed that the BTA6:58373887 T-allele activates a cryptic exonic splice site that eliminates three evolutionarily conserved amino acids from WDR19. Western blot analysis demonstrated that the BTA6:58373887 T-allele decreases protein expression. We make the remarkable observation that, in spite of negative effects on semen quality and bull fertility, the BTA6:58373887 T-allele has a frequency of 24% in the Brown Swiss population. Our findings are the first to uncover a variant that is associated with quantitative variation in semen quality and male fertility in cattle. In cattle farming, artificial insemination is the most common method of breeding. To ensure high fertilization rates, ejaculate quality and insemination success are closely monitored in artificial insemination bulls. We analyse semen quality, insemination success and microarray-called genotypes at more than 600,000 genome-wide SNP markers of 794 bulls to identify a recessive allele that compromises semen quality. We take advantage of whole-genome sequencing to pinpoint a variant in the coding sequence of WDR19 encoding WD repeat-containing protein 19 that activates a novel exonic splice site. Our results indicate that cryptic splicing in WDR19 is associated with reduced male reproductive performance. This is the first report of a variant that contributes to quantitative variation in bovine semen quality.
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Affiliation(s)
| | - Guanglin Niu
- Livestock Biotechnology, TU München, Freising, Germany
| | | | | | - Zih-Hua Fang
- Animal Genomics, ETH Zürich, Lindau, Switzerland
| | | | | | | | | | | | - Frauke Seehusen
- Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | | | | | - Ruedi Fries
- Animal Breeding, TU München, Freising, Germany
| | - Heinrich Bollwein
- Clinic of Reproductive Medicine, University of Zurich, Zürich, Switzerland
| | | | - Hubert Pausch
- Animal Genomics, ETH Zürich, Lindau, Switzerland
- * E-mail:
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Estimates of Autozygosity Through Runs of Homozygosity in Farmed Coho Salmon. Genes (Basel) 2020; 11:genes11050490. [PMID: 32365758 PMCID: PMC7290985 DOI: 10.3390/genes11050490] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 11/17/2022] Open
Abstract
The characterization of runs of homozygosity (ROH), using high-density single nucleotide polymorphisms (SNPs) allows inferences to be made about the past demographic history of animal populations and the genomic ROH has become a common approach to characterize the inbreeding. We aimed to analyze and characterize ROH patterns and compare different genomic and pedigree-based methods to estimate the inbreeding coefficient in two pure lines (POP A and B) and one recently admixed line (POP C) of coho salmon (Oncorhynchus kisutch) breeding nuclei, genotyped using a 200 K Affymetrix Axiom® myDesign Custom SNP Array. A large number and greater mean length of ROH were found for the two “pure” lines and the recently admixed line (POP C) showed the lowest number and smaller mean length of ROH. The ROH analysis for different length classes suggests that all three coho salmon lines the genome is largely composed of a high number of short segments (<4 Mb), and for POP C no segment >16 Mb was found. A high variable number of ROH, mean length and inbreeding values across chromosomes; positively the consequence of artificial selection. Pedigree-based inbreeding values tended to underestimate genomic-based inbreeding levels, which in turn varied depending on the method used for estimation. The high positive correlations between different genomic-based inbreeding coefficients suggest that they are consistent and may be more accurate than pedigree-based methods, given that they capture information from past and more recent demographic events, even when there are no pedigree records available.
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Bhati M, Kadri NK, Crysnanto D, Pausch H. Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data. BMC Genomics 2020; 21:27. [PMID: 31914939 PMCID: PMC6950892 DOI: 10.1186/s12864-020-6446-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 12/31/2019] [Indexed: 02/07/2023] Open
Abstract
Background Autochthonous cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution. Results We annotated 15,722,811 SNPs and 1,580,878 Indels including 10,738 and 2763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 × 10− 3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding derived from runs of homozygosity (ROH) was relatively low (FROH = 0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in OB cattle of more recent generations (FROH = 0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus. Conclusions We provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.
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Affiliation(s)
- Meenu Bhati
- Animal Genomics, ETH Zürich, Zürich, Switzerland.
