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Wang P, Ou G, Li G, Li H, Zhao T. Analysis of genetic diversity and structure of endangered Dengchuan cattle population using a single-nucleotide polymorphism chip. Anim Biotechnol 2024; 35:2349625. [PMID: 38733367 DOI: 10.1080/10495398.2024.2349625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024]
Abstract
This study aimed to evaluate the genetic diversity and structure within the Dengchuan cattle population and effectively protect and utilize their germplasm resources. Herein, the single-nucleotide polymorphisms (SNPs) of 100 Dengchuan cattle (46 bulls and 54 cows) were determined using the GGP Bovine 100K SNP Beadchip. The results showed that among the Dengchuan cattle, a total of 101,220 SNPs were detected, and there were 83,534 SNPs that passed quality control, of which 85.7% were polymorphic. The average genetic distance based on identity-by-state (IBS) within the conservation population of Dengchuan cattle was 0.26 ± 0.02. A total of 3,999 genome-length runs of homozygosity (ROHs) were detected in the Dengchuan cattle, with ROH lengths primarily concentrated in the range of 1-5 Mb, accounting for 87.02% of the total. The average inbreeding coefficient based on ROHs was 4.6%, within the conservation population of Dengchuan cattle, whereas it was 4.9% for bulls, and the Wright inbreeding coefficient (FIS) value was 2.4%, demonstrating a low level of inbreeding within the Dengchuan cattle population. Based on neighbor-joining tree analysis, the Dengchuan cattle could be divided into 16 families. In summary, the conservation population of Dengchuan cattle displays relatively abundant diversity and a moderate genetic relationship. Inbreeding was observed among a few individuals, but the overall inbreeding level of the population remained low. It is important to maintain this low level of inbreeding when introducing purebred bloodlines to expand the core group. This approach will ensure the long-term conservation of Dengchuan cattle germplasm resources and prevent loss of genetic diversity.
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Affiliation(s)
- Pingping Wang
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
- Co-Innovation Center for Cangshan Mountain and Erhai Lake Integrated Protection and Green Development of Yunnan Province, Dali University, Dali, Yuannan, China
| | - Guoyu Ou
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
- Co-Innovation Center for Cangshan Mountain and Erhai Lake Integrated Protection and Green Development of Yunnan Province, Dali University, Dali, Yuannan, China
| | - Genchang Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Huiying Li
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
- Co-Innovation Center for Cangshan Mountain and Erhai Lake Integrated Protection and Green Development of Yunnan Province, Dali University, Dali, Yuannan, China
| | - Tianzhang Zhao
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
- Co-Innovation Center for Cangshan Mountain and Erhai Lake Integrated Protection and Green Development of Yunnan Province, Dali University, Dali, Yuannan, China
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Wirth A, Duda J, Emmerling R, Götz KU, Birkenmaier F, Distl O. Analyzing Runs of Homozygosity Reveals Patterns of Selection in German Brown Cattle. Genes (Basel) 2024; 15:1051. [PMID: 39202411 PMCID: PMC11354284 DOI: 10.3390/genes15081051] [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: 07/14/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 09/03/2024] Open
Abstract
An increasing trend in ancestral and classical inbreeding coefficients as well as inbreeding depression for longevity were found in the German Brown population. In addition, the proportion of US Brown Swiss genes is steadily increasing in German Browns. Therefore, the aim of the present study was to analyze the presence and genomic localization of runs of homozygosity (ROH) in order to evaluate their associations with the proportion of US Brown Swiss genes and survival rates of cows to higher lactations. Genotype data were sampled in 2364 German Browns from 258 herds. The final data set included 49,693 autosomal SNPs. We identified on average 35.996 ± 7.498 ROH per individual with a mean length of 8.323 ± 1.181 Mb. The genomic inbreeding coefficient FROH was 0.122 ± 0.032 and it decreased to 0.074, 0.031 and 0.006, when genomic homozygous segments > 8 Mb (FROH>8), >16 Mb (FROH>16) and >32 Mb (FROH>32) were considered. New inbreeding showed the highest correlation with FROH>32, whereas ancestral inbreeding coefficients had the lowest correlations with FROH>32. The correlation between the classical inbreeding coefficient and FROH was 0.572. We found significantly lower FROH, FROH>4, FROH>8 and FIS for US Brown Swiss proportions <60% compared to >80%. Cows surviving to the 2nd, 4th, 6th, 8th, and 10th lactation had lower genomic inbreeding for FROH and up to FROH>32, which was due to a lower number of ROH and a shorter average length of ROH. The strongest ROH island and consensus ROH shared by 50% of the animals was found on BTA 6 at 85-88 Mb. The genes located in this genomic region were associated with longevity (NPFFR2 and ADAMTS3), udder health and morphology (SLC4A4, NPFFR2, GC and RASSF6), milk production, milk protein percentage, coagulation properties of milk and milking speed (CSN3). On BTA 2, a ROH island was detected only in animals with <60% US Brown Swiss genes. Genes within this region are predominantly important for dual-purpose cattle breeds including Original Browns. For cows reaching more than 9 lactations, an exclusive ROH island was identified on BTA 7 with genes assumed to be associated with longevity. The analysis indicated that genomic homozygous regions important for Original Browns are still present and also ROH containing genes affecting longevity may have been identified. The breeding of German Browns should prevent any further increase in genomic inbreeding and run a breeding program with balanced weights on production, robustness and longevity.
