1
|
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.
Collapse
|
2
|
Marina H, Pelayo R, Suárez-Vega A, Gutiérrez-Gil B, Esteban-Blanco C, Arranz JJ. Genome-wide association studies (GWAS) and post-GWAS analyses for technological traits in Assaf and Churra dairy breeds. J Dairy Sci 2021; 104:11850-11866. [PMID: 34454756 DOI: 10.3168/jds.2021-20510] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/05/2021] [Indexed: 12/30/2022]
Abstract
This study aimed to perform a GWAS to identify genomic regions associated with milk and cheese-making traits in Assaf and Churra dairy sheep breeds; second, it aimed to identify possible positional and functional candidate genes and their interactions through post-GWAS studies. For 2,020 dairy ewes from 2 breeds (1,039 Spanish Assaf and 981 Churra), milk samples were collected and analyzed to determine 6 milk production and composition traits and 6 traits related to milk coagulation properties and cheese yield. The genetic profiles of the ewes were obtained using a genotyping chip array that included 50,934 SNP markers. For both milk and cheese-making traits, separate single-breed GWAS were performed using GCTA software. The set of positional candidate genes identified via GWAS was subjected to guilt-by-association-based prioritization analysis with ToppGene software. Totals of 84 and 139 chromosome-wise significant associations for the 6 milk traits and the 6 cheese-making traits were identified in this study. No significant SNPs were found in common between the 2 studied breeds, possibly due to their genetic heterogeneity of the phenotypes under study. Additionally, 63 and 176 positional candidate genes were located in the genomic intervals defined as confidence regions in relation to the significant SNPs identified for the analyzed traits for Assaf and Churra breeds. After the functional prioritization analysis, 71 genes were identified as promising positional and functional candidate genes and proposed as targets of future research to identify putative causative variants in relation to the traits under examination. In addition, this multitrait study allowed us to identify variants that have a pleiotropic effect on both milk production and cheese-related traits. The incorporation of variants among the proposed functional and positional candidate genes into genomic selection strategies represent an interesting approach for achieving rapid genetic gains, specifically for those traits difficult to measure, such as cheese-making traits.
Collapse
Affiliation(s)
- H Marina
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - R Pelayo
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - A Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - B Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - C Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - J J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain.
| |
Collapse
|
3
|
Fountain ED, Zhou LC, Karklus A, Liu QX, Meyers J, Fontanilla IKC, Rafael EF, Yu JY, Zhang Q, Zhu XL, Pei EL, Yuan YH, Banes GL. Cross-Species Application of Illumina iScan Microarrays for Cost-Effective, High-Throughput SNP Discovery. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.629252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microarrays can be a cost-effective alternative to high-throughput sequencing for discovering novel single-nucleotide polymorphisms (SNPs). Illumina’s iScan platform dominates the market, but their commercial microarray products are designed for model organisms. Further, the platform outputs data in a proprietary format. This cannot be easily converted to human-readable genotypes or be merged with pre-existing data. To address this, we present and validate a novel pipeline to facilitate data analysis from cross-species application of Illumina microarrays. This facilitates the generation of a compatible VCF from iScan data and the merging of this with a second VCF comprising genotypes derived from other samples and sources. Our pipeline includes a custom script, iScanVCFMerge (presented as a Python package), which we validate using iScan data from three great ape genera. We conclude that cross-species application of microarrays can be a rapid, cost-effective approach for SNP discovery in non-model organisms. Our pipeline surmounts the common challenges of integrating iScan genotypes with pre-existing data.
Collapse
|
4
|
Sample identification and pedigree reconstruction in Wolverine (Gulo gulo) using SNP genotyping of non-invasive samples. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01208-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractFor conservation genetic studies using non-invasively collected samples, genome-wide data may be hard to acquire. Until now, such studies have instead mostly relied on analyses of traditional genetic markers such as microsatellites (SSRs). Recently, high throughput genotyping of single nucleotide polymorphisms (SNPs) has become available, expanding the use of genomic methods to include non-model species of conservation concern. We have developed a 96-marker SNP array for use in applied conservation monitoring of the Scandinavian wolverine (Gulo gulo) population. By genotyping more than a thousand non-invasively collected samples, we were able to obtain precise estimates of different types of genotyping errors and sample dropout rates. The SNP panel significantly outperforms the SSR markers (and DBY intron markers for sexing) both in terms of precision in genotyping, sex assignment and individual identification, as well as in the proportion of samples successfully genotyped. Furthermore, SNP genotyping offers a simplified laboratory and analysis pipeline with fewer samples needed to be repeatedly genotyped in order to obtain reliable consensus data. In addition, we utilised a unique opportunity to successfully demonstrate the application of SNP genotype data for reconstructing pedigrees in wild populations, by validating the method with samples from wild individuals with known relatedness. By offering a simplified workflow with improved performance, we anticipate this methodology will facilitate the use of non-invasive samples to improve genetic management of many different types of populations that have previously been challenging to survey.
Collapse
|
5
|
Mitochondrial DNA Analysis Clarifies Taxonomic Status of the Northernmost Snow Sheep ( Ovis nivicola) Population. Life (Basel) 2021; 11:life11030252. [PMID: 33803851 PMCID: PMC8003287 DOI: 10.3390/life11030252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 11/18/2022] Open
Abstract
Currently, the intraspecific taxonomy of snow sheep (Ovis nivicola) is controversial and needs to be specified using DNA molecular genetic markers. In our previous work using whole-genome single nucleotide polymorphism (SNP) analysis, we found that the population inhabiting Kharaulakh Ridge was genetically different from the other populations of Yakut subspecies to which it was usually referred. Here, our study was aimed at the clarification of taxonomic status of Kharaulakh snow sheep using mitochondrial cytochrome b gene. A total of 87 specimens from five different geographic locations of Yakut snow sheep as well as 20 specimens of other recognized subspecies were included in this study. We identified 19 haplotypes, two of which belonged to the population from Kharaulakh Ridge. Median-joining network and Bayesian tree analyses revealed that Kharaulakh population clustered separately from all the other Yakut snow sheep. The divergence time between Kharaulakh population and Yakut snow sheep was estimated as 0.48 ± 0.19 MYA. Thus, the study of the mtDNA cytb sequences confirmed the results of genome-wide SNP analysis. Taking into account the high degree of divergence of Kharaulakh snow sheep from other groups, identified by both nuclear and mitochondrial DNA markers, we propose to classify the Kharaulakh population as a separate subspecies.
Collapse
|
6
|
Getachew T, Haile A, Mészáros G, Rischkowsky B, Huson H, Gizaw S, Wurzinger M, Mwai A, Sölkner J. Genetic diversity, population structure and runs of homozygosity in Ethiopian short fat-tailed and Awassi sheep breeds using genome-wide 50k SNP markers. Livest Sci 2020. [DOI: 10.1016/j.livsci.2019.103899] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
7
|
Sim Z, Coltman DW. Heritability of Horn Size in Thinhorn Sheep. Front Genet 2019; 10:959. [PMID: 31681413 PMCID: PMC6797622 DOI: 10.3389/fgene.2019.00959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/09/2019] [Indexed: 12/31/2022] Open
Abstract
Understanding the genetic basis of fitness-related trait variation has long been of great interest to evolutionary biologists. Secondary sexual characteristics, such as horns in bovids, are particularly intriguing since they can be potentially affected by both natural and sexual selection. Until recently, however, the study of fitness-related quantitative trait variation in wild species has been hampered by a lack of genomic resources, pedigree, and/or phenotype data. Recent innovations in genomic technologies have enabled wildlife researchers to perform marker-based relatedness estimation and acquire adequate loci density, enabling both the “top-down” approach of quantitative genetics and the “bottom-up” approach of association studies to describe the genetic basis of fitness-related traits. Here we combine a cross species application of the OvineHD BeadChip and horn measurements (horn length, base circumference, and volume) from harvested thinhorn sheep to examine the heritability and to perform a genome-wide single-nucleotide polymorphism association study of horn size in the species. Thinhorn sheep are mountain ungulates that reside in the mountainous regions of northwestern North America. Thinhorn sheep males grow massive horns that determine the social rank and mating success. We found horn length, base circumference, and volume to be moderately heritable and two loci to be suggestively associated with horn length.
Collapse
Affiliation(s)
- Zijian Sim
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Fish and Wildlife Forensic Unit, Alberta Fish and Wildlife Enforcement Branch, Government of Alberta, Edmonton, AB, Canada
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
8
|
Minias P, Dunn PO, Whittingham LA, Johnson JA, Oyler-McCance SJ. Evaluation of a Chicken 600K SNP genotyping array in non-model species of grouse. Sci Rep 2019; 9:6407. [PMID: 31015535 PMCID: PMC6478925 DOI: 10.1038/s41598-019-42885-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/11/2019] [Indexed: 12/30/2022] Open
Abstract
The use of single nucleotide polymorphism (SNP) arrays to generate large SNP datasets for comparison purposes have recently become an attractive alternative to other genotyping methods. Although most SNP arrays were originally developed for domestic organisms, they can be effectively applied to wild relatives to obtain large panels of SNPs. In this study, we tested the cross-species application of the Affymetrix 600K Chicken SNP array in five species of North American prairie grouse (Centrocercus and Tympanuchus genera). Two individuals were genotyped per species for a total of ten samples. A high proportion (91%) of the total 580 961 SNPs were genotyped in at least one individual (73–76% SNPs genotyped per species). Principal component analysis with autosomal SNPs separated the two genera, but failed to clearly distinguish species within genera. Gene ontology analysis identified a set of genes related to morphogenesis and development (including genes involved in feather development), which may be primarily responsible for large phenotypic differences between Centrocercus and Tympanuchus grouse. Our study provided evidence for successful cross-species application of the chicken SNP array in grouse which diverged ca. 37 mya from the chicken lineage. As far as we are aware, this is the first reported application of a SNP array in non-passerine birds, and it demonstrates the feasibility of using commercial SNP arrays in research on non-model bird species.