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Whole genome detection of recent selection signatures in Sarabi cattle: a unique Iranian taurine breed. Genes Genomics 2019; 42:203-215. [DOI: 10.1007/s13258-019-00888-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/12/2019] [Indexed: 12/13/2022]
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Runs of Homozygosity and NetView analyses provide new insight into the genome-wide diversity and admixture of three German cattle breeds. PLoS One 2019; 14:e0225847. [PMID: 31800604 PMCID: PMC6892555 DOI: 10.1371/journal.pone.0225847] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/13/2019] [Indexed: 11/19/2022] Open
Abstract
Angler (RVA) and Red-and-White dual-purpose (RDN) cattle were in the past decades crossed with influential Red Holstein (RH) sires. However, genome-wide diversity studies in these breeds are lacking. The objective of the present study was to elucidate the genome-wide diversity and population structure of the three German cattle breeds. Using 40,851 single nucleotide polymorphism markers scored in 337 individuals, runs of homozygosity (ROH) were analysed in each breed. Clustering and a high-resolution network visualisation analyses were performed on an extended dataset that included 11 additional (outgroup) breeds. Genetic diversity levels were high with observed heterozygosity above 0.35 in all three breeds. Only RVA had a recent past effective population size (Ne) estimate above 100 at 5 generations ago. ROH length distribution followed a similar pattern across breeds and the majority of ROH were found in the length class of >5 to 10 Mb. Estimates of average inbreeding calculated from ROH (FROH) were 0.021 (RVA), 0.045 (RDN) and 0.053 (RH). Moderate to high positive correlations were found between FROH and pedigree inbreeding (FPED) and between FROH and inbreeding derived from the excess of homozygosity (FHOM), while the intercept of the regression of FROH on FPED was above zero. The population structure analysis showed strong evidence of admixture between RVA and RH. Introgression of RDN with RH genes was minimally detected and for the first time, the study uncovered Norwegian Red Cattle ancestry in RVA. Highly heterogeneous genetic background was found for RVA and RH and as expected, the breeds of the extended dataset effectively differentiated mostly based on geographical origin, validating our findings. The results of this study confirm the impact of RH sires on RVA and RDN populations. Furthermore, a close monitoring is suggested to curb further reduction of Ne in the breeds.
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Abstract
Genome-wide single nucleotide polymorphism (SNP) arrays can be used to explore homozygosity segments, where two haplotypes inherited from the parents are identical. In this study, we identified a total of 27,358 runs of homozygosity (ROH) with an average of 153 ROH events per animal in Chinese local cattle. The sizes of ROH events varied considerably ranging from 0.5 to 66 Mb, with an average length of 1.22 Mb. The highest average proportion of the genome covered by ROH (~11.54% of the cattle genome) was found in Nanda cattle (NDC) from South China, whereas the lowest average proportion (~3.1%) was observed in Yanhuang cattle (YHC). The average estimated FROH ranged from 0.03 in YHC to 0.12 in NDC. For each of three ROH classes with different sizes (Small 0.5-1 Mb, Medium 1-5 Mb and Large >5 Mb), the numbers and total lengths of ROH per individual showed considerable differences across breeds. Moreover, we obtained 993 to 3603 ROH hotspots (which were defined where ROH frequency at a SNP within each breed exceeded the 1% threshold) among eight cattle breeds. Our results also revealed several candidate genes embedded with ROH hotspots which may be related to environmental conditions and local adaptation. In conclusion, we generated baselines for homozygosity patterns in diverse Chinese cattle breeds. Our results suggested that selection has, at least partially, played a role with other factors in shaping the genomic patterns of ROH in Chinese local cattle and might provide valuable insights for understanding the genetic basis of economic and adaptive traits.
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Signer-Hasler H, Burren A, Ammann P, Drögemüller C, Flury C. Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds. Anim Genet 2019; 50:512-525. [PMID: 31365135 DOI: 10.1111/age.12828] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2019] [Indexed: 01/01/2023]
Abstract
A dataset consisting of 787 animals with high-density SNP chip genotypes (346 774 SNPs) and 939 animals with medium-density SNP chip genotypes (33 828 SNPs) from eight indigenous Swiss sheep breeds was analyzed to characterize population structure, quantify genomic inbreeding based on runs of homozygosity and identify selection signatures. In concordance with the recent known history of these breeds, the highest genetic diversity was observed in Engadine Red sheep and the lowest in Valais Blacknose sheep. Correlation between FPED and FROH was around 0.50 and thereby lower than that found in similar studies in cattle. Mean FROH estimates from medium-density data and HD data were highly correlated (0.95). Signatures of selection and candidate gene analysis revealed that the most prominent signatures of selection were found in the proximity of genes associated with body size (NCAPG, LCORL, LAP3, SPP1, PLAG1, ALOX12, TP53), litter size (SPP1), milk production (ABCG2, SPP1), coat color (KIT, ASIP, TBX3) and horn status (RXFP2). For the Valais Blacknose sheep, the private signatures in proximity of genes/QTL influencing body size, coat color and fatty acid composition were confirmed based on runs of homozygosity analysis. These private signatures underline the genetic uniqueness of the Valais Blacknose sheep breed. In conclusion, we identified differences in the genetic make-up of Swiss sheep breeds, and we present relevant candidate genes responsible for breed differentiation in locally adapted breeds.
