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Sukhija N, Malik AA, Devadasan JM, Dash A, Bidyalaxmi K, Ravi Kumar D, Kousalaya Devi M, Choudhary A, Kanaka KK, Sharma R, Tripathi SB, Niranjan SK, Sivalingam J, Verma A. Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India. Anim Biotechnol 2024; 35:2290521. [PMID: 38088885 DOI: 10.1080/10495398.2023.2290521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
The peculiarity of Indian cattle lies in milk quality, resistance to diseases and stressors as well as adaptability. The investigation addressed selection signatures in Gir and Tharparkar cattle, belonging to arid ecotypes of India. Double digest restriction-site associated DNA sequencing (ddRAD-seq) yielded nearly 26 million high-quality reads from unrelated seven Gir and seven Tharparkar cows. In all, 19,127 high-quality SNPs were processed for selection signature analysis. An approach involving within-population composite likelihood ratio (CLR) statistics and between-population FST statistics was used to capture selection signatures within and between the breeds, respectively. A total of 191 selection signatures were addressed using CLR and FST approaches. Selection signatures overlapping 86 and 73 genes were detected as Gir- and Tharparkar-specific, respectively. Notably, genes related to production (CACNA1D, GHRHR), reproduction (ESR1, RBMS3), immunity (NOSTRIN, IL12B) and adaptation (ADAM22, ASL) were annotated to selection signatures. Gene pathway analysis revealed genes in insulin/IGF pathway for milk production, gonadotropin releasing hormone pathway for reproduction, Wnt signalling pathway and chemokine and cytokine signalling pathway for adaptation. This is the first study where selection signatures are identified using ddRAD-seq in indicine cattle breeds. The study shall help in conservation and leveraging genetic improvements in Gir and Tharparkar cattle.
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Affiliation(s)
- Nidhi Sukhija
- ICAR-National Dairy Research Institute, Karnal, India
| | - Anoop Anand Malik
- TERI School of Advanced Studies, Delhi, India
- The Energy and Resources Institute, North Eastern Regional Centre, Guwahati, India
| | | | | | - Kangabam Bidyalaxmi
- ICAR-National Dairy Research Institute, Karnal, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - D Ravi Kumar
- ICAR-National Dairy Research Institute, Karnal, India
| | | | | | - K K Kanaka
- ICAR-National Dairy Research Institute, Karnal, India
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | | | | | | | - Archana Verma
- ICAR-National Dairy Research Institute, Karnal, India
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Ayalew W, Wu X, Tarekegn GM, Sisay Tessema T, Naboulsi R, Van Damme R, Bongcam-Rudloff E, Edea Z, Chu M, Enquahone S, Liang C, Yan P. Whole Genome Scan Uncovers Candidate Genes Related to Milk Production Traits in Barka Cattle. Int J Mol Sci 2024; 25:6142. [PMID: 38892330 PMCID: PMC11172929 DOI: 10.3390/ijms25116142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/23/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
In this study, our primary aim was to explore the genomic landscape of Barka cattle, a breed recognized for high milk production in a semi-arid environment, by focusing on genes with known roles in milk production traits. We employed genome-wide analysis and three selective sweep detection methods (ZFST, θπ ratio, and ZHp) to identify candidate genes associated with milk production and composition traits. Notably, ACAA1, P4HTM, and SLC4A4 were consistently identified by all methods. Functional annotation highlighted their roles in crucial biological processes such as fatty acid metabolism, mammary gland development, and milk protein synthesis. These findings contribute to understanding the genetic basis of milk production in Barka cattle, presenting opportunities for enhancing dairy cattle production in tropical climates. Further validation through genome-wide association studies and transcriptomic analyses is essential to fully exploit these candidate genes for selective breeding and genetic improvement in tropical dairy cattle.
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Affiliation(s)
- Wondossen Ayalew
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (W.A.); (X.W.); (M.C.)
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia
| | - Xiaoyun Wu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (W.A.); (X.W.); (M.C.)
| | - Getinet Mekuriaw Tarekegn
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia
- Scotland’s Rural College (SRUC), Easter Bush Campus, Roslin Institute Building, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Tesfaye Sisay Tessema
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia
| | - Rakan Naboulsi
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institute, Tomtebodavägen 18A, 17177 Stockholm, Sweden
| | - Renaud Van Damme
- Department of Animal Biosciences, Bioinformatics Section, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (E.B.-R.)
| | - Erik Bongcam-Rudloff
- Department of Animal Biosciences, Bioinformatics Section, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (E.B.-R.)
| | - Zewdu Edea
- Ethiopian Bio and Emerging Technology Institute, Addis Ababa P.O. Box 5954, Ethiopia;
| | - Min Chu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (W.A.); (X.W.); (M.C.)
| | - Solomon Enquahone
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia
| | - Chunnian Liang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (W.A.); (X.W.); (M.C.)
| | - Ping Yan
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (W.A.); (X.W.); (M.C.)
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Howe NS, Hale MC, Waters CD, Schaal SM, Shedd KR, Larson WA. Genomic evidence for domestication selection in three hatchery populations of Chinook salmon, Oncorhynchus tshawytscha. Evol Appl 2024; 17:e13656. [PMID: 38357359 PMCID: PMC10866082 DOI: 10.1111/eva.13656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
Fish hatcheries are widely used to enhance fisheries and supplement declining wild populations. However, substantial evidence suggests that hatchery fish are subject to differential selection pressures compared to their wild counterparts. Domestication selection, or adaptation to the hatchery environment, poses a risk to wild populations if traits specific to success in the hatchery environment have a genetic component and there is subsequent introgression between hatchery and wild fish. Few studies have investigated domestication selection in hatcheries on a genomic level, and even fewer have done so in parallel across multiple hatchery-wild population pairs. In this study, we used low-coverage whole-genome sequencing to investigate signals of domestication selection in three separate hatchery populations of Chinook salmon, Oncorhynchus tshawytscha, after approximately seven generations of divergence from their corresponding wild progenitor populations. We sequenced 192 individuals from populations across Southeast Alaska and estimated genotype likelihoods at over six million loci. We discovered a total of 14 outlier peaks displaying high genetic differentiation (F ST) between hatchery-wild pairs, although no peaks were shared across the three comparisons. Peaks were small (53 kb on average) and often displayed elevated absolute genetic divergence (D xy) and linkage disequilibrium, suggesting some level of domestication selection has occurred. Our study provides evidence that domestication selection can lead to genetic differences between hatchery and wild populations in only a few generations. Additionally, our data suggest that population-specific adaptation to hatchery environments likely occurs through different genetic pathways, even for populations with similar standing genetic variation. These results highlight the need to collect paired genotype-phenotype data to understand how domestication may be affecting fitness and to identify potential management practices that may mitigate genetic risks despite multiple pathways of domestication.
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Affiliation(s)
- Natasha S. Howe
- Department of BiologyTexas Christian UniversityFort WorthTexasUSA
| | - Matthew C. Hale
- Department of BiologyTexas Christian UniversityFort WorthTexasUSA
| | - Charles D. Waters
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
| | - Sara M. Schaal
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
| | - Kyle R. Shedd
- Alaska Department of Fish and Game, Division of Commercial FisheriesGene Conservation LaboratoryAnchorageAlaskaUSA
| | - Wesley A. Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
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Velayudhan SM, Alam S, Yin T, Brügemann K, Buerkert A, Sejian V, Bhatta R, Schlecht E, König S. Selective Sweeps in Cattle Genomes in Response to the Influence of Urbanization and Environmental Contamination. Genes (Basel) 2023; 14:2083. [PMID: 38003026 PMCID: PMC10671461 DOI: 10.3390/genes14112083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
A genomic study was conducted to identify the effects of urbanization and environmental contaminants with heavy metals on selection footprints in dairy cattle populations reared in the megacity of Bengaluru, South India. Dairy cattle reared along the rural-urban interface of Bengaluru with/without access to roughage from public lakeshores were selected. The genotyped animals were subjected to the cross-population-extended haplotype homozygosity (XP-EHH) methodology to infer selection sweeps caused by urbanization (rural, mixed, and urban) and environmental contamination with cadmium and lead. We postulated that social-ecological challenges contribute to mechanisms of natural selection. A number of selection sweeps were identified when comparing the genomes of cattle located in rural, mixed, or urban regions. The largest effects were identified on BTA21, displaying pronounced peaks for selection sweeps for all three urbanization levels (urban_vs_rural, urban_vs_mixed and rural_vs_mixed). Selection sweeps are located in chromosomal segments in close proximity to the genes lrand rab interactor 3 (RIN3), solute carrier family 24 member 4 (SLC24A4), tetraspanin 3 (TSPAN3), and proline-serine-threonine phosphatase interacting protein 1 (PSTPIP1). Functional enrichment analyses of the selection sweeps for all three comparisons revealed a number of gene ontology (GO) and KEGG terms, which were associated with reproduction, metabolism, and cell signaling-related functional mechanisms. Likewise, a number of the chromosomal segments under selection were observed when creating cattle groups according to cadmium and lead contaminations. Stronger and more intense positive selection sweeps were observed for the cadmium contaminated group, i.e., signals of selection on BTA 16 and BTA19 in close proximity to genes regulating the somatotropic axis (growth factor receptor bound protein 2 (GRB2) and cell ion exchange (chloride voltage-gated channel 6 (CLCN6)). A few novel, so far uncharacterized genes, mostly with effects on immune physiology, were identified. The lead contaminated group revealed sweeps which were annotated with genes involved in carcass traits (TNNC2, SLC12A5, and GABRA4), milk yield (HTR1D, SLCO3A1, TEK, and OPCML), reproduction (GABRA4), hypoxia/stress response (OPRD1 and KDR), cell adhesion (PCDHGC3), inflammatory response (ADORA2A), and immune defense mechanism (ALCAM). Thus, the findings from this study provide a deeper insight into the genomic regions under selection under the effects of urbanization and environmental contamination.
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Affiliation(s)
| | - Shahin Alam
- Animal Husbandry in the Tropics and Subtropics, University of Kassel and Georg-August-Universität Göttingen, Steinstr. 19, 37213 Witzenhausen, Germany
| | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Ludwigstraße 21 b, 35390 Giessen, Germany
| | - Kerstin Brügemann
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Ludwigstraße 21 b, 35390 Giessen, Germany
| | - Andreas Buerkert
- Organic Plant Production and Agroecosystems Research in the Tropics and Subtropics, University of Kassel, 37213 Witzenhausen, Germany
| | - Veerasamy Sejian
- National Institute of Animal Nutrition and Physiology (NIANP), Hosur Rd, Chennakeshava Nagar, Adugodi, Bengaluru 560030, India
| | - Raghavendra Bhatta
- National Institute of Animal Nutrition and Physiology (NIANP), Hosur Rd, Chennakeshava Nagar, Adugodi, Bengaluru 560030, India
| | - Eva Schlecht
- Animal Husbandry in the Tropics and Subtropics, University of Kassel and Georg-August-Universität Göttingen, Steinstr. 19, 37213 Witzenhausen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Ludwigstraße 21 b, 35390 Giessen, Germany
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Yang K, Zhang J, Zhao Y, Shao Y, Zhai M, Liu H, Zhang L. Whole Genome Resequencing Revealed the Genetic Relationship and Selected Regions among Baicheng-You, Beijing-You, and European-Origin Broilers. BIOLOGY 2023; 12:1397. [PMID: 37997996 PMCID: PMC10669838 DOI: 10.3390/biology12111397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]
Abstract
As the only two You-chicken breeds in China, Baicheng-You (BCY) and Beijing-You (BJY) chickens are famous for their good meat quality. However, so far, the molecular basis of germplasm of the two You-chicken breeds is not yet clear. The genetic relationship among BCY, BJY, and European-origin broilers (BRs) was analyzed using whole genome resequencing data to contribute to this issue. A total of 18,852,372 single nucleotide polymorphisms (SNPs) were obtained in this study. After quality control, 8,207,242 SNPs were applied to subsequent analysis. The data indicated that BJY chickens possessed distant distance with BRs (genetic differentiation coefficient (FST) = 0.1681) and BCY (FST = 0.1231), respectively, while BCY and BRs had a closer relationship (FST = 0.0946). In addition, by using FST, cross-population extended haplotype homozygosity (XP-EHH), and cross-population composite likelihood ratio (XP-CLR) methods, we found 374 selected genes between BJY and BRs chickens and 279 selected genes between BCY and BJY chickens, respectively, which contained a number of important candidates or genetic variations associated with feather growth and fat deposition of BJY chickens and potential disease resistance of BCY chickens. Our study demonstrates a genome-wide view of genetic diversity and differentiation among BCY, BJY, and BRs. These results may provide useful information on a molecular basis related to the special characteristics of these broiler breeds, thus enabling us to better understand the formation mechanism of Chinese-You chickens.
