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Rajawat D, Ghildiyal K, Sonejita Nayak S, Sharma A, Parida S, Kumar S, Ghosh AK, Singh U, Sivalingam J, Bhushan B, Dutt T, Panigrahi M. Genome-wide mining of diversity and evolutionary signatures revealed selective hotspots in Indian Sahiwal cattle. Gene 2024; 901:148178. [PMID: 38242377 DOI: 10.1016/j.gene.2024.148178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
The Sahiwal cattle breed is the best indigenous dairy cattle breed, and it plays a pivotal role in the Indian dairy industry. This is due to its exceptional milk-producing potential, adaptability to local tropical conditions, and its resilience to ticks and diseases. The study aimed to identify selective sweeps and estimate intrapopulation genetic diversity parameters in Sahiwal cattle using ddRAD sequencing-based genotyping data from 82 individuals. After applying filtering criteria, 78,193 high-quality SNPs remained for further analysis. The population exhibited an average minor allele frequency of 0.221 ± 0.119. Genetic diversity metrics, including observed (0.597 ± 0.196) and expected heterozygosity (0.433 ± 0.096), nucleotide diversity (0.327 ± 0.114), the proportion of polymorphic SNPs (0.726), and allelic richness (1.323 ± 0.134), indicated ample genomic diversity within the breed. Furthermore, an effective population size of 74 was observed in the most recent generation. The overall mean linkage disequilibrium (r2) for pairwise SNPs was 0.269 ± 0.057. Moreover, a greater proportion of short Runs of Homozygosity (ROH) segments were observed suggesting that there may be low levels of recent inbreeding in this population. The genomic inbreeding coefficients, computed using different inbreeding estimates (FHOM, FUNI, FROH, and FGROM), ranged from -0.0289 to 0.0725. Subsequently, we found 146 regions undergoing selective sweeps using five distinct statistical tests: Tajima's D, CLR, |iHS|, |iHH12|, and ROH. These regions, located in non-overlapping 500 kb windows, were mapped and revealed various protein-coding genes associated with enhanced immune systems and disease resistance (IFNL3, IRF8, BLK), as well as production traits (NRXN1, PLCE1, GHR). Notably, we identified interleukin 2 (IL2) on Chr17: 35217075-35223276 as a gene linked to tick resistance and uncovered a cluster of genes (HSPA8, UBASH3B, ADAMTS18, CRTAM) associated with heat stress. These findings indicate the evolutionary impact of natural and artificial selection on the environmental adaptation of the Sahiwal cattle population.
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Affiliation(s)
- Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Pharmacology & Toxicology Division, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Shive Kumar
- Department of Animal Genetics and Breeding, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - A K Ghosh
- Department of Animal Genetics and Breeding, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Umesh Singh
- ICAR Central Institute for Research on Cattle, Meerut, UP, India
| | | | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
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Calderón-Chagoya R, Vega-Murillo VE, García-Ruiz A, Ríos-Utrera Á, Martínez-Velázquez G, Montaño-Bermúdez M. Discovering Genomic Regions Associated with Reproductive Traits and Frame Score in Mexican Simmental and Simbrah Cattle Using Individual SNP and Haplotype Markers. Genes (Basel) 2023; 14:2004. [PMID: 38002947 PMCID: PMC10671695 DOI: 10.3390/genes14112004] [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: 09/08/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Reproductive efficiency stands as a critical determinant of profitability within beef production systems. The incorporation of molecular markers can expedite advancements in reproductive performance. While the use of SNPs in association analysis is prevalent, approaches centered on haplotypes can offer a more comprehensive insight. The study used registered Simmental and Simbrah cattle genotyped with the GGP Bovine 150 k panel. Phenotypes included scrotal circumference (SC), heifer fertility (HF), stayability (STAY), and frame score (FS). After quality control, 105,129 autosomal SNPs from 967 animals were used. Haplotype blocks were defined based on linkage disequilibrium. Comparison between haplotypes and SNPs for reproductive traits and FS was conducted using Bayesian and frequentist models. 23, 13, 7, and 2 SNPs exhibited associations with FS, SC, HF, and STAY, respectively. In addition, seven, eight, seven, and one haplotypes displayed associations with FS, SC, HF, and STAY, respectively. Within these delineated genomic segments, potential candidate genes were associated.
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Affiliation(s)
- René Calderón-Chagoya
- Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Ciudad de México 04510, Mexico;
- National Center for Disciplinary Research in Physiology and Animal Improvement, National Institute for Forestry, Agricultural and Livestock Research, Querétaro 76280, Mexico;
| | - Vicente Eliezer Vega-Murillo
- Faculty of Veterinary Medicine and Zootechnics, Veracruzana University, Veracruz 91710, Mexico; (V.E.V.-M.); (Á.R.-U.)
| | - Adriana García-Ruiz
- National Center for Disciplinary Research in Physiology and Animal Improvement, National Institute for Forestry, Agricultural and Livestock Research, Querétaro 76280, Mexico;
| | - Ángel Ríos-Utrera
- Faculty of Veterinary Medicine and Zootechnics, Veracruzana University, Veracruz 91710, Mexico; (V.E.V.-M.); (Á.R.-U.)
| | - Guillermo Martínez-Velázquez
- Experimental Field Santiago Ixcuintla, National Institute for Forestry, Agricultural and Livestock Research, Nayarit 63570, Mexico;
| | - Moisés Montaño-Bermúdez
- National Center for Disciplinary Research in Physiology and Animal Improvement, National Institute for Forestry, Agricultural and Livestock Research, Querétaro 76280, Mexico;
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Mourad AM, Hamdy RM, Esmail SM. Novel genomic regions on chromosome 5B controlling wheat powdery mildew seedling resistance under Egyptian conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1160657. [PMID: 37235018 PMCID: PMC10208068 DOI: 10.3389/fpls.2023.1160657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/27/2023] [Indexed: 05/28/2023]
Abstract
Wheat powdery mildew (PM) causes significant yield losses worldwide. None of the Egyptian wheat cultivars was detected to be highly resistant to such a severe disease. Therefore, a diverse spring wheat panel was evaluated for PM seedling resistance using different Bgt conidiospores collected from Egyptian fields in two growing seasons. The evaluation was done in two separate experiments. Highly significant differences were found between the two experiments suggesting the presence of different isolates populations. Highly significant differences were found among the tested genotypes confirming the ability to improve PM resistance using the recent panel. Genome-wide association study (GWAS) was done for each experiment separately and a total of 71 significant markers located within 36 gene models were identified. The majority of these markers are located on chromosome 5B. Haplotype block analysis identified seven blocks containing the significant markers on chromosome 5B. Five gene models were identified on the short arm of the chromosome. Gene enrichment analysis identified five and seven pathways based on the biological process and molecular functions respectively for the detected gene models. All these pathways are associated with disease resistance in wheat. The genomic regions on 5B seem to be novel regions that are associated with PM resistance under Egyptian conditions. Selection of superior genotypes was done and Grecian genotypes seem to be a good source for improving PM resistance under Egyptian conditions.
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Affiliation(s)
- Amira M.I. Mourad
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, OT Gatersleben, Germany
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Rania M. Hamdy
- Food Science and Technology Department, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Samar M. Esmail
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
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Dash S, Singh A, Dixit SP, Kumar A, Behera R. Exploring haplotype block structure, runs of homozygosity, and effective population size among dairy cattle breeds of India. Trop Anim Health Prod 2023; 55:129. [PMID: 36952060 DOI: 10.1007/s11250-023-03534-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 03/06/2023] [Indexed: 03/24/2023]
Abstract
The present study aimed to explore haplotype structure, runs of homozygosity (ROH), effective population size and persistence of gametic phase among three indigenous dairy cattle breeds, viz., Sahiwal (n = 19), Tharparkar (n = 17), and Gir (n = 16) by using BovineHD single nucleotide polymorphism (SNP) genotyping assay. The filtered SNPs after quality control ranged from 44% in Sahiwal to 53% in Gir. The highest number of haplotype blocks was observed in Tharparkar (15,640) and the lowest in Sahiwal (8027) spanning 17.3% and 7.8% of genome, respectively. The average block length was found close to 26 kb which suggests that multiple recombination events fragmented the ancestral haplotypes into smaller sizes. Gir cattle had the largest number of runs of homozygosity (ROH) regions (1762) followed by Tharparkar (1528) and Sahiwal (1138). Without pedigree information, inbreeding coefficients estimated from ROH (FROH) revealed that Gir had the highest FROH (0.099) proposing more inbreeding rate in this population. Effective population size (Ne) decreased slowly over the last 60 generations and at 13 generations ago; Ne was estimated as 70 for all the three dairy breeds. The highest gametic phase correlation (r = 0.78) was observed for Sahiwal and Tharparkar breed pair suggesting formulation of multi-breed reference population for successful implementation of genomic selection among dairy breeds. The decline in effective population size among native Indian cattle breeds may help in formulating strategies for conservation and genetic improvement of native germplasm for future use.
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Affiliation(s)
- Soumya Dash
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India.