Collapse
Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
| | - Peter O Dunn
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.,Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Linda A Whittingham
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Jeff A Johnson
- Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, Texas, USA
| | | |
Collapse
|
9
|
Jahner JP, Matocq MD, Malaney JL, Cox M, Wolff P, Gritts MA, Parchman TL. The genetic legacy of 50 years of desert bighorn sheep translocations. Evol Appl 2019; 12:198-213. [PMID: 30697334 PMCID: PMC6346675 DOI: 10.1111/eva.12708] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/16/2018] [Accepted: 08/18/2018] [Indexed: 12/20/2022] Open
Abstract
Conservation biologists have increasingly used translocations to mitigate population declines and restore locally extirpated populations. Genetic data can guide the selection of source populations for translocations and help evaluate restoration success. Bighorn sheep (Ovis canadensis) are a managed big game species that suffered widespread population extirpations across western North America throughout the early 1900s. Subsequent translocation programs have successfully re-established many formally extirpated bighorn herds, but most of these programs pre-date genetically informed management practices. The state of Nevada presents a particularly well-documented case of decline followed by restoration of extirpated herds. Desert bighorn sheep (O. c. nelsoni) populations declined to less than 3,000 individuals restricted to remnant herds in the Mojave Desert and a few locations in the Great Basin Desert. Beginning in 1968, the Nevada Department of Wildlife translocated ~2,000 individuals from remnant populations to restore previously extirpated areas, possibly establishing herds with mixed ancestries. Here, we examined genetic diversity and structure among remnant herds and the genetic consequences of translocation from these herds using a genotyping-by-sequencing approach to genotype 17,095 loci in 303 desert bighorn sheep. We found a signal of population genetic structure among remnant Mojave Desert populations, even across geographically proximate mountain ranges. Further, we found evidence of a genetically distinct, potential relict herd from a previously hypothesized Great Basin lineage of desert bighorn sheep. The genetic structure of source herds was clearly reflected in translocated populations. In most cases, herds retained genetic evidence of multiple translocation events and subsequent admixture when founded from multiple remnant source herds. Our results add to a growing literature on how population genomic data can be used to guide and monitor restoration programs.
Collapse
Affiliation(s)
| | - Marjorie D. Matocq
- Department of Natural Resources and Environmental Science, and Program in Ecology, Evolution, and Conservation BiologyUniversity of NevadaRenoNevada
| | - Jason L. Malaney
- Department of BiologyAustin Peay State UniversityClarksvilleTennessee
| | - Mike Cox
- Nevada Department of Wildlife, and Wild Sheep Working GroupWestern Association of Fish and Wildlife AgenciesRenoNevada
| | | | | | - Thomas L. Parchman
- Department of Biology, and Program in Ecology, Evolution, and Conservation BiologyUniversity of NevadaRenoNevada
| |
Collapse
|
10
|
Genetic diversity and population structure of domestic and wild reindeer (Rangifer tarandus L. 1758): A novel approach using BovineHD BeadChip. PLoS One 2018; 13:e0207944. [PMID: 30500861 PMCID: PMC6267972 DOI: 10.1371/journal.pone.0207944] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/08/2018] [Indexed: 01/04/2023] Open
Abstract
Reindeer (Rangifer tarandus L. 1758) are an essential element of the Russian Far North, providing a significant source of nutrition for the representatives of 18 ethnicities. The species has wild and domestic forms, which are in constant interaction. The aim of our study was to characterize the genetic structure of domestic and wild reindeer populations, using a genome-wide bovine genotyping array (BovineHD BeadChip). The wild reindeer samples were obtained from the western Taymyr Peninsula population and from the taiga and tundra populations in the Sakha Republic (Yakutia). The domestic populations included the Evenk, Even, and Chukotka-Khargin breeds of Yakutia and the Nenets breed from the Nenets Autonomous district and Murmansk region. The level of genetic diversity was higher for the wild population. Analyzing Neighbor-Net tree, multidimensional scaling, and Structure results, we observed strong genetic population structure and clear differentiation between domestic and wild populations. All regional populations of domestic reindeer were clearly separated, while wild reindeer showed similar genetic backgrounds. Nevertheless, we found contrasting patterns in the genetic structure of the tundra and taiga reindeer, in accordance with their morphological and ecological differences. Thus, our study revealed a clear genetic differentiation between domestic and wild reindeer populations. It provides novel insights into the genetic diversity and structure of reindeer populations, to support resource utilization and aid in the development of genetic improvement strategies and conservation programs for this species.
Collapse
|
11
|
Global genomic diversity and conservation priorities for domestic animals are associated with the economies of their regions of origin. Sci Rep 2018; 8:11677. [PMID: 30076315 PMCID: PMC6076285 DOI: 10.1038/s41598-018-30061-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 07/18/2018] [Indexed: 12/03/2022] Open
Abstract
Domestic animals play a key role in human survival and the development of civilization. However, the genetic resources of domestic animals are facing an alarming rate of erosion due to socioeconomic changes, economic globalization and financial constraints. In this study, through genome-wide SNP analysis, we estimated the heterozygosity, inbreeding coefficient, effective population size, and runs of homozygosity to identify the breeds facing the risk of extinction for sheep and cattle across the world. In particular, we quantified the contribution of 97 sheep breeds and 53 cattle breeds to genomic diversity (within-breed, between-breed and total) and prioritized the breeds for conservation. Additionally, we compared the average values of genomic diversity between breeds from regions (or countries) in different economic categories (underdeveloped, developing and developed), and found that breeds in developed regions exhibit significantly higher levels of total genomic diversity than those in underdeveloped and developing regions. Altogether, our results suggested that conservation priority should be given to breeds in developed regions to secure the future genomic diversity hotspots of domestic animal resources.
Collapse
|
12
|
Dotsev AV, Deniskova TE, Okhlopkov IM, Mészáros G, Sölkner J, Reyer H, Wimmers K, Brem G, Zinovieva NA. Genome-wide SNP analysis unveils genetic structure and phylogeographic history of snow sheep ( Ovis nivicola) populations inhabiting the Verkhoyansk Mountains and Momsky Ridge (northeastern Siberia). Ecol Evol 2018; 8:8000-8010. [PMID: 30250679 PMCID: PMC6144981 DOI: 10.1002/ece3.4350] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/23/2018] [Accepted: 05/30/2018] [Indexed: 01/01/2023] Open
Abstract
Insights into the genetic characteristics of a species provide important information for wildlife conservation programs. Here, we used the OvineSNP50 BeadChip developed for domestic sheep to examine population structure and evaluate genetic diversity of snow sheep (Ovis nivicola) inhabiting Verkhoyansk Range and Momsky Ridge. A total of 1,121 polymorphic SNPs were used to test 80 specimens representing five populations, including four populations of the Verkhoyansk Mountain chain: Kharaulakh Ridge-Tiksi Bay (TIK, n = 22), Orulgan Ridge (ORU, n = 22), the central part of Verkhoyansk Range (VER, n = 15), Suntar-Khayata Ridge (SKH, n = 13), and Momsky Ridge (MOM, n = 8). We showed that the studied populations were genetically structured according to a geographic pattern. Pairwise FST values ranged from 0.044 to 0.205. Admixture analysis identified K = 2 as the most likely number of ancestral populations. A Neighbor-Net tree showed that TIK was an isolated group related to the main network through ORU. TreeMix analysis revealed that TIK and MOM originated from two different ancestral populations and detected gene flow from MOM to ORU. This was supported by the f3 statistic, which showed that ORU is an admixed population with TIK and MOM/SKH heritage. Genetic diversity in the studied groups was increasing southward. Minimum values of observed (Ho) and expected (He) heterozygosity and allelic richness (Ar) were observed in the most northern population-TIK, and maximum values were observed in the most southern population-SKH. Thus, our results revealed clear genetic structure in the studied populations of snow sheep and showed that TIK has a different origin from MOM, SKH, and VER even though they are conventionally considered a single subspecies known as Yakut snow sheep (Ovis nivicola lydekkeri). Most likely, TIK was an isolated group during the Late Pleistocene glaciations of Verkhoyansk Range.
Collapse
Affiliation(s)
- Arsen V. Dotsev
- L.K. Ernst Federal Science Center for Animal HusbandryMoscow RegionPodolskRussian Federation
| | - Tatiana E. Deniskova
- L.K. Ernst Federal Science Center for Animal HusbandryMoscow RegionPodolskRussian Federation
| | | | - Gabor Mészáros
- Division of Livestock SciencesUniversity of Natural Resources and Life SciencesViennaAustria
| | - Johann Sölkner
- Division of Livestock SciencesUniversity of Natural Resources and Life SciencesViennaAustria
| | - Henry Reyer
- Institute of Genome BiologyLeibniz Institute for Farm Animal Biology (FBN)DummerstorfGermany
| | - Klaus Wimmers
- Institute of Genome BiologyLeibniz Institute for Farm Animal Biology (FBN)DummerstorfGermany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal HusbandryMoscow RegionPodolskRussian Federation
- Institute of Animal Breeding and GeneticsUniversity of Veterinary Medicine (VMU)ViennaAustria
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Science Center for Animal HusbandryMoscow RegionPodolskRussian Federation
| |
Collapse
|
13
|
RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding. G3-GENES GENOMES GENETICS 2018; 8:2709-2722. [PMID: 29954843 PMCID: PMC6071602 DOI: 10.1534/g3.118.200171] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level by around 400 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organization.
Collapse
|
14
|
Alvarenga AB, Rovadoscki GA, Petrini J, Coutinho LL, Morota G, Spangler ML, Pinto LFB, Carvalho GGP, Mourão GB. Linkage disequilibrium in Brazilian Santa Inês breed, Ovis aries. Sci Rep 2018; 8:8851. [PMID: 29892085 PMCID: PMC5995818 DOI: 10.1038/s41598-018-27259-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 05/25/2018] [Indexed: 11/13/2022] Open
Abstract
For genomic selection to be successful, there must be sufficient linkage disequilibrium between the markers and the causal mutations. The objectives of this study were to evaluate the extent of LD in ovine using the Santa Inês breed and to infer the minimum number of markers required to reach reasonable prediction accuracy. In total, 38,168 SNPs and 395 samples were used. The mean LD between adjacent marker pairs measured by r2 and |D′| were 0.166 and 0.617, respectively. LD values between adjacent marker pairs ranged from 0.135 to 0.194 and from 0.568 to 0.650 for r2 for |D′| across all chromosomes. The average r2 between all pairwise SNPs on each chromosome was 0.018. SNPs separated by between 0.10 to 0.20 Mb had an estimated average r2 equal to 0.1033. The identified haplotype blocks consisted of 2 to 21 markers. Moreover, estimates of average coefficients of inbreeding and effective population size were 0.04 and 96, respectively. LD estimated in this study was lower than that reported in other species and was characterized by short haplotype blocks. Our results suggest that the use of a higher density SNP panel is recommended for the implementation of genomic selection in the Santa Inês breed.
