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Le SV, de Las Heras-Saldana S, Alexandri P, Olmo L, Walkden-Brown SW, van der Werf JHJ. Genetic diversity, population structure and origin of the native goats in Central Laos. J Anim Breed Genet 2024; 141:531-549. [PMID: 38520124 DOI: 10.1111/jbg.12862] [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: 11/15/2023] [Revised: 02/14/2024] [Accepted: 03/10/2024] [Indexed: 03/25/2024]
Abstract
Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (FST: 0.011-0.043) and negligible inbreeding coefficients (FIS: -0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92-6.85 Mb, with short ROH segments (1-5 Mb length) being the most prevalent (66.34%). Longer ROH segments (20-40 and >40 Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low-inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features.
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Affiliation(s)
- Sang V Le
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Sara de Las Heras-Saldana
- AGBU, a Joint Venture of the NSW Department of Primary Industries and the University of New England, Armidale, New South Wales, Australia
| | - Panoraia Alexandri
- AGBU, a Joint Venture of the NSW Department of Primary Industries and the University of New England, Armidale, New South Wales, Australia
| | - Luisa Olmo
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Stephen W Walkden-Brown
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Julius H J van der Werf
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
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Vostry L, Vostra-Vydrova H, Moravcikova N, Kasarda R, Margetin M, Rychtarova J, Drzaic I, Shihabi M, Cubric-Curik V, Sölkner J, Curik I. Genomic analysis of conservation status, population structure and admixture in local Czech and Slovak dairy goat breeds. J Dairy Sci 2024:S0022-0302(24)00937-8. [PMID: 38908686 DOI: 10.3168/jds.2023-24607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 05/30/2024] [Indexed: 06/24/2024]
Abstract
While dairy goat production, characterized by traditional production on small farms, is an important source of income in the Czech Republic and Slovakia, locally adapted breeds have not been fully consolidated over the last 100 years due to large fluctuations in population size and inconsistent breeding programs that allowed for different crossbreeding strategies. Our main objective in this study was therefore to assess the conservation status of 4 Czech (Alpine Goat, White Shorthair, Brown Shorthair and Czech Landrace) and one Slovak (Slovak White Shorthair) local goat breeds, to analyze their population structure and admixture, and to estimate their relatedness to several neighboring breeds. Our analyses included 142 goats belonging to 5 local breeds genotyped with the Illumina 50K BeadChip and 618 previously genotyped animals representing 15 goat breeds from Austria and Switzerland (all analyses based on 46,862 autosomal SNPs and 760 animals). In general, the conservation status of the Czech and Slovak local goat breeds was satisfactory, with the exception of the Brown Shorthair goat, as the analyzed parameters (heterozygosity, haplotype richness, ROH-based inbreeding and effective population size) were mostly above the median of 20 breeds. However, for all 5 Czech and Slovakian breeds, an examination of historical effective population size indicated a substantial decline about 8 to 22 generations ago. In addition, our study revealed that the Czech and Slovakian breeds are not fully consolidated; for instance, White Shorthair and Brown Shorthair were not clearly distinguishable. Considerable admixture, especially in Czech Landrace (effective number of parental clusters equal to 4.2), and low but numerous migration rates from other Austrian and Swiss breeds were found. These results provide valuable insights for future breeding programs and genetic diversity management of local Czech and Slovak goat breeds.
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Affiliation(s)
- Lubos Vostry
- Czech University of Life Science Prague, Kamycka 129, 16500 Prague, Czech Republic.
| | - Hana Vostra-Vydrova
- Czech University of Life Science Prague, Kamycka 129, 16500 Prague, Czech Republic
| | - Nina Moravcikova
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Radovan Kasarda
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Milan Margetin
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Jana Rychtarova
- Institute of Animal Science, Přátelství 815, 104 00 Prague, Czech Republic
| | - Ivana Drzaic
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Mario Shihabi
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Vlatka Cubric-Curik
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Johan Sölkner
- University of Natural Resources & Life Sciences Vienna, Gregor-Mendel-Strasse 33, 1180 Vienna, Austria
| | - Ino Curik
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia; Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Guba Sándor u. 40, 7400 Kaposvár, Hungary.