- School of Crop Health Policy Support Research, ICAR-National Institute of Biotic Stress Management, Raipur, 493225, Chhattisgarh, India.
| | - Avtar Singh
- Animal Genetics and Breeding Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - S P Dixit
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Avnish Kumar
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Rajalaxmi Behera
- Regional Centre, ICAR-Directorate of Poultry Research, Bhubaneswar, 751003, Odisha, India
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Dlamini NM, Dzomba EF, Magawana M, Ngcamu S, Muchadeyi FC. Linkage Disequilibrium, Haplotype Block Structures, Effective Population Size and Genome-Wide Signatures of Selection of Two Conservation Herds of the South African Nguni Cattle. Animals (Basel) 2022; 12:ani12162133. [PMID: 36009722 PMCID: PMC9405234 DOI: 10.3390/ani12162133] [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: 05/05/2022] [Revised: 06/24/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
The Nguni cattle of South Africa are a Sanga breed, characterized by many eco-types and research populations that have been established in an effort to conserve the diversity within the breed. The aim of this study was to investigate the overall genetic diversity as well as similarities and differences within and between two conservation herds of the South African Nguni Cattle. Mean LD (r2) estimates were 0.413 ± 0.219 for Bartlow Combine and 0.402 ± 0.209 for Kokstad. Genome-wide average LD (r2) decreased with increasing genetic marker distance for both populations from an average of 0.76 ± 0.28 and 0.77 ± 0.27 at 0–1 kb bin to 0.31 ± 0.13 and 0.32 ± 0.13 at 900–1000 kb bin in Bartlow Combine and Kokstad populations, respectively. Variation in LD levels across autosomes was observed in both populations. The results showed higher levels of LD than previously reported in Nguni field populations and other South African breeds, especially at shorter marker distances of less than 20 kb. A total number of 77,305 and 66,237 haplotype blocks covering a total of 1570.09 Mb (61.99% genome coverage) and 1367.42 Mb (53.96% genome coverage) were detected in Bartlow Combine and Kokstad populations, respectively. A total of 18,449 haploblocks were shared between the two populations while 58,856 and 47,788 haploblocks were unique to Bartlow Combine and Kokstad populations, respectively. Effective population size (Ne) results demonstrated a rapid decrease in Ne across generations for both Bartlow Combine and Kokstad conservation herds. Two complementary methods, integrated haplotype score (iHS) and Extend Haplotype Homozygosity Test (XP-EHH), were implemented in this study to detect the selection signatures in the two herds. A total of 553 and 166 selected regions were identified in Bartlow Combine and Kokstad populations, respectively. DAVID and GO terms analysis of the regions under selection reported genes/QTLs associated with fertility, carcass weight, coat colour, immune response, and eye area pigmentation. Some genes, such as HCAR1, GNAI1, PIK3R3, WNT3, RAB5A, BOLA-N (Class IB MHC Antigen QA-2-Related), BOLA (Class IB MHC Antigen QA-2-Related), and Rab-8B, etc., were found in regions under selection in this study. Overall, the study implied reduced genetic diversity in the two herds calling for corrective measures to maintain the diversity of the South African Nguni cattle. This study presented a comprehensive analysis of the genomic architecture of South African Nguni cattle populations, providing essential genetic information of utility in the management of conservation flocks.
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Affiliation(s)
- Njabulo M. Dlamini
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa or
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, Pretoria 0110, South Africa
| | - Edgar F. Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa or
| | - Mpumelelo Magawana
- KZN Department of Agriculture & Rural Development, Private Bag X9059, Pietermaritzburg 3200, South Africa
| | - Sphamandla Ngcamu
- KZN Department of Agriculture & Rural Development, Private Bag X9059, Pietermaritzburg 3200, South Africa
| | - Farai C. Muchadeyi
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, Pretoria 0110, South Africa
- Correspondence:
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Rahimmadar S, Ghaffari M, Mokhber M, Williams JL. Linkage Disequilibrium and Effective Population Size of Buffalo Populations of Iran, Turkey, Pakistan, and Egypt Using a Medium Density SNP Array. Front Genet 2021; 12:608186. [PMID: 34950186 PMCID: PMC8689148 DOI: 10.3389/fgene.2021.608186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/03/2021] [Indexed: 11/21/2022] Open
Abstract
Linkage disequilibrium (LD) across the genome provides information to identify the genes and variations related to quantitative traits in genome-wide association studies (GWAS) and for the implementation of genomic selection (GS). LD can also be used to evaluate genetic diversity and population structure and reveal genomic regions affected by selection. LD structure and Ne were assessed in a set of 83 water buffaloes, comprising Azeri (AZI), Khuzestani (KHU), and Mazandarani (MAZ) breeds from Iran, Kundi (KUN) and Nili-Ravi (NIL) from Pakistan, Anatolian (ANA) buffalo from Turkey, and buffalo from Egypt (EGY). The values of corrected r2 (defined as the correlation between two loci) of adjacent SNPs for three pooled Iranian breeds (IRI), ANA, EGY, and two pooled Pakistani breeds (PAK) populations were 0.24, 0.28, 0.27, and 0.22, respectively. The corrected r2 between SNPs decreased with increasing physical distance from 100 Kb to 1 Mb. The LD values for IRI, ANA, EGY, and PAK populations were 0.16, 0.23, 0.24, and 0.21 for less than 100Kb, respectively, which reduced rapidly to 0.018, 0.042, 0.059, and 0.024, for a distance of 1 Mb. In all the populations, the decay rate was low for distances greater than 2Mb, up to the longest studied distance (15 Mb). The r2 values for adjacent SNPs in unrelated samples indicated that the Affymetrix Axiom 90 K SNP genomic array was suitable for GWAS and GS in these populations. The persistency of LD phase (PLDP) between populations was assessed, and results showed that PLPD values between the populations were more than 0.9 for distances of less than 100 Kb. The Ne in the recent generations has declined to the extent that breeding plans are urgently required to ensure that these buffalo populations are not at risk of being lost. We found that results are affected by sample size, which could be partially corrected for; however, additional data should be obtained to be confident of the results.
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Affiliation(s)
- Shirin Rahimmadar
- Department of Animal Science, Faculty of Agricultural Science, Urmia University, Urmia, Iran
| | - Mokhtar Ghaffari
- Department of Animal Science, Faculty of Agricultural Science, Urmia University, Urmia, Iran
| | - Mahdi Mokhber
- Department of Animal Science, Faculty of Agricultural Science, Urmia University, Urmia, Iran
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia.,Department of Animal Science, Food and Nutrition, Università Cattolica Del Sacro Cuore, Piacenza, Italy
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Helal MMU, Gill RA, Tang M, Yang L, Hu M, Yang L, Xie M, Zhao C, Cheng X, Zhang Y, Zhang X, Liu S. SNP- and Haplotype-Based GWAS of Flowering-Related Traits in Brassica napus. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112475. [PMID: 34834840 PMCID: PMC8619824 DOI: 10.3390/plants10112475] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 05/05/2023]
Abstract
Traits related to flowering time are the most promising agronomic traits that directly impact the seed yield and oil quality of rapeseed (Brassica napus L.). Developing early flowering and maturity rapeseed varieties is an important breeding objective in B. napus. Many studies have reported on days to flowering, but few have reported on budding, bolting, and the interval between bolting and DTF. Therefore, elucidating the genetic architecture of QTLs and genes regulating flowering time, we presented an integrated investigation on SNP and haplotype-based genome-wide association study of 373 diverse B. napus germplasm, which were genotyped by the 60K SNP array and were phenotyped in the four environments. The results showed that a total of 15 and 37 QTLs were detected from SNP and haplotype-based GWAS, respectively. Among them, seven QTL clusters were identified by haplotype-based GWAS. Moreover, three and eight environmentally stable QTLs were detected by SNP-GWAS and haplotype-based GWAS, respectively. By integrating the above two approaches and by co-localizing the four traits, ten (10) genomic regions were under selection on chromosomes A03, A07, A08, A10, C06, C07, and C08. Interestingly, the genomic regions FT.A07.1, FT.A08, FT.C06, and FT.C07 were identified as novel. In these ten regions, a total of 197 genes controlling FT were detected, of which 14 highly expressed DEGs were orthologous to 13 Arabidopsis thaliana genes after integration with transcriptome results. In a nutshell, the above results uncovered the genetic architecture of important agronomic traits related to flowering time and provided a basis for multiple molecular marker-trait associations in B. napus.
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Affiliation(s)
- MMU Helal
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Rafaqat Ali Gill
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Minqiang Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
- Key Laboratory of Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), College of Forestry, Hainan University, Haikou 570228, China
| | - Li Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Ming Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Lingli Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Meili Xie
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Chuanji Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Xiaohui Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
| | - Yuanyuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
- Correspondence: (Y.Z.); (X.Z.)
| | - Xiong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
- Correspondence: (Y.Z.); (X.Z.)
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (M.M.U.H.); (R.A.G.); (M.T.); (L.Y.); (M.H.); (L.Y.); (M.X.); (C.Z.); (X.C.); (S.L.)
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Xu Z, Mei S, Zhou J, Zhang Y, Qiao M, Sun H, Li Z, Li L, Dong B, Oyelami FO, Wu J, Peng X. Genome-Wide Assessment of Runs of Homozygosity and Estimates of Genomic Inbreeding in a Chinese Composite Pig Breed. Front Genet 2021; 12:720081. [PMID: 34539748 PMCID: PMC8440853 DOI: 10.3389/fgene.2021.720081] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/06/2021] [Indexed: 01/31/2023] Open
Abstract
The primary purpose of the current study was to assess the genetic diversity, runs of homozygosity (ROH) and ROH islands in a Chinese composite pig and explore hotspot regions for traces of selection. First, we estimated the length, number, and frequency of ROH in 262 Xidu black pigs using the Porcine SNP50 BeadChip and compared the estimates of inbreeding coefficients, which were calculated based on ROHs (FROH) and homozygosity (FHOM). Our result shows that a total of 7,248 ROH exceeding 1Mb were detected in 262 pigs. In addition, Sus scrofa chromosome (SSC) 8 and SSC10, respectively, has the highest and lowest chromosome coverage by ROH. These results suggest that inbreeding estimation based on total ROH may be a useful method, especially for crossbreed or composite populations. We also calculated an inbreeding coefficient of 0.077 from the total ROH. Eight ROH islands were found in this study. These ROH islands harbored genes associated with fat deposition, muscular development, reproduction, ear shape, and adaptation, such as TRAF7, IGFBP7, XPO1, SLC26A8, PPARD, and OR1F1. These findings may help to understand the effects of environmental and artificial selection on the genome structure of composite pigs. Our results provide a basis for subsequent genomic selection (GS), and provides a reference for the hybrid utilization of other pig breeds.
