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A continent-wide high genetic load in African buffalo revealed by clines in the frequency of deleterious alleles, genetic hitchhiking and linkage disequilibrium. PLoS One 2021; 16:e0259685. [PMID: 34882683 PMCID: PMC8659316 DOI: 10.1371/journal.pone.0259685] [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: 05/12/2021] [Accepted: 10/24/2021] [Indexed: 11/19/2022] Open
Abstract
A high genetic load can negatively affect population viability and increase susceptibility to diseases and other environmental stressors. Prior microsatellite studies of two African buffalo (Syncerus caffer) populations in South Africa indicated substantial genome-wide genetic load due to high-frequency occurrence of deleterious alleles. The occurrence of these alleles, which negatively affect male body condition and bovine tuberculosis resistance, throughout most of the buffalo's range were evaluated in this study. Using available microsatellite data (2-17 microsatellite loci) for 1676 animals from 34 localities (from 25°S to 5°N), we uncovered continent-wide frequency clines of microsatellite alleles associated with the aforementioned male traits. Frequencies decreased over a south-to-north latitude range (average per-locus Pearson r = -0.22). The frequency clines coincided with a multilocus-heterozygosity cline (adjusted R2 = 0.84), showing up to a 16% decrease in southern Africa compared to East Africa. Furthermore, continent-wide linkage disequilibrium (LD) at five linked locus pairs was detected, characterized by a high fraction of positive interlocus associations (0.66, 95% CI: 0.53, 0.77) between male-deleterious-trait-associated alleles. Our findings suggest continent-wide and genome-wide selection of male-deleterious alleles driven by an earlier observed sex-chromosomal meiotic drive system, resulting in frequency clines, reduced heterozygosity due to hitchhiking effects and extensive LD due to male-deleterious alleles co-occurring in haplotypes. The selection pressures involved must be high to prevent destruction of allele-frequency clines and haplotypes by LD decay. Since most buffalo populations are stable, these results indicate that natural mammal populations, depending on their genetic background, can withstand a high genetic load.
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Thorne JW, Murdoch BM, Freking BA, Redden RR, Murphy TW, Taylor JB, Blackburn HD. Evolution of the sheep industry and genetic research in the United States: opportunities for convergence in the twenty-first century. Anim Genet 2021; 52:395-408. [PMID: 33955573 PMCID: PMC8360125 DOI: 10.1111/age.13067] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2021] [Indexed: 12/14/2022]
Abstract
The continuous development and application of technology for genetic improvement is a key element for advancing sheep production in the United States. The US sheep industry has contracted over time but appears to be at a juncture where a greater utilization of technology can facilitate industry expansion to new markets and address inefficiencies in traditional production practices. Significant transformations include the increased value of lamb in relation to wool, and a downtrend in large-scale operations but a simultaneous rise in small flocks. Additionally, popularity of hair breeds not requiring shearing has surged, particularly in semi-arid and subtropical US environments. A variety of domestically developed composite breeds and newly established technological approaches are now widely available for the sheep industry to use as it navigates these ongoing transformations. These genetic resources can also address long-targeted areas of improvement such as growth, reproduction and parasite resistance. Moderate progress in production efficiency has been achieved by producers who have employed estimated breeding values, but widespread adoption of this technology has been limited. Genomic marker panels have recently shown promise for reducing disease susceptibility, identifying parentage and providing a foundation for marker-assisted selection. As the ovine genome is further explored and genomic assemblies are improved, the sheep research community in the USA can capitalize on new-found information to develop and apply genetic technologies to improve the production efficiency and profitability of the sheep industry.