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Affiliation(s)
- H Signer-Hasler
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Länggasse 85, 3052 , Zollikofen, Switzerland
| | - A Burren
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Länggasse 85, 3052 , Zollikofen, Switzerland
| | - P Ammann
- ProSpecieRara, Unter Brüglingen 6, 4052, Basel, Switzerland
| | - C Drögemüller
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland
| | - C Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Länggasse 85, 3052 , Zollikofen, Switzerland
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D’Ambrosio J, Phocas F, Haffray P, Bestin A, Brard-Fudulea S, Poncet C, Quillet E, Dechamp N, Fraslin C, Charles M, Dupont-Nivet M. Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding. Genet Sel Evol 2019; 51:26. [PMID: 31170906 PMCID: PMC6554922 DOI: 10.1186/s12711-019-0468-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 05/22/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Selective breeding is a relatively recent practice in aquaculture species compared to terrestrial livestock. Nevertheless, the genetic variability of farmed salmonid lines, which have been selected for several generations, should be assessed. Indeed, a significant decrease in genetic variability due to high selection intensity could have occurred, potentially jeopardizing the long-term genetic progress as well as the adaptive capacities of populations facing change(s) in the environment. Thus, it is important to evaluate the impact of selection practices on genetic diversity to limit future inbreeding. The current study presents an analysis of genetic diversity within and between six French rainbow trout (Oncorhynchus mykiss) experimental or commercial lines based on a medium-density single nucleotide polymorphism (SNP) chip and various molecular genetic indicators: fixation index (FST), linkage disequilibrium (LD), effective population size (Ne) and inbreeding coefficient derived from runs of homozygosity (ROH). RESULTS Our results showed a moderate level of genetic differentiation between selected lines (FST ranging from 0.08 to 0.15). LD declined rapidly over the first 100 kb, but then remained quite high at long distances, leading to low estimates of Ne in the last generation ranging from 24 to 68 depending on the line and methodology considered. These results were consistent with inbreeding estimates that varied from 10.0% in an unselected experimental line to 19.5% in a commercial line, and which are clearly higher than corresponding estimates in ruminants or pigs. In addition, strong variations in LD and inbreeding were observed along the genome that may be due to differences in local rates of recombination or due to key genes that tended to have fixed favorable alleles for domestication or production. CONCLUSIONS This is the first report on ROH for any aquaculture species. Inbreeding appeared to be moderate to high in the six French rainbow trout lines, due to founder effects at the start of the breeding programs, but also likely to sweepstakes reproductive success in addition to selection for the selected lines. Efficient management of inbreeding is a major goal in breeding programs to ensure that populations can adapt to future breeding objectives and SNP information can be used to manage the rate at which inbreeding builds up in the fish genome.
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Affiliation(s)
- Jonathan D’Ambrosio
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- SYSAAF Section Aquacole, Campus de Beaulieu, 35000 Rennes, France
| | - Florence Phocas
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Pierrick Haffray
- SYSAAF Section Aquacole, Campus de Beaulieu, 35000 Rennes, France
| | - Anastasia Bestin
- SYSAAF Section Aquacole, Campus de Beaulieu, 35000 Rennes, France
| | | | - Charles Poncet
- GDEC, INRA, Université Clermont-Auvergne, 63039 Clermont-Ferrand, France
| | - Edwige Quillet
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Nicolas Dechamp
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Clémence Fraslin
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- SYSAAF Section Aquacole, Campus de Beaulieu, 35000 Rennes, France
| | - Mathieu Charles
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Mei C, Junjvlieke Z, Raza SHA, Wang H, Cheng G, Zhao C, Zhu W, Zan L. Copy number variation detection in Chinese indigenous cattle by whole genome sequencing. Genomics 2019; 112:831-836. [PMID: 31145994 DOI: 10.1016/j.ygeno.2019.05.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/30/2019] [Accepted: 05/25/2019] [Indexed: 12/15/2022]
Abstract
Copy number variation (CNV) refers to a kind of structural variation, having functional and evolutionary effects on phenotypes. Thus far, further elucidation of the CNVs in different Chinese indigenous cattle breeds by whole genome sequencing have yet not been done. In this study, a comprehensive genomic analysis was performed on 75 cattle individuals including six Chinese indigenous cattle breeds and two non-native specialized beef cattle breeds. Based on the 11,486 CNVRs discovered, population analysis was performed, showed that all the cattle breeds clustered in to three clades, consistent with their lineages Bos taurus, Bos taurus × Bos indicus and Bos indicus. Importantly, a set of CNVRs related genes were found to be associated with the traits of interest, which include meat production or quality (CAST, ACTC1, etc.), adaption (BLA-DQB, EGLN2, etc.) and coat color (KIT, MITF, etc.). These results provide valuable full genome variation resources for Chinese bovine genome research and would be helpful for cattle breeding and selection programs in the future.