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Affiliation(s)
- Kai Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
| | - Jian Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Z.); (H.L.)
| | - Yuelei Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
| | - Yonggang Shao
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.S.); (M.Z.)
| | - Manjun Zhai
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.S.); (M.Z.)
| | - Huagui Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Z.); (H.L.)
| | - Lifan Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
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Martinez R, Bejarano D, Ramírez J, Ocampo R, Polanco N, Perez JE, Onofre HG, Rocha JF. Genomic variability and population structure of six Colombian cattle breeds. Trop Anim Health Prod 2023; 55:185. [PMID: 37130925 PMCID: PMC10154261 DOI: 10.1007/s11250-023-03574-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 03/29/2023] [Indexed: 05/04/2023]
Abstract
Analyses of the genetic diversity of indigenous cattle are essential for implementing conservation programs, promoting their sustainable use and maintaining productive advantages offered by these breeds in local conditions. The aim of this study was to investigate the genetic diversity and population structure of six Colombian cattle breeds: Blanco Orejinegro (BON), Costeño con Cuernos (CCC), Romosinuano (ROM), Sanmartinero (SAM), Casanareño (CAS), and Hartón del Valle (HDV). Two additional breed groups were included for comparison: Zebu (CEB) and a crossbreed of Colombian cattle breeds × Zebu. Genetic diversity within breeds was analyzed using expected heterozygosity (He), inbreeding coefficient (f), and runs of homozygosity (ROH). Population structure was assessed using model-based clustering (ADMIXTURE) and principal components analysis (PCA). Zebu cattle showed the lowest genetic diversity (He = 0.240). Breeds with the highest genetic diversity level were HDV and BON (He = 0.350 and 0.340, respectively). Inbreeding was lower for Colombian cattle breeds ranging between 0.005 and 0.045. Overall, the largest average genetic distance was found among the group of Colombian cattle breeds and Zebu, while the smallest was found between ROM and CCC. Model-based clustering revealed some level of admixture among HDV and CAS cattle which is consistent with their recent history. The results of the present study provide a useful insight on the genetic structure of Colombian cattle breeds.
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Affiliation(s)
- Rodrigo Martinez
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Diego Bejarano
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Julián Ramírez
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Ricardo Ocampo
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Mosquera, Cundinamarca, Colombia.
| | - Nelson Polanco
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Juan Esteban Perez
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Héctor Guillermo Onofre
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Juan Felipe Rocha
- Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Mosquera, Cundinamarca, Colombia
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Steyn Y, Lawlor T, Masuda Y, Tsuruta S, Legarra A, Lourenco D, Misztal I. Nonparallel genome changes within subpopulations over time contributed to genetic diversity within the US Holstein population. J Dairy Sci 2023; 106:2551-2572. [PMID: 36797192 DOI: 10.3168/jds.2022-21914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 10/03/2022] [Indexed: 02/16/2023]
Abstract
Maintaining genetic variation in a population is important for long-term genetic gain. The existence of subpopulations within a breed helps maintain genetic variation and diversity. The 20,990 genotyped animals, representing the breeding animals in the year 2014, were identified as the sires of animals born after 2010 with at least 25 progenies, and females measured for type traits within the last 2 yr of data. K-means clustering with 5 clusters (C1, C2, C3, C4, and C5) was applied to the genomic relationship matrix based on 58,990 SNP markers to stratify the selected candidates into subpopulations. The general higher inbreeding resulting from within-cluster mating than across-cluster mating suggests the successful stratification into genetically different groups. The largest cluster (C4) contained animals that were less related to each animal within and across clusters. The average fixation index was 0.03, indicating that the populations were differentiated, and allele differences across the subpopulations were not due to drift alone. Starting with the selected candidates within each cluster, a family unit was identified by tracing back through the pedigree, identifying the genotyped ancestors, and assigning them to a pseudogeneration. Each of the 5 families (F1, F2, F3, F4, and F5) was traced back for 10 generations, allowing for changes in frequency of individual SNPs over time to be observed, which we call allele frequencies change. Alternative procedures were used to identify SNPs changing in a parallel or nonparallel way across families. For example, markers that have changed the most in the whole population, markers that have changed differently across families, and genes previously identified as those that have changed in allele frequency. The genomic trajectory taken by each family involves selective sweeps, polygenic changes, hitchhiking, and epistasis. The replicate frequency spectrum was used to measure the similarity of change across families and showed that populations have changed differently. The proportion of markers that reversed direction in allele frequency change varied from 0.00 to 0.02 if the rate of change was greater than 0.02 per generation, or from 0.14 to 0.24 if the rate of change was greater than 0.005 per generation within each family. Cluster-specific SNP effects for stature were estimated using only females and applied to obtain indirect genomic predictions for males. Reranking occurs depending on SNP effects used. Additive genetic correlations between clusters show possible differences in populations. Further research is required to determine how this knowledge can be applied to maintain diversity and optimize selection decisions in the future.
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Affiliation(s)
- Y Steyn
- Department of Animal and Dairy Science, University of Georgia, 425 River Road, Athens 30602.
| | - T Lawlor
- Holstein Association USA Inc., Brattleboro, VT 05302
| | - Y Masuda
- Department of Animal and Dairy Science, University of Georgia, 425 River Road, Athens 30602
| | - S Tsuruta
- Department of Animal and Dairy Science, University of Georgia, 425 River Road, Athens 30602
| | - A Legarra
- GenPhySE, INRA, INPT, ENVT, Université de Toulouse, Castanet-Tolosan 31520, France
| | - D Lourenco
- Department of Animal and Dairy Science, University of Georgia, 425 River Road, Athens 30602
| | - I Misztal
- Department of Animal and Dairy Science, University of Georgia, 425 River Road, Athens 30602
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Assessment of Genetic Diversity, Runs of Homozygosity, and Signatures of Selection in Tropical Milking Criollo Cattle Using Pedigree and Genomic Data. Genes (Basel) 2022; 13:genes13101896. [PMID: 36292782 PMCID: PMC9602073 DOI: 10.3390/genes13101896] [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: 09/28/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022] Open
Abstract
The objective of this study was to evaluate the genetic diversity of the Tropical Milking Criollo cattle (TMC) breed in Mexico through parameters derived from pedigree and genomic information assessment. The pedigree file consisted of 3780 animals. Seventy-nine bovines were genotyped with the medium-density single nucleotide polymorphism chip and considered a reference population for pedigree analysis. The effective population size and the probability of gene origin used to assess the evolution of genetic diversity were calculated with pedigree information. Inbreeding coefficients were evaluated based on pedigree (FPed), the genomic relationship matrix (FGRM), and runs of homozygosity (FROH) of different length classes. The average inbreeding was 2.82 ± 2.66%, −0.7 ± 3.8%, and 10.9 ± 3.0% for FPED, FGRM, and FROH, respectively. Correlation between FPED and FROH was significant only for runs of homozygosity > 4 Mb, indicating the FPED of a population with an average equivalent complete generation of five only recovers the most recent inbreeding. The parameters of the probability of gene origin indicated the existence of genetic bottlenecks and the loss of genetic diversity in the history of the TMC cattle population; however, pedigree and genomic information revealed the existence of current sufficient genetic diversity to design a sustainable breeding program.
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Naji MM, Jiang Y, Utsunomiya YT, Rosen BD, Sölkner J, Wang C, Jiang L, Zhang Q, Zhang Y, Ding X, Mészáros G. Favored single nucleotide variants identified using whole genome Re-sequencing of Austrian and Chinese cattle breeds. Front Genet 2022; 13:974787. [PMID: 36238155 PMCID: PMC9552183 DOI: 10.3389/fgene.2022.974787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022] Open
Abstract
Cattle have been essential for the development of human civilization since their first domestication few thousand years ago. Since then, they have spread across vast geographic areas following human activities. Throughout generations, the cattle genome has been shaped with detectable signals induced by various evolutionary processes, such as natural and human selection processes and demographic events. Identifying such signals, called selection signatures, is one of the primary goals of population genetics. Previous studies used various selection signature methods and normalized the outputs score using specific windows, in kbp or based on the number of SNPs, to identify the candidate regions. The recent method of iSAFE claimed for high accuracy in pinpointing the candidate SNPs. In this study, we analyzed whole-genome resequencing (WGS) data of ten individuals from Austrian Fleckvieh (Bos taurus) and fifty individuals from 14 Chinese indigenous breeds (Bos taurus, Bos taurus indicus, and admixed). Individual WGS reads were aligned to the cattle reference genome of ARS. UCD1.2 and subsequently undergone single nucleotide variants (SNVs) calling pipeline using GATK. Using these SNVs, we examined the population structure using principal component and admixture analysis. Then we refined selection signature candidates using the iSAFE program and compared it with the classical iHS approach. Additionally, we run Fst population differentiation from these two cattle groups. We found gradual changes of taurine in north China to admixed and indicine to the south. Based on the population structure and the number of individuals, we grouped samples to Fleckvieh, three Chinese taurines (Kazakh, Mongolian, Yanbian), admixed individuals (CHBI_Med), indicine individuals (CHBI_Low), and a combination of admixed and indicine (CHBI) for performing iSAFE and iHS tests. There were more significant SNVs identified using iSAFE than the iHS for the candidate of positive selection and more detectable signals in taurine than in indicine individuals. However, combining admixed and indicine individuals decreased the iSAFE signals. From both within-population tests, significant SNVs are linked to the olfactory receptors, production, reproduction, and temperament traits in taurine cattle, while heat and parasites tolerance in the admixed individuals. Fst test suggests similar patterns of population differentiation between Fleckvieh and three Chinese taurine breeds against CHBI. Nevertheless, there are genes shared only among the Chinese taurine, such as PAX5, affecting coat color, which might drive the differences between these yellowish coated breeds, and those in the greater Far East region.
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Affiliation(s)
- Maulana M. Naji
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Yifan Jiang
- China Agricultural University, Beijing, China
| | - Yuri T. Utsunomiya
- Department of Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Araçatuba, Brazil
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, USDA‐ARS, Beltsville, MD, United States
| | - Johann Sölkner
- University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Li Jiang
- China Agricultural University, Beijing, China
| | - Qin Zhang
- China Agricultural University, Beijing, China
| | - Yi Zhang
- China Agricultural University, Beijing, China
| | - Xiangdong Ding
- China Agricultural University, Beijing, China
- *Correspondence: Xiangdong Ding, ; Gábor Mészáros,
| | - Gábor Mészáros
- University of Natural Resources and Life Sciences, Vienna, Austria
- *Correspondence: Xiangdong Ding, ; Gábor Mészáros,
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10
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Zare M, Atashi H, Hostens M. Genome-Wide Association Study for Lactation Performance in the Early and Peak Stages of Lactation in Holstein Dairy Cows. Animals (Basel) 2022; 12:ani12121541. [PMID: 35739877 PMCID: PMC9219502 DOI: 10.3390/ani12121541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/27/2022] [Accepted: 06/10/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Although genome-wide association studies (GWAS) have been carried out within a variety of cattle breeds, they are mainly based on the accumulated 305-day lactation yield traits estimated by summing the test-day recorded every day during the lactation period, or combining the weekly or monthly test-day records by linear interpolation. Since the additive genetic variance for milk yield and composition changes during lactation, the genetic effects of QTL related to these traits are not constant during the lactation period. Therefore, a better understanding of the genetic architecture of milk production traits in different lactation stages (e.g., beginning, peak, and end stages of lactation) is needed. The aim of this study was to detect genomic loci associated with lactation performance during 9 to 50 days in milk (DIM) in Holstein dairy cows. Candidate genes identified for milk production traits showed contrasting results between the EARLY and PEAK stages of lactation. Based on the results of this study, it can be concluded that in any genomic study it should be taken into account that the genetic effects of genes related to the lactation performance are not constant during the lactation period. Abstract This study aimed to detect genomic loci associated with the lactation performance during 9 to 50 days in milk (DIM) in Holstein dairy cows. Daily milk yield (MY), fat yield (FY), and protein yield (PY) during 9 to 50 DIM were recorded on 134 multiparous Holstein dairy cows distributed in four research herds. Fat- and protein-corrected milk (FPCM), fat-corrected milk (FCM), and energy-corrected milk (ECM) were predicted. The records collected during 9 to 25 DIM were put into the early stage of lactation (EARLY) and those collected during 26 to 50 DIM were put into the peak stage of lactation (PEAK). Then, the mean of traits in each cow included in each lactation stage (EARLY and PEAK) were estimated and used as phenotypic observations for the genome-wide association study. The included animals were genotyped with the Illumina BovineHD Genotyping BeadChip (Illumina Inc., San Diego, CA, USA) for a total of 777,962 single nucleotide polymorphisms (SNPs). After quality control, 585,109 variants were analyzed using GEMMA software in a mixed linear model. Although there was no SNP associated with traits included at the 5% genome-wide significance threshold, 18 SNPs were identified to be associated with milk yield and composition at the suggestive genome-wide significance threshold. Candidate genes identified for milk production traits showed contrasting results between the EARLY and PEAK stages of lactation. This suggests that differential sets of candidate genes underlie the phenotypic expression of the considered traits in the EARLY and PEAK stages of lactation. Although further functional studies are needed to validate our findings in independent populations, it can be concluded that in any genomic study it should be taken into account that the genetic effects of genes related to the lactation performance are not constant during the lactation period.
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Affiliation(s)
- Mahsa Zare
- Department of Animal Science, Shiraz University, Shiraz 7144113131, Iran; (M.Z.); (H.A.)
| | - Hadi Atashi
- Department of Animal Science, Shiraz University, Shiraz 7144113131, Iran; (M.Z.); (H.A.)
| | - Miel Hostens
- Department of Population Health Sciences, University of Utrecht, Yalelaan 7, 3584 CL Utrecht, The Netherlands
- Correspondence: ; Tel.: +31-30-253-1820
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11
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Magnier J, Druet T, Naves M, Ouvrard M, Raoul S, Janelle J, Moazami-Goudarzi K, Lesnoff M, Tillard E, Gautier M, Flori L. The genetic history of Mayotte and Madagascar cattle breeds mirrors the complex pattern of human exchanges in Western Indian Ocean. G3 GENES|GENOMES|GENETICS 2022; 12:6523972. [PMID: 35137043 PMCID: PMC8982424 DOI: 10.1093/g3journal/jkac029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
Despite their central economic and cultural role, the origin of cattle populations living in Indian Ocean islands still remains poorly documented. Here, we unravel the demographic and adaptive histories of the extant Zebus from the Mayotte and Madagascar islands using high-density SNP genotyping data. We found that these populations are very closely related and both display a predominant indicine ancestry. They diverged in the 16th century at the arrival of European people who transformed the trade network in the area. Their common ancestral cattle population originates from an admixture between an admixed African zebu population and an Indian zebu that occurred around the 12th century at the time of the earliest contacts between human African populations of the Swahili corridor and Austronesian people from Southeast Asia in Comoros and Madagascar. A steep increase in the estimated population sizes from the beginning of the 16th to the 17th century coincides with the expansion of the cattle trade. By carrying out genome scans for recent selection in the two cattle populations from Mayotte and Madagascar, we identified sets of candidate genes involved in biological functions (cancer, skin structure, and UV-protection, nervous system and behavior, organ development, metabolism, and immune response) broadly representative of the physiological adaptation to tropical conditions. Overall, the origin of the cattle populations from Western Indian Ocean islands mirrors the complex history of human migrations and trade in this area.