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Affiliation(s)
- J. W. Thorne
- Texas A&M AgriLife ExtensionTexas A&M UniversitySan AngeloTX76901USA
- Department of Animal, Veterinary and Food ScienceUniversity of IdahoMoscowID83844USA
| | - B. M. Murdoch
- Department of Animal, Veterinary and Food ScienceUniversity of IdahoMoscowID83844USA
| | - B. A. Freking
- United States Meat Animal Research CenterUnited States Department of Agriculture, Agricultural Research ServiceClay CenterNE68933‐0166USA
| | - R. R. Redden
- Texas A&M AgriLife ExtensionTexas A&M UniversitySan AngeloTX76901USA
| | - T. W. Murphy
- United States Meat Animal Research CenterUnited States Department of Agriculture, Agricultural Research ServiceClay CenterNE68933‐0166USA
| | - J. B. Taylor
- United States Sheep Experiment StationUnited States Department of Agriculture, Agricultural Research ServiceDuboisID83423USA
| | - H. D. Blackburn
- National Animal Germplasm ProgramUnited States Department of Agriculture, Agricultural Research ServiceFort CollinsCO80521USA
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Integration of georeferenced and genetic data for the management of biodiversity in sheep genetic resources in Brazil. Trop Anim Health Prod 2021; 53:126. [PMID: 33449218 DOI: 10.1007/s11250-021-02573-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 01/06/2021] [Indexed: 10/22/2022]
Abstract
There are few animal germplasm/gene bank collections in Brazil, and basic studies are needed to attend the future internal and external demands from international partners. The aim of this work was to validate a "proof of concept" that integrates spatial (georeferenced data) and genetic data regarding the local of origin from 3518 DNA samples from 17 different genetic groups or breeds of sheep in the Brazilian Germplasm bank. Spatialisation shows that not all genetic groups have samples in the bank, and collection is concentrated in the conservation nuclei spread nationwide. Only 21% of states with a specific breed have samples in the gene bank. The mean number of animals sampled per collection was 32, while the mean distance travelled to collect samples was 262 km from the conservation nuclei. For example, the Brazilian Somali were only collected in the conservation nucleus in Ceará State. No samples were collected to date for the Cariri breed, which is recognised by the Brazilian Ministry of Agriculture. Only two farms and one breed in the bank are from the northern region. Of the 27 states, there are samples in the gene bank of sheep from 13, so several states have no samples, requiring collection from herds outside the official system of conservation to make sure that studies using this germplasm realised are not biased. Significant genetic differences are seen above 332 km, which should guide future sampling efforts. Suggestions are given for improving the quantity, quality and diversity of samples in the gene bank.
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Abstract
Biobanking animal germplasm and tissues is a major component of conserving genetic resources. Effectively constructing such gene banks requires an understanding and evaluation of genetic resources, the ability to conserve various tissues through cryopreservation, and a robust information technology infrastructure to allow managers and potential users to fully understand and make use of the collection. Progress has been made internationally in developing national genetic resource collections. As these collections have been developed, it has become apparent that gene banks can serve a multitude of roles, thereby serving short- and long-term needs of research communities and industry. This article documents the development of gene banks and provides examples of how they have been used to date and the extent to which they have captured genetic diversity for future use.
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Affiliation(s)
- H D Blackburn
- National Animal Germplasm Program, Agricultural Research Service, US Department of Agriculture, Fort Collins, Colorado 80521, USA;
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Spangler GL, Rosen BD, Ilori MB, Hanotte O, Kim ES, Sonstegard TS, Burke JM, Morgan JLM, Notter DR, Van Tassell CP. Whole genome structural analysis of Caribbean hair sheep reveals quantitative link to West African ancestry. PLoS One 2017; 12:e0179021. [PMID: 28662044 PMCID: PMC5490989 DOI: 10.1371/journal.pone.0179021] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 05/23/2017] [Indexed: 01/05/2023] Open
Abstract
Hair sheep of Caribbean origin have become an important part of the U.S. sheep industry. Their lack of wool eliminates a number of health concerns and drastically reduces the cost of production. More importantly, Caribbean hair sheep demonstrate robust production performance even in the presence of drug-resistant gastrointestinal nematodes, a rising concern to the industry. Despite the growing importance of hair sheep in the Americas their genetic origins have remained speculative. Prior to this report no genetic studies were able to identify a unique geographical origin of hair sheep in the New World. Our study clarifies the African and European ancestry of Caribbean hair sheep. Whole-genome structural analysis was conducted on four established breeds of hair sheep from the Caribbean region. Using breeds representing Africa and Europe we establish an objective measure indicating Caribbean hair sheep are derived from Iberian and West African origins. Caribbean hair sheep result from West African introgression into established ecotypes of Iberian descent. Genotypes from 47,750 autosomal single nucleotide polymorphism markers scored in 290 animals were used to characterize the population structure of the St. Croix, Barbados Blackbelly, Morada Nova, and Santa Ines. Principal components, admixture, and phylogenetic analyses results correlate with historical patterns of colonization and trade. These patterns support co-migration of these sheep with humans.