Collapse
Affiliation(s)
- Amanda Botelho Alvarenga
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil
| | - Gregori Alberto Rovadoscki
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil
| | - Juliana Petrini
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil
| | - Gota Morota
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | | | | | | | - Gerson Barreto Mourão
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil.
| |
Collapse
|
15
|
Flesch EP, Rotella JJ, Thomson JM, Graves TA, Garrott RA. Evaluating sample size to estimate genetic management metrics in the genomics era. Mol Ecol Resour 2018; 18:1077-1091. [PMID: 29856123 DOI: 10.1111/1755-0998.12898] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 11/29/2022]
Abstract
Inbreeding and relationship metrics among and within populations are useful measures for genetic management of wild populations, but accuracy and precision of estimates can be influenced by the number of individual genotypes analysed. Biologists are confronted with varied advice regarding the sample size necessary for reliable estimates when using genomic tools. We developed a simulation framework to identify the optimal sample size for three widely used metrics to enable quantification of expected variance and relative bias of estimates and a comparison of results among populations. We applied this approach to analyse empirical genomic data for 30 individuals from each of four different free-ranging Rocky Mountain bighorn sheep (Ovis canadensis canadensis) populations in Montana and Wyoming, USA, through cross-species application of an Ovine array and analysis of approximately 14,000 single nucleotide polymorphisms (SNPs) after filtering. We examined intra- and interpopulation relationships using kinship and identity by state metrics, as well as FST between populations. By evaluating our simulation results, we concluded that a sample size of 25 was adequate for assessing these metrics using the Ovine array to genotype Rocky Mountain bighorn sheep herds. However, we conclude that a universal sample size rule may not be able to sufficiently address the complexities that impact genomic kinship and inbreeding estimates. Thus, we recommend that a pilot study and sample size simulation using R code we developed that includes empirical genotypes from a subset of populations of interest would be an effective approach to ensure rigour in estimating genomic kinship and population differentiation.
Collapse
Affiliation(s)
| | - Jay J Rotella
- Ecology Department, Montana State University, Bozeman, Montana
| | - Jennifer M Thomson
- Animal and Range Sciences Department, Montana State University, Bozeman, Montana
| | - Tabitha A Graves
- U.S. Geological Survey Glacier Field Station, Northern Rocky Mountain Science Center, West Glacier, Montana
| | | |
Collapse
|
16
|
Miller JM, Festa-Bianchet M, Coltman DW. Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium ® HD SNP BeadChip. PeerJ 2018; 6:e4364. [PMID: 29473002 PMCID: PMC5817937 DOI: 10.7717/peerj.4364] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/23/2018] [Indexed: 11/20/2022] Open
Abstract
Elucidating the genetic basis of fitness-related traits is a major goal of molecular ecology. Traits subject to sexual selection are particularly interesting, as non-random mate choice should deplete genetic variation and thereby their evolutionary benefits. We examined the genetic basis of three sexually selected morphometric traits in bighorn sheep (Ovis canadensis): horn length, horn base circumference, and body mass. These traits are of specific concern in bighorn sheep as artificial selection through trophy hunting opposes sexual selection. Specifically, horn size determines trophy status and, in most North American jurisdictions, if an individual can be legally harvested. Using between 7,994–9,552 phenotypic measures from the long-term individual-based study at Ram Mountain (Alberta, Canada), we first showed that all three traits are heritable (h2 = 0.15–0.23). We then conducted a genome-wide association study (GWAS) utilizing a set of 3,777 SNPs typed in 76 individuals using the Ovine Infinium® HD SNP BeadChip. We found suggestive association for body mass at a single locus (OAR9_91647990). The absence of strong associations with SNPs suggests that the traits are likely polygenic. These results represent a step forward for characterizing the genetic architecture of fitness related traits in sexually dimorphic ungulates.
Collapse
Affiliation(s)
- Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,Current affiliation: Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | | | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
17
|
Genomic diversity and population structure of three autochthonous Greek sheep breeds assessed with genome-wide DNA arrays. Mol Genet Genomics 2018; 293:753-768. [PMID: 29372305 DOI: 10.1007/s00438-018-1421-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/17/2018] [Indexed: 12/13/2022]
Abstract
In the present study, genome-wide genotyping was applied to characterize the genetic diversity and population structure of three autochthonous Greek breeds: Boutsko, Karagouniko and Chios. Dairy sheep are among the most significant livestock species in Greece numbering approximately 9 million animals which are characterized by large phenotypic variation and reared under various farming systems. A total of 96 animals were genotyped with the Illumina's OvineSNP50K microarray beadchip, to study the population structure of the breeds and develop a specialized panel of single-nucleotide polymorphisms (SNPs), which could distinguish one breed from the others. Quality control on the dataset resulted in 46,125 SNPs, which were used to evaluate the genetic structure of the breeds. Population structure was assessed through principal component analysis (PCA) and admixture analysis, whereas inbreeding was estimated based on runs of homozygosity (ROHs) coefficients, genomic relationship matrix inbreeding coefficients (FGRM) and patterns of linkage disequilibrium (LD). Associations between SNPs and breeds were analyzed with different inheritance models, to identify SNPs that distinguish among the breeds. Results showed high levels of genetic heterogeneity in the three breeds. Genetic distances among breeds were modest, despite their different ancestries. Chios and Karagouniko breeds were more genetically related to each other compared to Boutsko. Analysis revealed 3802 candidate SNPs that can be used to identify two-breed crosses and purebred animals. The present study provides, for the first time, data on the genetic background of three Greek indigenous dairy sheep breeds as well as a specialized marker panel that can be applied for traceability purposes as well as targeted genetic improvement schemes and conservation programs.
Collapse
|
18
|
Zhao YX, Yang J, Lv FH, Hu XJ, Xie XL, Zhang M, Li WR, Liu MJ, Wang YT, Li JQ, Liu YG, Ren YL, Wang F, Hehua EE, Kantanen J, Arjen Lenstra J, Han JL, Li MH. Genomic Reconstruction of the History of Native Sheep Reveals the Peopling Patterns of Nomads and the Expansion of Early Pastoralism in East Asia. Mol Biol Evol 2017. [PMID: 28645168 PMCID: PMC5850515 DOI: 10.1093/molbev/msx181] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
China has a rich resource of native sheep (Ovis aries) breeds associated with historical movements of several nomadic societies. However, the history of sheep and the associated nomadic societies in ancient China remains poorly understood. Here, we studied the genomic diversity of Chinese sheep using genome-wide SNPs, mitochondrial and Y-chromosomal variations in > 1,000 modern samples. Population genomic analyses combined with archeological records and historical ethnic demographics data revealed genetic signatures of the origins, secondary expansions and admixtures, of Chinese sheep thereby revealing the peopling patterns of nomads and the expansion of early pastoralism in East Asia. Originating from the Mongolian Plateau ∼5,000‒5,700 years ago, Chinese sheep were inferred to spread in the upper and middle reaches of the Yellow River ∼3,000‒5,000 years ago following the expansions of the Di-Qiang people. Afterwards, sheep were then inferred to reach the Qinghai-Tibetan and Yunnan-Kweichow plateaus ∼2,000‒2,600 years ago by following the north-to-southwest routes of the Di-Qiang migration. We also unveiled two subsequent waves of migrations of fat-tailed sheep into northern China, which were largely commensurate with the migrations of ancestors of Hui Muslims eastward and Mongols southward during the 12th‒13th centuries. Furthermore, we revealed signs of argali introgression into domestic sheep, extensive historical mixtures among domestic populations and strong artificial selection for tail type and other traits, reflecting various breeding strategies by nomadic societies in ancient China.
Collapse
Affiliation(s)
- Yong-Xin Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Xiao-Ju Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Min Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wen-Rong Li
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ming-Jun Liu
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Yu-Tao Wang
- College of Life and Geographic Sciences, Kashgar University, Kashgar, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - EEr Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| |
Collapse
|
19
|
Medvedev DG, Dotsev AV, Okhlopkov IM, Deniskova TE, Reyer H, Wimmers K, Brem G, Bagirov VA, Zinovieva NA. Genetic characteristics of Kodar snow sheep using SNP markers. CONTEMP PROBL ECOL+ 2017. [DOI: 10.1134/s1995425517060099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
20
|
Getachew T, Huson HJ, Wurzinger M, Burgstaller J, Gizaw S, Haile A, Rischkowsky B, Brem G, Boison SA, Mészáros G, Mwai AO, Sölkner J. Identifying highly informative genetic markers for quantification of ancestry proportions in crossbred sheep populations: implications for choosing optimum levels of admixture. BMC Genet 2017; 18:80. [PMID: 28836937 PMCID: PMC5571632 DOI: 10.1186/s12863-017-0526-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 06/19/2017] [Indexed: 01/08/2023] Open
Affiliation(s)
- Tesfaye Getachew
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Gregor Mendel Straße 33, A-1180, Vienna, Austria.,Animal Biodiversity Directorate, Ethiopian Biodiversity Institute, Addis Ababa, Ethiopia
| | - Heather J Huson
- Department of Animal Science, Cornell University, Ithaca, NY, USA
| | - Maria Wurzinger
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Gregor Mendel Straße 33, A-1180, Vienna, Austria
| | - Jörg Burgstaller
- Institute of Biotechnology in Animal Production, Department for Agro biotechnology, IFA, Konrad Lorenzstr. 20, 3430, Tulln, Austria
| | - Solomon Gizaw
- International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Aynalem Haile
- International Center for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Barbara Rischkowsky
- International Center for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Solomon Antwi Boison
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Gregor Mendel Straße 33, A-1180, Vienna, Austria.,Department of Breeding and Genetics, Nofima, Osloveien 1, 1430, Ås, Norway
| | - Gábor Mészáros
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Gregor Mendel Straße 33, A-1180, Vienna, Austria
| | - Ally Okeyo Mwai
- International Livestock Research Institute, Biotechnology Theme, Nairobi, Kenya
| | - Johann Sölkner
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Gregor Mendel Straße 33, A-1180, Vienna, Austria.
| |
Collapse
|
21
|
Barbato M, Hailer F, Orozco-terWengel P, Kijas J, Mereu P, Cabras P, Mazza R, Pirastru M, Bruford MW. Genomic signatures of adaptive introgression from European mouflon into domestic sheep. Sci Rep 2017; 7:7623. [PMID: 28790322 PMCID: PMC5548776 DOI: 10.1038/s41598-017-07382-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 06/22/2017] [Indexed: 11/09/2022] Open
Abstract
Mouflon (Ovis aries musimon) became extinct from mainland Europe after the Neolithic, but remnant populations from the Mediterranean islands of Corsica and Sardinia have been used for reintroductions across Europe since the 19th-century. Mouflon x sheep hybrids are larger-bodied than mouflon, potentially showing increased male reproductive success, but little is known about genomic levels of admixture, or about the adaptive significance of introgression between resident mouflon and local sheep breeds. Here we analysed Ovine medium-density SNP array genotypes of 92 mouflon from six geographic regions, along with data from 330 individuals of 16 domestic sheep breeds. We found lower levels of genetic diversity in mouflon than in domestic sheep, consistent with past bottlenecks in mouflon. Introgression signals were bidirectional and affected most mouflon and sheep populations, being strongest in one Sardinian mouflon population. Developing and using a novel approach to identify chromosomal regions with consistent introgression signals, we infer adaptive introgression from mouflon to domestic sheep related to immunity mechanisms, but not in the opposite direction. Further, we infer that Soay and Sarda sheep carry introgressed mouflon alleles involved in bitter taste perception and/or innate immunity. Our results illustrate the potential for adaptive introgression even among recently diverged populations.