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Affiliation(s)
- Zhong Xu
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Shuqi Mei
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Jiawei Zhou
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Yu Zhang
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Mu Qiao
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Hua Sun
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Zipeng Li
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Lianghua Li
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Binke Dong
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Favour Oluwapelumi Oyelami
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Junjing Wu
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Xianwen Peng
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
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9
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Marina H, Chitneedi P, Pelayo R, Suárez-Vega A, Esteban-Blanco C, Gutiérrez-Gil B, Arranz JJ. Study on the concordance between different SNP-genotyping platforms in sheep. Anim Genet 2021; 52:868-880. [PMID: 34515357 DOI: 10.1111/age.13139] [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] [Accepted: 08/28/2021] [Indexed: 12/12/2022]
Abstract
Different SNP genotyping technologies are commonly used in multiple studies to perform QTL detection, genotype imputation, and genomic predictions. Therefore, genotyping errors cannot be ignored, as they can reduce the accuracy of different procedures applied in genomic selection, such as genomic imputation, genomic predictions, and false-positive results in genome-wide association studies. Currently, whole-genome resequencing (WGR) also offers the potential for variant calling analysis and high-throughput genotyping. WGR might overshadow array-based genotyping technologies due to the larger amount and precision of the genomic information provided; however, its comparatively higher price per individual still limits its use in larger populations. Thus, the objective of this work was to evaluate the accuracy of the two most popular SNP-chip technologies, namely, Affymetrix and Illumina, for high-throughput genotyping in sheep considering high-coverage WGR datasets as references. Analyses were performed using two reference sheep genome assemblies, the popular Oar_v3.1 reference genome and the latest available version Oar_rambouillet_v1.0. Our results demonstrate that the genotypes from both platforms are suggested to have high concordance rates with the genotypes determined from reference WGR datasets (96.59% and 99.51% for Affymetrix and Illumina technologies, respectively). The concordance results provided in the current study can pinpoint low reproducible markers across multiple platforms used for sheep genotyping data. Comparing results using two reference genome assemblies also informs how genome assembly quality can influence genotype concordance rates among different genotyping platforms. Moreover, we describe an efficient pipeline to test the reliability of markers included in sheep SNP-chip panels against WGR datasets available on public databases. This pipeline may be helpful for discarding low-reliability markers before exploiting genomic information for gene mapping analyses or genomic prediction.
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Affiliation(s)
- H Marina
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - P Chitneedi
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - R Pelayo
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - A Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - C Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - B Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - J J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
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10
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Verardo LL, E Silva FF, Machado MA, do Carmo Panetto JC, de Lima Reis Faza DR, Otto PI, de Almeida Regitano LC, da Silva LOC, do Egito AA, do Socorro Maués Albuquerque M, Zanella R, da Silva MVGB. Genome-Wide Analyses Reveal the Genetic Architecture and Candidate Genes of Indicine, Taurine, Synthetic Crossbreds, and Locally Adapted Cattle in Brazil. Front Genet 2021; 12:702822. [PMID: 34386042 PMCID: PMC8353373 DOI: 10.3389/fgene.2021.702822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/30/2021] [Indexed: 11/24/2022] Open
Abstract
Cattle population history, breeding systems, and geographic subdivision may be reflected in runs of homozygosity (ROH), effective population size (Ne), and linkage disequilibrium (LD) patterns. Thus, the assessment of this information has become essential to the implementation of genomic selection on purebred and crossbred cattle breeding programs. In this way, we assessed the genotype of 19 cattle breeds raised in Brazil belonging to taurine, indicine, synthetic crossbreds, and Iberian-derived locally adapted ancestries to evaluate the overall LD decay patterns, Ne, ROH, and breed composition. We were able to obtain a general overview of the genomic architecture of cattle breeds currently raised in Brazil and other tropical countries. We found that, among the evaluated breeds, different marker densities should be used to improve the genomic prediction accuracy and power of genome-wide association studies. Breeds showing low Ne values indicate a recent inbreeding, also reflected by the occurrence of longer ROH, which demand special attention in the matting schemes to avoid extensive inbreeding. Candidate genes (e.g., ABCA7, PENK, SPP1, IFNAR1, IFNAR2, SPEF2, PRLR, LRRTM1, and LRRTM4) located in the identified ROH islands were evaluated, highlighting biological processes involved with milk production, behavior, rusticity, and fertility. Furthermore, we were successful in obtaining the breed composition regarding the taurine and indicine composition using single-nucleotide polymorphism (SNP) data. Our results were able to observe in detail the genomic backgrounds that are present in each breed and allowed to better understand the various contributions of ancestor breeds to the modern breed composition to the Brazilian cattle.
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Affiliation(s)
- Lucas Lima Verardo
- Animal Breeding Lab, Department of Animal Science, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Brazil
| | | | | | | | | | - Pamela Itajara Otto
- Department of Animal Science, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | | | | | | | | | - Ricardo Zanella
- Department of Veterinary Medicine, Universidade de Passo Fundo, Passo Fundo, Brazil
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11
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El Hou A, Rocha D, Venot E, Blanquet V, Philippe R. Long-range linkage disequilibrium in French beef cattle breeds. Genet Sel Evol 2021; 53:63. [PMID: 34301193 PMCID: PMC8306006 DOI: 10.1186/s12711-021-00657-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Linkage disequilibrium (LD) is a key parameter to study the history of populations and to identify and fine map quantitative trait loci (QTL) and it has been studied for many years in animal populations. The advent of new genotyping technologies has allowed whole-genome LD studies in most cattle populations. However, to date, long-range LD (LRLD) between distant variants on the genome has not been investigated in detail in cattle. Here, we present the first comprehensive study of LRLD in French beef cattle by analysing data on 672 Charolais (CHA), 462 Limousine (LIM) and 326 Blonde d'Aquitaine (BLA) individuals that were genotyped on the Illumina BovineHD Beadchip. Furthermore, whole-genome LD and haplotype block structure were analysed in these three breeds. RESULTS We computed linkage disequilibrium (r2) values for 5.9, 5.6 and 6.0 billion pairs of SNPs on the 29 autosomes of CHA, LIM and BLA, respectively. Mean r2 values drop to less than 0.1 for distances between SNPs greater than 120 kb. However, for the first time, we detected the existence of LRLD in the three main French beef breeds. In total, 598, 266, and 795 LRLD events (r2 ≥ 0.6) were detected in CHA, LIM and BLA, respectively. Each breed had predominantly population-specific LRLD interactions, although shared LRLD events occurred in a number of regions (55 LRLD events were shared between two breeds and nine between the three breeds). Examples of possible functional gene interactions and QTL co-location were observed with some of these LRLD events, which suggests epistatic selection. CONCLUSIONS We identified long-range linkage disequilibrium for the first time in French beef cattle populations. Epistatic selection may be the main source of the observed LRLD events, but other forces may also be involved. LRLD information should be accounted for in genome-wide association studies.
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Affiliation(s)
- Abdelmajid El Hou
- INRAE, PEIRENE EA7500, USC1061 GAMAA, Université de Limoges, 87060, Limoges, France
| | - Dominique Rocha
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Eric Venot
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Véronique Blanquet
- INRAE, PEIRENE EA7500, USC1061 GAMAA, Université de Limoges, 87060, Limoges, France
| | - Romain Philippe
- INRAE, PEIRENE EA7500, USC1061 GAMAA, Université de Limoges, 87060, Limoges, France.
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12
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Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, Xu Q, Brito LF. Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. Front Genet 2021; 12:604823. [PMID: 33613634 PMCID: PMC7887320 DOI: 10.3389/fgene.2021.604823] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.
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Affiliation(s)
- Pedro H. F. Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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13
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Saravanan KA, Panigrahi M, Kumar H, Parida S, Bhushan B, Gaur GK, Kumar P, Dutt T, Mishra BP, Singh RK. Genome-wide assessment of genetic diversity, linkage disequilibrium and haplotype block structure in Tharparkar cattle breed of India. Anim Biotechnol 2020; 33:297-311. [PMID: 32730141 DOI: 10.1080/10495398.2020.1796696] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Knowledge about genetic diversity is very essential for the management and sustainable utilization of livestock genetic resources. In this study, we presented a comprehensive genome-wide analysis of genetic diversity, ROH, inbreeding, linkage disequilibrium, effective population size and haplotype block structure in Tharparkar cattle of India. A total of 24 Tharparkar animals used in this study were genotyped with Illumina BovineSNP50 array. After quality control, 22,825 biallelic SNPs were retained, which were in HWE, MAF > 0.05 and genotyping rate >90%. The overall mean observed (HO) and expected heterozygosity (HE) were 0.339 ± 0.156 and 0.325 ± 0.129, respectively. The average minor allele frequency was 0.234 with a standard deviation of ± 0.131. We identified a total of 1832 ROH segments and the highest autosomal coverage of 13.87% was observed on chromosome 23. The genomic inbreeding coefficients estimates by FROH, FHOM, FGRM and FUNI were 0.0589, 0.0215, 0.0532 and 0.0160 respectively. The overall mean linkage disequilibrium (LD) for a total of 133,532 pairwise SNPs measured by D' and r2 was 0.6452 and 0.1339, respectively. In addition, we observed a gradual decline in effective population size over the past generations.
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Affiliation(s)
- K A Saravanan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Subhashree Parida
- Division of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - G K Gaur
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Pushpendra Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - B P Mishra
- Division of Animal Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - R K Singh
- Division of Animal Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
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14
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Hao D, Thomsen B, Bai J, Peng S, Lan X, Huang Y, Wang X, Chen H. Expression profiles of the MXD3 gene and association of sequence variants with growth traits in Xianan and Qinchuan cattle. Vet Med Sci 2020; 6:399-409. [PMID: 32141244 PMCID: PMC7397896 DOI: 10.1002/vms3.251] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/07/2020] [Accepted: 01/24/2020] [Indexed: 01/17/2023] Open
Abstract
Max dimerization protein 3 (MXD3) belongs to the MYC superfamily of basic helix‐loop‐helix leucine zipper transcription factors, and MXD3‐MAX heterodimers can bind to promoters of target genes to modulate their expression. The aim of this study was to determine the MXD3 mRNA expression levels in various cattle tissues comprising heart, liver, spleen, lung, kidney, Longissimus dorsi muscle and subcutaneous fat in Chinese Qinchuan and Xianan cattle breeds. The RT‐qPCR data showed that the MXD3 gene was variably expressed between all tissues and at levels that were significantly different between two breeds (p < .05). We used the polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) method to investigate the possible association between single‐nucleotide polymorphisms (SNP) within the MXD3 gene and five different growth traits in cattle. We found two intronic SNPs (g.2694 C>T and g.3801 T>C) and one SNP in 3′untranslated region (3′UTR) (g.6263 G>A) of MXD3 gene. Association analysis revealed strong associations between pairwise and triple SNP combinations and the growth traits. Based on these results, we suggest that MXD3 polymorphisms could be useful as molecular markers in the Chinese beef cattle breeding program.