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Affiliation(s)
- Gordon L. Spangler
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | | | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Eui-Soo Kim
- Acceligen of Recombinetics Incorporated, Saint Paul, Minnesota, United States of America
| | - Tad S. Sonstegard
- Acceligen of Recombinetics Incorporated, Saint Paul, Minnesota, United States of America
| | - Joan M. Burke
- Dale Bumpers Small Farms Research Station, Agricultural Research Service, United States Department of Agriculture, Booneville, Arkansas, United States of America
| | - James L. M. Morgan
- Katahdin Hair Sheep International, Fayetteville, Arkansas, United States of America
| | - David R. Notter
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
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Short tandem repeat (STR) based genetic diversity and relationship of domestic sheep breeds with primitive wild Punjab Urial sheep ( Ovis vignei punjabiensis ). Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2016.12.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kardos M, Taylor HR, Ellegren H, Luikart G, Allendorf FW. Genomics advances the study of inbreeding depression in the wild. Evol Appl 2016; 9:1205-1218. [PMID: 27877200 PMCID: PMC5108213 DOI: 10.1111/eva.12414] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 08/05/2016] [Indexed: 12/12/2022] Open
Abstract
Inbreeding depression (reduced fitness of individuals with related parents) has long been a major focus of ecology, evolution, and conservation biology. Despite decades of research, we still have a limited understanding of the strength, underlying genetic mechanisms, and demographic consequences of inbreeding depression in the wild. Studying inbreeding depression in natural populations has been hampered by the inability to precisely measure individual inbreeding. Fortunately, the rapidly increasing availability of high-throughput sequencing data means it is now feasible to measure the inbreeding of any individual with high precision. Here, we review how genomic data are advancing our understanding of inbreeding depression in the wild. Recent results show that individual inbreeding and inbreeding depression can be measured more precisely with genomic data than via traditional pedigree analysis. Additionally, the availability of genomic data has made it possible to pinpoint loci with large effects contributing to inbreeding depression in wild populations, although this will continue to be a challenging task in many study systems due to low statistical power. Now that reliably measuring individual inbreeding is no longer a limitation, a major focus of future studies should be to more accurately quantify effects of inbreeding depression on population growth and viability.