Collapse
Affiliation(s)
- Mario Barbato
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, Piacenza, Italy. .,School of Biosciences, Cardiff University, CF10 3AX, Cardiff, Wales, UK.
| | - Frank Hailer
- School of Biosciences, Cardiff University, CF10 3AX, Cardiff, Wales, UK
| | | | - James Kijas
- CSIRO Agriculture, St Lucia, Brisbane, 4067, QLD, Australia
| | - Paolo Mereu
- Department of Biomedical Sciences, and Centre for Biotechnology Development and Biodiversity Research, University of Sassari, V.le San Pietro 43, Sassari, Italy
| | - Pierangela Cabras
- Istituto Zooprofilattico Sperimentale della Sardegna, Tortolí, Ogliastra, Italy
| | - Raffaele Mazza
- Laboratorio Genetica e Servizi - Associazione Italiana Allevatori, Cremona, Italy
| | - Monica Pirastru
- Department of Biomedical Sciences, and Centre for Biotechnology Development and Biodiversity Research, University of Sassari, V.le San Pietro 43, Sassari, Italy
| | - Michael W Bruford
- School of Biosciences, Cardiff University, CF10 3AX, Cardiff, Wales, UK
| |
Collapse
|
22
|
Estimates of linkage disequilibrium and effective population sizes in Chinese Merino (Xinjiang type) sheep by genome-wide SNPs. Genes Genomics 2017; 39:733-745. [PMID: 28706593 PMCID: PMC5486679 DOI: 10.1007/s13258-017-0539-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 03/19/2017] [Indexed: 12/14/2022]
Abstract
Knowledge of linkage disequilibrium (LD) is important for effective genome-wide association studies and accurate genomic prediction. Chinese Merino (Xinjiang type) is well-known fine wool sheep breed. However, the extent of LD across the genome remains unexplored. In this study, we calculated autosomal LD based on genome-wide SNPs of 635 Chinese Merino (Xinjiang type) sheep by Illumina Ovine SNP50 BeadChip. A moderate level of LD (r2 ≥ 0.25) across the whole genome was observed at short distances of 0–10 kb. Further, the ancestral effective population size (Ne) was analyzed by extent of LD and found that Ne increased with the increase of generations and declined rapidly within the most recent 50 generations, which is consistent with the history of Chinese Merino sheep breeding, initiated in 1971. We also noted that even when the effective population size was estimated across different single chromosomes, Ne only ranged from 140.36 to 183.33 at five generations in the past, exhibiting a rapid decrease compared with that at ten generations in the past. These results indicated that the genetic diversity in Chinese Merino sheep recently decreased and proper protective measures should be taken to maintain the diversity. Our datasets provided essential genetic information to track molecular variations which potentially contribute to phenotypic variation in Chinese Merino sheep.
Collapse
|
23
|
McKinney GJ, Larson WA, Seeb LW, Seeb JE. RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al
. (2016). Mol Ecol Resour 2017; 17:356-361. [DOI: 10.1111/1755-0998.12649] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/20/2016] [Accepted: 12/20/2016] [Indexed: 01/26/2023]
Affiliation(s)
- Garrett J. McKinney
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
| | - Wesley A. Larson
- U.S. Geological Survey; Wisconsin Cooperative Fishery Research Unit; College of Natural Resources; University of Wisconsin-Stevens Point; 800 Reserve St. Stevens Point WI 54481 USA
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
| | - James E. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
| |
Collapse
|
24
|
Lowry DB, Hoban S, Kelley JL, Lotterhos KE, Reed LK, Antolin MF, Storfer A. Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation. Mol Ecol Resour 2016; 17:142-152. [PMID: 27860289 DOI: 10.1111/1755-0998.12635] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/23/2016] [Accepted: 09/02/2016] [Indexed: 12/26/2022]
Abstract
Understanding how and why populations evolve is of fundamental importance to molecular ecology. Restriction site-associated DNA sequencing (RADseq), a popular reduced representation method, has ushered in a new era of genome-scale research for assessing population structure, hybridization, demographic history, phylogeography and migration. RADseq has also been widely used to conduct genome scans to detect loci involved in adaptive divergence among natural populations. Here, we examine the capacity of those RADseq-based genome scan studies to detect loci involved in local adaptation. To understand what proportion of the genome is missed by RADseq studies, we developed a simple model using different numbers of RAD-tags, genome sizes and extents of linkage disequilibrium (length of haplotype blocks). Under the best-case modelling scenario, we found that RADseq using six- or eight-base pair cutting restriction enzymes would fail to sample many regions of the genome, especially for species with short linkage disequilibrium. We then surveyed recent studies that have used RADseq for genome scans and found that the median density of markers across these studies was 4.08 RAD-tag markers per megabase (one marker per 245 kb). The length of linkage disequilibrium for many species is one to three orders of magnitude less than density of the typical recent RADseq study. Thus, we conclude that genome scans based on RADseq data alone, while useful for studies of neutral genetic variation and genetic population structure, will likely miss many loci under selection in studies of local adaptation.
Collapse
Affiliation(s)
- David B Lowry
- Plant Biology Laboratories, Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Sean Hoban
- The Morton Arboretum, Lisle, IL, USA.,National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, TN, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, 430 Nahant Rd., Nahant, MA, 01908, USA
| | - Laura K Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35406, USA
| | - Michael F Antolin
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| |
Collapse
|
25
|
Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing. Mamm Biol 2016. [DOI: 10.1016/j.mambio.2016.07.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
26
|
Deniskova TE, Okhlopkov IM, Sermyagin AA, Gladyr' EA, Bagirov VA, Sölkner J, Mamaev NV, Brem G, Zinov'eva NA. Whole genome SNP scanning of snow sheep (Ovis nivicola). DOKL BIOCHEM BIOPHYS 2016; 469:288-93. [PMID: 27599514 DOI: 10.1134/s1607672916040141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Indexed: 11/23/2022]
Abstract
This is the first report performing the whole genome SNP scanning of snow sheep (Ovis nivicola). Samples of snow sheep (n = 18) collected in six different regions of the Republic of Sakha (Yakutia) from 64° to 71° N. For SNP genotyping, we applied Ovine 50K SNP BeadChip (Illumina, United States), designed for domestic sheep. The total number of genotyped SNPs (call rate 90%) was 47796 (88.1% of total SNPs), wherein 1006 SNPs were polymorphic (2.1%). Principal component analysis (PCA) showed the clear differentiation within the species O. nivicola: studied individuals were distributed among five distinct arrays corresponding to the geographical locations of sampling points. Our results demonstrate that the DNA chip designed for domestic sheep can be successfully used to study the allele pool and the genetic structure of snow sheep populations.
Collapse
Affiliation(s)
- T E Deniskova
- Biotechnology and Molecular Diagnostics Center, Ernst All-Russia Institute of Animal Husbandry, pos. Dubrovitsy, Podol'sk district, Moscow oblast, 142132, Russia.
| | - I M Okhlopkov
- Biotechnology and Molecular Diagnostics Center, Ernst All-Russia Institute of Animal Husbandry, pos. Dubrovitsy, Podol'sk district, Moscow oblast, 142132, Russia.,Institute of Biological Problems of Cryolithozone, Siberian Branch, Russian Academy of Sciences, ul. Lenina 41, Yakutsk, 677980, Russia
| | - A A Sermyagin
- Biotechnology and Molecular Diagnostics Center, Ernst All-Russia Institute of Animal Husbandry, pos. Dubrovitsy, Podol'sk district, Moscow oblast, 142132, Russia
| | - E A Gladyr'
- Biotechnology and Molecular Diagnostics Center, Ernst All-Russia Institute of Animal Husbandry, pos. Dubrovitsy, Podol'sk district, Moscow oblast, 142132, Russia
| | - V A Bagirov
- Biotechnology and Molecular Diagnostics Center, Ernst All-Russia Institute of Animal Husbandry, pos. Dubrovitsy, Podol'sk district, Moscow oblast, 142132, Russia
| | - J Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Augasse 2-6, Vienna, A-1090, Austria
| | - N V Mamaev
- Institute of Biological Problems of Cryolithozone, Siberian Branch, Russian Academy of Sciences, ul. Lenina 41, Yakutsk, 677980, Russia
| | - G Brem
- Biotechnology and Molecular Diagnostics Center, Ernst All-Russia Institute of Animal Husbandry, pos. Dubrovitsy, Podol'sk district, Moscow oblast, 142132, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Veterinärplatz, Vienna, A-1210, Austria
| | - N A Zinov'eva
- Biotechnology and Molecular Diagnostics Center, Ernst All-Russia Institute of Animal Husbandry, pos. Dubrovitsy, Podol'sk district, Moscow oblast, 142132, Russia
| |
Collapse
|
27
|
Städele V, Vigilant L. Strategies for determining kinship in wild populations using genetic data. Ecol Evol 2016; 6:6107-20. [PMID: 27648229 PMCID: PMC5016635 DOI: 10.1002/ece3.2346] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 01/17/2023] Open
Abstract
Knowledge of kin relationships between members of wild animal populations has broad application in ecology and evolution research by allowing the investigation of dispersal dynamics, mating systems, inbreeding avoidance, kin recognition, and kin selection as well as aiding the management of endangered populations. However, the assessment of kinship among members of wild animal populations is difficult in the absence of detailed multigenerational pedigrees. Here, we first review the distinction between genetic relatedness and kinship derived from pedigrees and how this makes the identification of kin using genetic data inherently challenging. We then describe useful approaches to kinship classification, such as parentage analysis and sibship reconstruction, and explain how the combined use of marker systems with biparental and uniparental inheritance, demographic information, likelihood analyses, relatedness coefficients, and estimation of misclassification rates can yield reliable classifications of kinship in groups with complex kin structures. We outline alternative approaches for cases in which explicit knowledge of dyadic kinship is not necessary, but indirect inferences about kinship on a group- or population-wide scale suffice, such as whether more highly related dyads are in closer spatial proximity. Although analysis of highly variable microsatellite loci is still the dominant approach for studies on wild populations, we describe how the long-awaited use of large-scale single-nucleotide polymorphism and sequencing data derived from noninvasive low-quality samples may eventually lead to highly accurate assessments of varying degrees of kinship in wild populations.