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Affiliation(s)
- Jessica Magnier
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Montpellier 34398, France
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R, Faculty of Veterinary Medicine, University of Liège, Liège 4000, Belgium
| | | | | | | | - Jérôme Janelle
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Saint-Pierre 97410, France
| | | | - Matthieu Lesnoff
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Montpellier 34398, France
| | - Emmanuel Tillard
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Saint-Pierre 97410, France
| | - Mathieu Gautier
- CBGP, INRAE, CIRAD, IRD, L’Institut Agro, University of Montpellier, Montferrier sur Lez 34988, France
| | - Laurence Flori
- SELMET, INRAE, CIRAD, L’Institut Agro, University of Montpellier, Montpellier 34398, France
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12
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Cesarani A, Gaspa G, Correddu F, Dimauro C, Macciotta NPP. Unravelling the effect of environment on the genome of Sarda breed ewes using Runs of Homozygosity. J Anim Breed Genet 2022; 139:292-306. [PMID: 34984736 DOI: 10.1111/jbg.12666] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/15/2021] [Accepted: 12/22/2021] [Indexed: 02/04/2023]
Abstract
Natural adaptation and artificial selection have shaped the genome of modern livestock breeds. Among SNP-based metrics that are used to detect signatures of selection at genome-wide level, runs of homozygosity (ROH) are getting increasing popularity. In this paper, ROH distribution and features of a sample of 823 Sarda breed ewes farmed at different levels of altitude are analysed to investigate the effect of the environment on the patterns of homozygosity. A total of 46,829 (33,087 unique) ROH were detected. OAR2 exhibited the largest average number of ROH per animal. The most frequent ROH (OAR27, 38.9-44.2 Mb) was shared by 327. ROH length was statistically affected (p < 0.001) by both the altitude and temperature of the place where the flock was located. The highest probability of a SNP falling in a ROH was observed for hill ewes, whereas the smallest one for mountain. A total of 457 SNP exceeded the 99th percentile of the ROH count per SNP distribution and were considered significant. These markers mapped in eight chromosomes and they clustered into 17 ROH islands, where 80 candidate genes were mapped. Results of this study highlighted differences in the ROH distribution and features among sheep farmed in flocks located at different levels of altitude, confirming the role of environmental adaptability in shaping the genome of this breed.
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Affiliation(s)
- Alberto Cesarani
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy.,Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA
| | - Giustino Gaspa
- Department of Agricultural, Forestry and Alimentary Sciences, University of Torino, Grugliasco, Italy
| | - Fabio Correddu
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy
| | - Corrado Dimauro
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy
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13
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Bang NN, Hayes BJ, Lyons RE, Randhawa IAS, Gaughan JB, McNeill DM. Genomic diversity and breed composition of Vietnamese smallholder dairy cows. J Anim Breed Genet 2021; 139:145-160. [PMID: 34559415 DOI: 10.1111/jbg.12651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 11/29/2022]
Abstract
Vietnamese smallholder dairy cows (VDC) are the result of crossbreeding between different zebu (ZEB) and taurine dairy breeds through many undefined generations. Thus, the predominant breed composition of VDC is currently unknown. This study aimed to evaluate the level of genetic diversity and breed composition of VDC. The SNP data of 344 animals from 32 farms located across four dairy regions of Vietnam were collected and merged with genomic reference data, which included three ZEB breeds: Red Sindhi, Sahiwal and Brahman, three taurine breeds: Holstein (HOL), Jersey (JER) and Brown Swiss (BSW), and a composite breed: Chinese Yellow cattle. Diversity and admixture analyses were applied to the merged data set. The VDC were not excessively inbred, as indicated by very low inbreeding coefficients (Wright's FIS ranged from -0.017 to 0.003). The genetic fractions in the test herds suggested that the VDC are primarily composed of HOL (85.0%); however, JER (6.0%), BSW 5.3%) and ZEB (4.5%) had also contributed. Furthermore, major genotype groupings in the test herds were pure HOL (48%), B3:15/16HOL_1/16ZEB (22%) and B2:7/8HOL_1/8ZEB (12%). The genetic makeup of the VDC is mainly components of various dairy breeds but also has a small percentage of ZEB; thus, the VDC could be a good genetic base for selecting high milk-producing cows with some degree of adaptation to tropical conditions.
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Affiliation(s)
- Nguyen N Bang
- School of Veterinary Science, The University of Queensland, Gatton, Qld, Australia.,Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Qld, Australia
| | - Russell E Lyons
- School of Veterinary Science, The University of Queensland, Gatton, Qld, Australia
| | - Imtiaz A S Randhawa
- School of Veterinary Science, The University of Queensland, Gatton, Qld, Australia
| | - John B Gaughan
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, Qld, Australia
| | - David M McNeill
- School of Veterinary Science, The University of Queensland, Gatton, Qld, Australia
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14
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Johnsson M, Jungnickel MK. Evidence for and localization of proposed causative variants in cattle and pig genomes. Genet Sel Evol 2021; 53:67. [PMID: 34461824 PMCID: PMC8404348 DOI: 10.1186/s12711-021-00662-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/20/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND This paper reviews the localization of published potential causative variants in contemporary pig and cattle reference genomes, and the evidence for their causality. In spite of the difficulties inherent to the identification of causative variants from genetic mapping and genome-wide association studies, researchers in animal genetics have proposed putative causative variants for several traits relevant to livestock breeding. RESULTS For this review, we read the literature that supports potential causative variants in 13 genes (ABCG2, DGAT1, GHR, IGF2, MC4R, MSTN, NR6A1, PHGK1, PRKAG3, PLRL, RYR1, SYNGR2 and VRTN) in cattle and pigs, and localized them in contemporary reference genomes. We review the evidence for their causality, by aiming to separate the evidence for the locus, the proposed causative gene and the proposed causative variant, and report the bioinformatic searches and tactics needed to localize the sequence variants in the cattle or pig genome. CONCLUSIONS Taken together, there is usually good evidence for the association at the locus level, some evidence for a specific causative gene at eight of the loci, and some experimental evidence for a specific causative variant at six of the loci. We recommend that researchers who report new potential causative variants use referenced coordinate systems, show local sequence context, and submit variants to repositories.
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Affiliation(s)
- Martin Johnsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07 Uppsala, Sweden
| | - Melissa K. Jungnickel
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG Scotland, UK
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15
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Illa SK, Mukherjee S, Nath S, Mukherjee A. Genome-Wide Scanning for Signatures of Selection Revealed the Putative Genomic Regions and Candidate Genes Controlling Milk Composition and Coat Color Traits in Sahiwal Cattle. Front Genet 2021; 12:699422. [PMID: 34306039 PMCID: PMC8299338 DOI: 10.3389/fgene.2021.699422] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
Background In the evolutionary time scale, selection shapes the genetic variation and alters the architecture of genome in the organisms. Selection leaves detectable signatures at the genomic coordinates that provide clues about the protein-coding regions. Sahiwal is a valuable indicine cattle adapted to tropical environments with desirable milk attributes. Insights into the genomic regions under putative selection may reveal the molecular mechanisms affecting the quantitative and other important traits. To understand this, the present investigation was undertaken to explore signatures of selection in the genome of Sahiwal cattle using a medium-density genotyping INDUS chip. Result De-correlated composite of multiple selection signals (DCMS), which combines five different univariate statistics, was computed in the dataset to detect the signatures of selection in the Sahiwal genome. Gene annotations, Quantitative Trait Loci (QTL) enrichment, and functional analyses were carried out for the identification of significant genomic regions. A total of 117 genes were identified, which affect a number of important economic traits. The QTL enrichment analysis highlighted 14 significant [False Discovery Rate (FDR)-corrected p-value ≤ 0.05] regions on chromosomes BTA 1, 3, 6, 11, 20, and 21. The top three enriched QTLs were found on BTA 6, 20, and 23, which are associated with exterior, health, milk production, and reproduction traits. The present study on selection signatures revealed some key genes related with coat color (PDGFRA, KIT, and KDR), facial pigmentation (LEF), milk fat percent (MAP3K1, HADH, CYP2U1, and SGMS2), sperm membrane integrity (OSTC), lactation persistency (MRPS30, NNT, CCL28, HMGCS1, NIM1K, ZNF131, and CCDC152), milk yield (GHR and ZNF469), reproduction (NKX2-1 and DENND1A), and bovine tuberculosis susceptibility (RNF144B and PAPSS1). Further analysis of candidate gene prioritization identified four hub genes, viz., KIT, KDR, MAP3K1, and LEF, which play a role in coat color, facial pigmentation, and milk fat percentage in cattle. Gene enrichment analysis revealed significant Gene ontology (GO) terms related to breed-specific coat color and milk fat percent. Conclusion The key candidate genes and putative genomic regions associated with economic traits were identified in Sahiwal using single nucleotide polymorphism data and the DCMS method. It revealed selection for milk production, coat color, and adaptability to tropical climate. The knowledge about signatures of selection and candidate genes affecting phenotypes have provided a background information that can be further utilized to understand the underlying mechanism involved in these traits in Sahiwal cattle.
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Affiliation(s)
- Satish Kumar Illa
- Division of Animal Genetics and Breeding, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
| | - Sabyasachi Mukherjee
- Division of Animal Genetics and Breeding, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
| | - Sapna Nath
- Artificial Breeding Research Center, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
| | - Anupama Mukherjee
- Division of Animal Genetics and Breeding, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
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16
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Thakor PB, Hinsu AT, Bhatia DR, Shah TM, Nayee N, Sudhakar A, Rank DN, Joshi CG. High-throughput genotype-based population structure analysis of selected buffalo breeds. Transl Anim Sci 2021; 5:txab033. [PMID: 33981962 PMCID: PMC8103726 DOI: 10.1093/tas/txab033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 05/01/2021] [Indexed: 11/29/2022] Open
Abstract
India is considered as the home tract of some of the best buffalo breeds. However, the genetic structure of the Indian river buffalo is poorly understood. Hence, there is a need to characterize the populations and understand the genetic structure of various buffalo breeds for selection and to design breeding strategies. In this study, we have analyzed genetic variability and population structure of seven buffalo breeds from their respective geographical regions using Axiom Buffalo Genotyping Array. Diversity, as measured by expected heterozygosity, ranged from 0.364 in Surti to 0.384 in Murrah breed, and pair-wise FST values revealed the lowest genetic distance between Murrah and Nili-Ravi (0.0022), while the highest between Surti and Pandharpuri (0.030). Principal component analysis and structure analysis unveiled the differentiation of Surti, Pandharpuri, and Jaffarabadi in first two principal components and at K = 4, respectively, while remaining breeds were grouped together as a separate single cluster and admixed. Murrah and Mehsana showed early linkage disequilibrium (LD) decay, while Surti breed showed late decay. In LD blocks to quantitative trait locis (QTLs) concordance analysis, 4.65% of concordance was observed with 873 LD blocks overlapped with 2,330 QTLs. Overall, total 4,090 markers were identified from all LD blocks for six types of traits. Results of this study indicated that these single-nucleotide polymorphism (SNP) markers could differentiate phenotypically distinct breeds like Surti, Pandharpuri, and Jaffarabadi but not others. So, there is a need to develop SNP chip based on SNP markers identified by sequence information of local breeds.
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Affiliation(s)
- Prakash B Thakor
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India
| | - Ankit T Hinsu
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India
| | - Dhruv R Bhatia
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India
| | - Tejas M Shah
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India
| | - Nilesh Nayee
- National Dairy Development Board, Anand 388001, India
| | - A Sudhakar
- National Dairy Development Board, Anand 388001, India
| | - Dharamshibhai N Rank
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India.,Gujarat Biotechnology Research Centre, Gandhinagar 382017, India
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17
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Burbidge CA, Ford CM, Melino VJ, Wong DCJ, Jia Y, Jenkins CLD, Soole KL, Castellarin SD, Darriet P, Rienth M, Bonghi C, Walker RP, Famiani F, Sweetman C. Biosynthesis and Cellular Functions of Tartaric Acid in Grapevines. FRONTIERS IN PLANT SCIENCE 2021; 12:643024. [PMID: 33747023 PMCID: PMC7970118 DOI: 10.3389/fpls.2021.643024] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/09/2021] [Indexed: 05/29/2023]
Abstract
Tartaric acid (TA) is an obscure end point to the catabolism of ascorbic acid (Asc). Here, it is proposed as a "specialized primary metabolite", originating from carbohydrate metabolism but with restricted distribution within the plant kingdom and lack of known function in primary metabolic pathways. Grapes fall into the list of high TA-accumulators, with biosynthesis occurring in both leaf and berry. Very little is known of the TA biosynthetic pathway enzymes in any plant species, although recently some progress has been made in this space. New technologies in grapevine research such as the development of global co-expression network analysis tools and genome-wide association studies, should enable more rapid progress. There is also a lack of information regarding roles for this organic acid in plant metabolism. Therefore this review aims to briefly summarize current knowledge about the key intermediates and enzymes of TA biosynthesis in grapes and the regulation of its precursor, ascorbate, followed by speculative discussion around the potential roles of TA based on current knowledge of Asc metabolism, TA biosynthetic enzymes and other aspects of fruit metabolism.
