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Oleksyk TK, Wolfsberger WW, Weber AM, Shchubelka K, Oleksyk OT, Levchuk O, Patrus A, Lazar N, Castro-Marquez SO, Hasynets Y, Boldyzhar P, Neymet M, Urbanovych A, Stakhovska V, Malyar K, Chervyakova S, Podoroha O, Kovalchuk N, Rodriguez-Flores JL, Zhou W, Medley S, Battistuzzi F, Liu R, Hou Y, Chen S, Yang H, Yeager M, Dean M, Mills RE, Smolanka V. Genome diversity in Ukraine. Gigascience 2021; 10:6079618. [PMID: 33438729 PMCID: PMC7804371 DOI: 10.1093/gigascience/giaa159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/21/2020] [Accepted: 12/15/2020] [Indexed: 01/21/2023] Open
Abstract
Background The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. Results The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population. Conclusions Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.
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Affiliation(s)
- Taras K Oleksyk
- Department of Biological Sciences, Uzhhorod National University, 32 Voloshyna Str., Uzhhorod 88000, Ukraine.,Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA
| | - Walter W Wolfsberger
- Department of Biological Sciences, Uzhhorod National University, 32 Voloshyna Str., Uzhhorod 88000, Ukraine.,Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA
| | - Alexandra M Weber
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Khrystyna Shchubelka
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA.,Department of Medicine, Uzhhorod National University, Uzhhorod 88000, Ukraine
| | - Olga T Oleksyk
- A. Novak Transcarpathian Regional Clinical Hospital, Uzhhorod 88000, Ukraine
| | | | | | | | - Stephanie O Castro-Marquez
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA
| | - Yaroslava Hasynets
- Department of Biological Sciences, Uzhhorod National University, 32 Voloshyna Str., Uzhhorod 88000, Ukraine
| | - Patricia Boldyzhar
- Department of Medicine, Uzhhorod National University, Uzhhorod 88000, Ukraine
| | - Mikhailo Neymet
- Velyka Kopanya Family Hospital, Transcarpatia 90330, Ukraine
| | | | | | - Kateryna Malyar
- I.I.Mechnikov Dnipro Regional Clinical Hospital, Dnipro 49000, Ukraine
| | | | | | - Natalia Kovalchuk
- Rivne Regional Specialized Hospital of Radiation Protection, Rivne 33028, Ukraine
| | | | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah Medley
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA
| | - Fabia Battistuzzi
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA
| | - Ryan Liu
- BGI Shenzhen, Shenzhen, 518083, China
| | - Yong Hou
- BGI Shenzhen, Shenzhen, 518083, China
| | - Siru Chen
- BGI Shenzhen, Shenzhen, 518083, China
| | | | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Volodymyr Smolanka
- Department of Medicine, Uzhhorod National University, Uzhhorod 88000, Ukraine
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Bakhtiarizadeh MR, Alamouti AA. RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep. Sci Rep 2020; 10:13525. [PMID: 32782325 PMCID: PMC7419499 DOI: 10.1038/s41598-020-70527-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/27/2020] [Indexed: 01/09/2023] Open
Abstract
Genetic basis of fat deposition in sheep tail have not been completely elucidated yet. Understanding the genetic mechanisms controlling fat-tail size can improve breeding strategies to modulate fat deposition. RNA sequencing has made it possible to discover genetic variants that may underlie various phenotypic differences. Hence, to identify genetic variants that are important for describing different fat-tail phenotypes in sheep, RNA sequencing was used for single nucleotide polymorphism (SNP) calling in two Iranian sheep breeds (Lori-Bakhtiari, fat-tailed; n = 4, vs Zel, thin-tailed; n = 4). Using a stringent pipeline, a total of 112,344 known SNPs were genotyped, of which 30,550 and 42,906 SNPs were shared by at least two Lori-Bakhtiari and Zel, respectively. Comparing these SNPs showed 2,774 (including 209 missense and 25 deleterious SNPs) and 10,470 (including 1,054 missense and 116 deleterious SNPs) breed-specific SNPs in Lori-Bakhtiari and Zel sheep, respectively. Potential breed-specific SNPs were detected by considering those located in QTL regions associated with fatness or reported as important candidates in previous similar studies. Of the breed-specific SNPs, 724 and 2,905 were located in the QTL regions. Functional enrichment analysis of the affected genes revealed several enriched gene ontologies and KEGG pathways related to fat metabolism. Based on the results, several affected genes were proposed to be strongly linked with fat deposition such as DGAT2, ACSL1, ACACA, ADIPOQ, ACLY, FASN, CPT2, SCD, ADCY6, PER3, CSF1R, SLC22A4, GFPT1, CDS2, BMP6, ACSS2, ELOVL6, HOXA10 and FABP4. Moreover, several SNPs were found in the candidate genes related to fatty acid oxidation introducing them as promising candidates responsible for lower fat content in tail of Zel. Our findings provided new insights into the genetic mechanisms of fat deposition in sheep, which can serve to designing appropriate breeding programs.