Collapse
Affiliation(s)
- Veronika Städele
- Department of PrimatologyMax Planck Institute for Evolutionary AnthropologyDeutscher Platz 6D‐04103LeipzigGermany
| | - Linda Vigilant
- Department of PrimatologyMax Planck Institute for Evolutionary AnthropologyDeutscher Platz 6D‐04103LeipzigGermany
| |
Collapse
|
28
|
Roffler GH, Amish SJ, Smith S, Cosart T, Kardos M, Schwartz MK, Luikart G. SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate. Mol Ecol Resour 2016; 16:1147-64. [PMID: 27327375 DOI: 10.1111/1755-0998.12560] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 06/04/2016] [Accepted: 06/07/2016] [Indexed: 11/30/2022]
Abstract
Identification of genes underlying genomic signatures of natural selection is key to understanding adaptation to local conditions. We used targeted resequencing to identify SNP markers in 5321 candidate adaptive genes associated with known immunological, metabolic and growth functions in ovids and other ungulates. We selectively targeted 8161 exons in protein-coding and nearby 5' and 3' untranslated regions of chosen candidate genes. Targeted sequences were taken from bighorn sheep (Ovis canadensis) exon capture data and directly from the domestic sheep genome (Ovis aries v. 3; oviAri3). The bighorn sheep sequences used in the Dall's sheep (Ovis dalli dalli) exon capture aligned to 2350 genes on the oviAri3 genome with an average of 2 exons each. We developed a microfluidic qPCR-based SNP chip to genotype 476 Dall's sheep from locations across their range and test for patterns of selection. Using multiple corroborating approaches (lositan and bayescan), we detected 28 SNP loci potentially under selection. We additionally identified candidate loci significantly associated with latitude, longitude, precipitation and temperature, suggesting local environmental adaptation. The three methods demonstrated consistent support for natural selection on nine genes with immune and disease-regulating functions (e.g. Ovar-DRA, APC, BATF2, MAGEB18), cell regulation signalling pathways (e.g. KRIT1, PI3K, ORRC3), and respiratory health (CYSLTR1). Characterizing adaptive allele distributions from novel genetic techniques will facilitate investigation of the influence of environmental variation on local adaptation of a northern alpine ungulate throughout its range. This research demonstrated the utility of exon capture for gene-targeted SNP discovery and subsequent SNP chip genotyping using low-quality samples in a nonmodel species.
Collapse
Affiliation(s)
- Gretchen H Roffler
- Alaska Science Center, U.S. Geological Survey, 4210 University Drive, Anchorage, AK, 99508, USA.,Wildlife Biology Program, Department of Ecosystem Sciences and Conservation, College of Forestry and Conservation, University of Montana, Missoula, MT, 59812, USA
| | - Stephen J Amish
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Seth Smith
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Ted Cosart
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Marty Kardos
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA.,Evolutionary Biology Centre, Uppsala University, SE-75236, Uppsala, Sweden
| | - Michael K Schwartz
- Evolutionary Biology Centre, Uppsala University, SE-75236, Uppsala, Sweden.,US Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, 800 E. Beckwith Ave., Missoula, MT, 59801, USA
| | - Gordon Luikart
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA.,Flathead Lake Biological Station, University of Montana, Polson, MT, 59860, USA
| |
Collapse
|
29
|
Sim Z, Hall JC, Jex B, Hegel TM, Coltman DW. Genome-wide set of SNPs reveals evidence for two glacial refugia and admixture from postglacial recolonization in an alpine ungulate. Mol Ecol 2016; 25:3696-705. [DOI: 10.1111/mec.13701] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 04/16/2016] [Accepted: 05/02/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Zijian Sim
- Department of Biological Sciences; University of Alberta; Edmonton Alberta Canada
| | - Jocelyn C. Hall
- Department of Biological Sciences; University of Alberta; Edmonton Alberta Canada
| | - Bill Jex
- Ministry of Forests, Lands and Natural Resource Operations; Bag 5000 - 3726 Alfred Ave Smithers British Columbia Canada
| | - Troy M. Hegel
- Yukon Department of Environment; PO Box 2703 Whitehorse Yukon Canada Y1A2C6
| | - David W. Coltman
- Department of Biological Sciences; University of Alberta; Edmonton Alberta Canada
| |
Collapse
|
30
|
Elevated Linkage Disequilibrium and Signatures of Soft Sweeps Are Common in Drosophila melanogaster. Genetics 2016; 203:863-80. [PMID: 27098909 DOI: 10.1534/genetics.115.184002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 03/25/2016] [Indexed: 12/20/2022] Open
Abstract
The extent to which selection and demography impact patterns of genetic diversity in natural populations of Drosophila melanogaster is yet to be fully understood. We previously observed that linkage disequilibrium (LD) at scales of ∼10 kb in the Drosophila Genetic Reference Panel (DGRP), consisting of 145 inbred strains from Raleigh, North Carolina, measured both between pairs of sites and as haplotype homozygosity, is elevated above neutral demographic expectations. We also demonstrated that signatures of strong and recent soft sweeps are abundant. However, the extent to which these patterns are specific to this derived and admixed population is unknown. It is also unclear whether these patterns are a consequence of the extensive inbreeding performed to generate the DGRP data. Here we analyze LD statistics in a sample of >100 fully-sequenced strains from Zambia; an ancestral population to the Raleigh population that has experienced little to no admixture and was generated by sequencing haploid embryos rather than inbred strains. We find an elevation in long-range LD and haplotype homozygosity compared to neutral expectations in the Zambian sample, thus showing the elevation in LD is not specific to the DGRP data set. This elevation in LD and haplotype structure remains even after controlling for possible confounders including genomic inversions, admixture, population substructure, close relatedness of individual strains, and recombination rate variation. Furthermore, signatures of partial soft sweeps similar to those found in the DGRP as well as partial hard sweeps are common in Zambia. These results suggest that while the selective forces and sources of adaptive mutations may differ in Zambia and Raleigh, elevated long-range LD and signatures of soft sweeps are generic in D. melanogaster.
Collapse
|
31
|
Kharzinova V, Sermyagin AA, Gladyr EA, Brem G, Zinovieva NA. Response to “Cross-Species Application of SNP Chips is Not Suitable for Identifying Runs of Homozygosity” by Shafer, Miller, and Kardos. J Hered 2016; 107:196-7. [DOI: 10.1093/jhered/esv139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 12/25/2015] [Indexed: 11/13/2022] Open
|
32
|
Shafer ABA, Miller JM, Kardos M. Cross-Species Application of SNP Chips is Not Suitable for Identifying Runs of Homozygosity. J Hered 2016; 107:193-5. [PMID: 26774056 PMCID: PMC5994971 DOI: 10.1093/jhered/esv137] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 11/24/2015] [Accepted: 12/21/2015] [Indexed: 11/12/2022] Open
Abstract
Cross-species application of single-nucleotide polymorphism (SNP) chips is a valid, relatively cost-effective alternative to the high-throughput sequencing methods generally required to obtain a genome-wide sampling of polymorphisms. Kharzinova et al. (2015) examined the applicability of SNP chips developed in domestic bovids (cattle and sheep) to a semi-wild cervid (reindeer). The ancestors of bovids and cervids diverged between 20 and 30 million years ago (Hassanin and Douzery 2003; Bibi et al. 2013). Empirical work has shown that for a SNP chip developed in a bovid and applied to a cervid species, approximately 50% genotype success with 1% of the loci being polymorphic is expected (Miller et al. 2012). The genotyping of Kharzinova et al. (2015) follows this pattern; however, these data are not appropriate for identifying runs of homozygosity (ROH) and can be problematic for estimating linkage disequilibrium (LD) and we caution readers in this regard.
Collapse
Affiliation(s)
- Aaron B A Shafer
- From the Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, SE-75236 Uppsala, Sweden (Shafer and Kardos); and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT (Miller).
| | - Joshua M Miller
- From the Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, SE-75236 Uppsala, Sweden (Shafer and Kardos); and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT (Miller)
| | - Marty Kardos
- From the Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, SE-75236 Uppsala, Sweden (Shafer and Kardos); and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT (Miller)
| |
Collapse
|
33
|
Deniskova TE, Sermyagin AA, Bagirov VA, Okhlopkov IM, Gladyr EA, Ivanov RV, Brem G, Zinovieva NA. Comparative analysis of the effectiveness of STR and SNP markers for intraspecific and interspecific differentiation of the genus Ovis. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416010026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
34
|
Kharzinova VR, Sermyagin AA, Gladyr EA, Okhlopkov IM, Brem G, Zinovieva NA. A Study of Applicability of SNP Chips Developed for Bovine and Ovine Species to Whole-Genome Analysis of Reindeer Rangifer tarandus. J Hered 2015; 106:758-61. [PMID: 26447215 DOI: 10.1093/jhered/esv081] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 09/14/2015] [Indexed: 12/20/2022] Open
Abstract
Two sets of commercially available single nucleotide polymorphisms (SNPs) developed for cattle (BovineSNP50 BeadChip) and sheep (OvineSNP50 BeadChip) have been trialed for whole-genome analysis of 4 female samples of Rangifer tarandus inhabiting Russia. We found out that 43.0% of bovine and 47.0% of Ovine SNPs could be genotyped, while only 5.3% and 2.03% of them were respectively polymorphic. The scored and the polymorphic SNPs were identified on each bovine and each ovine chromosome, but their distribution was not unique. The maximal value of runs of homozygosity (ROH) was 30.93Mb (for SNPs corresponding to bovine chromosome 8) and 80.32Mb (for SNPs corresponding to ovine chromosome 7). Thus, the SNP chips developed for bovine and ovine species can be used as a powerful tool for genome analysis in reindeer R. tarandus.