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Affiliation(s)
| | | | | | - Darren Chern Jan Wong
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Yong Jia
- Western Barley Genetic Alliance, Murdoch University, Perth, WA, Australia
| | | | - Kathleen Lydia Soole
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Simone Diego Castellarin
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Philippe Darriet
- Université Bordeaux, Unité de recherche OEnologie, EA 4577, USC 1366 INRAE, Institut des Sciences de la Vigne et du Vin, Villenave d’Ornon, France
| | - Markus Rienth
- University of Sciences and Art Western Switzerland, Changins College for Viticulture and Oenology, Nyon, Switzerland
| | - Claudio Bonghi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Robert Peter Walker
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Franco Famiani
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Crystal Sweetman
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
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18
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Eydivandi S, Roudbar MA, Ardestani SS, Momen M, Sahana G. A selection signatures study among Middle Eastern and European sheep breeds. J Anim Breed Genet 2021; 138:574-588. [PMID: 33453096 DOI: 10.1111/jbg.12536] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/25/2020] [Accepted: 12/26/2020] [Indexed: 01/26/2023]
Abstract
Selection, both natural and artificial, leaves patterns on the genome during domestication of animals and leads to changes in allele frequencies among populations. Detecting genomic regions influenced by selection in livestock may assist in understanding the processes involved in genome evolution and discovering genomic regions related to traits of economic and ecological interests. In the current study, genetic diversity analyses were conducted on 34,206 quality-filtered SNP positions from 450 individuals in 15 sheep breeds, including six indigenous breeds from the Middle East, namely Iranian Balouchi, Afshari, Moghani, Qezel, Karakas and Norduz, and nine breeds from Europe, namely East Friesian Sheep, Ile de France, Mourerous, Romane, Swiss Mirror, Spaelsau, Suffolk, Comisana and Engadine Red Sheep. The SNP genotype data generated by the Illumina OvineSNP50 Genotyping BeadChip array were used in this analysis. We applied two complementary statistical analyses, FST (fixation index) and xp-EHH (cross-population extended haplotype homozygosity), to detect selection signatures in Middle Eastern and European sheep populations. FST and xp-EHH detected 629 and 256 genes indicating signatures of selection, respectively. Genomic regions identified using FST and xp-EHH contained the CIDEA, HHATL, MGST1, FADS1, RTL1 and DGKG genes, which were reported earlier to influence a number of economic traits. Both FST and xp-EHH approaches identified 60 shared genes as the signatures of selection, including four candidate genes (NT5E, ADA2, C8A and C8B) that were enriched for two significant Gene Ontology (GO) terms associated with the adenosine metabolic procedure. Knowledge about the candidate genomic regions under selective pressure in sheep breeds may facilitate identification of the underlying genes and enhance our understanding on these genes role in local adaptation.
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Affiliation(s)
- Sirous Eydivandi
- Department of Animal Science, Behbahan Branch, Islamic Azad University, Behbahan, Iran.,Faculty of Technical Sciences, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Mahmoud Amiri Roudbar
- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Dezful, Iran
| | | | - Mehdi Momen
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Goutam Sahana
- Faculty of Technical Sciences, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
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19
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Singh A, Mehrotra A, Gondro C, Romero ARDS, Pandey AK, Karthikeyan A, Bashir A, Mishra BP, Dutt T, Kumar A. Signatures of Selection in Composite Vrindavani Cattle of India. Front Genet 2020; 11:589496. [PMID: 33391343 PMCID: PMC7775581 DOI: 10.3389/fgene.2020.589496] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/01/2020] [Indexed: 12/31/2022] Open
Abstract
Vrindavani is an Indian composite cattle breed developed by crossbreeding taurine dairy breeds with native indicine cattle. The constituent breeds were selected for higher milk production and adaptation to the tropical climate. However, the selection response for production and adaptation traits in the Vrindavani genome is not explored. In this study, we provide the first overview of the selection signatures in the Vrindavani genome. A total of 96 Vrindavani cattle were genotyped using the BovineSNP50 BeadChip and the SNP genotype data of its constituent breeds were collected from a public database. Within-breed selection signatures in Vrindavani were investigated using the integrated haplotype score (iHS). The Vrindavani breed was also compared to each of its parental breeds to discover between-population signatures of selection using two approaches, cross-population extended haplotype homozygosity (XP-EHH) and fixation index (FST). We identified 11 common regions detected by more than one method harboring genes such as LRP1B, TNNI3K, APOB, CACNA2D1, FAM110B, and SPATA17 associated with production and adaptation. Overall, our results suggested stronger selective pressure on regions responsible for adaptation compared to milk yield.
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Affiliation(s)
- Akansha Singh
- Animal Genetics Division, Indian Council of Agricultural Research (ICAR)-Indian Veterinary Research Institute, Bareilly, India
| | - Arnav Mehrotra
- Animal Genetics Division, Indian Council of Agricultural Research (ICAR)-Indian Veterinary Research Institute, Bareilly, India
| | - Cedric Gondro
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | | | - Ashwni Kumar Pandey
- Animal Genetics Division, Indian Council of Agricultural Research (ICAR)-Indian Veterinary Research Institute, Bareilly, India
| | - A Karthikeyan
- Animal Genetics Division, Indian Council of Agricultural Research (ICAR)-Indian Veterinary Research Institute, Bareilly, India
| | - Aamir Bashir
- Animal Genetics Division, Indian Council of Agricultural Research (ICAR)-Indian Veterinary Research Institute, Bareilly, India
| | - B P Mishra
- Animal Biotechnology, Indian Council of Agricultural Research (ICAR)-Indian Veterinary Research Institute, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management, Indian Council of Agricultural Research (ICAR)-Indian Veterinary Research Institute, Bareilly, India
| | - Amit Kumar
- Animal Genetics Division, Indian Council of Agricultural Research (ICAR)-Indian Veterinary Research Institute, Bareilly, India
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20
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Islam S, Reddy UK, Natarajan P, Abburi VL, Bajwa AA, Imran M, Zahoor MY, Abdullah M, Bukhari AM, Iqbal S, Ashraf K, Nadeem A, Rehman H, Rashid I, Shehzad W. Population demographic history and population structure for Pakistani Nili-Ravi breeding bulls based on SNP genotyping to identify genomic regions associated with male effects for milk yield and body weight. PLoS One 2020; 15:e0242500. [PMID: 33232358 PMCID: PMC7685427 DOI: 10.1371/journal.pone.0242500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 11/03/2020] [Indexed: 11/20/2022] Open
Abstract
The domestic Nili-Ravi water buffalo (Bubalus bubalis) is the best dairy animal contributing 68% to total milk production in Pakistan. In this study, we identified genome-wide single nucleotide polymorphisms (SNPs) to estimate various population genetic parameters such as diversity, pairwise population differentiation, linkage disequilibrium (LD) distribution and for genome-wide association study for milk yield and body weight traits in the Nili-Ravi dairy bulls that they may pass on to their daughters who are retained for milking purposes. The genotyping by sequencing approach revealed 13,039 reference genome-anchored SNPs with minor allele frequency of 0.05 among 167 buffalos. Population structure analysis revealed that the bulls were grouped into two clusters (K = 2), which indicates the presence of two different lineages in the Pakistani Nili-Ravi water buffalo population, and we showed the extent of admixture of these two lineages in our bull collection. LD analysis revealed 4169 significant SNP associations, with an average LD decay of 90 kb for these buffalo genome. Genome-wide association study involved a multi-locus mixed linear model for milk yield and body weight to identify genome-wide male effects. Our study further illustrates the utility of the genotyping by sequencing approach for identifying genomic regions to uncover additional demographic complexity and to improve the complex dairy traits of the Pakistani Nili-Ravi water buffalo population that would provide the lot of economic benefits to dairy industry.
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Affiliation(s)
- Saher Islam
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Umesh K. Reddy
- Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Purushothaman Natarajan
- Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Venkata Lakshmi Abburi
- Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Amna Arshad Bajwa
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Imran
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Yasir Zahoor
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Abdullah
- Department of Livestock Production, University of Veterinary and Animal Sciences, Pattoki, Pakistan
| | - Aamir Mehmood Bukhari
- Semen Production Unit, Qadirabad, District Sahiwal, Pakistan
- Livestock and Dairy Development Department, Government of the Punjab, Lahore, Pakistan
| | - Sajid Iqbal
- Semen Production Unit, Qadirabad, District Sahiwal, Pakistan
- Livestock and Dairy Development Department, Government of the Punjab, Lahore, Pakistan
| | - Kamran Ashraf
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Asif Nadeem
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Habibur Rehman
- Department of Physiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Imran Rashid
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Wasim Shehzad
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
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21
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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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22
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Rovelli G, Ceccobelli S, Perini F, Demir E, Mastrangelo S, Conte G, Abeni F, Marletta D, Ciampolini R, Cassandro M, Bernabucci U, Lasagna E. The genetics of phenotypic plasticity in livestock in the era of climate change: a review. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1809540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Giacomo Rovelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Francesco Perini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
| | - Eymen Demir
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Giuseppe Conte
- Dipartimento di Scienze Agrarie, Alimentari e Agro-Ambientali, University of Pisa, Pisa, Italy
| | - Fabio Abeni
- Centro di ricerca Zootecnia e Acquacoltura, Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA), Lodi, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | | | - Martino Cassandro
- Dipartimento di Agronomia, Animali, Alimenti, Risorse naturali e Ambiente, University of Padova, Legnaro, Italy
| | - Umberto Bernabucci
- Dipartimento di Scienze Agrarie e Forestali, Università della Tuscia, Viterbo, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
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Aliloo H, Mrode R, Okeyo AM, Gibson JP. Ancestral Haplotype Mapping for GWAS and Detection of Signatures of Selection in Admixed Dairy Cattle of Kenya. Front Genet 2020; 11:544. [PMID: 32582285 PMCID: PMC7296079 DOI: 10.3389/fgene.2020.00544] [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: 10/24/2019] [Accepted: 05/06/2020] [Indexed: 12/11/2022] Open
Abstract
Understanding the genetic structure of adaptation and productivity in challenging environments is necessary for designing breeding programs that suit such conditions. Crossbred dairy cattle in East Africa resulting from over 60 years of crossing exotic dairy breeds with indigenous cattle plus inter se matings form a highly variable admixed population. This population has been subject to natural selection in response to environmental stresses, such as harsh climate, low-quality feeds, poor management, and strong disease challenge. Here, we combine two complementary sets of analyses, genome-wide association (GWA) and signatures of selection (SoS), to identify genomic regions that contribute to variation in milk yield and/or contribute to adaptation in admixed dairy cattle of Kenya. Our GWA separates SNP effects due to ancestral origin of alleles from effects due to within-population linkage disequilibrium. The results indicate that many genomic regions contributed to the high milk production potential of modern dairy breeds with no region having an exceptional effect. For SoS, we used two haplotype-based tests to compare haplotype length variation within admixed and between admixed and East African Shorthorn Zebu cattle populations. The integrated haplotype score (iHS) analysis identified 16 candidate regions for positive selection in the admixed cattle while the between population Rsb test detected 24 divergently selected regions in the admixed cattle compared to East African Shorthorn Zebu. We compare the results from GWA and SoS in an attempt to validate the most significant SoS results. Only four candidate regions for SoS intersect with GWA regions using a low stringency test. The identified SoS candidate regions harbored genes in several enriched annotation clusters and overlapped with previously found QTLs and associations for different traits in cattle. If validated, the GWA and SoS results indicate potential for SNP-based genomic selection for genetic improvement of smallholder crossbred cattle.
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Affiliation(s)
- Hassan Aliloo
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Raphael Mrode
- Animal Biosciences, International Livestock Research Institute, Nairobi, Kenya.,Animal and Veterinary Science, Scotland's Rural College, Edinburgh, United Kingdom
| | - A M Okeyo
- Animal Biosciences, International Livestock Research Institute, Nairobi, Kenya
| | - John P Gibson
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
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24
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Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data. Animals (Basel) 2020; 10:ani10061005. [PMID: 32521830 PMCID: PMC7341496 DOI: 10.3390/ani10061005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 12/31/2022] Open
Abstract
Simple Summary The Bardigiano horse is a native Italian breed bred for living in rural areas, traditionally used in agriculture. The breed counts about 3000 horses, and it is nowadays mainly used for recreational purposes. The relatively small size and the closed status of the breed raise the issue of monitoring genetic diversity. We therefore characterized the breed’s genetic diversity based on molecular data. We showed a critical reduction of genetic variability mainly driven by past bottlenecks. We also highlighted homozygous genomic regions that might be the outcome of directional selection in recent years, in line with the conversion of Bardigiano horses from agricultural to riding purposes. Abstract Horses are nowadays mainly used for sport and leisure activities, and several local breeds, traditionally used in agriculture, have been exposed to a dramatic loss in population size and genetic diversity. The loss of genetic diversity negatively impacts individual fitness and reduces the potential long-term survivability of a breed. Recent advances in molecular biology and bioinformatics have allowed researchers to explore biodiversity one step further. This study aimed to evaluate the loss of genetic variability and identify genomic regions under selection pressure in the Bardigiano breed based on GGP Equine70k SNP data. The effective population size based on Linkage Disequilibrium (Ne) was equal to 39 horses, and it showed a decline over time. The average inbreeding based on runs of homozygosity (ROH) was equal to 0.17 (SD = 0.03). The majority of the ROH were relatively short (91% were ≤2 Mbp long), highlighting the occurrence of older inbreeding, rather than a more recent occurrence. A total of eight ROH islands, shared among more than 70% of the Bardigiano horses, were found. Four of them mapped to known quantitative trait loci related to morphological traits (e.g., body size and coat color) and disease susceptibility. This study provided the first genome-wide scan of genetic diversity and selection signatures in an Italian native horse breed.