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Affiliation(s)
| | - Ali A Alamouti
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
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54
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Boyrie L, Moreau C, Frugier F, Jacquet C, Bonhomme M. A linkage disequilibrium-based statistical test for Genome-Wide Epistatic Selection Scans in structured populations. Heredity (Edinb) 2020; 126:77-91. [PMID: 32728044 DOI: 10.1038/s41437-020-0349-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 01/16/2023] Open
Abstract
The quest for signatures of selection using single nucleotide polymorphism (SNP) data has proven efficient to uncover genes involved in conserved and/or adaptive molecular functions, but none of the statistical methods were designed to identify interacting alleles as targets of selective processes. Here, we propose a statistical test aimed at detecting epistatic selection, based on a linkage disequilibrium (LD) measure accounting for population structure and heterogeneous relatedness between individuals. SNP-based ([Formula: see text]) and window-based ([Formula: see text]) statistics fit a Student distribution, allowing to test the significance of correlation coefficients. As a proof of concept, we use SNP data from the Medicago truncatula symbiotic legume plant and uncover a previously unknown gene coadaptation between the MtSUNN (Super Numeric Nodule) receptor and the MtCLE02 (CLAVATA3-Like) signaling peptide. We also provide experimental evidence supporting a MtSUNN-dependent negative role of MtCLE02 in symbiotic root nodulation. Using human HGDP-CEPH SNP data, our new statistical test uncovers strong LD between SLC24A5 (skin pigmentation) and EDAR (hairs, teeth, sweat glands development) world-wide, which persists after correction for population structure and relatedness in Central South Asian populations. This result suggests that epistatic selection or coselection could have contributed to the phenotypic make-up in some human populations. Applying this approach to genome-wide SNP data will facilitate the identification of coadapted gene networks in model or non-model organisms.
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Affiliation(s)
- Léa Boyrie
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Castanet-Tolosan, France
| | - Corentin Moreau
- Institute of Plant Sciences-Paris Saclay (IPS2), Centre National de la Recherche Scientifique, Univ Paris-Sud, Univ Paris-Diderot, Univ d'Evry, Institut National de la Recherche Agronomique, Université Paris-Saclay, 91192, Gif-sur-Yvette, France
| | - Florian Frugier
- Institute of Plant Sciences-Paris Saclay (IPS2), Centre National de la Recherche Scientifique, Univ Paris-Sud, Univ Paris-Diderot, Univ d'Evry, Institut National de la Recherche Agronomique, Université Paris-Saclay, 91192, Gif-sur-Yvette, France
| | - Christophe Jacquet
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Castanet-Tolosan, France
| | - Maxime Bonhomme
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Castanet-Tolosan, France.