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Affiliation(s)
- Anna Wirth
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany;
| | - Jürgen Duda
- Landeskuratorium der Erzeugerringe für Tierische Veredelung in Bayern e.V. (LKV), 80687 München, Germany;
| | - Reiner Emmerling
- Bavarian State Research Center for Agriculture, Institute of Animal Breeding, 85586 Poing-Grub, Germany; (R.E.); (K.-U.G.)
| | - Kay-Uwe Götz
- Bavarian State Research Center for Agriculture, Institute of Animal Breeding, 85586 Poing-Grub, Germany; (R.E.); (K.-U.G.)
| | - Franz Birkenmaier
- Amt für Ernährung, Landwirtschaft und Forsten, 87439 Kempten, Germany;
| | - Ottmar Distl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany;
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Hu M, Shi L, Yi W, Li F, Yan S. Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data. Anim Biosci 2024; 37:461-470. [PMID: 38271971 PMCID: PMC10915192 DOI: 10.5713/ab.23.0304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/13/2023] [Accepted: 11/28/2023] [Indexed: 01/27/2024] Open
Abstract
OBJECTIVE The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits. METHODS To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, Fst, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions. RESULTS The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, Fst, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity. CONCLUSION In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.
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Affiliation(s)
- Mingyue Hu
- Department of Animal Science, Jilin University, Changchun 130062,
China
| | - Lulu Shi
- Department of Animal Science, Jilin University, Changchun 130062,
China
| | - Wenfeng Yi
- Department of Animal Science, Jilin University, Changchun 130062,
China
| | - Feng Li
- Shandong Binzhou Animal Science & Veterinary Medicine Academy, Binzhou, 256600,
China
| | - Shouqing Yan
- Department of Animal Science, Jilin University, Changchun 130062,
China
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Smaragdov MG. Identification of homozygosity-rich regions in the Holstein genome. Vavilovskii Zhurnal Genet Selektsii 2023; 27:471-479. [PMID: 37808215 PMCID: PMC10556852 DOI: 10.18699/vjgb-23-57] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/03/2023] [Accepted: 02/27/2023] [Indexed: 10/10/2023] Open
Abstract
In this study, 371 Holstein cows from six herds and 26 Holstein bulls, which were used in these herds, were genotyped by the Illumina BovineSNP50 array. For runs of homozygosity (ROH) identification, consecutive and sliding runs were performed by the detectRUNS and Plink software. The missing calls did not significantly affect the ROH data. The mean number of ROH identified by consecutive runs was 95.4 ± 2.7, and that by sliding runs was 86.0 ± 2.6 in cows, while this number for Holstein bulls was lower 58.9 ± 1.9. The length of the ROH segments varied from 1 Mb to over 16 Mb, with the largest number of ROH having a length of 1-2 Mb. Of the 29 chromosomes, BTA 14, BTA 16, and BTA 7 were the most covered by ROH. The mean coefficient of inbreeding across the herds was 0.111 ± 0.003 and 0.104 ± 0.004 based on consecutive and sliding runs, respectively, and 0.078 ± 0.005 for bulls based on consecutive runs. These values do not exceed those for Holstein cattle in North America. The results of this study confirmed the more accurate identification of ROH by consecutive runs, and also that the number of allowed heterozygous SNPs may have a significant effect on ROH data.