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Naval-Sánchez M, Porto-Neto LR, Cardoso DF, Hayes BJ, Daetwyler HD, Kijas J, Reverter A. Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB. Genet Sel Evol 2020; 52:27. [PMID: 32460767 PMCID: PMC7251699 DOI: 10.1186/s12711-020-00546-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 05/11/2020] [Indexed: 01/14/2023] Open
Abstract
Background Distinct domestication events, adaptation to different climatic zones, and divergent selection in productive traits have shaped the genomic differences between taurine and indicine cattle. In this study, we assessed the impact of artificial selection and environmental adaptation by comparing whole-genome sequences from European taurine and Asian indicine breeds and from African cattle. Next, we studied the impact of divergent selection by exploiting predicted and experimental functional annotation of the bovine genome. Results We identified selective sweeps in beef cattle taurine and indicine populations, including a 430-kb selective sweep on indicine cattle chromosome 5 that is located between 47,670,001 and 48,100,000 bp and spans five genes, i.e. HELB, IRAK3, ENSBTAG00000026993, GRIP1 and part of HMGA2. Regions under selection in indicine cattle display significant enrichment for promoters and coding genes. At the nucleotide level, sites that show a strong divergence in allele frequency between European taurine and Asian indicine are enriched for the same functional categories. We identified nine single nucleotide polymorphisms (SNPs) in coding regions that are fixed for different alleles between subspecies, eight of which were located within the DNA helicase B (HELB) gene. By mining information from the 1000 Bull Genomes Project, we found that HELB carries mutations that are specific to indicine cattle but also found in taurine cattle, which are known to have been subject to indicine introgression from breeds, such as N’Dama, Anatolian Red, Marchigiana, Chianina, and Piedmontese. Based on in-house genome sequences, we proved that mutations in HELB segregate independently of the copy number variation HMGA2-CNV, which is located in the same region. Conclusions Major genomic sequence differences between Bos taurus and Bos indicus are enriched for promoter and coding regions. We identified a 430-kb selective sweep in Asian indicine cattle located on chromosome 5, which carries SNPs that are fixed in indicine populations and located in the coding sequences of the HELB gene. HELB is involved in the response to DNA damage including exposure to ultra-violet light and is associated with reproductive traits and yearling weight in tropical cattle. Thus, HELB likely contributed to the adaptation of tropical cattle to their harsh environment.
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Affiliation(s)
- Marina Naval-Sánchez
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia. .,Institute of Molecular Biosciences, The University of Queensland, 306 Carmody Road, St. Lucia, Brisbane, QLD, 4067, Australia.
| | - Laercio R Porto-Neto
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Diercles F Cardoso
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia.,Department of Animal Science, School of Agricultural and Veterinarian Sciences, Sao Paulo State University (UNESP), Jaboticabal, SP, Brazil.,Centre for Genetic Improvement of Livestock, University of Guelph, 50 Stone Road East, Guelph, ON, N1G2W1, Canada
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4067, Australia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - James Kijas
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Antonio Reverter
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
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Beche E, Gillman JD, Song Q, Nelson R, Beissinger T, Decker J, Shannon G, Scaboo AM. Nested association mapping of important agronomic traits in three interspecific soybean populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1039-1054. [PMID: 31974666 DOI: 10.1007/s00122-019-03529-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/30/2019] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE Glycine soja germplasm can be used to successfully introduce new alleles with the potential to add valuable new genetic diversity to the current elite soybean gene pool. Given the demonstrated narrow genetic base of the US soybean production, it is essential to identify beneficial alleles from exotic germplasm, such as wild soybean, to enhance genetic gain for favorable traits. Nested association mapping (NAM) is an approach to population development that permits the comparison of allelic effects of the same QTL in multiple parents. Seed yield, plant maturity, plant height and plant lodging were evaluated in a NAM panel consisting of 392 recombinant inbred lines derived from three biparental interspecific soybean populations in eight environments during 2016 and 2017. Nested association mapping, combined with linkage mapping, identified three major QTL for plant maturity in chromosomes 6, 11 and 12 associated with alleles from wild soybean resulting in significant increases in days to maturity. A significant QTL for plant height was identified on chromosome 13 with the allele increasing plant height derived from wild soybean. A significant grain yield QTL was detected on chromosome 17, and the allele from Glycine soja had a positive effect of 166 kg ha-1; RIL's with the wild soybean allele yielded on average 6% more than the lines carrying the Glycine max allele. These findings demonstrate the usefulness and potential of alleles from wild soybean germplasm to enhance important agronomic traits in a soybean breeding program.
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Affiliation(s)
- Eduardo Beche
- Division of Plant Science, University of Missouri, Columbia, MO, USA
| | | | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA
| | - Randall Nelson
- Department of Crop Sciences, University of Illinois, 1101 W. Peabody Dr, Urbana, IL, 61801, USA
- USDA-Agricultural Research Service, 1101 W. Peabody Dr, Urbana, IL, 61801, USA
| | - Tim Beissinger
- Center for Integrated Breeding Research, Georg-August-Universität, Göttingen, Germany
| | - Jared Decker
- Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - Grover Shannon
- Division of Plant Science, University of Missouri, Columbia, MO, USA
| | - Andrew M Scaboo
- Division of Plant Science, University of Missouri, Columbia, MO, USA.
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Comparative selection signature analyses identify genomic footprints in Reggiana cattle, the traditional breed of the Parmigiano-Reggiano cheese production system. Animal 2020; 14:921-932. [PMID: 31928542 DOI: 10.1017/s1751731119003318] [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] [Indexed: 12/20/2022] Open
Abstract
Reggiana is an autochthonous cattle breed reared mainly in the province of Reggio Emilia, located in the North of Italy. Reggiana cattle (originally a triple-purpose population largely diffused in the North of Italy) are characterised by a typical solid red coat colour. About 2500 cows of this breed are currently registered to its herd book. Reggiana is now considered a dual-purpose breed even if it is almost completely dedicated to the production of a mono-breed branded Protected Designation of Origin Parmigiano-Reggiano cheese, which is the main driver of the sustainable conservation of this local genetic resource. In this study, we provided the first overview of genomic footprints that characterise Reggiana and define the diversity of this local cattle breed. A total of 168 Reggiana sires (all bulls born over 35 years for which semen was available) and other 3321 sires from 3 cosmopolitan breeds (Brown, Holstein and Simmental) were genotyped with the Illumina BovineSNP50 panel. ADMIXTURE analysis suggested that Reggiana breed might have been influenced, at least in part, by the other three breeds included in this study. Selection signatures in the Reggiana genome were identified using three statistical approaches based on allele frequency differences among populations or on properties of haplotypes segregating in the populations (fixation index (FST); integrated haplotype score; cross-population extended haplotype homozygosity). We identified several regions under peculiar selection in the Reggiana breed, particularly on bovine chromosome (BTA) 6 in the KIT gene region, that is known to be involved in coat colour pattern distribution, and within the region of the LAP3, NCAPG and LCORL genes, that are associated with stature, conformation and carcass traits. Another already known region that includes the PLAG1 gene (BTA14), associated with conformation traits, showed a selection signature in the Reggiana cattle. On BTA18, a signal of selection included the MC1R gene that causes the red coat colour in cattle. Other selection sweeps were in regions, with high density of quantitative trait loci for milk production traits (on BTA20) and in several other large regions that might have contributed to shape and define the Reggiana genome (on BTA17 and BTA29). All these results, overall, indicate that the Reggiana genome might still contain several signs of its multipurpose and non-specialised utilisation, as already described for other local cattle populations, in addition to footprints derived by its ancestral origin and by its adaptation to the specialised Parmigiano-Reggiano cheese production system.
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Liu L, Cui H, Xing S, Zhao G, Wen J. Effect of Divergent Selection for Intramuscular Fat Content on Muscle Lipid Metabolism in Chickens. Animals (Basel) 2019; 10:ani10010004. [PMID: 31861430 PMCID: PMC7023311 DOI: 10.3390/ani10010004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 12/22/2022] Open
Abstract
Simple Summary Intramuscular fat is an important factor affecting meat quality and consumer acceptance. Appropriate increases in the intramuscular fat content contribute to the improvement of meat quality, and genetic selection is an effective method to increase the intramuscular fat content in chickens. In this study, chicken lines divergently selected for their intramuscular fat content were used to investigate the mechanisms behind differential intramuscular fat deposition. These results found in this study may contribute to the improvement of meat quality in chickens. Abstract Intramuscular fat (IMF)—an important factor affecting meat quality—can be appropriately increased by genetic selection. Chicken lines divergently selected for IMF content were used in this study to investigate the mechanisms behind differential IMF deposition. Sixty 15th generation chickens were genotyped using the IASCHICK 55K single nucleotide polymorphism (SNP) chip. After quality control, 59 chickens and 36,893 SNPs were available for subsequent analysis. Population structure assessment indicated that the lines were genetically differentiated. Based on the top 1% paired fixation index values, three pathways were significantly (p < 0.05) enriched, and nine genes were considered candidate genes for differential IMF deposition. Differences between the lines in the expressions of representative genes involved in the above pathways were detected in 16th generation chickens. This study suggests that genetic selection for increased IMF in the pectoralis major muscle may enhance fatty acid synthesis, transport, and esterification, and reduce triglyceride hydrolysis. The peroxisome proliferator-activated receptor (PPAR) signaling pathway, glycerolipid metabolism, and fatty acid degradation pathway may have contributed to the differences in IMF deposition between the lines. These results contribute to the understanding of the genetic mechanisms behind IMF deposition, and the improvement of chicken meat quality.
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Affiliation(s)
- Lu Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.L.); (H.C.); (S.X.)
- State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Huanxian Cui
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.L.); (H.C.); (S.X.)
- State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Siyuan Xing
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.L.); (H.C.); (S.X.)
- State Key Laboratory of Animal Nutrition, Beijing 100193, China
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6708WD, The Netherlands
| | - Guiping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.L.); (H.C.); (S.X.)
- State Key Laboratory of Animal Nutrition, Beijing 100193, China
- Correspondence: (G.Z.); (J.W.); Tel.: +86-10-6281-5856 (J.W.)
| | - Jie Wen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.L.); (H.C.); (S.X.)
- State Key Laboratory of Animal Nutrition, Beijing 100193, China
- Correspondence: (G.Z.); (J.W.); Tel.: +86-10-6281-5856 (J.W.)
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Flori L, Moazami-Goudarzi K, Alary V, Araba A, Boujenane I, Boushaba N, Casabianca F, Casu S, Ciampolini R, Coeur D'Acier A, Coquelle C, Delgado JV, El-Beltagi A, Hadjipavlou G, Jousselin E, Landi V, Lauvie A, Lecomte P, Ligda C, Marinthe C, Martinez A, Mastrangelo S, Menni D, Moulin CH, Osman MA, Pineau O, Portolano B, Rodellar C, Saïdi-Mehtar N, Sechi T, Sempéré G, Thévenon S, Tsiokos D, Laloë D, Gautier M. A genomic map of climate adaptation in Mediterranean cattle breeds. Mol Ecol 2019; 28:1009-1029. [PMID: 30593690 DOI: 10.1111/mec.15004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 12/12/2022]
Abstract
Domestic species such as cattle (Bos taurus taurus and B. t. indicus) represent attractive biological models to characterize the genetic basis of short-term evolutionary response to climate pressure induced by their post-domestication history. Here, using newly generated dense SNP genotyping data, we assessed the structuring of genetic diversity of 21 autochtonous cattle breeds from the whole Mediterranean basin and performed genome-wide association analyses with covariables discriminating the different Mediterranean climate subtypes. This provided insights into both the demographic and adaptive histories of Mediterranean cattle. In particular, a detailed functional annotation of genes surrounding variants associated with climate variations highlighted several biological functions involved in Mediterranean climate adaptation such as thermotolerance, UV protection, pathogen resistance or metabolism with strong candidate genes identified (e.g., NDUFB3, FBN1, METTL3, LEF1, ANTXR2 and TCF7). Accordingly, our results suggest that main selective pressures affecting cattle in Mediterranean area may have been related to variation in heat and UV exposure, in food resources availability and in exposure to pathogens, such as anthrax bacteria (Bacillus anthracis). Furthermore, the observed contribution of the three main bovine ancestries (indicine, European and African taurine) in these different populations suggested that adaptation to local climate conditions may have either relied on standing genomic variation of taurine origin, or adaptive introgression from indicine origin, depending on the local breed origins. Taken together, our results highlight the genetic uniqueness of local Mediterranean cattle breeds and strongly support conservation of these populations.