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Masila EM, Ogada SO, Ogali IN, Kennedy GM, Too EK, Ommeh CS. Mitochondrial DNA D-Loop Polymorphisms among the Galla Goats Reveals Multiple Maternal Origins with Implication on the Functional Diversity of the HSP70 Gene. Genet Res (Camb) 2024; 2024:5564596. [PMID: 38348366 PMCID: PMC10861283 DOI: 10.1155/2024/5564596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/15/2024] Open
Abstract
Despite much attention given to the history of goat evolution in Kenya, information on the origin, demographic history, dispersal route, and genetic diversity of Galla goats remains unclear. Here, we examined the genetic background, diversity, demographic history, and population genetic variation of Galla goats using mtDNA D-loop and HSP70 single-nucleotide polymorphism markers. The results revealed 90 segregating sites and 68 haplotypes in a 600-bp mtDNA D-loop sequence. The overall mean mitochondrial haplotype diversity was 0.993. The haplotype diversities ranged between 0.8939 ± 0.0777 and 1.0000 ± 0.0221 in all populations supporting high genetic diversity. Mitochondrial phylogenetic analysis revealed three Galla goat haplogroups (A, G, and D), supporting multiple maternal ancestries, of which haplogroup A was the most predominant. Analysis of molecular variance (AMOVA) showed considerable variation within populations at 94.39%, evidence of high genetic diversity. Bimodal mismatch distribution patterns were observed while most populations recorded negative results for Tajima and Fu's Fs neutrality tests supporting population expansion. Genetic variation among populations was also confirmed using HSP70 gene fragment sequences, where six polymorphic sites which defined 21 haplotypes were discovered. Analysis of molecular variance revealed a significant FST index value of 0.134 and a high FIS index value of 0.746, an indication of inbreeding. This information will pave the way for conservation strategies and informed breeding to improve Galla or other goat breeds for climate-smart agriculture.
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Affiliation(s)
- Ednah M. Masila
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Juja, Kenya
- Veterinary Science Research Institute (VSRI), Kenya Agricultural Livestock and Research Organization (KALRO), P.O. Box 32-00902, Nairobi, Kenya
| | - Stephen O. Ogada
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Juja, Kenya
| | - Irene N. Ogali
- Veterinary Science Research Institute (VSRI), Kenya Agricultural Livestock and Research Organization (KALRO), P.O. Box 32-00902, Nairobi, Kenya
| | - Grace M. Kennedy
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Juja, Kenya
| | - Eric K. Too
- Veterinary Science Research Institute (VSRI), Kenya Agricultural Livestock and Research Organization (KALRO), P.O. Box 32-00902, Nairobi, Kenya
| | - Cecily S. Ommeh
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Juja, Kenya
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Ning C, Xie K, Huang J, Di Y, Wang Y, Yang A, Hu J, Zhang Q, Wang D, Fan X. Marker density and statistical model designs to increase accuracy of genomic selection for wool traits in Angora rabbits. Front Genet 2022; 13:968712. [PMID: 36118881 PMCID: PMC9478554 DOI: 10.3389/fgene.2022.968712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
The Angora rabbit, a well-known breed for fiber production, has been undergoing traditional breeding programs relying mainly on phenotypes. Genomic selection (GS) uses genomic information and promises to accelerate genetic gain. Practically, to implement GS in Angora rabbit breeding, it is necessary to evaluate different marker densities and GS models to develop suitable strategies for an optimized breeding pipeline. Considering a lack in microarray, low-coverage sequencing combined with genotype imputation was used to boost the number of SNPs across the rabbit genome. Here, in a population of 629 Angora rabbits, a total of 18,577,154 high-quality SNPs were imputed (imputation accuracy above 98%) based on low-coverage sequencing of 3.84X genomic coverage, and wool traits and body weight were measured at 70, 140 and 210 days of age. From the original markers, 0.5K, 1K, 3K, 5K, 10K, 50K, 100K, 500K, 1M and 2M were randomly selected and evaluated, resulting in 50K markers as the baseline for the heritability estimation and genomic prediction. Comparing to the GS performance of single-trait models, the prediction accuracy of nearly all traits could be improved by multi-trait models, which might because multiple-trait models used information from genetically correlated traits. Furthermore, we observed high significant negative correlation between the increased prediction accuracy from single-trait to multiple-trait models and estimated heritability. The results indicated that low-heritability traits could borrow more information from correlated traits and hence achieve higher prediction accuracy. The research first reported heritability estimation in rabbits by using genome-wide markers, and provided 50K as an optimal marker density for further microarray design, genetic evaluation and genomic selection in Angora rabbits. We expect that the work could provide strategies for GS in early selection, and optimize breeding programs in rabbits.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Dan Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Xinzhong Fan
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