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Affiliation(s)
- Dan Hao
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling, Shaanxi, China.,Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Bo Thomsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Jiangsong Bai
- College of Veterinary Medicine, China Agricultural University, Beijing, China.,Beijing Zhongnongtongchuang (ZNTC) Biotechnology Co., Ltd, Beijing, China
| | - Shujun Peng
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling, Shaanxi, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling, Shaanxi, China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling, Shaanxi, China
| | - Xiao Wang
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling, Shaanxi, China
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15
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Jasielczuk I, Gurgul A, Szmatoła T, Semik-Gurgul E, Pawlina-Tyszko K, Szyndler-Nędza M, Blicharski T, Szulc K, Skrzypczak E, Bugno-Poniewierska M. Comparison of linkage disequilibrium, effective population size and haplotype blocks in Polish Landrace and Polish native pig populations. Livest Sci 2020. [DOI: 10.1016/j.livsci.2019.103887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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16
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Mouresan EF, González-Rodríguez A, Cañas-Álvarez JJ, Munilla S, Altarriba J, Díaz C, Baró JA, Molina A, Lopez-Buesa P, Piedrafita J, Varona L. Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain. Front Genet 2019; 10:1170. [PMID: 31824571 PMCID: PMC6880760 DOI: 10.3389/fgene.2019.01170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 10/23/2019] [Indexed: 01/14/2023] Open
Abstract
In organisms with sexual reproduction, genetic diversity, and genome evolution are governed by meiotic recombination caused by crossing-over, which is known to vary within the genome. In this study, we propose a simple method to estimate the recombination rate that makes use of the persistency of linkage disequilibrium (LD) phase among closely related populations. The biological material comprised 171 triplets (sire/dam/offspring) from seven populations of autochthonous beef cattle in Spain (Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta, and Rubia Gallega), which were genotyped for 777,962 SNPs with the BovineHD BeadChip. After standard quality filtering, we reconstructed the haplotype phases in the parental individuals and calculated the LD by the correlation -r- between each pair of markers that had a genetic distance < 1 Mb. Subsequently, these correlations were used to calculate the persistency of LD phase between each pair of populations along the autosomal genome. Therefore, the distribution of the recombination rate along the genome can be inferred since the effect of the number of generations of divergence should be equivalent throughout the genome. In our study, the recombination rate was highest in the largest chromosomes and at the distal portion of the chromosomes. In addition, the persistency of LD phase was highly heterogeneous throughout the genome, with a ratio of 25.4 times between the estimates of the recombination rates from the genomic regions that had the highest (BTA18-7.1 Mb) and the lowest (BTA12-42.4 Mb) estimates. Finally, an overrepresentation enrichment analysis (ORA) showed differences in the enriched gene ontology (GO) terms between the genes located in the genomic regions with estimates of the recombination rate over (or below) the 95th (or 5th) percentile throughout the autosomal genome.
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Affiliation(s)
- Elena Flavia Mouresan
- Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain
| | | | | | - Sebastián Munilla
- Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain.,Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
| | - Juan Altarriba
- Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain
| | - Clara Díaz
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Jesús A Baró
- Instituto Agroalimentario de Aragón (IA2), Zaragoza, Spain
| | - Antonio Molina
- Departamento de Ciencias Agroforestales, Universidad de Valladolid, Valladolid, Spain
| | - Pascual Lopez-Buesa
- Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain
| | - Jesús Piedrafita
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Luis Varona
- Departamento de Anatomía, Embriología y Genética Animal, Universidad de Zaragoza, Zaragoza, Spain
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17
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Fallahi MH, Shahrbabak HM, Shahrbabak MM, Arpanahi RA, Gholami S. Detection of Haplotypic Structure for Genome of Azerbaijani Buffalo Using High Density SNP Markers. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419080040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Montes DE, Braz CU, Ribeiro AMF, Cavani L, Barbero MMD, Albuquerque LG, Curi RA, Oliveira HN. Selection signatures in candidate genes and QTL for reproductive traits in Nellore heifers. Anim Reprod Sci 2019; 207:1-8. [PMID: 31266598 DOI: 10.1016/j.anireprosci.2019.06.004] [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: 11/06/2018] [Revised: 03/18/2019] [Accepted: 06/04/2019] [Indexed: 12/19/2022]
Abstract
The identification of selection signature genes may help to detect genomic regions that underwent artificial selection and contributed to phenotypic diversity. The aim of this study, therefore, was to detect selection signatures in candidate genes and quantitative trait locus (QTL) for reproductive traits in a Nellore population being selected for sexual precocity. A total of 2035 Nellore heifers, sourced from breeding programs focused on sexual precocity, were used. Candidate genes and some specific QTL related to reproductive traits were chosen based on published literature and Animal QTL databases, respectively, for investigation whether these regions were affected by selection. Selection signature DNA sequences were detected in the selected regions using the extended haplotype homozygosity (EHH) and relative extended haplotype homozygosity (REHH) methods. From 22,241 single nucleotide polymorphisms (SNPs) located in the candidate genes and QTL, 17,312 SNPs generated 2756 haplotype blocks. A total of 7518 EHH tests were analyzed using haplotypes with a frequency of more than 25%, for which there were 39 tests that were significant for REHH (P<0.01). Selection signature DNA sequences were detected that contained several QTLs for important reproductive traits in cattle, suggesting that reproductive traits may have been affected by selection for sexual precocity in this population. Forty-six genes were located in the selection signature regions, whereas 24 genes participated in important biological processes or pathways that may underlie sexual precocity. These results indicate there are possible molecular mechanisms related to sexual precocity in the Nellore breed.
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Affiliation(s)
- Donicer E Montes
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil; Universidad de Sucre, Facultad de Ciencias Agropecuarias, Departamento de Zootecnia, Sincelejo, Colombia
| | - Camila U Braz
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil
| | - André M F Ribeiro
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil
| | - Lígia Cavani
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil
| | - Marina M D Barbero
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil
| | - Lucia G Albuquerque
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil
| | - Rogério A Curi
- São Paulo State University (UNESP), School of Veterinary Medicine and Animal Science, Campus (Botucatu), Department of Animal Improvement and Nutrition, Brazil
| | - Henrique N Oliveira
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil.
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Mokhber M, Shahrbabak MM, Sadeghi M, Shahrbabak HM, Stella A, Nicolzzi E, Williams JL. Study of whole genome linkage disequilibrium patterns of Iranian water buffalo breeds using the Axiom Buffalo Genotyping 90K Array. PLoS One 2019; 14:e0217687. [PMID: 31150486 PMCID: PMC6544294 DOI: 10.1371/journal.pone.0217687] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 05/16/2019] [Indexed: 01/21/2023] Open
Abstract
Accuracy of genome-wide association studies, and the successful implementation of genomic selection depends on the level of linkage disequilibrium (LD) across the genome and also the persistence of LD phase between populations. In the present study LD between adjacent SNPs and LD decay between SNPs was calculated in three Iranian water buffalo populations. Persistence of LD phase was evaluated across these populations and effective population size (Ne) was estimated from corrected r2 information. A set of 404 individuals from three Iranian buffalo populations were genotyped with the Axiom Buffalo Genotyping 90K Array. Average r2 and |D'| between adjacent SNP pairs across all chromosomes was 0.27 and 0.66 for AZI, 0.29 and 0.68 for KHU, and 0.32 and 0.72 for MAZ. The LD between the SNPs decreased with increasing physical distance from 100Kb to 1Mb between markers, from 0.234 to 0.018 for AZI, 0.254 to 0.034 for KHU, and 0.297 to 0.119 for MAZ, respectively. These results indicate that a density of 90K SNP is sufficient for genomic analyses relying on long range LD (e.g. GWAS and genomic selection). The persistence of LD phase decreased with increasing marker distances across all the populations, but remained above 0.8 for AZI and KHU for marker distances up to 100Kb. For multi-breed genomic evaluation, the 90K SNP panel is suitable for AZI and KHU buffalo breeds. Estimated effective population sizes for AZI, KHU and MAZ were 477, 212 and 32, respectively, for recent generations. The estimated effective population sizes indicate that the MAZ is at risk and requires careful management.
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Affiliation(s)
- Mahdi Mokhber
- Department of Animal Science, Faculty of Agriculture, Urmia University, Urmia, Iran
- * E-mail:
| | - Mohammad Moradi Shahrbabak
- Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, Karaj, Iran
| | - Mostafa Sadeghi
- Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, Karaj, Iran
| | - Hossein Moradi Shahrbabak
- Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, Karaj, Iran
| | | | | | - John L. Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia, Australia
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Chhotaray S, Panigrahi M, Pal D, Ahmad SF, Bhanuprakash V, Kumar H, Parida S, Bhushan B, Gaur GK, Mishra BP, Singh RK. Genome-wide estimation of inbreeding coefficient, effective population size and haplotype blocks in Vrindavani crossbred cattle strain of India. BIOL RHYTHM RES 2019. [DOI: 10.1080/09291016.2019.1600266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Supriya Chhotaray
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Dhan Pal
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Sheikh Firdous Ahmad
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - V. Bhanuprakash
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, Indian Veterinary Research Institute, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - G. K. Gaur
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - B. P. Mishra
- Division of Animal Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - R. K. Singh
- Division of Animal Biotechnology, Indian Veterinary Research Institute, Bareilly, India
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21
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Xu L, Zhu B, Wang Z, Xu L, Liu Y, Chen Y, Zhang L, Gao X, Gao H, Zhang S, Xu L, Li J. Evaluation of Linkage Disequilibrium, Effective Population Size and Haplotype Block Structure in Chinese Cattle. Animals (Basel) 2019; 9:ani9030083. [PMID: 30845681 PMCID: PMC6466336 DOI: 10.3390/ani9030083] [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: 01/18/2019] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Evaluation of the population structure and linkage disequilibrium can offer important insights to fully understand the genetic diversity and population history of cattle, which can enable us to appropriately design and implement GWAS and GS in cattle. In this study, we characterized the extent of genome-wide LD and the haplotype block structure, and estimated the persistence of phase of Chinese indigenous cattle with Illumina BovineHD BeadChip. According to our study, 58K, 87K, 95K, 52K, and 52K markers would be necessary for SCHC, NCC, SWC, SIM, and WAG, respectively, in the implementation of GWAS and GS and combining a multipopulation with high persistence of phase is feasible for the implication of genomic selection for Chinese beef cattle. Abstract Understanding the linkage disequilibrium (LD) across the genome, haplotype structure, and persistence of phase between breeds can enable us to appropriately design and implement the genome-wide association (GWAS) and genomic selection (GS) in beef cattle. We estimated the extent of genome-wide LD, haplotype block structure, and the persistence of phase in 10 Chinese cattle population using high density BovinHD BeadChip. The overall LD measured by r2 between adjacent SNPs were 0.60, 0.67, 0.58, 0.73, and 0.71 for South Chinese cattle (SCHC), North Chinese cattle (NCC), Southwest Chinese cattle (SWC), Simmental (SIM), and Wagyu (WAG). The highest correlation (0.53) for persistence of phase across groups was observed for SCHC vs. SWC at distances of 0–50 kb, while the lowest correlation was 0.13 for SIM vs. SCHC at the same distances. In addition, the estimated current effective population sizes were 27, 14, 31, 34, and 43 for SCHC, NCC, SWC, SIM, and WAG, respectively. Our result showed that 58K, 87K, 95K, 52K, and 52K markers were required for implementation of GWAS and GS in SCHC, NCC, SWC, SIM, and WAG, respectively. Also, our findings suggested that the implication of genomic selection for multipopulation with high persistence of phase is feasible for Chinese cattle.