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Affiliation(s)
- Laurence Flori
- SELMET, INRA, CIRAD, University of Montpellier, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | | | - Véronique Alary
- SELMET, INRA, CIRAD, University of Montpellier, Montpellier SupAgro, University of Montpellier, Montpellier, France.,CIRAD, UMR SELMET, ICARDA, Rabat, Morocco
| | - Abdelillah Araba
- Institut Agronomique et Vétérinaire Hassan II, Département de Productions et de Biotechnologies Animales, Rabat, Morocco
| | - Ismaïl Boujenane
- Institut Agronomique et Vétérinaire Hassan II, Département de Productions et de Biotechnologies Animales, Rabat, Morocco
| | - Nadjet Boushaba
- Université d'Oran "Mohamed Boudiaf", Département de Génétique Moléculaire Appliquée, Oran, Algeria
| | | | - Sara Casu
- Agris-Sardegna Servizio Ricerca per la Zootecnica, Olmedo, Italy
| | | | | | | | | | | | | | | | - Vincenzo Landi
- Animal Breeding Consulting SL, Laboratorio de Genetica Molecular Aplicada, Cordoba, Spain
| | - Anne Lauvie
- SELMET, INRA, CIRAD, University of Montpellier, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Philippe Lecomte
- SELMET, INRA, CIRAD, University of Montpellier, Montpellier SupAgro, University of Montpellier, Montpellier, France.,CIRAD, UMR SELMET, Montpellier, France
| | - Christina Ligda
- HAO-Demeter, Veterinary Research Institute, Thessaloniki, Greece
| | | | - Amparo Martinez
- Animal Breeding Consulting SL, Laboratorio de Genetica Molecular Aplicada, Cordoba, Spain
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Dalal Menni
- Institut Agronomique et Vétérinaire Hassan II, Département de Productions et de Biotechnologies Animales, Rabat, Morocco
| | - Charles-Henri Moulin
- SELMET, INRA, CIRAD, University of Montpellier, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | | | | | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Clementina Rodellar
- LAGENBIO, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza-CITA, Zaragoza, Spain
| | - Nadhira Saïdi-Mehtar
- Université d'Oran "Mohamed Boudiaf", Département de Génétique Moléculaire Appliquée, Oran, Algeria
| | - Tiziana Sechi
- Agris-Sardegna Servizio Ricerca per la Zootecnica, Olmedo, Italy
| | - Guilhem Sempéré
- INTERTRYP, University of Montpellier, CIRAD, IRD, Montpellier, France.,CIRAD, UMR INTERTRYP, Montpellier, France
| | - Sophie Thévenon
- INTERTRYP, University of Montpellier, CIRAD, IRD, Montpellier, France.,CIRAD, UMR INTERTRYP, Montpellier, France
| | | | - Denis Laloë
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Mathieu Gautier
- CBGP, INRA, CIRAD, IRD, University of Montpellier, Montferrier-sur-Lez, France.,Institut de Biologie Computationnelle (IBC), Montpellier, France
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Alshawi A, Essa A, Al-Bayatti S, Hanotte O. Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and Environmental Traits in Iraqi Cattle. Front Genet 2019; 10:609. [PMID: 31379916 PMCID: PMC6646475 DOI: 10.3389/fgene.2019.00609] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 06/11/2019] [Indexed: 01/03/2023] Open
Abstract
The Near East cattle are adapted to different agro-ecological zones including desert areas, mountains habitats, and humid regions along the Tigris and Euphrates rivers system. The region was one of the earliest and most significant areas of cattle husbandry. Currently, four main breeds of Iraqi cattle are recognized. Among these, the Jenoubi is found in the southern more humid part of Iraq, while the Rustaqi is found in the middle and drier region of the country. Despite their importance, Iraqi cattle have up to now been poorly characterized at the genome level. Here, we report at a genome-wide level the diversity and signature of positive selection in these two breeds. Thirty-five unrelated Jenoubi cattle, sampled in the Maysan and Basra regions, and 60 Rustaqi cattle, from around Baghdad and Babylon, were genotyped using the Illumina Bovine HD BeadChip (700K). Genetic population structure and diversity level were studied using principal component analysis (PCA), expected heterozygosity (He), observed heterozygosity (Ho), and admixture. Signatures of selection were studied using extended haplotype homozygosity (EHH) (iHS and Rsb) and inter-population Wright's Fst. The results of PCA and admixture analysis, including European taurine, Asian indicine, African indicine, and taurine indicate that the two breeds are crossbreed zebu × taurine, with more zebu background in Jenoubi cattle compared with Rustaqi. The Rustaqi has the greatest mean heterozygosity (He = 0.37) among all breeds. iHS and Rsb signatures of selection analyses identify 68 candidate genes under positive selection in the two Iraqi breeds, while Fst analysis identifies 220 candidate genes including genes related to the innate and acquired immunity responses, different environmental selection pressures (e.g., tick resistance and heat stress), and genes of commercial interest (e.g., marbling score).
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Affiliation(s)
- Akil Alshawi
- Division of Cells, Organisms and Molecular Genetics, School of Life Sciences, Faculty of Medicine and Health Sciences, University Park Campus, University of Nottingham, Nottingham, United Kingdom.,Department of Internal and Preventive Veterinary Medicine, College of Veterinary Medicine, University of Baghdad, Iraqi Ministry of Higher Education and Scientific Research, Baghdad, Iraq
| | - Abdulameer Essa
- Animal Genetics Resources Department, Directorate of Animal Resources, the Ministry of Iraqi Agriculture, Baghdad, Iraq
| | - Sahar Al-Bayatti
- Animal Genetics Resources Department, Directorate of Animal Resources, the Ministry of Iraqi Agriculture, Baghdad, Iraq
| | - Olivier Hanotte
- Division of Cells, Organisms and Molecular Genetics, School of Life Sciences, Faculty of Medicine and Health Sciences, University Park Campus, University of Nottingham, Nottingham, United Kingdom.,LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
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Genome-wide scan reveals genetic divergence and diverse adaptive selection in Chinese local cattle. BMC Genomics 2019; 20:494. [PMID: 31200634 PMCID: PMC6570941 DOI: 10.1186/s12864-019-5822-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 05/21/2019] [Indexed: 01/18/2023] Open
Abstract
Background Understanding the population structure and genetic bases of well-adapted cattle breeds to local environments is one of the most essential tasks to develop appropriate genetic improvement programs. Results We performed a comprehensive study to investigate the population structure, divergence and selection signatures at genome-wide level in diverse Chinese local cattle using Bovine HD SNPs array, including two breeds from North China, one breed from Northwest China, three breeds from Southwest China and two breeds from South China. Population genetic analyses revealed the genetic structures of these populations were mostly related to the geographic locations. Notably, we detected 294 and 1263 candidate regions under selection using the di and iHS approaches, respectively. A series of group-specific and breed-specific candidate genes were identified, which are involved in immune response, sexual maturation, stature related, birth and bone weight, embryonic development, coat colors and adaptation. Furthermore, haplotype diversity and network pattern for candidate genes, including LPGAT1, LCORL, PPP1R8, RXFP2 and FANCA, suggest that these genes have been under differential selection pressures in various environmental conditions. Conclusions Our results shed insights into diverse selection during breed formation in Chinese local cattle. These findings may promote the application of genome-assisted breeding for well-adapted local breeds with economic and ecological importance. Electronic supplementary material The online version of this article (10.1186/s12864-019-5822-y) contains supplementary material, which is available to authorized users.
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Tijjani A, Utsunomiya YT, Ezekwe AG, Nashiru O, Hanotte O. Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle. Front Genet 2019; 10:442. [PMID: 31231417 PMCID: PMC6558954 DOI: 10.3389/fgene.2019.00442] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 04/29/2019] [Indexed: 01/01/2023] Open
Abstract
Like most West African Bos taurus, the shorthorn Muturu is under threat of replacement or crossbreeding with zebu. Their populations are now reduced to a few hundred breeding individuals and they are considered endangered. So far, the genetic variation and genetic basis of the trypanotolerant Muturu environmental adaptation have not been assessed. Here, we present genome-wide candidate positive selection signatures in Muturu following within-population iHS and between population Rsb signatures of selection analysis. We compared the results in Muturu with the ones obtained in N’Dama, a West African longhorn trypanotolerant taurine, and in two European taurine (Holstein and Jersey). The results reveal candidate signatures of selection regions in Muturu including genes linked to the innate (e.g., TRIM10, TRIM15, TRIM40, and TRIM26) and the adaptive (e.g., JSP.1, BOLA-DQA2, BOLA-DQA5, BOLA-DRB3, and BLA-DQB) immune responses. The most significant regions are identified on BTA 23 at the bovine major histocompatibility complex (MHC) (iHS analysis) and on BTA 12 at genes including a heat tolerance gene (INTS6) (Rsb analysis). Other candidate selected regions include genes related to growth traits/stature (e.g., GHR and GHRHR), coat color (e.g., MITF and KIT), feed efficiency (e.g., ZRANB3 and MAP3K5) and reproduction (e.g., RFX2, SRY, LAP3, and GPX5). Genes under common signatures of selection regions with N’Dama, including for adaptive immunity and heat tolerance, suggest shared mechanisms of adaptation to environmental challenges for these two West African taurine cattle. Interestingly, out of the 242,910 SNPs identified within the candidate selected regions in Muturu, 917 are missense SNPs (0.4%), with an unequal distribution across 273 genes. Fifteen genes including RBBP8, NID1, TEX15, LAMA3, TRIM40, and OR12D3 comprise 220 missense variants, each between 11 and 32. Our results, while providing insights into the candidate genes under selection in Muturu, are paving the way to the identification of genes and their polymorphisms linked to the unique tropical adaptive traits of the West Africa taurine, including trypanotolerance.
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Affiliation(s)
- Abdulfatai Tijjani
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University Park Campus, University of Nottingham, Nottingham, United Kingdom.,Center for Genomics Research and Innovation, National Biotechnology Development Agency, Abuja, Nigeria.,International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Yuri Tani Utsunomiya
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, São Paulo, Brazil
| | - Arinze G Ezekwe
- Department of Animal Science, Faculty of Agriculture, University of Nigeria, Nsukka, Nigeria
| | - Oyekanmi Nashiru
- Center for Genomics Research and Innovation, National Biotechnology Development Agency, Abuja, Nigeria
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University Park Campus, University of Nottingham, Nottingham, United Kingdom.,International Livestock Research Institute, Addis Ababa, Ethiopia
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Na W, Yu JQ, Xu ZC, Zhang XY, Yang LL, Cao ZP, Li H, Zhang H. Important candidate genes for abdominal fat content identified by linkage disequilibrium and fixation index information. Poult Sci 2019; 98:581-589. [PMID: 30285249 DOI: 10.3382/ps/pey426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 08/21/2018] [Indexed: 11/20/2022] Open
Abstract
Selection for rapid growth in chickens has always been accompanied by increased fat deposition and excessive fat deposition, especially abdominal fat, cannot only decrease feed efficiency but also cause many diseases. Finding the candidate genes associated with abdominal fat deposition is essential for breeding. To identify these candidate genes, we applied linkage disequilibrium and selection signature analysis using chicken 60 k single nucleotide polymorphism (SNP) chips in two broiler lines divergently selected for abdominal fat content for 11 generations. After quality control, 46,033 SNPs were left for analysis. Using these SNPs, we found that r2 was 0.06 to 0.14 in the lean line and 0.07 to 0.13 in the fat line for all 28 chromosomes (except GGA16). Pairwise SNP distances <25 kb showed a mean r2 = 0.33 in the lean line and r2 = 0.32 in the fat line. The fixation index (FST) analysis was carried out and 46 SNPs with the top 0.1% of the FST value was detected as the loci with selection signatures. Besides FST, hapFLK was also used to detect selection signatures for abdominal fat content. A total of 11 genes, including transient receptor potential cation channel subfamily C member 4, estrogen related receptor gamma, fibroblast growth factor 13, G-protein-signaling modulator 2, RAR related orphan receptor A, phospholipase A2 group X, mitochondrial ribosomal protein L28, metadherin, calcitonin receptor like receptor, serine/threonine kinase 39, and nuclear factor I A, were detected as the important candidate genes for abdominal fat deposition based on their basic functions. The results of the present study may benefit the understanding of genetic mechanism of abdominal fat deposition in chicken.
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Affiliation(s)
- Wei Na
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province.,College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Jia-Qiang Yu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province.,College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Zi-Chun Xu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province.,College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Xin-Yang Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province.,College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Li-Li Yang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province.,College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Zhi-Ping Cao
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province.,College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province.,College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Hui Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province.,College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
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Su S, Li H, Du F, Zhang C, Li X, Jing X, Liu L, Li Z, Yang X, Xu P, Yuan X, Zhu J, Bouzoualegh R. Combined QTL and Genome Scan Analyses With the Help of 2b-RAD Identify Growth-Associated Genetic Markers in a New Fast-Growing Carp Strain. Front Genet 2018; 9:592. [PMID: 30581452 PMCID: PMC6293859 DOI: 10.3389/fgene.2018.00592] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 11/15/2018] [Indexed: 11/17/2022] Open
Abstract
Common carp is one of the oldest and most popular cultured freshwater fish species both globally and in China. In a previous study, we used a carp strain with a long breeding tradition in China, named Huanghe, to create a new fast-growing strain by selection for fast growth for 6 years. The growth performance at 8 months of age has been improved by 20.84%. To achieve this, we combined the best linear unbiased prediction with marker-assisted selection techniques. Recent progress in genome-wide association studies and genomic selection in livestock breeding inspired common carp breeders to consider genome-based breeding approaches. In this study, we developed a 2b-RAD sequence assay as a means of investigating the quantitative trait loci in common carp. A total of 4,953,017,786 clean reads were generated for 250 specimens (average reads/specimen = 19,812,071) with BsaXI Restriction Enzyme. From these, 56,663 SNPs were identified, covering 50 chromosomes and 3,377 scaffolds. Principal component analysis indicated that selection and control groups are relatively clearly distinct. Top 1% of Fst values was selected as the threshold signature of artificial selection. Among the 244 identified loci, genes associated with sex-related factors and nutritional metabolism (especially fat metabolism) were annotated. Eighteen QTL were associated with growth parameters. Body length at 3 months of age and body weight (both at 3 and 8 months) were controlled by polygenic effects, but body size (length, depth, width) at 8 months of age was controlled mainly by several loci with major effects. Importantly, a single shared QTL (IGF2 gene) partially controlled the body length, depth, and width. By merging the above results, we concluded that mainly the genes related to neural pathways, sex and fatty acid metabolism contributed to the improved growth performance of the new Huanghe carp strain. These findings are one of the first investigations into the potential use of genomic selection in the breeding of common carp. Moreover, our results show that combining the Fst, QTL mapping and CRISPR–Cas9 methods can be an effective way to identify important novel candidate molecular markers in economic breeding programs.