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Affiliation(s)
- Chugang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zainaguli Junjvlieke
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | | | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Chuping Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Wenjuan Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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Bieber A, Wallenbeck A, Leiber F, Fuerst-Waltl B, Winckler C, Gullstrand P, Walczak J, Wójcik P, Neff AS. Production level, fertility, health traits, and longevity in local and commercial dairy breeds under organic production conditions in Austria, Switzerland, Poland, and Sweden. J Dairy Sci 2019; 102:5330-5341. [PMID: 30954255 DOI: 10.3168/jds.2018-16147] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/06/2019] [Indexed: 11/19/2022]
Abstract
Our aim was to map the performance of local (native) dairy cattle breeds in Austria, Switzerland, Poland, and Sweden with regard to production, fertility, longevity, and health-associated traits and to compare them with commercial (modern) breeds. For this purpose, we analyzed test-day records (July 1, 2011, to June 30, 2014) and treatment records (Austria, Sweden) of cows managed on organic farms. We performed country-wise comparisons of 123,415 lactations from Original Braunvieh (OB) and Grey Cattle (AL) with Braunvieh (BV; Brown Swiss blood >60%) in Switzerland; AL with BV (Brown Swiss blood >50%) in Austria; Polish Black and White (ZB), Polish Red and White (ZR), and Polish Red (RP) with Polish Holstein Friesian (PHF) in Poland; and Swedish Red (SRB) with Swedish Holstein (SH) in Sweden. Average milk yields were substantially lower for local compared with commercial breeds in all countries; differences ranged from 750 kg (Sweden) to 1,822 kg (Austria), albeit on very different average levels. Local breeds showed a longer productive lifetime by 0.64, 0.83, 1.42, and 0.20 lactations in Switzerland, Austria, Poland, and Sweden, respectively, again on very different levels in each country. Regarding fertility traits, calving interval was shorter in local than in commercial breeds by 13 (Sweden), 14 (Switzerland), and 20 d (Austria, Poland). Insemination index was lower in certain local breeds by 0.15 (Switzerland), 0.14 (Austria), 0.21 (Poland), and 0.13 (Sweden). Several local breeds showed a lower proportion of cows with >100,000 somatic cells/mL. This was the case in Switzerland (OB 24.2%; BV 35.8%), Austria (AL 25.3%; BV 36.9%), and Sweden (SRB 42.4%; SH 43.4%). In contrast, the respective proportion in Poland exceeded 82% in all breeds except the commercial PHF (76.1%). In Sweden, lactations with veterinary treatments were considerably less prevalent in SRB (15.6%) than in SH (21.7%). In Austria, breeds differed only in treatments for udder disorders, which favored AL. In conclusion, the markedly lower milk yields of local breeds are partly counterbalanced by (somewhat inconsistent) advantages in longevity, fertility, and health traits across 4 European countries. This indicates that the robustness of local breeds can contribute to improved sustainability of organic dairy systems.
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Affiliation(s)
- Anna Bieber
- Department of Livestock Sciences, Research Institute of Organic Agriculture (FiBL), 5070 Frick, Switzerland.
| | - Anna Wallenbeck
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), 750 07 Uppsala, Sweden; Department of Animal Environment and Health, Swedish University of Agricultural Sciences (SLU), 532 31 Skara, Sweden
| | - Florian Leiber
- Department of Livestock Sciences, Research Institute of Organic Agriculture (FiBL), 5070 Frick, Switzerland
| | - Birgit Fuerst-Waltl
- University of Natural Resources and Life Sciences Vienna (BOKU), 1180 Vienna, Austria
| | - Christoph Winckler
- University of Natural Resources and Life Sciences Vienna (BOKU), 1180 Vienna, Austria
| | - Patricia Gullstrand
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), 750 07 Uppsala, Sweden
| | - Jacek Walczak
- National Research Institute of Animal Production, 32-083 Balice, Poland
| | - Piotr Wójcik
- National Research Institute of Animal Production, 32-083 Balice, Poland
| | - Anet Spengler Neff
- Department of Livestock Sciences, Research Institute of Organic Agriculture (FiBL), 5070 Frick, Switzerland
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