Collapse
Affiliation(s)
- Veronika R Kharzinova
- From the L.K. Ernst Institute for Animal Husbandry, Dubrovitzy Estate, 60, Podolsk district, Moscow region, Podolsk 142132, Russia (Kharzinova, Sermyagin, Gladyr, Brem, and Zinovieva); Science Institute of Biological Problems Cryolithozone, Yakutsk 677980, Russia (Okhlopkov); and Institute for Animal Breeding and Genetics, VMU, A-1210 Vienna, Austria (Brem).
| | - Alexander A Sermyagin
- From the L.K. Ernst Institute for Animal Husbandry, Dubrovitzy Estate, 60, Podolsk district, Moscow region, Podolsk 142132, Russia (Kharzinova, Sermyagin, Gladyr, Brem, and Zinovieva); Science Institute of Biological Problems Cryolithozone, Yakutsk 677980, Russia (Okhlopkov); and Institute for Animal Breeding and Genetics, VMU, A-1210 Vienna, Austria (Brem)
| | - Elena A Gladyr
- From the L.K. Ernst Institute for Animal Husbandry, Dubrovitzy Estate, 60, Podolsk district, Moscow region, Podolsk 142132, Russia (Kharzinova, Sermyagin, Gladyr, Brem, and Zinovieva); Science Institute of Biological Problems Cryolithozone, Yakutsk 677980, Russia (Okhlopkov); and Institute for Animal Breeding and Genetics, VMU, A-1210 Vienna, Austria (Brem)
| | - Innokentiy M Okhlopkov
- From the L.K. Ernst Institute for Animal Husbandry, Dubrovitzy Estate, 60, Podolsk district, Moscow region, Podolsk 142132, Russia (Kharzinova, Sermyagin, Gladyr, Brem, and Zinovieva); Science Institute of Biological Problems Cryolithozone, Yakutsk 677980, Russia (Okhlopkov); and Institute for Animal Breeding and Genetics, VMU, A-1210 Vienna, Austria (Brem)
| | - Gottfried Brem
- From the L.K. Ernst Institute for Animal Husbandry, Dubrovitzy Estate, 60, Podolsk district, Moscow region, Podolsk 142132, Russia (Kharzinova, Sermyagin, Gladyr, Brem, and Zinovieva); Science Institute of Biological Problems Cryolithozone, Yakutsk 677980, Russia (Okhlopkov); and Institute for Animal Breeding and Genetics, VMU, A-1210 Vienna, Austria (Brem)
| | - Natalia A Zinovieva
- From the L.K. Ernst Institute for Animal Husbandry, Dubrovitzy Estate, 60, Podolsk district, Moscow region, Podolsk 142132, Russia (Kharzinova, Sermyagin, Gladyr, Brem, and Zinovieva); Science Institute of Biological Problems Cryolithozone, Yakutsk 677980, Russia (Okhlopkov); and Institute for Animal Breeding and Genetics, VMU, A-1210 Vienna, Austria (Brem)
| |
Collapse
|
35
|
Miller JM, Poissant J, Malenfant RM, Hogg JT, Coltman DW. Temporal dynamics of linkage disequilibrium in two populations of bighorn sheep. Ecol Evol 2015; 5:3401-12. [PMID: 26380673 PMCID: PMC4569035 DOI: 10.1002/ece3.1612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Linkage disequilibrium (LD) is the nonrandom association of alleles at two markers. Patterns of LD have biological implications as well as practical ones when designing association studies or conservation programs aimed at identifying the genetic basis of fitness differences within and among populations. However, the temporal dynamics of LD in wild populations has received little empirical attention. In this study, we examined the overall extent of LD, the effect of sample size on the accuracy and precision of LD estimates, and the temporal dynamics of LD in two populations of bighorn sheep (Ovis canadensis) with different demographic histories. Using over 200 microsatellite loci, we assessed two metrics of multi-allelic LD, D', and χ ('2). We found that both populations exhibited high levels of LD, although the extent was much shorter in a native population than one that was founded via translocation, experienced a prolonged bottleneck post founding, followed by recent admixture. In addition, we observed significant variation in LD in relation to the sample size used, with small sample sizes leading to depressed estimates of the extent of LD but inflated estimates of background levels of LD. In contrast, there was not much variation in LD among yearly cross-sections within either population once sample size was accounted for. Lack of pronounced interannual variability suggests that researchers may not have to worry about interannual variation when estimating LD in a population and can instead focus on obtaining the largest sample size possible.
Collapse
Affiliation(s)
- Joshua M Miller
- Department of Biological Sciences, University of Alberta Edmonton, Alberta, Canada
| | - Jocelyn Poissant
- Centre for Ecology and Conservation, University of Exeter Penryn Campus, UK
| | - René M Malenfant
- Department of Biological Sciences, University of Alberta Edmonton, Alberta, Canada
| | - John T Hogg
- Montana Conservation Science Institute 5200 Upper Miller Creek Road, Missoula, Montana, USA
| | - David W Coltman
- Department of Biological Sciences, University of Alberta Edmonton, Alberta, Canada
| |
Collapse
|
36
|
Oliveira R, Randi E, Mattucci F, Kurushima JD, Lyons LA, Alves PC. Toward a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris). Heredity (Edinb) 2015; 115:195-205. [PMID: 26103945 DOI: 10.1038/hdy.2015.25] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 12/13/2014] [Accepted: 02/03/2015] [Indexed: 01/16/2023] Open
Abstract
Endemic gene pools have been severely endangered by human-mediated hybridization, which is posing new challenges in the conservation of several vertebrate species. The endangered European wildcat is an example of this problem, as several natural populations are suffering introgression of genes from the domestic cat. The implementation of molecular methods for detecting hybridization is crucial for supporting appropriate conservation programs on the wildcat. In this study, genetic variation at 158 single-nucleotide polymorphisms (SNPs) was analyzed in 139 domestic cats, 130 putative European wildcats and 5 captive-bred hybrids (N=274). These SNPs were variable both in wild (HE=0.107) and domestic cats (HE=0.340). Although we did not find any SNP that was private in any population, 22 SNPs were monomorphic in wildcats and pairwise FCT values revealed marked differences between domestic and wildcats, with the most divergent 35 loci providing an average FCT>0.74. The power of all the loci to accurately identify admixture events and discriminate the different hybrid categories was evaluated. Results from simulated and real genotypes show that the 158 SNPs provide successful estimates of admixture, with 100% hybrid individuals (two to three generations in the past) being correctly identified in STRUCTURE and over 92% using the NEWHYBRIDS' algorithm. None of the unclassified cats were wrongly allocated to another hybrid class. Thirty-five SNPs, showing the highest FCT values, provided the most parsimonious panel for robust inferences of parental and first generations of admixed ancestries. This approach may be used to further reconstruct the evolution of wildcat populations and, hopefully, to develop sound conservation guidelines for its legal protection in Europe.
Collapse
Affiliation(s)
- R Oliveira
- 1] CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO-Laboratório Associado, Vairão, Portugal [2] Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - E Randi
- 1] Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Bologna, Italy [2] Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - F Mattucci
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Bologna, Italy
| | - J D Kurushima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - L A Lyons
- 1] Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA [2] Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri-Columbia, Columbia, MI, USA
| | - P C Alves
- 1] CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO-Laboratório Associado, Vairão, Portugal [2] Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal [3] Wildlife Biology Program, University of Montana, Missoula, MT, USA
| |
Collapse
|
37
|
Miller JM, Moore SS, Stothard P, Liao X, Coltman DW. Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis). BMC Genomics 2015; 16:397. [PMID: 25990117 PMCID: PMC4438629 DOI: 10.1186/s12864-015-1618-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/05/2015] [Indexed: 02/08/2023] Open
Abstract
Background Whole genome sequences (WGS) have proliferated as sequencing technology continues to improve and costs decline. While many WGS of model or domestic organisms have been produced, a growing number of non-model species are also being sequenced. In the absence of a reference, construction of a genome sequence necessitates de novo assembly which may be beyond the ability of many labs due to the large volumes of raw sequence data and extensive bioinformatics required. In contrast, the presence of a reference WGS allows for alignment which is more tractable than assembly. Recent work has highlighted that the reference need not come from the same species, potentially enabling a wide array of species WGS to be constructed using cross-species alignment. Here we report on the creation a draft WGS from a single bighorn sheep (Ovis canadensis) using alignment to the closely related domestic sheep (Ovis aries). Results Two sequencing libraries on SOLiD platforms yielded over 865 million reads, and combined alignment to the domestic sheep reference resulted in a nearly complete sequence (95% coverage of the reference) at an average of 12x read depth (104 SD). From this we discovered over 15 million variants and annotated them relative to the domestic sheep reference. We then conducted an enrichment analysis of those SNPs showing fixed differences between the reference and sequenced individual and found significant differences in a number of gene ontology (GO) terms, including those associated with reproduction, muscle properties, and bone deposition. Conclusion Our results demonstrate that cross-species alignment enables the creation of novel WGS for non-model organisms. The bighorn sheep WGS will provide a resource for future resequencing studies or comparative genomics. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1618-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Joshua M Miller
- Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Stephen S Moore
- Centre for Animal Science, Queensland Alliance for Agriculture & Food Innovation, University of Queensland, St Lucia, QLD, Australia. .,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Xiaoping Liao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
| | - David W Coltman
- Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada.
| |
Collapse
|
38
|
Lv FH, Agha S, Kantanen J, Colli L, Stucki S, Kijas JW, Joost S, Li MH, Ajmone Marsan P. Adaptations to climate-mediated selective pressures in sheep. Mol Biol Evol 2014; 31:3324-43. [PMID: 25249477 PMCID: PMC4245822 DOI: 10.1093/molbev/msu264] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Following domestication, sheep (Ovis aries) have become essential farmed animals across the world through adaptation to a diverse range of environments and varied production systems. Climate-mediated selective pressure has shaped phenotypic variation and has left genetic "footprints" in the genome of breeds raised in different agroecological zones. Unlike numerous studies that have searched for evidence of selection using only population genetics data, here, we conducted an integrated coanalysis of environmental data with single nucleotide polymorphism (SNP) variation. By examining 49,034 SNPs from 32 old, autochthonous sheep breeds that are adapted to a spectrum of different regional climates, we identified 230 SNPs with evidence for selection that is likely due to climate-mediated pressure. Among them, 189 (82%) showed significant correlation (P ≤ 0.05) between allele frequency and climatic variables in a larger set of native populations from a worldwide range of geographic areas and climates. Gene ontology analysis of genes colocated with significant SNPs identified 17 candidates related to GTPase regulator and peptide receptor activities in the biological processes of energy metabolism and endocrine and autoimmune regulation. We also observed high linkage disequilibrium and significant extended haplotype homozygosity for the core haplotype TBC1D12-CH1 of TBC1D12. The global frequency distribution of the core haplotype and allele OAR22_18929579-A showed an apparent geographic pattern and significant (P ≤ 0.05) correlations with climatic variation. Our results imply that adaptations to local climates have shaped the spatial distribution of some variants that are candidates to underpin adaptive variation in sheep.