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Affiliation(s)
- M G Smaragdov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Science Center for Animal Husbandry, St. Petersburg, Pushkin, Russia
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Zegeye T, Belay G, Vallejo-Trujillo A, Han J, Hanotte O. Genome-wide diversity and admixture of five indigenous cattle populations from the Tigray region of northern Ethiopia. Front Genet 2023; 14:1050365. [PMID: 37600659 PMCID: PMC10432725 DOI: 10.3389/fgene.2023.1050365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 07/14/2023] [Indexed: 08/22/2023] Open
Abstract
The Tigray region, where we found around eight per cent of the indigenous cattle population of Ethiopia, is considered as the historic centre of the country, with the ancient pre-Aksumite and Aksumite civilisations in contact with the civilisations of the Fertile Crescent and the Indian subcontinent. Here, we used whole genome sequencing data to characterise the genomic diversity, relatedness, and admixture of five cattle populations (Abergelle, Arado, Begait, Erob, and Raya) indigenous to the Tigray region of Ethiopia. We detected 28 to 29 million SNPs and 2.7 to 2.9 million indels in each population, of which 7% of SNPs and 34% of indels were novel. Functional annotation of the variants showed around 0.01% SNPs and 0.22%-0.27% indels in coding regions. Enrichment analysis of genes overlapping missense private SNPs revealed 20 significant GO terms and KEGG pathways that were shared by or specific to breeds. They included important genes associated with morphology (SCN4A, TAS1R2 and KCNG4), milk yield (GABRG1), meat quality (MMRN2, VWC2), feed efficiency (PCDH8 and SLC26A3), immune response (LAMC1, PCDH18, CELSR1, TLR6 and ITGA5), heat resistance (NPFFR1 and HTR7) and genes belonging to the olfactory gene family, which may be related to adaptation to harsh environments. Tigray indigenous cattle are very diverse. Their genome-wide average nucleotide diversity ranged from 0.0035 to 0.0036. The number of heterozygous SNPs was about 0.6-0.7 times higher than homozygous ones. The within-breed average number of ROHs ranged from 777.82 to 1000.45, with the average sum of the length of ROHs ranging from 122.01 Mbp to 163.88 Mbp. The genomic inbreeding coefficients differed among animals and breeds, reaching up to 10% in some Begait and Raya animals. Tigray indigenous cattle shared a common ancestry with Asian indicine (85.6%-88.7%) and African taurine (11.3%-14.1%) cattle, with very small, if any, European taurine introgression. This study identified high within-breed genetic diversity representing an opportunity for breeding improvement programs and, also, significant novel variants that could increase the number of known cattle variants, an important contribution to the knowledge of domestic cattle genetic diversity.
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Affiliation(s)
- Tsadkan Zegeye
- Mekelle Agricultural Research Center, Tigray Agricultural Research Institute, Mekelle, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Live Gene—CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Adriana Vallejo-Trujillo
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jianlin Han
- Live Gene—CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Olivier Hanotte
- Live Gene—CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
- Cells, Organism and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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Zsolnai A, Egerszegi I, Rózsa L, Mezőszentgyörgyi D, Anton I. Position of Hungarian Merino among other Merinos, within-breed genetic similarity network and markers associated with daily weight gain. Anim Biosci 2023; 36:10-18. [PMID: 35760405 PMCID: PMC9834658 DOI: 10.5713/ab.21.0459] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 05/18/2022] [Indexed: 01/27/2023] Open
Abstract
OBJECTIVE In this study, we aimed to position the Hungarian Merino among other Merino-derived sheep breeds, explore the characteristics of our sampled animals' genetic similarity network within the breed, and highlight single nucleotide polymorphisms (SNPs) associated with daily weight-gain. METHODS Hungarian Merino (n = 138) was genotyped on Ovine SNP50 Bead Chip (Illumina, San Diego, CA, USA) and positioned among 30 Merino and Merino-derived breeds (n = 555). Population characteristics were obtained via PLINK, SVS, Admixture, and Treemix software, within-breed network was analysed with python networkx 2.3 library. Daily weight gain of Hungarian Merino was standardised to 60 days and was collected from the database of the Association of Hungarian Sheep and Goat Breeders. For the identification of loci associated with daily weight gain, a multi-locus mixed-model was used. RESULTS Supporting the breed's written history, the closest breeds to Hungarian Merino were Estremadura and Rambouillet (pairwise FST values are 0.035 and 0.036, respectively). Among Hungarian Merino, a highly centralised connectedness has been revealed by network analysis of pairwise values of identity-by-state, where the animal in the central node had a betweenness centrality value equal to 0.936. Probing of daily weight gain against the SNP data of Hungarian Merinos revealed five associated loci. Two of them, OAR8_17854216.1 and s42441.1 on chromosome 8 and 9 (-log10P>22, false discovery rate<5.5e-20) and one locus on chromosome 20, s28948.1 (-log10P = 13.46, false discovery rate = 4.1e-11), were close to the markers reported in other breeds concerning daily weight gain, six-month weight, and post-weaning gain. CONCLUSION The position of Hungarian Merino among other Merino breeds has been determined. We have described the similarity network of the individuals to be applied in breeding practices and highlighted several markers useful for elevating the daily weight gain of Hungarian Merino.