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Chokoe TC, Hadebe K, Muchadeyi FC, Nephawe KA, Dzomba EF, Mphahlele TD, Matelele TC, Mtileni BJ. Conservation status and historical relatedness of South African communal indigenous goat populations using a genome-wide single-nucleotide polymorphism marker. Front Genet 2022; 13:909472. [PMID: 36017496 PMCID: PMC9395594 DOI: 10.3389/fgene.2022.909472] [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: 03/31/2022] [Accepted: 06/27/2022] [Indexed: 11/18/2022] Open
Abstract
Indigenous goats form the majority of populations in smallholder, low input, low output production systems and are considered an important genetic resource due to their adaptability to different production environments and support of communal farming. Effective population size (Ne), inbreeding levels, and the runs of homozygosity (ROHs) are effective tools for exploring the genetic diversity and understanding the demographic history in efforts to support breeding strategies to use and conserve genetic resources. Across populations, the current Ne of Gauteng was the lowest at 371 animals, while the historical Ne across populations suggests that the ancestor Ne has decreased by 53.86%, 44.58%, 42.16%, and 41.16% in Free State (FS), North West (NW), Limpopo (LP), and Gauteng (GP), respectively, over the last 971 generations. Genomic inbreeding levels related to ancient kinship (FROH > 5 Mb) were highest in FS (0.08 ± 0.09) and lowest in the Eastern Cape (EC) (0.02 ± 0.02). A total of 871 ROH island regions which include important environmental adaptation and hermo-tolerance genes such as IL10RB, IL23A, FGF9, IGF1, EGR1, MTOR, and MAPK3 were identified (occurring in over 20% of the samples) in FS (n = 37), GP (n = 42), and NW (n = 2) populations only. The mean length of ROH across populations was 7.76 Mb and ranged from 1.61 Mb in KwaZulu-Natal (KZN) to 98.05 Mb (GP and NW). The distribution of ROH according to their size showed that the majority (n = 1949) of the detected ROH were > 5 Mb in length compared to the other categories. Assuming two hypothetical ancestral populations, the populations from KZN and LP are revealed, supporting PC 1. The genomes of KZN and LP share a common origin but have substantial admixture from the EC and NW populations. The findings revealed that the occurrence of high Ne and autozygosity varied largely across breeds in communal indigenous goat populations at recent and ancient events when a genome-wide single-nucleotide polymorphism (SNP) marker was used. The use of Illumina goat SNP50K BeadChip shows that there was a migration route of communal indigenous goat populations from the northern part (LP) of South Africa to the eastern areas of the KZN that confirmed their historical relatedness and coincides with the migration periods of the Bantu nation.
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Affiliation(s)
- T. C. Chokoe
- Farm Animal Genetic Resources, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
- School of Agriculture & Environmental Sciences, University of Limpopo, Polokwane, South Africa
- *Correspondence: T. C. Chokoe,
| | - K. Hadebe
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - F. C. Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - K. A. Nephawe
- Department of Animal Sciences, Tshwane University of Technology, Pretoria, South Africa
| | - E. F. Dzomba
- Discipline of Genetics, School of Life Sciences, University of Kwazulu-Natal, Scottsville, South African
| | - T. D. Mphahlele
- Farm Animal Genetic Resources, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
| | - T. C. Matelele
- Farm Animal Genetic Resources, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
| | - B. J. Mtileni
- Department of Animal Sciences, Tshwane University of Technology, Pretoria, South Africa
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Luigi-Sierra MG, Fernández A, Martínez A, Guan D, Delgado JV, Álvarez JF, Landi V, Such FX, Jordana J, Saura M, Amills M. Genomic patterns of homozygosity and inbreeding depression in Murciano-Granadina goats. J Anim Sci Biotechnol 2022; 13:35. [PMID: 35264251 PMCID: PMC8908635 DOI: 10.1186/s40104-022-00684-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/19/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Inbreeding depression can adversely affect traits related to fitness, reproduction and productive performance. Although current research suggests that inbreeding levels are generally low in most goat breeds, the impact of inbreeding depression on phenotypes of economic interest has only been investigated in a few studies based on genealogical data. RESULTS We genotyped 1040 goats with the Goat SNP50 BeadChip. This information was used to estimate different molecular inbreeding coefficients and characterise runs of homozygosity and homozygosity patterns. We detected 38 genomic regions with increased homozygosity as well as 8 ROH hotspots mapping to chromosomes 1, 2, 4, 6, 14, 16 and 17. Eight hundred seventeen goats with available records for dairy traits were analysed to evaluate the potential consequences of inbreeding depression on milk phenotypes. Four regions on chromosomes 8 and 25 were significantly associated with inbreeding depression for the natural logarithm of the somatic cell count. Notably, these regions contain several genes related with immunity, such as SYK, IL27, CCL19 and CCL21. Moreover, one region on chromosome 2 was significantly associated with inbreeding depression for milk yield. CONCLUSIONS Although genomic inbreeding levels are low in Murciano-Granadina goats, significant evidence of inbreeding depression for the logarithm of the somatic cell count, a phenotype closely associated with udder health and milk yield, have been detected in this population. Minimising inbreeding would be expected to augment economic gain by increasing milk yield and reducing the incidence of mastitis, which is one of the main causes of dairy goat culling.