Collapse
Affiliation(s)
- Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Saif Agha
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland Department of Animal Science, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Juha Kantanen
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland Department of Biology, University of Eastern Finland, Kuopio, Finland
| | - Licia Colli
- Istituto di Zootecnica, Facoltà di Agraria, Università Cattolica del Sacro Cuore, Piacenza, Italy Biodiversity and Ancient DNA Research Center-BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - James W Kijas
- CSIRO Livestock Industries, St Lucia, Brisbane, Qld, Australia
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Paolo Ajmone Marsan
- Istituto di Zootecnica, Facoltà di Agraria, Università Cattolica del Sacro Cuore, Piacenza, Italy Biodiversity and Ancient DNA Research Center-BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| |
Collapse
|
39
|
Zhao F, Wang G, Zeng T, Wei C, Zhang L, Wang H, Zhang S, Liu R, Liu Z, Du L. Estimations of genomic linkage disequilibrium and effective population sizes in three sheep populations. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
40
|
Mastrangelo S, Di Gerlando R, Tolone M, Tortorici L, Sardina MT, Portolano B. Genome wide linkage disequilibrium and genetic structure in Sicilian dairy sheep breeds. BMC Genet 2014; 15:108. [PMID: 25928374 PMCID: PMC4197223 DOI: 10.1186/s12863-014-0108-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/29/2014] [Indexed: 11/19/2022] Open
Abstract
Background The recent availability of sheep genome-wide SNP panels allows providing background information concerning genome structure in domestic animals. The aim of this work was to investigate the patterns of linkage disequilibrium (LD), the genetic diversity and population structure in Valle del Belice, Comisana, and Pinzirita dairy sheep breeds using the Illumina Ovine SNP50K Genotyping array. Results Average r2 between adjacent SNPs across all chromosomes was 0.155 ± 0.204 for Valle del Belice, 0.156 ± 0.208 for Comisana, and 0.128 ± 0.188 for Pinzirita breeds, and some variations in LD value across chromosomes were observed, in particular for Valle del Belice and Comisana breeds. Average values of r2 estimated for all pairwise combinations of SNPs pooled over all autosomes were 0.058 ± 0.023 for Valle del Belice, 0.056 ± 0.021 for Comisana, and 0.037 ± 0.017 for Pinzirita breeds. The LD declined as a function of distance and average r2 was lower than the values observed in other sheep breeds. Consistency of results among the several used approaches (Principal component analysis, Bayesian clustering, FST, Neighbor networks) showed that while Valle del Belice and Pinzirita breeds formed a unique cluster, Comisana breed showed the presence of substructure. In Valle del Belice breed, the high level of genetic differentiation within breed, the heterogeneous cluster in Admixture analysis, but at the same time the highest inbreeding coefficient, suggested that the breed had a wide genetic base with inbred individuals belonging to the same flock. The Sicilian breeds were characterized by low genetic differentiation and high level of admixture. Pinzirita breed displayed the highest genetic diversity (He, Ne) whereas the lowest value was found in Valle del Belice breed. Conclusions This study has reported for the first time estimates of LD and genetic diversity from a genome-wide perspective in Sicilian dairy sheep breeds. Our results indicate that breeds formed non-overlapping clusters and are clearly separated populations and that Comisana sheep breed does not constitute a homogenous population. The information generated from this study has important implications for the design and applications of association studies as well as for development of conservation and/or selection breeding programs. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0108-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Viale delle Scienze, 90128, Palermo, Italy.
| | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Viale delle Scienze, 90128, Palermo, Italy.
| | - Marco Tolone
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Viale delle Scienze, 90128, Palermo, Italy.
| | - Lina Tortorici
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Viale delle Scienze, 90128, Palermo, Italy.
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Viale delle Scienze, 90128, Palermo, Italy.
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Viale delle Scienze, 90128, Palermo, Italy.
| | | |
Collapse
|
41
|
Yang J, Shikano T, Li MH, Merilä J. Genome-wide linkage disequilibrium in nine-spined stickleback populations. G3 (BETHESDA, MD.) 2014; 4:1919-29. [PMID: 25122668 PMCID: PMC4199698 DOI: 10.1534/g3.114.013334] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 08/09/2014] [Indexed: 11/18/2022]
Abstract
Variation in the extent and magnitude of genome-wide linkage disequilibrium (LD) among populations residing in different habitats has seldom been studied in wild vertebrates. We used a total of 109 microsatellite markers to quantify the level and patterns of genome-wide LD in 13 Fennoscandian nine-spined stickleback (Pungitius pungitius) populations from four (viz. marine, lake, pond, and river) different habitat types. In general, high magnitude (D' > 0.5) of LD was found both in freshwater and marine populations, and the magnitude of LD was significantly greater in inland freshwater than in marine populations. Interestingly, three coastal freshwater populations located in close geographic proximity to the marine populations exhibited similar LD patterns and genetic diversity as their marine neighbors. The greater levels of LD in inland freshwater compared with marine and costal freshwater populations can be explained in terms of their contrasting demographic histories: founder events, long-term isolation, small effective sizes, and population bottlenecks are factors likely to have contributed to the high levels of LD in the inland freshwater populations. In general, these findings shed new light on the patterns and extent of variation in genome-wide LD, as well as the ecological and evolutionary factors driving them.
Collapse
Affiliation(s)
- Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Takahito Shikano
- Ecological Genetics Research Unit, Department of Biosciences, FIN-00014 University of Helsinki, Finland
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Juha Merilä
- Ecological Genetics Research Unit, Department of Biosciences, FIN-00014 University of Helsinki, Finland
| |
Collapse
|
42
|
Liu S, Sun L, Li Y, Sun F, Jiang Y, Zhang Y, Zhang J, Feng J, Kaltenboeck L, Kucuktas H, Liu Z. Development of the catfish 250K SNP array for genome-wide association studies. BMC Res Notes 2014; 7:135. [PMID: 24618043 PMCID: PMC3995806 DOI: 10.1186/1756-0500-7-135] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 02/28/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Quantitative traits, such as disease resistance, are most often controlled by a set of genes involving a complex array of regulation. The dissection of genetic basis of quantitative traits requires large numbers of genetic markers with good genome coverage. The application of next-generation sequencing technologies has allowed discovery of over eight million SNPs in catfish, but the challenge remains as to how to efficiently and economically use such SNP resources for genetic analysis. RESULTS In this work, we developed a catfish 250K SNP array using Affymetrix Axiom genotyping technology. The SNPs were obtained from multiple sources including gene-associated SNPs, anonymous genomic SNPs, and inter-specific SNPs. A set of 640K high-quality SNPs obtained following specific requirements of array design were submitted. A panel of 250,113 SNPs was finalized for inclusion on the array. The performance evaluated by genotyping individuals from wild populations and backcross families suggested the good utility of the catfish 250K SNP array. CONCLUSIONS This is the first high-density SNP array for catfish. The array should be a valuable resource for genome-wide association studies (GWAS), fine QTL mapping, high-density linkage map construction, haplotype analysis, and whole genome-based selection.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA.
| |
Collapse
|
43
|
The application of genome-wide SNP genotyping methods in studies on livestock genomes. J Appl Genet 2014; 55:197-208. [PMID: 24566962 DOI: 10.1007/s13353-014-0202-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/14/2014] [Accepted: 02/04/2014] [Indexed: 01/07/2023]
Abstract
Animal genomics is currently undergoing dynamic development, which is driven by the flourishing of high-throughput genome analysis methods. Recently, a large number of animals has been genotyped with the use of whole-genome genotyping assays in the course of genomic selection programmes. The results of such genotyping can also be used for studies on different aspects of livestock genome functioning and diversity. In this article, we review the recent literature concentrating on various aspects of animal genomics, including studies on linkage disequilibrium, runs of homozygosity, selection signatures, copy number variation and genetic differentiation of animal populations. Our work is aimed at providing insight into certain achievements of animal genomics and to arouse interest in basic research on the complexity and structure of the genomes of livestock.
Collapse
|
44
|
Ekblom R, Wennekes P, Horsburgh GJ, Burke T. Characterization of the house sparrow (Passer domesticus) transcriptome: a resource for molecular ecology and immunogenetics. Mol Ecol Resour 2014; 14:636-46. [PMID: 24345231 DOI: 10.1111/1755-0998.12213] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/04/2013] [Accepted: 12/11/2013] [Indexed: 11/30/2022]
Abstract
The house sparrow (Passer domesticus) is an important model species in ecology and evolution. However, until recently, genomic resources for molecular ecological projects have been lacking in this species. Here, we present transcriptome sequencing data (RNA-Seq) from three different house sparrow tissues (spleen, blood and bursa). These tissues were specifically chosen to obtain a diverse representation of expressed genes and to maximize the yield of immune-related gene functions. After de novo assembly, 15,250 contigs were identified, representing sequence data from a total of 8756 known avian genes (as inferred from the closely related zebra finch). The transcriptome assembly contain sequence data from nine manually annotated MHC genes, including an almost complete MHC class I coding sequence. There were 407, 303 and 68 genes overexpressed in spleen, blood and bursa, respectively. Gene ontology terms related to ribosomal function were associated with overexpression in spleen and oxygen transport functions with overexpression in blood. In addition to the transcript sequences, we provide 327 gene-linked microsatellites (SSRs) with sufficient flanking sequences for primer design, and 3177 single-nucleotide polymorphisms (SNPs) within genes, that can be used in follow-up molecular ecology studies of this ecological well-studied species.