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Affiliation(s)
- Attila Zsolnai
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Herceghalom, 2053,
Hungary,National Centre for Biodiversity and Gene Conservation, Gödöllő, 2100,
Hungary,Corresponding Author: Attila Zsolnai, Tel: +36-70-491-7824, E-mail:
| | - István Egerszegi
- Department of Animal Husbandry Technology and Animal Welfare, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Gödöllő, 2100,
Hungary
| | - László Rózsa
- Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Keszthely, 8360,
Hungary
| | - Dávid Mezőszentgyörgyi
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Herceghalom, 2053,
Hungary
| | - István Anton
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Herceghalom, 2053,
Hungary
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Schmid M, Stock J, Bennewitz J, Wellmann R. Improving the Accuracy of Multi-Breed Prediction in Admixed Populations by Accounting for the Breed Origin of Haplotype Segments. Front Genet 2022; 13:840815. [PMID: 35401683 PMCID: PMC8987492 DOI: 10.3389/fgene.2022.840815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
Numerically small breeds have often been upgraded with mainstream breeds. This historic introgression predisposes the breeds for joint genomic evaluations with mainstream breeds. The linkage disequilibrium structure differs between breeds. The marker effects of a haplotype segment may, therefore, depend on the breed from which the haplotype segment originates. An appropriate method for genomic evaluation would account for this dependency. This study proposes a method for the computation of genomic breeding values for small admixed breeds that incorporate phenotypic and genomic information from large introgressed breeds by considering the breed origin of alleles (BOA) in the evaluation. The proposed BOA model classifies haplotype segments according to their origins and assumes different but correlated SNP effects for the different origins. The BOA model was compared in a simulation study to conventional within-breed genomic best linear unbiased prediction (GBLUP) and conventional multi-breed GBLUP models. The BOA model outperformed within-breed GBLUP as well as multi-breed GBLUP in most cases.
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Affiliation(s)
- Markus Schmid
- Institute of Animal Science, Department of Animal Genetics and Breeding, University of Hohenheim, Stuttgart, Germany
| | - Joana Stock
- Institute of Animal Science, Department of Animal Genetics and Breeding, University of Hohenheim, Stuttgart, Germany
| | - Jörn Bennewitz
- Institute of Animal Science, Department of Animal Genetics and Breeding, University of Hohenheim, Stuttgart, Germany
| | - Robin Wellmann
- Institute of Animal Science, Department of Animal Genetics and Breeding, University of Hohenheim, Stuttgart, Germany
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Slagboom M, Milkevych V, Liu H, Thomasen JR, Kargo M, Schmidtmann C. Conservation of local Red cattle breeds by collaboration with a mainstream Red dairy cattle breed. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.104936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Fabbri MC, Dadousis C, Tiezzi F, Maltecca C, Lozada-Soto E, Biffani S, Bozzi R. Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity. PLoS One 2021; 16:e0248087. [PMID: 34695128 PMCID: PMC8544844 DOI: 10.1371/journal.pone.0248087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 10/06/2021] [Indexed: 11/18/2022] Open
Abstract
In the present study, GeneSeek GGP-LDv4 33k single nucleotide polymorphism chip was used to detect runs of homozygosity (ROH) in eight Italian beef cattle breeds, six breeds with distribution limited to Tuscany (Calvana, Mucca Pisana, Pontremolese) or Sardinia (Sarda, Sardo Bruna and Sardo Modicana) and two cosmopolitan breeds (Charolais and Limousine). ROH detection analyses were used to estimate autozygosity and inbreeding and to identify genomic regions with high frequency of ROH, which might reflect selection signatures. Comparative analysis among breeds revealed differences in length and distribution of ROH and inbreeding levels. The Charolais, Limousine, Sarda, and Sardo Bruna breeds were found to have a high frequency of short ROH (~ 15.000); Calvana and Mucca Pisana presented also runs longer than 16 Mbp. The highest level of average genomic inbreeding was observed in Tuscan breeds, around 0.3, while Sardinian and cosmopolitan breeds showed values around 0.2. The population structure and genetic distances were analyzed through principal component and multidimensional scaling analyses, and resulted in a clear separation among the breeds, with clusters related to productive purposes. The frequency of ROH occurrence revealed eight breed-specific genomic regions where genes of potential selective and conservative interest are located (e.g. MYOG, CHI3L1, CHIT1 (BTA16), TIMELESS, APOF, OR10P1, OR6C4, OR2AP1, OR6C2, OR6C68, CACNG2 (BTA5), COL5A2 and COL3A1 (BTA2)). In all breeds, we found the largest proportion of homozygous by descent segments to be those that represent inbreeding events that occurred around 32 generations ago, with Tuscan breeds also having a significant proportion of segments relating to more recent inbreeding.