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Affiliation(s)
- María Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7,5, 28040, Madrid, Spain
| | - Amparo Martínez
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | | | | | - Vincenzo Landi
- Department of Veterinary Medicine, University of Bari ''Aldo Moro", 62 per Casamassima km. 3, 70010, Valenzano, SP, Italy
| | - Francesc Xavier Such
- Group of Research in Ruminants (G2R), Department of Animal and Food Science, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - María Saura
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7,5, 28040, Madrid, Spain.
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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The SNP-Based Profiling of Montecristo Feral Goat Populations Reveals a History of Isolation, Bottlenecks, and the Effects of Management. Genes (Basel) 2022; 13:genes13020213. [PMID: 35205258 PMCID: PMC8872249 DOI: 10.3390/genes13020213] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
The Montecristo wild goat is an endangered feral population that has been on the homonymous island in the Tuscan Archipelago since ancient times. The origins of Montecristo goats are still debated, with authors dating their introduction either back to Neolithic times or between the 6th and 13th century of the Common Era. To investigate the evolutionary history and relationships of this population we assembled a 50K SNP dataset including 55 Mediterranean breeds and two nuclei of Montecristo goats sampled on the island and from an ex situ conservation project. Diversity levels, gene flow, population structure, and genetic relationships were assessed through multiple approaches. The insular population scored the lowest values of both observed and expected heterozygosity, highlighting reduced genetic variation, while the ex situ nucleus highlighted a less severe reduction. Multivariate statistics, network, and population structure analyses clearly separated the insular nucleus from all other breeds, including the population of Montecristo goats from the mainland. Moreover, admixture and gene flow analyses pinpointed possible genetic inputs received by the two Montecristo goat nuclei from different sources, while Runs of Homozygosity (ROHs) indicated an ancient bottleneck/founder effect in the insular population and recent extensive inbreeding in the ex situ one. Overall, our results suggest that Montecristo goats experienced several demographic fluctuations combined with admixture events over time and highlighted a noticeable differentiation between the two nuclei.
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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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Goyache F, Pérez-Pardal L, Fernández I, Traoré A, Menéndez-Arias NA, Álvarez I. Ancient autozygous segments subject to positive selection suggest adaptive immune responses in West African cattle. Gene 2021; 803:145899. [PMID: 34400278 DOI: 10.1016/j.gene.2021.145899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 11/19/2022]
Abstract
Small-sized and trypanotolerant West African taurine (Bos taurus) cattle are a unique case of human-mediated process of adaptation to a challenging environment. Extensive gene flow with Sahelian zebu (B. indicus), bigger and with some resistance to tick attack, occurred for centuries and allowed the apparition of stable crossbred populations (sanga) having intermediate characteristics. Up to 237 individuals belonging to 10 different taurine, zebu and sanga cattle populations sampled in Benin, Burkina Faso and Niger were typed using the BovineHD BeadChip of Illumina to identify signatures of selection, assessed using three different Extended-Haplotype-Homozygosity-based statistics, overlapping with ancient, originated 1024 or 2048 generations ago, Homozygosity-By-Descent segments in the cattle genome. Candidate genomic regions were defined ensuring their importance within cattle type and using zebu as reference. Functional annotation analysis identified four statistically significant Annotation Clusters in taurine cattle (from ACt1 to ACt4), one (ACs1) in sanga, and another (ACz1) in zebu cattle, fitting well with expectations. ACt1 included genes primarily associated with innate immunity; ACt2 involved bitter taste receptor genes of importance to adaptation to changing environments; ACt3 included 68 genes coding ATP-binding proteins, some of them located on trypanotolerance-related QTL regions, that can partially underlie immune response and the additive mechanism of trypanotolerance; ACt4 was associated with growth and small size (NPPC gene); ACs1 included genes involved in immune response; and ACz1 is related with ectoparasite resistance. Our results provide a new set of genomic areas and candidate genes giving new insights on the genomic impact of adaptation in West African cattle.