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Affiliation(s)
- Lei Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
- Institute of Animal Husbandry and Veterinary Research, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
| | - Bo Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Zezhao Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Ling Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Ying Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Yan Chen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Lupei Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Xue Gao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Huijiang Gao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Lingyang Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Junya Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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22
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Deng T, Liang A, Liu J, Hua G, Ye T, Liu S, Campanile G, Plastow G, Zhang C, Wang Z, Salzano A, Gasparrini B, Cassandro M, Riaz H, Liang X, Yang L. Genome-Wide SNP Data Revealed the Extent of Linkage Disequilibrium, Persistence of Phase and Effective Population Size in Purebred and Crossbred Buffalo Populations. Front Genet 2019; 9:688. [PMID: 30671082 PMCID: PMC6332145 DOI: 10.3389/fgene.2018.00688] [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: 07/03/2018] [Accepted: 12/11/2018] [Indexed: 02/04/2023] Open
Abstract
Linkage disequilibrium (LD) is a useful parameter for guiding the accuracy and power of both genome-wide association studies (GWAS) and genomic selection (GS) among different livestock species. The present study evaluated the extent of LD, persistence of phase and effective population size (Ne) for the purebred (Mediterranean buffalo; n = 411) and crossbred [Mediterranean × Jianghan × Nili-Ravi buffalo, n = 9; Murrah × Nili-Ravi × local (Xilin or Fuzhong) buffalo, n = 36] buffalo populations using the 90K Buffalo SNP genotyping array. The results showed that the average square of correlation coefficient (r 2) between adjacent SNP was 0.13 ± 0.19 across all autosomes for purebred and 0.09 ± 0.13 for crossbred, and the most rapid decline in LD was observed over the first 200 kb. Estimated r 2 ≥ 0.2 extended up to ~50 kb in crossbred and 170 kb in purebred populations, while average r 2 values ≥0.3 were respectively observed in the ~10 and 60 kb in the crossbred and purebred populations. The largest phase correlation (R P, C = 0.47) was observed at the distance of 100 kb, suggesting that this phase was not actively preserved between the two populations. Estimated Ne for the purebred and crossbred population at the current generation was 387 and 113 individuals, respectively. These findings may provide useful information to guide the GS and GWAS in buffaloes.
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Affiliation(s)
- Tingxian Deng
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Aixin Liang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Jiajia Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Guohua Hua
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Tingzhu Ye
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Shenhe Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Giuseppe Campanile
- Department of Veterinary Medicine and Animal Productions, University of Naples "Federico II", Naples, Italy
| | - Graham Plastow
- Department of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Chunyan Zhang
- Department of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Department of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Angela Salzano
- Department of Veterinary Medicine and Animal Productions, University of Naples "Federico II", Naples, Italy
| | - Bianca Gasparrini
- Department of Veterinary Medicine and Animal Productions, University of Naples "Federico II", Naples, Italy
| | - Martino Cassandro
- Department of Agronomy Food Natural Resources Animal Environmental, University of Padova, Legnaro, Italy
| | - Hasan Riaz
- Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal, Pakistan
| | - Xianwei Liang
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Liguo Yang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
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23
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Nandolo W, Utsunomiya YT, Mészáros G, Wurzinger M, Khayadzadeh N, Torrecilha RBP, Mulindwa HA, Gondwe TN, Waldmann P, Ferenčaković M, Garcia JF, Rosen BD, Bickhart D, van Tassell CP, Curik I, Sölkner J. Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances. Genet Sel Evol 2018; 50:43. [PMID: 30134820 PMCID: PMC6106898 DOI: 10.1186/s12711-018-0414-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 07/30/2018] [Indexed: 12/22/2022] Open
Abstract
Background Runs of homozygosity (ROH) islands are stretches of homozygous sequence in the genome of a large proportion of individuals in a population. Algorithms for the detection of ROH depend on the similarity of haplotypes. Coverage gaps and copy number variants (CNV) may result in incorrect identification of such similarity, leading to the detection of ROH islands where none exists. Misidentified hemizygous regions will also appear as homozygous based on sequence variation alone. Our aim was to identify ROH islands influenced by marker coverage gaps or CNV, using Illumina BovineHD BeadChip (777 K) single nucleotide polymorphism (SNP) data for Austrian Brown Swiss, Tyrol Grey and Pinzgauer cattle. Methods ROH were detected using clustering, and ROH islands were determined from population inbreeding levels for each marker. CNV were detected using a multivariate copy number analysis method and a hidden Markov model. SNP coverage gaps were defined as genomic regions with intermarker distances on average longer than 9.24 kb. ROH islands that overlapped CNV regions (CNVR) or SNP coverage gaps were considered as potential artefacts. Permutation tests were used to determine if overlaps between CNVR with copy losses and ROH islands were due to chance. Diversity of the haplotypes in the ROH islands was assessed by haplotype analyses. Results In Brown Swiss, Tyrol Grey and Pinzgauer, we identified 13, 22, and 24 ROH islands covering 26.6, 389.0 and 35.8 Mb, respectively, and we detected 30, 50 and 71 CNVR derived from CNV by using both algorithms, respectively. Overlaps between ROH islands, CNVR or coverage gaps occurred for 7, 14 and 16 ROH islands, respectively. About 37, 44 and 52% of the ROH islands coverage in Brown Swiss, Tyrol Grey and Pinzgauer, respectively, were affected by copy loss. Intersections between ROH islands and CNVR were small, but significantly larger compared to ROH islands at random locations across the genome, implying an association between ROH islands and CNVR. Haplotype diversity for reliable ROH islands was lower than for ROH islands that intersected with copy loss CNVR. Conclusions Our findings show that a significant proportion of the ROH islands in the bovine genome are artefacts due to CNV or SNP coverage gaps. Electronic supplementary material The online version of this article (10.1186/s12711-018-0414-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wilson Nandolo
- Division of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Gregor-Mendel Strasse 33, 1180, Vienna, Austria.,Lilongwe University of Agriculture and Natural Resources, P. O. Box 219, Lilongwe, Malawi
| | - Yuri T Utsunomiya
- School of Agricultural and Veterinarian Sciences, Jaboticabal, Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (UNESP), São Paulo, Brazil
| | - Gábor Mészáros
- Division of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Gregor-Mendel Strasse 33, 1180, Vienna, Austria.
| | - Maria Wurzinger
- Division of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Gregor-Mendel Strasse 33, 1180, Vienna, Austria
| | - Negar Khayadzadeh
- Division of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Gregor-Mendel Strasse 33, 1180, Vienna, Austria
| | - Rafaela B P Torrecilha
- School of Agricultural and Veterinarian Sciences, Jaboticabal, Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (UNESP), São Paulo, Brazil
| | - Henry A Mulindwa
- National Livestock Resources Research Institute, P.O Box 96, Tororo, Uganda
| | - Timothy N Gondwe
- Lilongwe University of Agriculture and Natural Resources, P. O. Box 219, Lilongwe, Malawi
| | - Patrik Waldmann
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
| | - Maja Ferenčaković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - José F Garcia
- School of Agricultural and Veterinarian Sciences, Jaboticabal, Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (UNESP), São Paulo, Brazil.,School of Veterinary Medicine, Araçatuba, Department of Support, Production and Animal Health, São Paulo State University (UNESP), São Paulo, Brazil
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705-2350, USA
| | - Derek Bickhart
- Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705-2350, USA
| | - Curt P van Tassell
- Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705-2350, USA
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - Johann Sölkner
- Division of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Gregor-Mendel Strasse 33, 1180, Vienna, Austria
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24
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Lashmar S, Visser C, van Marle-Köster E, Muchadeyi F. Genomic diversity and autozygosity within the SA Drakensberger beef cattle breed. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.04.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Mourad AMI, Sallam A, Belamkar V, Wegulo S, Bowden R, Jin Y, Mahdy E, Bakheit B, El-Wafaa AA, Poland J, Baenziger PS. Genome-Wide Association Study for Identification and Validation of Novel SNP Markers for Sr6 Stem Rust Resistance Gene in Bread Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:380. [PMID: 29636761 PMCID: PMC5881291 DOI: 10.3389/fpls.2018.00380] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 03/08/2018] [Indexed: 05/03/2023]
Abstract
Stem rust (caused by Puccinia graminis f. sp. tritici Erikss. & E. Henn.), is a major disease in wheat (Triticum aestivium L.). However, in recent years it occurs rarely in Nebraska due to weather and the effective selection and gene pyramiding of resistance genes. To understand the genetic basis of stem rust resistance in Nebraska winter wheat, we applied genome-wide association study (GWAS) on a set of 270 winter wheat genotypes (A-set). Genotyping was carried out using genotyping-by-sequencing and ∼35,000 high-quality SNPs were identified. The tested genotypes were evaluated for their resistance to the common stem rust race in Nebraska (QFCSC) in two replications. Marker-trait association identified 32 SNP markers, which were significantly (Bonferroni corrected P < 0.05) associated with the resistance on chromosome 2D. The chromosomal location of the significant SNPs (chromosome 2D) matched the location of Sr6 gene which was expected in these genotypes based on pedigree information. A highly significant linkage disequilibrium (LD, r2 ) was found between the significant SNPs and the specific SSR marker for the Sr6 gene (Xcfd43). This suggests the significant SNP markers are tagging Sr6 gene. Out of the 32 significant SNPs, eight SNPs were in six genes that are annotated as being linked to disease resistance in the IWGSC RefSeq v1.0. The 32 significant SNP markers were located in nine haplotype blocks. All the 32 significant SNPs were validated in a set of 60 different genotypes (V-set) using single marker analysis. SNP markers identified in this study can be used in marker-assisted selection, genomic selection, and to develop KASP (Kompetitive Allele Specific PCR) marker for the Sr6 gene. HIGHLIGHTS Novel SNPs for Sr6 gene, an important stem rust resistant gene, were identified and validated in this study. These SNPs can be used to improve stem rust resistance in wheat.