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Affiliation(s)
- Marty Kardos
- Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | | | - Hans Ellegren
- Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Gordon Luikart
- Division of Biological SciencesUniversity of MontanaMissoulaMTUSA
- Flathead Lake Biological StationDivision of Biological SciencesUniversity of MontanaPolsonMTUSA
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E GX, Zhong T, Ma YH, Gao HJ, He JN, Liu N, Zhao YJ, Zhang JH, Huang YF. Conservation genetics in Chinese sheep: diversity of fourteen indigenous sheep (Ovis aries) using microsatellite markers. Ecol Evol 2016; 6:810-7. [PMID: 26865968 PMCID: PMC4739567 DOI: 10.1002/ece3.1891] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 11/13/2015] [Accepted: 11/23/2015] [Indexed: 11/10/2022] Open
Abstract
The domestic sheep (Ovis aries) has been an economically and culturally important farm animal species since its domestication around the world. A wide array of sheep breeds with abundant phenotypic diversity exists including domestication and selection as well as the indigenous breeds may harbor specific features as a result of adaptation to their environment. The objective of this study was to investigate the population structure of indigenous sheep in a large geographic location of the Chinese mainland. Six microsatellites were genotyped for 611 individuals from 14 populations. The mean number of alleles (±SD) ranged from 7.00 ± 3.69 in Gangba sheep to 10.50 ± 4.23 in Tibetan sheep. The observed heterozygote frequency (±SD) within a population ranged from 0.58 ± 0.03 in Gangba sheep to 0.71 ± 0.03 in Zazakh sheep and Minxian black fur sheep. In addition, there was a low pairwise difference among the Minxian black fur sheep, Mongolian sheep, Gansu alpine merino, and Lanzhou fat-tailed sheep. Bayesian analysis with the program STRUCTURE showed support for 3 clusters, revealing a vague genetic clustering pattern with geographic location. The results of the current study inferred high genetic diversity within these native sheep in the Chinese mainland.
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Affiliation(s)
- Guang-Xin E
- College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization Southwest University Chongqing 400716 China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan province Sichuan Agricultural University Chengdu Sichuan 625014 China
| | - Yue-Hui Ma
- Institute of Animal Science Chinese Academy of Agricultural Sciences (CAAS) Beijing 100193 China
| | - Hui-Jiang Gao
- Institute of Animal Science Chinese Academy of Agricultural Sciences (CAAS) Beijing 100193 China
| | - Jian-Ning He
- College of Animal Science and Technology Qingdao Agricultural University Qingdao 266109 China
| | - Nan Liu
- College of Animal Science and Technology Qingdao Agricultural University Qingdao 266109 China
| | - Yong-Ju Zhao
- College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization Southwest University Chongqing 400716 China
| | - Jia-Hua Zhang
- College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization Southwest University Chongqing 400716 China
| | - Yong-Fu Huang
- College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization Southwest University Chongqing 400716 China
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Carvalho GMC, Paiva SR, Araújo AM, Mariante A, Blackburn HD. Genetic structure of goat breeds from Brazil and the United States: Implications for conservation and breeding programs1. J Anim Sci 2015; 93:4629-36. [DOI: 10.2527/jas.2015-8974] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Crispim BDA, Seno LDO, Egito AAD, Vargas Junior FMD, Grisolia AB. Application of microsatellite markers for breeding and genetic conservation of herds of Pantaneiro sheep. ELECTRON J BIOTECHN 2014. [DOI: 10.1016/j.ejbt.2014.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Blackburn HD, Plante Y, Rohrer G, Welch EW, Paiva SR. Impact of genetic drift on access and benefit sharing under the Nagoya Protocol: the case of the Meishan pig. J Anim Sci 2014; 92:1405-11. [PMID: 24496834 DOI: 10.2527/jas.2013-7274] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genetic drift (GD) randomly impacts small breeds and imported populations. Therefore, it can impact policies that affect conservation of animal genetic resources. This paper evaluates GD for a population of Meishan pigs imported into the United States and explores the ramifications of GD on access and benefit sharing of genetic resources under the Nagoya Protocol (NP) of the United Nations' Convention on Biological Diversity. The NP was motivated by concerns about fair and equitable benefit sharing of genetic resources across life forms. In this experiment, 35 microsatellite markers were used to quantify the level of GD that occurred between Meishan pigs (Meishan-China; n = 22) imported into the United States in the late 1980s and contemporary Meishan (Meishan-US; n = 42), which have been randomly bred since importation. The Meishan-US consisted of 2 subpopulations (Meishan-MARC and Meishan-ISU). Five other breeds were also included in the analysis to serve as reference populations: Fengjing and Minzhu, which were imported with Meishan-China, and Duroc, Berkshire, and Yorkshire from the United States. Mean shift in allele frequency was 0.11 (SE = 0.019) due to GD for Meishan-US vs. Meishan-China with some loci having changed allele frequencies by greater than 0.20. Principle coordinate analysis confirmed divergence among the Meishan populations. Model-based clustering tended to place the U.S. and Chinese breeds into 2 distinct clusters, likely due to differences in allele frequencies between U.S. and Chinese breeds. Contemporary Meishan-US has become differentiated from the original imported animals due to GD. Attributing future performance of Meishan-US to Meishan-China, as set forth by NP, is problematic due to GD. As an imported breed becomes established there will be an increasing number of breeders who may have different selection goals and private treaty contracts will govern the exchange of stock between them. Therefore, considering biological phenomena and social dynamics simultaneously draws into question whether a rigorous access and benefit sharing protocol as envisioned in the NP will be operational.