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Affiliation(s)
- Shengyan Su
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Hengde Li
- Ministry of Agriculture Key Laboratory of Aquatic Genomics, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Center for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
| | - Fukuan Du
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Chengfeng Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xinyuan Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xiaojun Jing
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Liyue Liu
- China Zebrafish Resource Center, Wuhan, China
| | - Zhixun Li
- Henan Academy of Fishery Sciences, Zhengzhou, China
| | - Xingli Yang
- Henan Academy of Fishery Sciences, Zhengzhou, China
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xinhua Yuan
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Jian Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Raouf Bouzoualegh
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
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35
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Comparing polymorphism of 86 candidate genes putatively involved in domestication of sheep, between wild and domestic Iranian sheep. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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36
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Kim K, Jung J, Caetano-Anollés K, Sung S, Yoo D, Choi BH, Kim HC, Jeong JY, Cho YM, Park EW, Choi TJ, Park B, Lim D, Kim H. Artificial selection increased body weight but induced increase of runs of homozygosity in Hanwoo cattle. PLoS One 2018; 13:e0193701. [PMID: 29561881 PMCID: PMC5862439 DOI: 10.1371/journal.pone.0193701] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 02/19/2018] [Indexed: 12/02/2022] Open
Abstract
Artificial selection has been demonstrated to have a rapid and significant effect on the phenotype and genome of an organism. However, most previous studies on artificial selection have focused solely on genomic sequences modified by artificial selection or genomic sequences associated with a specific trait. In this study, we generated whole genome sequencing data of 126 cattle under artificial selection, and 24,973,862 single nucleotide variants to investigate the relationship among artificial selection, genomic sequences and trait. Using runs of homozygosity detected by the variants, we showed increase of inbreeding for decades, and at the same time demonstrated a little influence of recent inbreeding on body weight. Also, we could identify ~0.2 Mb runs of homozygosity segment which may be created by recent artificial selection. This approach may aid in development of genetic markers directly influenced by artificial selection, and provide insight into the process of artificial selection.
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Affiliation(s)
- Kwondo Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak Gu, Seoul, Republic of Korea
- C&K genomics, C-1008, H businesspark, 26, Beobwon-ro 9-gil, Songpa-gu, Seoul, Republic of Korea
| | - Jaehoon Jung
- C&K genomics, C-1008, H businesspark, 26, Beobwon-ro 9-gil, Songpa-gu, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Kwan-ak Gu, Seoul, Republic of Korea
| | - Kelsey Caetano-Anollés
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Samsun Sung
- C&K genomics, C-1008, H businesspark, 26, Beobwon-ro 9-gil, Songpa-gu, Seoul, Republic of Korea
| | - DongAhn Yoo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak Gu, Seoul, Republic of Korea
- C&K genomics, C-1008, H businesspark, 26, Beobwon-ro 9-gil, Songpa-gu, Seoul, Republic of Korea
| | - Bong-Hwan Choi
- National Institute of Animal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Hyung-Chul Kim
- National Institute of Animal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Jin-Young Jeong
- National Institute of Animal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Yong-Min Cho
- National Institute of Animal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Eung-Woo Park
- National Institute of Animal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Tae-Jeong Choi
- National Institute of Animal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Byoungho Park
- National Institute of Animal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Dajeong Lim
- National Institute of Animal Science, Rural Development Administration, Wanju, Republic of Korea
- * E-mail: (HK); (DL)
| | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak Gu, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Kwan-ak Gu, Seoul, Republic of Korea
- * E-mail: (HK); (DL)
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Browett S, McHugo G, Richardson IW, Magee DA, Park SDE, Fahey AG, Kearney JF, Correia CN, Randhawa IAS, MacHugh DE. Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed. Front Genet 2018. [PMID: 29520297 PMCID: PMC5827531 DOI: 10.3389/fgene.2018.00051] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP array data to evaluate genomic diversity within the Kerry population and between Kerry cattle and other European breeds. Patterns of genetic differentiation and gene flow among breeds using phylogenetic trees with ancestry graphs highlighted historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (Ne) revealed a demographic trend of diminishing Ne over time and that recent estimated Ne values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (FROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland.
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Affiliation(s)
- Sam Browett
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Gillian McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | | | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | | | - Alan G Fahey
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | | | - Carolina N Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Imtiaz A S Randhawa
- Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, Australia
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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38
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Genome-wide identification of runs of homozygosity islands and associated genes in local dairy cattle breeds. Animal 2018; 12:2480-2488. [DOI: 10.1017/s1751731118000629] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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39
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Campos BM, do Carmo AS, da Silva TBR, Verardo LL, de Simoni Gouveia JJ, Mendes Malhado CH, Barbosa da Silva MVG, Souza Carneiro PL. Identification of artificial selection signatures in Caracu breed lines selected for milk production and meat production. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.10.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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40
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Zhao YX, Yang J, Lv FH, Hu XJ, Xie XL, Zhang M, Li WR, Liu MJ, Wang YT, Li JQ, Liu YG, Ren YL, Wang F, Hehua EE, Kantanen J, Arjen Lenstra J, Han JL, Li MH. Genomic Reconstruction of the History of Native Sheep Reveals the Peopling Patterns of Nomads and the Expansion of Early Pastoralism in East Asia. Mol Biol Evol 2017. [PMID: 28645168 PMCID: PMC5850515 DOI: 10.1093/molbev/msx181] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
China has a rich resource of native sheep (Ovis aries) breeds associated with historical movements of several nomadic societies. However, the history of sheep and the associated nomadic societies in ancient China remains poorly understood. Here, we studied the genomic diversity of Chinese sheep using genome-wide SNPs, mitochondrial and Y-chromosomal variations in > 1,000 modern samples. Population genomic analyses combined with archeological records and historical ethnic demographics data revealed genetic signatures of the origins, secondary expansions and admixtures, of Chinese sheep thereby revealing the peopling patterns of nomads and the expansion of early pastoralism in East Asia. Originating from the Mongolian Plateau ∼5,000‒5,700 years ago, Chinese sheep were inferred to spread in the upper and middle reaches of the Yellow River ∼3,000‒5,000 years ago following the expansions of the Di-Qiang people. Afterwards, sheep were then inferred to reach the Qinghai-Tibetan and Yunnan-Kweichow plateaus ∼2,000‒2,600 years ago by following the north-to-southwest routes of the Di-Qiang migration. We also unveiled two subsequent waves of migrations of fat-tailed sheep into northern China, which were largely commensurate with the migrations of ancestors of Hui Muslims eastward and Mongols southward during the 12th‒13th centuries. Furthermore, we revealed signs of argali introgression into domestic sheep, extensive historical mixtures among domestic populations and strong artificial selection for tail type and other traits, reflecting various breeding strategies by nomadic societies in ancient China.
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Affiliation(s)
- Yong-Xin Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Xiao-Ju Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Min Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wen-Rong Li
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ming-Jun Liu
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Yu-Tao Wang
- College of Life and Geographic Sciences, Kashgar University, Kashgar, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - EEr Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
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41
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Signer-Hasler H, Burren A, Neuditschko M, Frischknecht M, Garrick D, Stricker C, Gredler B, Bapst B, Flury C. Population structure and genomic inbreeding in nine Swiss dairy cattle populations. Genet Sel Evol 2017; 49:83. [PMID: 29115934 PMCID: PMC5674839 DOI: 10.1186/s12711-017-0358-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 10/26/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Domestication, breed formation and intensive selection have resulted in divergent cattle breeds that likely exhibit their own genomic signatures. In this study, we used genotypes from 27,612 autosomal single nucleotide polymorphisms to characterize population structure based on 9214 sires representing nine Swiss dairy cattle populations: Brown Swiss (BS), Braunvieh (BV), Original Braunvieh (OB), Holstein (HO), Red Holstein (RH), Swiss Fleckvieh (SF), Simmental (SI), Eringer (ER) and Evolèner (EV). Genomic inbreeding (F ROH) and signatures of selection were determined by calculating runs of homozygosity (ROH). The results build the basis for a better understanding of the genetic development of Swiss dairy cattle populations and highlight differences between the original populations (i.e. OB, SI, ER and EV) and those that have become more popular in Switzerland as currently reflected by their larger populations (i.e. BS, BV, HO, RH and SF). RESULTS The levels of genetic diversity were highest and lowest in the SF and BS breeds, respectively. Based on F ST values, we conclude that, among all pairwise comparisons, BS and HO (0.156) differ more than the other pairs of populations. The original Swiss cattle populations OB, SI, ER, and EV are clearly genetically separated from the Swiss cattle populations that are now more common and represented by larger numbers of cows. Mean levels of F ROH ranged from 0.027 (ER) to 0.091 (BS). Three of the original Swiss cattle populations, ER (F ROH: 0.027), OB (F ROH: 0.029), and SI (F ROH: 0.039), showed low levels of genomic inbreeding, whereas it was much higher in EV (F ROH: 0.074). Private signatures of selection for the original Swiss cattle populations are reported for BTA4, 5, 11 and 26. CONCLUSIONS The low levels of genomic inbreeding observed in the original Swiss cattle populations ER, OB and SI compared to the other breeds are explained by a lesser use of artificial insemination and greater use of natural service. Natural service results in more sires having progeny at each generation and thus this breeding practice is likely the major reason for the remarkable levels of genetic diversity retained within these populations. The fact that the EV population is regionally restricted and its small census size of herd-book cows explain its high level of genomic inbreeding.
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Affiliation(s)
- Heidi Signer-Hasler
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Alexander Burren
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | | | - Mirjam Frischknecht
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
- Qualitas AG, Zug, Switzerland
| | | | | | | | | | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
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42
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Genome-wide genetic structure and differentially selected regions among Landrace, Erhualian, and Meishan pigs using specific-locus amplified fragment sequencing. Sci Rep 2017; 7:10063. [PMID: 28855565 PMCID: PMC5577042 DOI: 10.1038/s41598-017-09969-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 08/02/2017] [Indexed: 12/22/2022] Open
Abstract
As typical Chinese indigenous pig breeds, Erhualian and Meishan have been widely used to produce new strain or breed in the world. However, the genetic basis of characteristics of these pig breeds is still limited. Moreover, considering cost and output of sequencing, it is necessary to further develop cost-effective method for pig genome screening. To contribute on this issue, we developed a SLAF-seq (specific-locus amplified fragment sequencing) method for pigs and applied it to analyze the genetic difference among Landrace, Erhualian, and Meishan pigs. A total of 453.75 million reads were produced by SLAF-seq. After quality-control, 165,670 SNPs (single nucleotide polymorphisms) were used in further analysis. The results showed that Landrace had distinct genetic relationship compared to Erhualian (FST = 0.5480) and Meishan (FST = 0.5800), respectively, while Erhualian and Meishan held the relatively close genetic relationship (FST = 0.2335). Furthermore, a genome-wide scanning revealed 268 differentially selected regions (DSRs) with 855 genes and 256 DSRs with 347 genes between Landrace and the two Chinese indigenous pig breeds and between Erhualian and Meishan, respectively. This study provides a new cost-effective method for pig genome study and might contribute to a better understanding on the formation mechanism of genetic difference among pigs with different geographical origins.
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43
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Manirakiza J, Hatungumukama G, Thévenon S, Gautier M, Besbes B, Flori L, Detilleux J. Effect of genetic European taurine ancestry on milk yield of Ankole-Holstein crossbred dairy cattle in mixed smallholders system of Burundi highlands. Anim Genet 2017; 48:544-550. [PMID: 28833335 DOI: 10.1111/age.12578] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2017] [Indexed: 12/31/2022]
Abstract
Different breeding systems associated with specific bovine genetic resources have coexisted in Burundi. To prepare for the development of a national action plan for the improvement of bovine genetic resources in Burundi, we aimed at performing genetic characterization of Ankole and Ankole × European crossbred individuals and assessing the effect of European ancestry on milk productivity of cows kept under the mixed crops livestock system. To that end, we genotyped 37 Ankole and 138 crossbred individuals on 42 636 SNPs and combined these genotypes with those from 21 cattle breeds, representative of the bovine genetic diversity. We also measured milk yield not suckled and estimated suckled milk. Given the results, we confirmed the indicine × African taurine admixed origin of the Ankole in Burundi and showed that crossbred individuals present a high proportion of European ancestry (i.e. 57% on average). As the proportion of European ancestry increased, milk yield increased by 0.03 ± 0.01 l/day, at a lower extent than expected. We also observed that breeders were unable to correctly evaluate the European proportion in their livestock. Our results may provide useful information for objective dairy breeding in Burundi. As an example, an ex-situ conservation program of Ankole within the framework of value chains is proposed as an accompanying strategy to improve the sustainability of the crossbreeding program.