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Affiliation(s)
- Amira M. I. Mourad
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Ahmed Sallam
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Stephen Wegulo
- Department of Plant Pathology, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Robert Bowden
- United States Department of Agriculture-Agricultural Research Service, Manhattan, KS, United States
| | - Yue Jin
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, United States
| | - Ezzat Mahdy
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Bahy Bakheit
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Atif A. El-Wafaa
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Jesse Poland
- Plant Sciences Center, Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Peter S. Baenziger
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
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26
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Mourad AMI, Sallam A, Belamkar V, Wegulo S, Bowden R, Jin Y, Mahdy E, Bakheit B, El-Wafaa AA, Poland J, Baenziger PS. Genome-Wide Association Study for Identification and Validation of Novel SNP Markers for Sr6 Stem Rust Resistance Gene in Bread Wheat. FRONTIERS IN PLANT SCIENCE 2018. [PMID: 29636761 DOI: 10.3389/fpls.2018.00380/full] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
UNLABELLED Stem rust (caused by Puccinia graminis f. sp. tritici Erikss. & E. Henn.), is a major disease in wheat (Triticum aestivium L.). However, in recent years it occurs rarely in Nebraska due to weather and the effective selection and gene pyramiding of resistance genes. To understand the genetic basis of stem rust resistance in Nebraska winter wheat, we applied genome-wide association study (GWAS) on a set of 270 winter wheat genotypes (A-set). Genotyping was carried out using genotyping-by-sequencing and ∼35,000 high-quality SNPs were identified. The tested genotypes were evaluated for their resistance to the common stem rust race in Nebraska (QFCSC) in two replications. Marker-trait association identified 32 SNP markers, which were significantly (Bonferroni corrected P < 0.05) associated with the resistance on chromosome 2D. The chromosomal location of the significant SNPs (chromosome 2D) matched the location of Sr6 gene which was expected in these genotypes based on pedigree information. A highly significant linkage disequilibrium (LD, r2 ) was found between the significant SNPs and the specific SSR marker for the Sr6 gene (Xcfd43). This suggests the significant SNP markers are tagging Sr6 gene. Out of the 32 significant SNPs, eight SNPs were in six genes that are annotated as being linked to disease resistance in the IWGSC RefSeq v1.0. The 32 significant SNP markers were located in nine haplotype blocks. All the 32 significant SNPs were validated in a set of 60 different genotypes (V-set) using single marker analysis. SNP markers identified in this study can be used in marker-assisted selection, genomic selection, and to develop KASP (Kompetitive Allele Specific PCR) marker for the Sr6 gene. HIGHLIGHTS Novel SNPs for Sr6 gene, an important stem rust resistant gene, were identified and validated in this study. These SNPs can be used to improve stem rust resistance in wheat.
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Affiliation(s)
- Amira M I Mourad
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Ahmed Sallam
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Stephen Wegulo
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Robert Bowden
- United States Department of Agriculture-Agricultural Research Service, Manhattan, KS, United States
| | - Yue Jin
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, United States
| | - Ezzat Mahdy
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Bahy Bakheit
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Atif A El-Wafaa
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Jesse Poland
- Plant Sciences Center, Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Peter S Baenziger
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
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27
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Buzanskas ME, Grossi DDA, Ventura RV, Schenkel FS, Chud TCS, Stafuzza NB, Rola LD, Meirelles SLC, Mokry FB, Mudadu MDA, Higa RH, da Silva MVGB, de Alencar MM, Regitano LCDA, Munari DP. Candidate genes for male and female reproductive traits in Canchim beef cattle. J Anim Sci Biotechnol 2017; 8:67. [PMID: 28852499 PMCID: PMC5569548 DOI: 10.1186/s40104-017-0199-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 07/13/2017] [Indexed: 01/20/2023] Open
Abstract
Background Beef cattle breeding programs in Brazil have placed greater emphasis on the genomic study of reproductive traits of males and females due to their economic importance. In this study, genome-wide associations were assessed for scrotal circumference at 210 d of age, scrotal circumference at 420 d of age, age at first calving, and age at second calving, in Canchim beef cattle. Data quality control was conducted resulting in 672,778 SNPs and 392 animals. Results Associated SNPs were observed for scrotal circumference at 420 d of age (435 SNPs), followed by scrotal circumference at 210 d of age (12 SNPs), age at first calving (six SNPs), and age at second calving (four SNPs). We investigated whether significant SNPs were within genic or surrounding regions. Biological processes of genes were associated with immune system, multicellular organismal process, response to stimulus, apoptotic process, cellular component organization or biogenesis, biological adhesion, and reproduction. Conclusions Few associations were observed for scrotal circumference at 210 d of age, age at first calving, and age at second calving, reinforcing their polygenic inheritance and the complexity of understanding the genetic architecture of reproductive traits. Finding many associations for scrotal circumference at 420 d of age in various regions of the Canchim genome also reveals the difficulty of targeting specific candidate genes that could act on fertility; nonetheless, the high linkage disequilibrium between loci herein estimated could aid to overcome this issue. Therefore, all relevant information about genomic regions influencing reproductive traits may contribute to target candidate genes for further investigation of causal mutations and aid in future genomic studies in Canchim cattle to improve the breeding program. Electronic supplementary material The online version of this article (doi:10.1186/s40104-017-0199-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marcos Eli Buzanskas
- Departamento de Zootecnia, Universidade Federal da Paraíba (UFPB), Areia, Paraíba 58397-000 Brazil
| | | | | | - Flavio Schramm Schenkel
- Department of Animal and Poultry Science, University of Guelph, Centre for Genetic Improvement of Livestock (CGIL), Guelph, ON N1G 2W1 Canada
| | - Tatiane Cristina Seleguim Chud
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo 14884-900 Brazil
| | - Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo 14884-900 Brazil
| | - Luciana Diniz Rola
- Departamento de Zootecnia, Núcleo de Pesquisa e Conservação de Cervídeos, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo 14884-900 Brazil
| | | | - Fabiana Barichello Mokry
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Carlos, São Paulo 13565-905 Brazil
| | | | | | | | | | | | - Danísio Prado Munari
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo 14884-900 Brazil
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Mouresan E, González-Rodríguez A, Cañas-Álvarez J, Díaz C, Altarriba J, Baro J, Piedrafita J, Molina A, Toro M, Varona L. On the haplotype diversity along the genome in Spanish beef cattle populations. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.04.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Dash S, Singh A, Bhatia AK, Jayakumar S, Sharma A, Singh S, Ganguly I, Dixit SP. Evaluation of Bovine High-Density SNP Genotyping Array in Indigenous Dairy Cattle Breeds. Anim Biotechnol 2017. [PMID: 28636460 DOI: 10.1080/10495398.2017.1329150] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In total 52 samples of Sahiwal ( 19 ), Tharparkar ( 17 ), and Gir ( 16 ) were genotyped by using BovineHD SNP chip to analyze minor allele frequency (MAF), genetic diversity, and linkage disequilibrium among these cattle. The common SNPs of BovineHD and 54K SNP Chips were also extracted and evaluated for their performance. Only 40%-50% SNPs of these arrays was found informative for genetic analysis in these cattle breeds. The overall mean of MAF for SNPs of BovineHD SNPChip was 0.248 ± 0.006, 0.241 ± 0.007, and 0.242 ± 0.009 in Sahiwal, Tharparkar and Gir, respectively, while that for 54K SNPs was on lower side. The average Reynold's genetic distance between breeds ranged from 0.042 to 0.055 based on BovineHD Beadchip, and from 0.052 to 0.084 based on 54K SNP Chip. The estimates of genetic diversity based on HD and 54K chips were almost same and, hence, low density chip seems to be good enough to decipher genetic diversity of these cattle breeds. The linkage disequilibrium started decaying (r2 < 0.2) at 140 kb inter-marker distance and, hence, a 20K low density customized SNP array from HD chip could be designed for genomic selection in these cattle else the 54K Bead Chip as such will be useful.
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Affiliation(s)
- S Dash
- a ICAR- National Dairy Research Institute , Karnal , Haryana , India
| | - A Singh
- a ICAR- National Dairy Research Institute , Karnal , Haryana , India
| | - A K Bhatia
- b ICAR- National Bureau of Animal Genetic Resources , Karnal , Haryana , India
| | - S Jayakumar
- b ICAR- National Bureau of Animal Genetic Resources , Karnal , Haryana , India
| | - A Sharma
- b ICAR- National Bureau of Animal Genetic Resources , Karnal , Haryana , India
| | - S Singh
- b ICAR- National Bureau of Animal Genetic Resources , Karnal , Haryana , India
| | - I Ganguly
- b ICAR- National Bureau of Animal Genetic Resources , Karnal , Haryana , India
| | - S P Dixit
- b ICAR- National Bureau of Animal Genetic Resources , Karnal , Haryana , India
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Estimates of linkage disequilibrium and effective population sizes in Chinese Merino (Xinjiang type) sheep by genome-wide SNPs. Genes Genomics 2017; 39:733-745. [PMID: 28706593 PMCID: PMC5486679 DOI: 10.1007/s13258-017-0539-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 03/19/2017] [Indexed: 12/14/2022]
Abstract
Knowledge of linkage disequilibrium (LD) is important for effective genome-wide association studies and accurate genomic prediction. Chinese Merino (Xinjiang type) is well-known fine wool sheep breed. However, the extent of LD across the genome remains unexplored. In this study, we calculated autosomal LD based on genome-wide SNPs of 635 Chinese Merino (Xinjiang type) sheep by Illumina Ovine SNP50 BeadChip. A moderate level of LD (r2 ≥ 0.25) across the whole genome was observed at short distances of 0–10 kb. Further, the ancestral effective population size (Ne) was analyzed by extent of LD and found that Ne increased with the increase of generations and declined rapidly within the most recent 50 generations, which is consistent with the history of Chinese Merino sheep breeding, initiated in 1971. We also noted that even when the effective population size was estimated across different single chromosomes, Ne only ranged from 140.36 to 183.33 at five generations in the past, exhibiting a rapid decrease compared with that at ten generations in the past. These results indicated that the genetic diversity in Chinese Merino sheep recently decreased and proper protective measures should be taken to maintain the diversity. Our datasets provided essential genetic information to track molecular variations which potentially contribute to phenotypic variation in Chinese Merino sheep.