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Affiliation(s)
- Maria Chiara Fabbri
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
- * E-mail:
| | - Christos Dadousis
- Dipartimento di Scienze Medico‐Veterinarie, Università di Parma, Parma, Italy
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States of America
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States of America
| | - Emmanuel Lozada-Soto
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States of America
| | - Stefano Biffani
- Institute of Agricultural Biology and Biotechnology (CNR), Milano, Italy
| | - Riccardo Bozzi
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
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Is the metabolic power paradigm ecologically valid within elite Gaelic football? SPORT SCIENCES FOR HEALTH 2021. [DOI: 10.1007/s11332-020-00707-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Addo S, Klingel S, Thaller G, Hinrichs D. Genetic diversity and the application of runs of homozygosity-based methods for inbreeding estimation in German White-headed Mutton sheep. PLoS One 2021; 16:e0250608. [PMID: 33956807 PMCID: PMC8101715 DOI: 10.1371/journal.pone.0250608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 04/09/2021] [Indexed: 11/19/2022] Open
Abstract
The German White-headed Mutton (GWM) sheep is a monitoring population believed to have been improved through crosses with other breeds, e.g., Texel (TXL) and French Berrichone du Cher (BDC). The primary aim of the study was to analyse genetic diversity and breed composition of GWM sheep. Furthermore, different measures of computing inbreeding from the runs of homozygosity (ROH) were investigated. Data for GWM consisted of pedigree information on 19,000 animals and 40,753 quality filtered SNPs on 46 individuals. Additionally, publicly available genotype data on 209 individuals belonging to nine sheep breeds were included in the analysis. Due to evenness of SNPs spacing and proportionality of the number of SNPs in each autosome to autosome length, a high correlation (rp = 0.99) was found between genomic inbreeding coefficients computed based on the length of ROH (FROH_L) and those computed relative to the number of SNPs in ROH (FROH_N). Total inbreeding was partitioned into values for individual chromosomes revealing the highest levels of inbreeding on chromosomes 1, 2 and 3. Correlations between the ROH-based inbreeding measures and pedigree inbreeding reached 0.82. The observed heterozygosity estimate in GWM was high (0.39), however, the breed suffered low level of effective population size (~50) from a genomic viewpoint. Moreover, effective number of founders (186), and effective number of ancestors (144) implied disequilibrium of founder contribution and a genetic bottleneck in the breed. Multidimensional scaling and network visualisation analyses revealed close connectedness of GWM to BDC and German Texel (GTX). A model-based admixture analysis consistently indicated the flow of genes from other breeds, particularly BDC to GWM. Our analyses highlight the mixed genetic background of GWM sheep and furthermore, suggest a close monitoring of the breed to consolidate its genetic diversity while averting further reduction in the effective population size.