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Affiliation(s)
- Félix Goyache
- SERIDA-Deva, Camino de Rioseco 1225, E-33394-Gijón, Spain.
| | | | - Iván Fernández
- SERIDA-Deva, Camino de Rioseco 1225, E-33394-Gijón, Spain
| | - Amadou Traoré
- Institut de l'Environnement et des Recherches Agricoles (INERA), Ouagadougou 04 BP 8645, Burkina Faso
| | | | - Isabel Álvarez
- SERIDA-Deva, Camino de Rioseco 1225, E-33394-Gijón, Spain
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Biodiversity of Russian Local Sheep Breeds Based on Pattern of Runs of Homozygosity. DIVERSITY 2021. [DOI: 10.3390/d13080360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Russian sheep breeds traditionally raised in specific environments are valuable parts of sociocultural heritage and economic component of the regions. However, the import of commercial breeds negatively influences the population sizes of local sheep populations and might lead to biodiversity loss. Estimation of the runs of homozygosity (ROH) in local sheep genomes is an informative tool to address their current genetic state. In this work, we aimed to address the ROH distribution and to estimate genome inbreeding based on SNP data to evaluate genetic diversity in Russian local sheep breeds. Materials for this study included SNP-genotypes from twenty-seven Russian local sheep breeds which were generated using the Illumina OvineSNP50 BeadChip (n = 391) or the Illumina Ovine Infinium HD BeadChip (n = 315). A consecutive runs method was used to calculate ROH which were estimated for each animal and then categorized in the ROH length classes. The ROH were found in all breeds. The mean ROH length varied from 86 to 280 Mb, while the ROH number ranged from 37 to 123. The genomic inbreeding coefficient varied from 0.033 to 0.106. Our findings provide evidence of low to moderate genomic inbreeding in major local sheep populations.
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Ouédraogo D, Ouédraogo-Koné S, Yougbaré B, Soudré A, Zoma-Traoré B, Mészáros G, Khayatzadeh N, Traoré A, Sanou M, Mwai OA, Wurzinger M, Burger PA, Sölkner J. Population structure, inbreeding and admixture in local cattle populations managed by community-based breeding programs in Burkina Faso. J Anim Breed Genet 2021; 138:379-388. [PMID: 33609004 PMCID: PMC8248134 DOI: 10.1111/jbg.12529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/16/2020] [Accepted: 11/23/2020] [Indexed: 12/30/2022]
Abstract
High-throughput genomic markers provide an opportunity to assess important indicators of genetic diversity for populations managed in livestock breeding programs. While well-structured breeding programs are common in developed countries, in developing country situations, especially in West Africa, on-farm performance and pedigree recordings are rare, and thus, genomic markers provide insights to the levels of genetic diversity, inbreeding and introgression by other breeds. In this study, we analysed key population parameters such as population structure, admixture and levels of inbreeding in three neighbouring populations of African taurine and taurine × Zebu crosses managed by community-based breeding programs in the South-West of Burkina Faso. The three populations were pure Baoulé (called Lobi locally) in sedentary production systems, Baoulé x Zebu crossbreds in sedentary systems and Zebu × Baoulé crossbreds in transhumant production systems, respectively. The total sample analysed included 631 animals and 38,207 single nucleotide polymorphisms after quality control. Results of principal component and admixture analyses confirmed the genetic background of two distinct ancestral populations (taurine and zebuine) and levels of admixture in all three breeding populations, including the presumably pure Baoulé group of animals. Inbreeding levels were moderate, compared to European dairy and beef cattle populations and higher than those of Brazilian Nellore cattle. Very few animals with inbreeding levels indicating parent-offspring or full sib mating were observed, and inbreeding levels indicating half sib mating were also rare. For the management of breeding populations, farmers were advised to exchange best young bulls. The crossbreeding levels of presumably pure Baoulé animals are of concern to the breeding program due to the high level of endangerment of pure African taurine cattle populations across West Africa. Future rounds of bull selection in the community-based breeding program will make use of genomic information about admixture levels.