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Study on the introgression of beef breeds in Canchim cattle using single nucleotide polymorphism markers. PLoS One 2017; 12:e0171660. [PMID: 28182737 PMCID: PMC5300224 DOI: 10.1371/journal.pone.0171660] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/24/2017] [Indexed: 11/19/2022] Open
Abstract
The aim of this study was to evaluate the level of introgression of breeds in the Canchim (CA: 62.5% Charolais—37.5% Zebu) and MA genetic group (MA: 65.6% Charolais—34.4% Zebu) cattle using genomic information on Charolais (CH), Nelore (NE), and Indubrasil (IB) breeds. The number of animals used was 395 (CA and MA), 763 (NE), 338 (CH), and 37 (IB). The Bovine50SNP BeadChip from Illumina panel was used to estimate the levels of introgression of breeds considering the Maximum likelihood, Bayesian, and Single Regression method. After genotype quality control, 32,308 SNPs were considered in the analysis. Furthermore, three thresholds to prune out SNPs in linkage disequilibrium higher than 0.10, 0.05, and 0.01 were considered, resulting in 15,286, 7,652, and 1,582 SNPs, respectively. For k = 2, the proportion of taurine and indicine varied from the expected proportion based on pedigree for all methods studied. For k = 3, the Regression method was able to differentiate the animals in three main clusters assigned to each purebred breed, showing more reasonable according to its biological viewpoint. Analyzing the data considering k = 2 seems to be more appropriate for Canchim-MA animals due to its biological interpretation. The usage of 32,308 SNPs in the analyses resulted in similar findings between the estimated and expected breed proportions. Using the Regression approach, a contribution of Indubrasil was observed in Canchim-MA when k = 3 was considered. Genetic parameter estimation could account for this breed composition information as a source of variation in order to improve the accuracy of genetic models. Our findings may help assemble appropriate reference populations for genomic prediction for Canchim-MA in order to improve prediction accuracy. Using the information on the level of introgression in each individual could also be useful in breeding or crossing design to improve individual heterosis in crossbred cattle.
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Linkage disequilibrium and haplotype block structure in Limousin, Simmental and native Polish Red cattle. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Niu H, Zhu B, Guo P, Zhang W, Xue J, Chen Y, Zhang L, Gao H, Gao X, Xu L, Li J. Estimation of linkage disequilibrium levels and haplotype block structure in Chinese Simmental and Wagyu beef cattle using high-density genotypes. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Urbinati I, Stafuzza NB, Oliveira MT, Chud TCS, Higa RH, Regitano LCDA, de Alencar MM, Buzanskas ME, Munari DP. Selection signatures in Canchim beef cattle. J Anim Sci Biotechnol 2016; 7:29. [PMID: 27158491 PMCID: PMC4858954 DOI: 10.1186/s40104-016-0089-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/24/2016] [Indexed: 11/10/2022] Open
Abstract
Background Recent technological advances in genomics have allowed the genotyping of cattle through single nucleotide polymorphism (SNP) panels. High-density SNP panels possess greater genome coverage and are useful for the identification of conserved regions of the genome due to selection, known as selection signatures (SS). The SS are detectable by different methods, such as the extended haplotype homozygosity (EHH); and the integrated haplotype score (iHS), which is derived from the EHH. The aim of this study was to identify SS regions in Canchim cattle (composite breed), genotyped with high-density SNP panel. Results A total of 687,655 SNP markers and 396 samples remained for SS analysis after the genotype quality control. The iHS statistic for each marker was transformed into piHS for better interpretation of the results. Chromosomes BTA5 and BTA14 showed piHS > 5, with 39 and nine statistically significant SNPs (P < 0.00001), respectively. For the candidate selection regions, iHS values were computed across the genome and averaged within non-overlapping windows of 500 Kb. We have identified genes that play an important role in metabolism, melanin biosynthesis (pigmentation), and embryonic and bone development. Conclusions The observation of SS indicates that the selection processes performed in Canchim, as well as in the founder breeds (i.e. Charolais), are maintaining specific genomic regions, particularly on BTA5 and BTA14. These selection signatures regions could be associated with Canchim characterization. Electronic supplementary material The online version of this article (doi:10.1186/s40104-016-0089-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ismael Urbinati
- Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
| | - Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
| | - Marcos Túlio Oliveira
- Departamento de Tecnologia, UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
| | - Tatiane Cristina Seleguim Chud
- Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
| | | | | | | | - Marcos Eli Buzanskas
- Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
| | - Danísio Prado Munari
- Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
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Mudadu MA, Porto-Neto LR, Mokry FB, Tizioto PC, Oliveira PSN, Tullio RR, Nassu RT, Niciura SCM, Tholon P, Alencar MM, Higa RH, Rosa AN, Feijó GLD, Ferraz ALJ, Silva LOC, Medeiros SR, Lanna DP, Nascimento ML, Chaves AS, Souza ARDL, Packer IU, Torres RAA, Siqueira F, Mourão GB, Coutinho LL, Reverter A, Regitano LCA. Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle. BMC Genomics 2016; 17:235. [PMID: 26979536 PMCID: PMC4791965 DOI: 10.1186/s12864-016-2535-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nelore is the major beef cattle breed in Brazil with more than 130 million heads. Genome-wide association studies (GWAS) are often used to associate markers and genomic regions to growth and meat quality traits that can be used to assist selection programs. An alternative methodology to traditional GWAS that involves the construction of gene network interactions, derived from results of several GWAS is the AWM (Association Weight Matrices)/PCIT (Partial Correlation and Information Theory). With the aim of evaluating the genetic architecture of Brazilian Nelore cattle, we used high-density SNP genotyping data (~770,000 SNP) from 780 Nelore animals comprising 34 half-sibling families derived from highly disseminated and unrelated sires from across Brazil. The AWM/PCIT methodology was employed to evaluate the genes that participate in a series of eight phenotypes related to growth and meat quality obtained from this Nelore sample. RESULTS Our results indicate a lack of structuring between the individuals studied since principal component analyses were not able to differentiate families by its sires or by its ancestral lineages. The application of the AWM/PCIT methodology revealed a trio of transcription factors (comprising VDR, LHX9 and ZEB1) which in combination connected 66 genes through 359 edges and whose biological functions were inspected, some revealing to participate in biological growth processes in literature searches. CONCLUSIONS The diversity of the Nelore sample studied is not high enough to differentiate among families neither by sires nor by using the available ancestral lineage information. The gene networks constructed from the AWM/PCIT methodology were a useful alternative in characterizing genes and gene networks that were allegedly influential in growth and meat quality traits in Nelore cattle.
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Affiliation(s)
- Maurício A Mudadu
- Embrapa Agricultural Informatics, Av. André Tosello, 209, Campinas, SP, Brazil. .,Embrapa Southeast Livestock, Rodovia Washington Luiz, Km 234, São Carlos, SP, Brazil.