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Affiliation(s)
- J Manirakiza
- Faculté d'Agronomie et de Bio-Ingénierie, Université du Burundi, B.P. 2940, Bujumbura, Burundi
| | - G Hatungumukama
- Faculté d'Agronomie et de Bio-Ingénierie, Université du Burundi, B.P. 2940, Bujumbura, Burundi
| | - S Thévenon
- UMR INTERTRYP, CIRAD, F34398, Montpellier, France
| | - M Gautier
- UMR CBGP (INRA/CIRAD/IRD/Supagro), INRA, F34988, Montferrier-sur-Lez, France.,IBC, Institut de Biologie Computationnelle, 34095, Montpellier, France
| | - B Besbes
- Animal Production and Health Division, FAO, Viale delle Terme di Caracalla, 00153, Rome, Italy
| | - L Flori
- UMR INTERTRYP, CIRAD, F34398, Montpellier, France.,AgroParisTech, GABI, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Montpellier SupAgro, SELMET, CIRAD, INRA, 34398, Montpellier, France
| | - J Detilleux
- FARAH, Productions Durables, Université de Liège, 4000, Liège, Belgium
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44
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Kasarapu P, Porto-Neto LR, Fortes MRS, Lehnert SA, Mudadu MA, Coutinho L, Regitano L, George A, Reverter A. The Bos taurus-Bos indicus balance in fertility and milk related genes. PLoS One 2017; 12:e0181930. [PMID: 28763475 PMCID: PMC5538644 DOI: 10.1371/journal.pone.0181930] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/10/2017] [Indexed: 12/16/2022] Open
Abstract
Numerical approaches to high-density single nucleotide polymorphism (SNP) data are often employed independently to address individual questions. We linked independent approaches in a bioinformatics pipeline for further insight. The pipeline driven by heterozygosity and Hardy-Weinberg equilibrium (HWE) analyses was applied to characterize Bos taurus and Bos indicus ancestry. We infer a gene co-heterozygosity network that regulates bovine fertility, from data on 18,363 cattle with genotypes for 729,068 SNP. Hierarchical clustering separated populations according to Bos taurus and Bos indicus ancestry. The weights of the first principal component were subjected to Normal mixture modelling allowing the estimation of a gene’s contribution to the Bos taurus-Bos indicus axis. We used deviation from HWE, contribution to Bos indicus content and association to fertility traits to select 1,284 genes. With this set, we developed a co-heterozygosity network where the group of genes annotated as fertility-related had significantly higher Bos indicus content compared to other functional classes of genes, while the group of genes associated with milk production had significantly higher Bos taurus content. The network analysis resulted in capturing novel gene associations of relevance to bovine domestication events. We report transcription factors that are likely to regulate genes associated with cattle domestication and tropical adaptation. Our pipeline can be generalized to any scenarios where population structure requires scrutiny at the molecular level, particularly in the presence of a priori set of genes known to impact a phenotype of evolutionary interest such as fertility.
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Affiliation(s)
- Parthan Kasarapu
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, Brisbane, Queensland, Australia
| | - Laercio R. Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, Brisbane, Queensland, Australia
| | - Marina R. S. Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sigrid A. Lehnert
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, Brisbane, Queensland, Australia
| | | | - Luiz Coutinho
- Centro de Genomica Funcional ESALQ, University of São Paulo, Piracicaba, Sao Paulo, Brazil
| | - Luciana Regitano
- Embrapa Southeast Livestock, Rodovia Washington Luiz, São Carlos, Sao Paulo, Brazil
| | - Andrew George
- CSIRO, DATA61, Ecosciences Precinct Brisbane, Brisbane, Queensland, Australia
| | - Antonio Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, Brisbane, Queensland, Australia
- * E-mail:
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45
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Sequence analysis of chromosome 1 revealed different selection patterns between Chinese wild mice and laboratory strains. Mol Genet Genomics 2017. [PMID: 28631230 DOI: 10.1007/s00438-017-1335-z] [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: 10/19/2022]
Abstract
Both natural and artificial selection play a critical role in animals' adaptation to the environment. Detection of the signature of selection in genomic regions can provide insights for understanding the function of specific phenotypes. It is generally assumed that laboratory mice may experience intense artificial selection while wild mice more natural selection. However, the differences of selection signature in the mouse genome and underlying genes between wild and laboratory mice remain unclear. In this study, we used two mouse populations: chromosome 1 (Chr 1) substitution lines (C1SLs) derived from Chinese wild mice and mouse genome project (MGP) sequenced inbred strains and two selection detection statistics: Fst and Tajima's D to identify the signature of selection footprint on Chr 1. For the differentiation between the C1SLs and MGP, 110 candidate selection regions containing 47 protein coding genes were detected. A total of 149 selection regions which encompass 7.215 Mb were identified in the C1SLs by Tajima's D approach. While for the MGP, we identified nearly twice selection regions (243) compared with the C1SLs which accounted for 13.27 Mb Chr 1 sequence. Through functional annotation, we identified several biological processes with significant enrichment including seven genes in the olfactory transduction pathway. In addition, we searched the phenotypes associated with the 47 candidate selection genes identified by Fst. These genes were involved in behavior, growth or body weight, mortality or aging, and immune systems which align well with the phenotypic differences between wild and laboratory mice. Therefore, the findings would be helpful for our understanding of the phenotypic differences between wild and laboratory mice and applications for using this new mouse resource (C1SLs) for further genetics studies.
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46
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Bahbahani H, Tijjani A, Mukasa C, Wragg D, Almathen F, Nash O, Akpa GN, Mbole-Kariuki M, Malla S, Woolhouse M, Sonstegard T, Van Tassell C, Blythe M, Huson H, Hanotte O. Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu. Front Genet 2017. [PMID: 28642786 PMCID: PMC5462927 DOI: 10.3389/fgene.2017.00068] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The East African Shorthorn Zebu (EASZ) cattle are ancient hybrid between Asian zebu × African taurine cattle preferred by local farmers due to their adaptability to the African environment. The genetic controls of these adaptabilities are not clearly understood yet. Here, we genotyped 92 EASZ samples from Kenya (KEASZ) with more than 770,000 SNPs and sequenced the genome of a pool of 10 KEASZ. We observe an even admixed autosomal zebu × taurine genomic structure in the population. A total of 101 and 165 candidate regions of positive selection, based on genome-wide SNP analyses (meta-SS, Rsb, iHS, and ΔAF) and pooled heterozygosity (Hp) full genome sequence analysis, are identified, in which 35 regions are shared between them. A total of 142 functional variants, one novel, have been detected within these regions, in which 30 and 26 were classified as of zebu and African taurine origins, respectively. High density genome-wide SNP analysis of zebu × taurine admixed cattle populations from Uganda and Nigeria show that 25 of these regions are shared between KEASZ and Uganda cattle, and seven regions are shared across the KEASZ, Uganda, and Nigeria cattle. The identification of common candidate regions allows us to fine map 18 regions. These regions intersect with genes and QTL associated with reproduction and environmental stress (e.g., immunity and heat stress) suggesting that the genome of the zebu × taurine admixed cattle has been uniquely selected to maximize hybrid fitness both in terms of reproduction and survivability.
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Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait UniversityKuwait, Kuwait
| | - Abdulfatai Tijjani
- School of Life Sciences, University of NottinghamNottingham, United Kingdom.,Centre for Genomics Research and Innovation, National Biotechnology Development AgencyAbuja, Nigeria
| | | | - David Wragg
- Centre for Tropical Livestock Genetics and Health, Roslin InstituteEdinburgh, United Kingdom
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal UniversityAl-Hasa, Saudi Arabia
| | - Oyekanmi Nash
- Centre for Genomics Research and Innovation, National Biotechnology Development AgencyAbuja, Nigeria
| | - Gerald N Akpa
- Department of Animal Science, Ahmadu Bello UniversityZaria, Nigeria
| | - Mary Mbole-Kariuki
- School of Life Sciences, University of NottinghamNottingham, United Kingdom
| | - Sunir Malla
- Deep Seq Department, University of NottinghamNottingham, United Kingdom
| | - Mark Woolhouse
- Ashworth Laboratories, Centre for Immunity, Infection and Evolution, University of EdinburghEdinburgh, United Kingdom
| | | | - Curtis Van Tassell
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research ServiceBeltsville, MD, United States
| | - Martin Blythe
- Deep Seq Department, University of NottinghamNottingham, United Kingdom
| | - Heather Huson
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research ServiceBeltsville, MD, United States
| | - Olivier Hanotte
- School of Life Sciences, University of NottinghamNottingham, United Kingdom.,International Livestock Research Institute (ILRI)Addis Ababa, Ethiopia
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47
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Association study and expression analysis of CYP4A11 gene copy number variation in Chinese cattle. Sci Rep 2017; 7:46599. [PMID: 28492277 PMCID: PMC5425913 DOI: 10.1038/srep46599] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 03/22/2017] [Indexed: 11/09/2022] Open
Abstract
The identification of copy number variations (CNVs) allow us to explore genomic polymorphisms. In recent years, significant progress in understanding CNVs has been made in studies of human and animals, however, association and expression studies of CNVs are still in the early stage. It was previously reported that the Cytochrome P-450 4A11 (CYP4A11) gene is located within a copy number variable region (CNVR) that encompasses quantitative trait loci (QTLs) for economic traits like meat quality and milk production. So, this study was performed to determine the presence of CYP4A11 CNV in six distinct cattle breeds, identify its relationship with growth, and explore the biological effects of gene expression. For three CYP4A11 CNV types, Normal was more frequent than Gain or Loss. Association analysis revealed a positive effect of CYP4A11 copy number on growth traits (P < 0.05). One-way analysis of variance (ANOVA) analysis revealed that more CYP4A11 copies increased the gene expression level. Moreover, overexpression of CYP4A11 in vitro revealed its effect on lipid deposit. The data provide evidence for the functional role of CYP4A11 CNV and provide the basis for future applications in cattle breeding.
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48
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de Simoni Gouveia JJ, Paiva SR, McManus CM, Caetano AR, Kijas JW, Facó O, Azevedo HC, de Araujo AM, de Souza CJH, Yamagishi MEB, Carneiro PLS, Braga Lôbo RN, de Oliveira SMP, da Silva MVG. Genome-wide search for signatures of selection in three major Brazilian locally adapted sheep breeds. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.01.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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49
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Lim D, Choi BH, Cho YM, Chai HH, Jang GW, Gondro C, Jeoung YH, Lee SH. Analysis of extended haplotype in Korean cattle (Hanwoo) population. BMB Rep 2017; 49:514-9. [PMID: 27470211 PMCID: PMC5227145 DOI: 10.5483/bmbrep.2016.49.9.074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Indexed: 12/22/2022] Open
Abstract
Korean cattle (Hanwoo) are categorized into three breeds based on color: brown, brindle, and black. Among these breeds, brown Hanwoo has been subjected to intensive selection to improve meat traits. To identify genetic traces driven by recent selection in brown Hanwoo, we scanned the genomes of brown and brindle Hanwoo using a bovine SNP chip. We identified 17 candidate selection signatures in brown Hanwoo and sequenced four candidate regions from 10 individuals each of brown and brindle Hanwoo. In particular, non-synonymous SNPs in the ADSL gene (K88M, L189H, and R302Q) might have had mutational effects on protein structure as a result of altering the purine pathway during nucleotide breakdown. The ADSL gene was previously reported to affect meat quality and yield in livestock. Meat quality and yield are main breeding goals for brown Hanwoo, and our results support a potential causal influence of non-synonymous SNPs in the ADSL gene. [BMB Reports 2016; 49(9): 514-519]
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Affiliation(s)
- Dajeong Lim
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 55365, Korea
| | - Bong Hwan Choi
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 55365, Korea
| | - Yong Min Cho
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 55365, Korea
| | - Han Ha Chai
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 55365, Korea
| | - Gul Won Jang
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 55365, Korea
| | - Cedric Gondro
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Yeoung Ho Jeoung
- Hanwoo Department, Korea Animal Improvement Association, Seoul 06668, Korea
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chung Nam National University, Daejeon 34134, Korea
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50
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Chen S, Kaeppler SM, Vogel KP, Casler MD. Selection Signatures in Four Lignin Genes from Switchgrass Populations Divergently Selected for In Vitro Dry Matter Digestibility. PLoS One 2016; 11:e0167005. [PMID: 27893787 PMCID: PMC5125650 DOI: 10.1371/journal.pone.0167005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/07/2016] [Indexed: 12/28/2022] Open
Abstract
Switchgrass is undergoing development as a dedicated cellulosic bioenergy crop. Fermentation of lignocellulosic biomass to ethanol in a bioenergy system or to volatile fatty acids in a livestock production system is strongly and negatively influenced by lignification of cell walls. This study detects specific loci that exhibit selection signatures across switchgrass breeding populations that differ in in vitro dry matter digestibility (IVDMD), ethanol yield, and lignin concentration. Allele frequency changes in candidate genes were used to detect loci under selection. Out of the 183 polymorphisms identified in the four candidate genes, twenty-five loci in the intron regions and four loci in coding regions were found to display a selection signature. All loci in the coding regions are synonymous substitutions. Selection in both directions were observed on polymorphisms that appeared to be under selection. Genetic diversity and linkage disequilibrium within the candidate genes were low. The recurrent divergent selection caused excessive moderate allele frequencies in the cycle 3 reduced lignin population as compared to the base population. This study provides valuable insight on genetic changes occurring in short-term selection in the polyploid populations, and discovered potential markers for breeding switchgrass with improved biomass quality.
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Affiliation(s)
- Shiyu Chen
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Shawn M. Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Energy, Great Lakes Bioenergy Research Center, Madison, Wisconsin, United States of America
| | - Kenneth P. Vogel
- USDA-ARS, Grain, Forage, and Bioenergy Research Unit, Lincoln, Nebraska, United States of America
- Department of Agronomy & Horticulture, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Michael D. Casler
- Department of Energy, Great Lakes Bioenergy Research Center, Madison, Wisconsin, United States of America
- USDA-ARS, U.S. Dairy Forage Research Center, Madison, Wisconsin, United States of America
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