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Affiliation(s)
- H D Blackburn
- National Animal Germplasm Program, National Center for Genetic Resources Preservation ARS-USDA, Fort Collins, CO 80521
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Agaviezor BO, Peters SO, Adefenwa MA, Yakubu A, Adebambo OA, Ozoje MO, Ikeobi CO, Wheto M, Ajayi OO, Amusan SA, Ekundayo OJ, Sanni TM, Okpeku M, Onasanya GO, De Donato M, Ilori BM, Kizilkaya K, Imumorin IG. Morphological and microsatellite DNA diversity of Nigerian indigenous sheep. J Anim Sci Biotechnol 2012; 3:38. [PMID: 23176051 PMCID: PMC3563600 DOI: 10.1186/2049-1891-3-38] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 11/01/2012] [Indexed: 11/10/2022] Open
Abstract
Background Sheep is important in the socio-economic lives of people around the world. It is estimated that more than half of our once common livestock breeds are now endangered. Since genetic characterization of Nigerian sheep is still lacking, we analyzed ten morphological traits on 402 animals and 15 microsatellite DNA markers in 384 animals of the 4 Nigerian sheep breeds to better understand genetic diversity for breeding management and germplasm conservation. Results Morphological traits of Uda and Balami were significantly (P < 0.05) higher than Yankasa, which were both higher than West African Dwarf (WAD) sheep. Stepwise discriminant analysis showed tail length, rump height, chest girth, ear length and chest depth as the most discriminating variables for classification. Mahalanobis distances show the least differentiation between Uda and Balami and the largest between WAD and Balami sheep. While 93.3% of WAD sheep were correctly assigned to their source genetic group, 63.9% of Yankasa, 61.2% of Balami and 45.2% of Uda were classified correctly by nearest neighbour discriminant analysis. The overall high Polymorphism Information Content (PIC) of all microsatellite markers ranged from 0.751 to 0.927 supporting their use in genetic characterization. Expected heterozygosity was high for all loci (0.783 to 0.93). Mean heterozygote deficiency across all populations (0.171 to 0.534) possibly indicate significant inbreeding (P < 0.05). Mean values for FST, FIT and FIS statistics across all loci were 0.088, 0.394 and 0.336 respectively. Yankasa and Balami are the most closely related breeds (DA = 0.184) while WAD and Balami are the farthest apart breeds (DA = 0.665), which is coincident with distance based on morphological analysis and population structure assessed by STRUCTURE. Conclusions These results suggest that within-breed genetic variation in Nigerian sheep is higher than between-breeds and may be a valuable tool for genetic improvement and conservation. The higher genetic variability in Yankasa suggests the presence of unique ancestral alleles reflecting the presence of certain functional genes which may result in better adaptability in more agro-ecological zones of Nigeria. These genetic characteristics are potentially useful in planning improvement and conservation strategies in Nigerian indigenous sheep.
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Affiliation(s)
- Phil Hedrick
- School of Life Sciences, Arizona State University, Tempe, AZ 85287
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15
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Genetic diversity of Ovis aries populations near domestication centers and in the New World. Genetica 2011; 139:1169-78. [DOI: 10.1007/s10709-011-9619-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 11/12/2011] [Indexed: 11/25/2022]
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