| | - Laercio R Porto-Neto
- Commonwealth Scientific and Industrial Research Organization - Agriculture, 306 Carmody Road, Brisbane, QLD, Australia
| | - Fabiana B Mokry
- Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washington Luiz, Km 235, São Carlos, SP, Brazil
| | - Polyana C Tizioto
- Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washington Luiz, Km 235, São Carlos, SP, Brazil
| | - Priscila S N Oliveira
- Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washington Luiz, Km 235, São Carlos, SP, Brazil
| | - Rymer R Tullio
- Embrapa Southeast Livestock, Rodovia Washington Luiz, Km 234, São Carlos, SP, Brazil
| | - Renata T Nassu
- Embrapa Southeast Livestock, Rodovia Washington Luiz, Km 234, São Carlos, SP, Brazil
| | - Simone C M Niciura
- Embrapa Southeast Livestock, Rodovia Washington Luiz, Km 234, São Carlos, SP, Brazil
| | - Patrícia Tholon
- Embrapa Southeast Livestock, Rodovia Washington Luiz, Km 234, São Carlos, SP, Brazil
| | - Maurício M Alencar
- Embrapa Southeast Livestock, Rodovia Washington Luiz, Km 234, São Carlos, SP, Brazil
| | - Roberto H Higa
- Embrapa Agricultural Informatics, Av. André Tosello, 209, Campinas, SP, Brazil
| | - Antônio N Rosa
- Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande, MS, Brazil
| | - Gélson L D Feijó
- Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande, MS, Brazil
| | - André L J Ferraz
- State University of Mato Grosso do Sul, Rodovia Uems-Aquidauana km 12, Aquidauana, MS, Brazil
| | - Luiz O C Silva
- Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande, MS, Brazil
| | | | - Dante P Lanna
- Department of Animal Science, University of São Paulo, Av. Padua Dias, 11306, Piracicaba, SP, Brazil
| | - Michele L Nascimento
- Department of Animal Science, University of São Paulo, Av. Padua Dias, 11306, Piracicaba, SP, Brazil
| | - Amália S Chaves
- Department of Animal Science, University of São Paulo, Av. Padua Dias, 11306, Piracicaba, SP, Brazil
| | - Andrea R D L Souza
- Faculdade de Medicina Veterinaria e Zootecnia, Federal University of Mato Grosso do Sul, Av. Senador Filinto Müller, 2443, Campo Grande, MS, Brazil
| | - Irineu U Packer
- Department of Animal Science, University of São Paulo, Av. Padua Dias, 11306, Piracicaba, SP, Brazil
| | | | - Fabiane Siqueira
- Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande, MS, Brazil
| | - Gerson B Mourão
- Department of Animal Science, University of São Paulo, Av. Padua Dias, 11306, Piracicaba, SP, Brazil
| | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo, Av. Padua Dias, 11306, Piracicaba, SP, Brazil
| | - Antonio Reverter
- Commonwealth Scientific and Industrial Research Organization - Agriculture, 306 Carmody Road, Brisbane, QLD, Australia
| | - Luciana C A Regitano
- Embrapa Southeast Livestock, Rodovia Washington Luiz, Km 234, São Carlos, SP, Brazil
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Karimi K, Esmailizadeh Koshkoiyeh A, Gondro C. Comparison of linkage disequilibrium levels in Iranian indigenous cattle using whole genome SNPs data. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2015; 57:47. [PMID: 26705480 PMCID: PMC4690407 DOI: 10.1186/s40781-015-0080-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 12/22/2015] [Indexed: 12/15/2022]
Abstract
BACKGROUND Knowledge of linkage disequilibrium (LD) levels among different populations can be used to detect genetic diversity and to investigate the historical changes in population sizes. Availability of large numbers of SNP through new sequencing technologies has provided opportunities for extensive researches in quantifying LD patterns in cattle breeds. The aim of this study was to compare the extent of linkage disequilibrium among Iranian cattle breeds using high density SNP genotyping data. RESULTS A total of 70 samples, representing seven Iranian indigenous cattle breeds, were genotyped for 777962 SNPs. The average values of LD based on the r(2) criterion were computed by grouping all syntenic SNP pairwises for inter-marker distances from 0 Kb up to 1 Mb using three distance sets. Average r(2) above 0.3 was observed at distances less than 30 Kb for Sistani and Kermani, 20 Kb for Najdi, Taleshi, Kurdi and Sarabi, and 10 Kb for Mazandarani. The LD levels were considerably different among the Iranian cattle breeds and the difference in LD extent was more detectable between the studied breeds at longer distances. Lower level of LD was observed for Mazandarani breed as compared to other breeds indicating larger ancestral population size in this breed. Kermani breed continued to have more slowly LD decay than all of the other breeds after 3 Kb distances. More slowly LD decay was observed in Kurdi and Sarabi breeds at larger distances (>100 Kb) showing that population decline has been more intense in more recent generations for these populations. CONCLUSIONS A wide genetic diversity and different historical background were well reflected in the LD levels among Iranian cattle breeds. More LD fluctuation was observed in the shorter distances (less than 10 Kb) in different cattle populations. Despite of the sample size effects, High LD levels found in this study were in accordance with the presence of inbreeding and population decline in Iranian cattle breeds.
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Affiliation(s)
- Karim Karimi
- />Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133 Iran
- />Young Researchers Society, Shahid Bahonar University of Kerman, Kerman, PB 76169-133 Iran
| | - Ali Esmailizadeh Koshkoiyeh
- />Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133 Iran
| | - Cedric Gondro
- />School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
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Wang MD, Dzama K, Hefer CA, Muchadeyi FC. Genomic population structure and prevalence of copy number variations in South African Nguni cattle. BMC Genomics 2015; 16:894. [PMID: 26531252 PMCID: PMC4632335 DOI: 10.1186/s12864-015-2122-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 10/22/2015] [Indexed: 12/21/2022] Open
Abstract
Background Copy number variations (CNVs) are modifications in DNA structure comprising of deletions, duplications, insertions and complex multi-site variants. Although CNVs are proven to be involved in a variety of phenotypic discrepancies, the full extent and consequence of CNVs is yet to be understood. To date, no such genomic characterization has been performed in indigenous South African Nguni cattle. Nguni cattle are recognized for their ability to sustain harsh environmental conditions while exhibiting enhanced resistance to disease and parasites and are thought to comprise of up to nine different ecotypes. Methods Illumina BovineSNP50 Beadchip data was utilized to investigate genomic population structure and the prevalence of CNVs in 492 South African Nguni cattle. PLINK, ADMIXTURE, R, gPLINK and Haploview software was utilized for quality control, population structure and haplotype block determination. PennCNV hidden Markov model identified CNVs and genes contained within and 10 Mb downstream from reported CNVs. PANTHER and Ensembl databases were subsequently utilized for gene annotation analyses. Results Population structure analyses on Nguni cattle revealed 5 sub-populations with a possible sub-structure evident at K equal to 8. Four hundred and thirty three CNVs that formed 334 CNVRs ranging from 30 kb to 1 Mb in size are reported. Only 231 of the 492 animals demonstrated CNVRs. Two hundred and eighty nine genes were observed within CNVRs identified. Of these 149, 28, 44, 2 and 14 genes were unique to sub-populations A, B, C, D and E respectively. Gene ontology analyses demonstrated a number of pathways to be represented by respective genes, including immune response, response to abiotic stress and biological regulation processess. Conclusions CNVs may explain part of the phenotypic diversity and the enhanced adaptation evident in Nguni cattle. Genes involved in a number of cellular components, biological processes and molecular functions are reported within CNVRs identified. The significance of such CNVRs and the possible effect thereof needs to be ascertained and may hold interesting insight into the functional and adaptive consequence of CNVs in cattle. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2122-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Magretha Diane Wang
- Department of Animal Sciences, University of Stellenbosch, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa. .,Biotechnology Platform, Agricultural Research Council, Private Bag X5, Onderstepoort, 0110, South Africa.
| | - Kennedy Dzama
- Department of Animal Sciences, University of Stellenbosch, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa.
| | - Charles A Hefer
- Biotechnology Platform, Agricultural Research Council, Private Bag X5, Onderstepoort, 0110, South Africa.
| | - Farai C Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Private Bag X5, Onderstepoort, 0110, South Africa.
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Bruford MW, Ginja C, Hoffmann I, Joost S, Orozco-terWengel P, Alberto FJ, Amaral AJ, Barbato M, Biscarini F, Colli L, Costa M, Curik I, Duruz S, Ferenčaković M, Fischer D, Fitak R, Groeneveld LF, Hall SJG, Hanotte O, Hassan FU, Helsen P, Iacolina L, Kantanen J, Leempoel K, Lenstra JA, Ajmone-Marsan P, Masembe C, Megens HJ, Miele M, Neuditschko M, Nicolazzi EL, Pompanon F, Roosen J, Sevane N, Smetko A, Štambuk A, Streeter I, Stucki S, Supakorn C, Telo Da Gama L, Tixier-Boichard M, Wegmann D, Zhan X. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025. Front Genet 2015; 6:314. [PMID: 26539210 PMCID: PMC4612686 DOI: 10.3389/fgene.2015.00314] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/05/2015] [Indexed: 12/20/2022] Open
Abstract
Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that “…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity.” However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.
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Affiliation(s)
- Michael W Bruford
- School of Biosciences, Cardiff University Cardiff, UK ; Sustainable Places Research Institute, Cardiff University Cardiff, UK
| | - Catarina Ginja
- Faculdade de Ciências, Centro de Ecologia, Evolução e Alterações Ambientais (CE3C), Universidade de Lisboa Lisboa, Portugal ; Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do Porto, Campus Agrário de Vairão Portugal
| | - Irene Hoffmann
- Food and Agriculture Organization of the United Nations, Animal Genetic Resources Branch, Animal Production and Health Division Rome, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Florian J Alberto
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes Grenoble, France
| | - Andreia J Amaral
- Faculty of Sciences, BioISI- Biosystems and Integrative Sciences Institute, University of Lisbon Campo Grande, Portugal
| | - Mario Barbato
- School of Biosciences, Cardiff University Cardiff, UK
| | | | - Licia Colli
- BioDNA Centro di Ricerca sulla Biodiversità a sul DNA Antico, Istituto di Zootecnica, Università Cattolica del Sacro Cuore di Piacenza Italy
| | - Mafalda Costa
- School of Biosciences, Cardiff University Cardiff, UK
| | - Ino Curik
- Faculty of Agriculture, University of Zagreb Zagreb, Croatia
| | - Solange Duruz
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Daniel Fischer
- Natural Resources Institute Finland (Luke), Green Technology Jokioinen, Finland
| | - Robert Fitak
- Institut für Populationsgenetik Vetmeduni, Vienna, Austria
| | | | | | - Olivier Hanotte
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Faiz-Ul Hassan
- School of Life Sciences, University of Nottingham Nottingham, UK ; Department of Animal Breeding and Genetics, University of Agriculture Faisalabad, Pakistan
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp Antwerp, Belgium
| | - Laura Iacolina
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Denmark
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Green Technology Jokioinen, Finland ; Department of Biology, University of Eastern Finland Kuopio, Finland
| | - Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Paolo Ajmone-Marsan
- BioDNA Centro di Ricerca sulla Biodiversità a sul DNA Antico, Istituto di Zootecnica, Università Cattolica del Sacro Cuore di Piacenza Italy
| | - Charles Masembe
- Institute of the Environment and Natural Resources, Makerere University Kampala, Uganda
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Centre, Wageningen University Wageningen, Netherlands
| | - Mara Miele
- School of Planning and Geography, Cardiff University Cardiff, UK
| | | | | | - François Pompanon
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes Grenoble, France
| | - Jutta Roosen
- TUM School of Management, Technische Universität München Munich, Germany
| | - Natalia Sevane
- Department of Animal Production, Veterinary Faculty, Universidad Complutense de Madrid Madrid, Spain
| | | | - Anamaria Štambuk
- Department of Biology, Faculty of Science, University of Zagreb Zagreb, Croatia
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, UK
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - China Supakorn
- School of Life Sciences, University of Nottingham Nottingham, UK ; School of Agricultural Technology, Walailak University Tha Sala, Thailand
| | - Luis Telo Da Gama
- Centre of Research in Animal Health (CIISA) - Faculty of Veterinary Medicine, University of Lisbon Lisbon, Portugal
| | | | - Daniel Wegmann
- Department of Biology, University of Fribourg Fribourg, Switzerland
| | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Beijing, China ; Cardiff University - Institute of Zoology, Joint Laboratory for Biocomplexity Research Beijing, China
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