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Affiliation(s)
- Sowah Addo
- Institute of Animal Breeding and Husbandry, Kiel University, Kiel, Germany
- Department of Animal Breeding, University of Kassel, Witzenhausen, Germany
- * E-mail:
| | - Stefanie Klingel
- Arche Warder, Center for Rare and Endangered Domestic Animals, Warder, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Kiel University, Kiel, Germany
| | - Dirk Hinrichs
- Department of Animal Breeding, University of Kassel, Witzenhausen, Germany
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Gautason E, Schönherz AA, Sahana G, Guldbrandtsen B. Genomic inbreeding and selection signatures in the local dairy breed Icelandic Cattle. Anim Genet 2021; 52:251-262. [PMID: 33829515 DOI: 10.1111/age.13058] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2021] [Indexed: 12/21/2022]
Abstract
Icelandic Cattle is the only dairy cattle breed native to Iceland. It currently numbers ca. 26 000 breeding females. We used 50k genotypes of over 8000 Icelandic Cattle to estimate genomic and pedigree-based inbreeding and to detect selection signatures using the integrated haplotype score. We used 47 Icelandic bulls genotyped with a 770k SNP chip to estimate LD decay for comparison with other Nordic dairy cattle breeds. We detected ROHs on the autosomes and computed ROH-based autosomal inbreeding coefficients. Average inbreeding coefficients according to pedigree and ROHs were 0.0621 and 0.101. Effective population sizes for the years 2009-2017 according to pedigree, ROHs, genomic relationship matrix, excess of homozygosity and individual increase in inbreeding were 81, 65, 60, 58 and 92 respectively. We identified three regions and six candidate genes that showed a signature of selection according to the integrated haplotype score (P < 0.05) on chromosomes 1, 16 and 23. The LD structure of Icelandic Cattle is shaped by a long period of isolation and a small founder population. The estimate of LD at distances closer than 0.3 Mb is lower in Icelandic Cattle than in Danish Jersey, but is higher than in Danish Holstein and Red Nordic Dairy Cattle breeds. Our findings show that inbreeding rates in Icelandic Cattle currently are sustainable according to FAO guidelines, and our results do not indicate severe historical inbreeding.
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Affiliation(s)
- E Gautason
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark
| | - A A Schönherz
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark.,Department of Animal Science, Aarhus University, Tjele, 8830, Denmark
| | - G Sahana
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark
| | - B Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark.,Department of Animal Sciences, University of Bonn, Endenicher Allee 15, Bonn, 53115, Germany
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13
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Schmidtmann C, Schönherz A, Guldbrandtsen B, Marjanovic J, Calus M, Hinrichs D, Thaller G. Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe. Genet Sel Evol 2021; 53:23. [PMID: 33676402 PMCID: PMC7936461 DOI: 10.1186/s12711-021-00613-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Background Local cattle breeds need special attention, as they are valuable reservoirs of genetic diversity. Appropriate breeding decisions and adequate genomic management of numerically smaller populations are required for their conservation. At this point, the analysis of dense genome-wide marker arrays provides encompassing insights into the genomic constitution of livestock populations. We have analyzed the genetic characterization of ten cattle breeds originating from Germany, The Netherlands and Denmark belonging to the group of red dairy breeds in Northern Europe. The results are intended to provide initial evidence on whether joint genomic breeding strategies of these populations will be successful. Results Traditional Danish Red and Groningen White-Headed were the most genetically differentiated breeds and their populations showed the highest levels of inbreeding. In contrast, close genetic relationships and shared ancestry were observed for the populations of German Red and White Dual-Purpose, Dutch Meuse-Rhine-Yssel, and Dutch Deep Red breeds, reflecting their common histories. A considerable amount of gene flow from Red Holstein to German Angler and to German Red and White Dual-Purpose was revealed, which is consistent with frequent crossbreeding to improve productivity of these local breeds. In Red Holstein, marked genomic signatures of selection were reported on chromosome 18, suggesting directed selection for important breeding goal traits. Furthermore, tests for signatures of selection between Red Holstein, Red and White Dual-Purpose, and Meuse-Rhine-Yssel uncovered signals for all investigated pairs of populations. The corresponding genomic regions, which were putatively under different selection pressures, harboured various genes which are associated with traits such as milk and beef production, mastitis and female fertility. Conclusions This study provides comprehensive knowledge on the genetic constitution and genomic connectedness of divergent red cattle populations in Northern Europe. The results will help to design and optimize breeding strategies. A joint genomic evaluation including some of the breeds studied here seems feasible.