Collapse
Affiliation(s)
- Robert Ekblom
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, Uppsala, SE-75236, Sweden; Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | | | | | | |
Collapse
|
45
|
Estimating genome-wide heterozygosity: effects of demographic history and marker type. Heredity (Edinb) 2013; 112:240-7. [PMID: 24149650 DOI: 10.1038/hdy.2013.99] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 09/04/2013] [Accepted: 09/16/2013] [Indexed: 01/03/2023] Open
Abstract
Heterozygosity-fitness correlations (HFCs) are often used to link individual genetic variation to differences in fitness. However, most studies examining HFCs find weak or no correlations. Here, we derive broad theoretical predictions about how many loci are needed to adequately measure genomic heterozygosity assuming different levels of identity disequilibrium (ID), a proxy for inbreeding. We then evaluate the expected ability to detect HFCs using an empirical data set of 200 microsatellites and 412 single nucleotide polymorphisms (SNPs) genotyped in two populations of bighorn sheep (Ovis canadensis), with different demographic histories. In both populations, heterozygosity was significantly correlated across marker types, although the strength of the correlation was weaker in a native population compared with one founded via translocation and later supplemented with additional individuals. Despite being bi-allelic, SNPs had similar correlations to genome-wide heterozygosity as microsatellites in both populations. For both marker types, this association became stronger and less variable as more markers were considered. Both populations had significant levels of ID; however, estimates were an order of magnitude lower in the native population. As with heterozygosity, SNPs performed similarly to microsatellites, and precision and accuracy of the estimates of ID increased as more loci were considered. Although dependent on the demographic history of the population considered, these results illustrate that genome-wide heterozygosity, and therefore HFCs, are best measured by a large number of markers, a feat now more realistically accomplished with SNPs than microsatellites.
Collapse
|
46
|
Li MH, Tiirikka T, Kantanen J. A genome-wide scan study identifies a single nucleotide substitution in ASIP associated with white versus non-white coat-colour variation in sheep (Ovis aries). Heredity (Edinb) 2013; 112:122-31. [PMID: 24022497 DOI: 10.1038/hdy.2013.83] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 07/02/2013] [Accepted: 07/04/2013] [Indexed: 12/21/2022] Open
Abstract
In sheep, coat colour (and pattern) is one of the important traits of great biological, economic and social importance. However, the genetics of sheep coat colour has not yet been fully clarified. We conducted a genome-wide association study of sheep coat colours by genotyping 47 303 single-nucleotide polymorphisms (SNPs) in the Finnsheep population in Finland. We identified 35 SNPs associated with all the coat colours studied, which cover genomic regions encompassing three known pigmentation genes (TYRP1, ASIP and MITF) in sheep. Eighteen of these associations were confirmed in further tests between white versus non-white individuals, but none of the 35 associations were significant in the analysis of only non-white colours. Across the tests, the s66432.1 in ASIP showed significant association (P=4.2 × 10(-11) for all the colours; P=2.3 × 10(-11) for white versus non-white colours) with the variation in coat colours and strong linkage disequilibrium with other significant variants surrounding the ASIP gene. The signals detected around the ASIP gene were explained by differences in white versus non-white alleles. Further, a genome scan for selection for white coat pigmentation identified a strong and striking selection signal spanning ASIP. Our study identified the main candidate gene for the coat colour variation between white and non-white as ASIP, an autosomal gene that has been directly implicated in the pathway regulating melanogenesis. Together with ASIP, the two other newly identified genes (TYRP1 and MITF) in the Finnsheep, bordering associated SNPs, represent a new resource for enriching sheep coat-colour genetics and breeding.
Collapse
Affiliation(s)
- M-H Li
- 1] Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland [2] Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - T Tiirikka
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
| | - J Kantanen
- 1] Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland [2] Department of Biology, University of Eastern Finland, Kuopio, Finland
| |
Collapse
|
47
|
Hoffman JI, Thorne MAS, McEwing R, Forcada J, Ogden R. Cross-amplification and validation of SNPs conserved over 44 million years between seals and dogs. PLoS One 2013; 8:e68365. [PMID: 23874599 PMCID: PMC3712990 DOI: 10.1371/journal.pone.0068365] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 05/28/2013] [Indexed: 01/17/2023] Open
Abstract
High-density SNP arrays developed for humans and their companion species provide a rapid and convenient tool for generating SNP data in closely-related non-model organisms, but have not yet been widely applied to phylogenetically divergent taxa. Consequently, we used the CanineHD BeadChip to genotype 24 Antarctic fur seal (Arctocephalus gazella) individuals. Despite seals and dogs having diverged around 44 million years ago, 33,324 out of 173,662 loci (19.2%) could be genotyped, of which 173 were polymorphic and clearly interpretable. Two SNPs were validated using KASP genotyping assays, with the resulting genotypes being 100% concordant with those obtained from the high-density array. Two loci were also confirmed through in silico visualisation after mapping them to the fur seal transcriptome. Polymorphic SNPs were distributed broadly throughout the dog genome and did not differ significantly in proximity to genes from either monomorphic SNPs or those that failed to cross-amplify in seals. However, the nearest genes to polymorphic SNPs were significantly enriched for functional annotations relating to energy metabolism, suggesting a possible bias towards conserved regions of the genome.
Collapse
Affiliation(s)
- Joseph I. Hoffman
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, North Rhine-Westphalia, Germany
- * E-mail:
| | - Michael A. S. Thorne
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom
| | - Rob McEwing
- Wildgenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, United Kingdom
| | - Jaume Forcada
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom
| | - Rob Ogden
- Wildgenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, United Kingdom
| |
Collapse
|
48
|
Zhang L, Mousel MR, Wu X, Michal JJ, Zhou X, Ding B, Dodson MV, El-Halawany NK, Lewis GS, Jiang Z. Genome-wide genetic diversity and differentially selected regions among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep. PLoS One 2013; 8:e65942. [PMID: 23762451 PMCID: PMC3677876 DOI: 10.1371/journal.pone.0065942] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/30/2013] [Indexed: 11/18/2022] Open
Abstract
Sheep are among the major economically important livestock species worldwide because the animals produce milk, wool, skin, and meat. In the present study, the Illumina OvineSNP50 BeadChip was used to investigate genetic diversity and genome selection among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds from the United States. After quality-control filtering of SNPs (single nucleotide polymorphisms), we used 48,026 SNPs, including 46,850 SNPs on autosomes that were in Hardy-Weinberg equilibrium and 1,176 SNPs on chromosome × for analysis. Phylogenetic analysis based on all 46,850 SNPs clearly separated Suffolk from Rambouillet, Columbia, Polypay, and Targhee, which was not surprising as Rambouillet contributed to the synthesis of the later three breeds. Based on pair-wise estimates of FST, significant genetic differentiation appeared between Suffolk and Rambouillet (FST = 0.1621), while Rambouillet and Targhee had the closest relationship (FST = 0.0681). A scan of the genome revealed 45 and 41 differentially selected regions (DSRs) between Suffolk and Rambouillet and among Rambouillet-related breed populations, respectively. Our data indicated that regions 13 and 24 between Suffolk and Rambouillet might be good candidates for evaluating breed differences. Furthermore, ovine genome v3.1 assembly was used as reference to link functionally known homologous genes to economically important traits covered by these differentially selected regions. In brief, our present study provides a comprehensive genome-wide view on within- and between-breed genetic differentiation, biodiversity, and evolution among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds. These results may provide new guidance for the synthesis of new breeds with different breeding objectives.
Collapse
Affiliation(s)
- Lifan Zhang
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Michelle R. Mousel
- USDA/ARS US Sheep Experiment Station, Dubois, Idaho, United States of America
| | - Xiaolin Wu
- Department of Dairy Science, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jennifer J. Michal
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Xiang Zhou
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Bo Ding
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Michael V. Dodson
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Nermin K. El-Halawany
- Cell Biology Department, Division of Genetic Engineering and Biotechnology, National Research Center, Dokki, Gueza, Egypt
| | - Gregory S. Lewis
- USDA/ARS US Sheep Experiment Station, Dubois, Idaho, United States of America
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
- * E-mail:
| |
Collapse
|
49
|
Albaina A, Iriondo M, Velado I, Laconcha U, Zarraonaindia I, Arrizabalaga H, Pardo MA, Lutcavage M, Grant WS, Estonba A. Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure. Anim Genet 2013; 44:678-92. [PMID: 23668670 DOI: 10.1111/age.12051] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2013] [Indexed: 10/26/2022]
Abstract
The optimal management of the commercially important, but mostly over-exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna (BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure than has been provided by previous molecular methods. Despite numerous studies of both species, their population structures remain controversial. This study reports the development of single nucleotide polymorphisms (SNPs) in albacore and BFT and the application of these SNPs to survey genetic variability across the geographic ranges of these tunas. A total of 616 SNPs were discovered in 35 albacore tuna by comparing sequences of 54 nuclear DNA fragments. A panel of 53 SNPs yielded FST values ranging from 0.0 to 0.050 between samples after genotyping 460 albacore collected throughout the distribution of this species. No significant heterogeneity was detected within oceans, but between-ocean comparisons (Atlantic, Pacific and Indian oceans along with Mediterranean Sea) were significant. Additionally, a 17-SNP panel was developed in Atlantic BFT by cross-species amplification in 107 fish. This limited number of SNPs discriminated between samples from the two major spawning areas of Atlantic BFT (FST = 0.116). The SNP markers developed in this study can be used to genotype large numbers of fish without the need for standardizing alleles among laboratories.
Collapse
Affiliation(s)
- A Albaina
- Genetika, Antropologia Fisikoa eta Animalien Fisiologia Saila, Zientzia eta Teknologia Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), P.O. Box 48940, Leioa, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Hagen IJ, Billing AM, Rønning B, Pedersen SA, Pärn H, Slate J, Jensen H. The easy road to genome‐wide medium density
SNP
screening in a non‐model species: development and application of a 10 K
SNP
‐chip for the house sparrow (
P
asser domesticus
). Mol Ecol Resour 2013; 13:429-39. [DOI: 10.1111/1755-0998.12088] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/11/2013] [Accepted: 01/15/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Ingerid J. Hagen
- Department of Biology Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim NO‐7491 Norway
| | - Anna M. Billing
- Department of Biology Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim NO‐7491 Norway
| | - Bernt Rønning
- Department of Biology Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim NO‐7491 Norway
| | - Sindre A. Pedersen
- Department of Biology Norwegian University of Science and Technology Trondheim NO‐7491 Norway
| | - Henrik Pärn
- Department of Biology Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim NO‐7491 Norway
| | - Jon Slate
- Department of Animal and Plant Sciences University of Sheffield Western Bank Sheffield S10 2TN UK
| | - Henrik Jensen
- Department of Biology Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim NO‐7491 Norway
| |
Collapse
|