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Affiliation(s)
- Dominique Ouédraogo
- Institut du Développement Rural (IDR), Université Nazi Boni (UNB), Bobo-Dioulasso, Burkina Faso.,Division of Livestock Sciences, Department of Sustainable Agricultural System, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Salifou Ouédraogo-Koné
- Institut du Développement Rural (IDR), Université Nazi Boni (UNB), Bobo-Dioulasso, Burkina Faso
| | - Bernadette Yougbaré
- Division of Livestock Sciences, Department of Sustainable Agricultural System, University of Natural Resources and Life Sciences, Vienna, Austria.,Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Albert Soudré
- Unité de Formation et de Recherche en Sciences et Technologies (UFR/ST), Université Norbert Zongo, Koudougou, Burkina Faso
| | - Bienvenue Zoma-Traoré
- Institut du Développement Rural (IDR), Université Nazi Boni (UNB), Bobo-Dioulasso, Burkina Faso.,Division of Livestock Sciences, Department of Sustainable Agricultural System, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gábor Mészáros
- Division of Livestock Sciences, Department of Sustainable Agricultural System, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Negar Khayatzadeh
- Division of Livestock Sciences, Department of Sustainable Agricultural System, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Amadou Traoré
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Moumouni Sanou
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Okeyo Ally Mwai
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Maria Wurzinger
- Division of Livestock Sciences, Department of Sustainable Agricultural System, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine Vienna, Vienna
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural System, University of Natural Resources and Life Sciences, Vienna, Austria
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Álvarez I, Fernández I, Traoré A, Pérez-Pardal L, Menéndez-Arias NA, Goyache F. Ancient Homozygosity Segments in West African Djallonké Sheep Inform on the Genomic Impact of Livestock Adaptation to the Environment. Animals (Basel) 2020; 10:E1178. [PMID: 32664651 PMCID: PMC7401600 DOI: 10.3390/ani10071178] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 12/22/2022] Open
Abstract
A sample of Burkina Faso Djallonké (West African Dwarf) sheep was analyzed to identify stretches of homozygous segments (runs of homozygosity; ROH) overlapping with ancient homozygosity-by-descent (HBD) segments. HBD segments were considered ancient if they were likely to be inherited from ancestors living from 1024 to 2048 generations ago, roughly coinciding with the time in which sheep entered into West Africa. It is hypothesized that such homozygous segments can inform on the effect of the sheep genome of human-mediated selection for adaptation to this harsh environment. PLINK analyses allowed to identify a total of 510 ROH segments in 127 different individuals that could be summarized into 124 different ROH. A total of 32,968 HBD segments were identified on 119 individuals using the software ZooRoH. HBD segments inherited from ancestors living 1024 and 2048 generations ago were identified on 61 individuals. The overlap between consensus ROH identified using PLINK and HBD fragments putatively assigned to generations 1024 and 2048 gave 108 genomic areas located on 17 different ovine chromosomes which were considered candidate regions for gene-annotation enrichment analyses. Functional annotation allowed to identify six statistically significant functional clusters involving 50 candidate genes. Cluster 1 was involved in homeostasis and coagulation; functional clusters 2, 3, and 6 were associated to innate immunity, defense against infections, and white blood cells proliferation and migration, respectively; cluster 4 was involved in parasite resistance; and functional cluster 5, formed by 20 genes, was involved in response to stress. The current analysis confirms the importance of genomic areas associated to immunity, disease resistance, and response to stress for adaptation of sheep to the challenging environment of humid Sub-Saharan West Africa.
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Affiliation(s)
- Isabel Álvarez
- Servicio Regional de Investigación y Desarrollo Agroalimentario, E-33394 Gijón, Spain; (I.Á.); (I.F.); (N.A.M.-A.)
| | - Iván Fernández
- Servicio Regional de Investigación y Desarrollo Agroalimentario, E-33394 Gijón, Spain; (I.Á.); (I.F.); (N.A.M.-A.)
| | - Amadou Traoré
- Institut de l’Environnement et des RecherchesAgricoles (INERA), 8645 Ouagadougou BP, Burkina Faso;
| | | | - Nuria A. Menéndez-Arias
- Servicio Regional de Investigación y Desarrollo Agroalimentario, E-33394 Gijón, Spain; (I.Á.); (I.F.); (N.A.M.-A.)
| | - Félix Goyache
- Servicio Regional de Investigación y Desarrollo Agroalimentario, E-33394 Gijón, Spain; (I.Á.); (I.F.); (N.A.M.-A.)
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