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Affiliation(s)
- Christin Schmidtmann
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098, Kiel, Germany.
| | - Anna Schönherz
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark.,Department of Animal Science, Aarhus University, 8830, Tjele, Denmark
| | - Bernt Guldbrandtsen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark.,Department of Animal Sciences, Department of Animal Breeding and Husbandry, University of Bonn, 53115, Bonn, Germany
| | - Jovana Marjanovic
- Animal Breeding and Genomics, Wageningen University and Research, 6700AH, Wageningen, The Netherlands
| | - Mario Calus
- Animal Breeding and Genomics, Wageningen University and Research, 6700AH, Wageningen, The Netherlands
| | - Dirk Hinrichs
- Department of Animal Breeding, University of Kassel, 37213, Witzenhausen, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098, Kiel, Germany
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Sumreddee P, Toghiani S, Hay EH, Roberts A, Aggrey SE, Rekaya R. Runs of homozygosity and analysis of inbreeding depression. J Anim Sci 2021; 98:5979489. [PMID: 33180906 DOI: 10.1093/jas/skaa361] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/07/2020] [Indexed: 01/24/2023] Open
Abstract
Pedigree information was traditionally used to assess inbreeding. The availability of high-density marker panels provides an alternative to assess inbreeding, particularly in the presence of incomplete and error-prone pedigrees. Assessment of autozygosity across chromosomal segments using runs of homozygosity (ROH) has emerged as a valuable tool to estimate inbreeding due to its general flexibility and ability to quantify the chromosomal contribution to genome-wide inbreeding. Unfortunately, the identification of ROH segments is sensitive to the parameters used during the search process. These parameters are heuristically set, leading to significant variation in the results. The minimum length required to identify an ROH segment has major effects on the estimation of inbreeding and inbreeding depression, yet it is arbitrarily set. To overcome this limitation, a search algorithm to approximate mutation enrichment was developed to determine the minimum length of ROH segments. It consists of finding genome segments with significant effect differences in trait means between animals with high and low burdens of autozygous intervals with a specific length. The minimum length could be determined heuristically as the smallest interval at which a significant signal is detected. The proposed method was tested in an inbred Hereford cattle population genotyped for 30,220 SNPs. Phenotypes recorded for six traits were used for the approximation of mutation loads. The estimated minimum length was around 1 Mb for yearling weight (YW) and average daily gain (ADG) and 4 Mb for birth weight and weaning weight. These trait-specific thresholds estimated using the proposed method could be attributed to a trait-dependent effect of homozygosity. The detection of significant inbreeding effects was well aligned with the estimated thresholds, especially for YW and ADG. Although highly deleterious alleles are expected to be more frequent in recent inbreeding (long ROH), short ROH segments (<5 Mb) could contain a large number of less deleterious mutations with substantial joint effects on some traits (YW and ADG). Our results highlight the importance of accurate estimation of the ROH-based inbreeding and the necessity to consider a trait-specific minimum length threshold for the identification of ROH segments in inbreeding depression analyses. These thresholds could be determined using the proposed method provided the availability of phenotypic information.
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Affiliation(s)
| | - Sajjad Toghiani
- Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, MD
| | - El Hamidi Hay
- Fort Keogh Livestock and Range Research Laboratory, USDA Agricultural Research Service, Miles City, MT
| | - Andrew Roberts
- Fort Keogh Livestock and Range Research Laboratory, USDA Agricultural Research Service, Miles City, MT
| | - Samuel E Aggrey
- Department of Poultry Science, University of Georgia, Athens, GA.,Institute of Bioinformatics, University of Georgia, Athens, GA
| | - Romdhane Rekaya
- Department of Animal and Dairy Science, University of Georgia, Athens, GA.,Institute of Bioinformatics, University of Georgia, Athens, GA.,Department of Statistics, University of Georgia, Athens, GA
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15
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The effect of a periodized small-sided games intervention in hurling on physical and physiological measures of performance. SPORT SCIENCES FOR HEALTH 2021. [DOI: 10.1007/s11332-020-00703-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Zinovieva NA, Dotsev AV, Sermyagin AA, Deniskova TE, Abdelmanova AS, Kharzinova VR, Sölkner J, Reyer H, Wimmers K, Brem G. Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis. PLoS One 2020; 15:e0242200. [PMID: 33196682 PMCID: PMC7668599 DOI: 10.1371/journal.pone.0242200] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.
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Affiliation(s)
- Natalia Anatolievna Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
- * E-mail:
| | - Arsen Vladimirovich Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Alexander Alexandrovich Sermyagin
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Tatiana Evgenievna Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Alexandra Sergeevna Abdelmanova
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Veronika Ruslanovna Kharzinova
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology [FBN], Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology [FBN], Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine [VMU], Vienna, Austria
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