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55
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Cádiz MI, López ME, Díaz-Domínguez D, Cáceres G, Yoshida GM, Gomez-Uchida D, Yáñez JM. Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus). Sci Rep 2020; 10:11514. [PMID: 32661317 PMCID: PMC7359307 DOI: 10.1038/s41598-020-68064-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 06/16/2020] [Indexed: 01/24/2023] Open
Abstract
Nile tilapia belongs to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs and domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be detected at the molecular level. In this work, signatures of selection were identified using genome-wide SNP data, by two haplotype-based (iHS and Rsb) and one FST based method. Whole-genome re-sequencing of 326 individuals from three strains (A, B and C) of farmed tilapia maintained in Brazil and Costa Rica was carried out using Illumina HiSeq 2500 technology. After applying conventional SNP-calling and quality-control filters, ~ 1.3 M high-quality SNPs were inferred and used as input for the iHS, Rsb and FST based methods. We detected several candidate genes putatively subjected to selection in each strain. A considerable number of these genes are associated with growth (e.g. NCAPG, KLF3, TBC1D1, TTN), early development (e.g. FGFR3, PFKFB3), and immunity traits (e.g. NLRC3, PIGR, MAP1S). These candidate genes represent putative genomic landmarks that could be associated to traits of biological and commercial interest in farmed Nile tilapia.
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Affiliation(s)
- María I Cádiz
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, 8820808, La Pintana, Santiago, Chile.,Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, 8820808, La Pintana, Santiago, Chile
| | - María E López
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, 8820808, La Pintana, Santiago, Chile.,Department of Animal Breeding and Genetics, Swedish University of Agriculturall Sciences, Uppsala, Sweden
| | - Diego Díaz-Domínguez
- Departamento de Ciencias de la Computación, Universidad de Chile, Santiago, Chile
| | - Giovanna Cáceres
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, 8820808, La Pintana, Santiago, Chile.,Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, 8820808, La Pintana, Santiago, Chile
| | - Grazyella M Yoshida
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, 8820808, La Pintana, Santiago, Chile
| | - Daniel Gomez-Uchida
- Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Núcleo Milenio INVASAL, Concepción, Chile
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, 8820808, La Pintana, Santiago, Chile. .,Núcleo Milenio INVASAL, Concepción, Chile.
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56
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Kim SJ, Ha JW, Kim H. Genome-Wide Identification of Discriminative Genetic Variations in Beef and Dairy Cattle via an Information-Theoretic Approach. Genes (Basel) 2020; 11:genes11060678. [PMID: 32580275 PMCID: PMC7350245 DOI: 10.3390/genes11060678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 11/23/2022] Open
Abstract
Analyzing the associations between genotypic changes and phenotypic traits on a genome-wide scale can contribute to understanding the functional roles of distinct genetic variations during breed development. We performed a whole-genome analysis of Angus and Jersey cattle breeds using conditional mutual information, which is an information-theoretic method estimating the conditional independency among multiple factor variables. The proposed conditional mutual information-based approach allows breed-discriminative genetic variations to be explicitly identified from tens of millions of SNP (single nucleotide polymorphism) positions on a genome-wide scale while minimizing the usage of prior knowledge. Using this data-driven approach, we identified biologically relevant functional genes, including breed-specific variants for cattle traits such as beef and dairy production. The identified lipid-related genes were shown to be significantly associated with lipid and triglyceride metabolism, fat cell differentiation, and muscle development. In addition, we confirmed that milk-related genes are involved in mammary gland development, lactation, and mastitis-associated processes. Our results provide the distinct properties of Angus and Jersey cattle at a genome-wide level. Moreover, this study offers important insights into discovering unrevealed genetic variants for breed-specific traits and the identification of genetic signatures of diverse cattle breeds with respect to target breed-specific properties.
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Affiliation(s)
- Soo-Jin Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea;
| | - Jung-Woo Ha
- Clova AI Research, NAVER Corp., Seongnam 13561, Korea;
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea;
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
- C&K Genomics, Seoul 05836, Korea
- Correspondence: ; Tel.: +82-2880-4803
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57
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Abstract
An experiment of divergent selection for intramuscular fat was carried out at Universitat Politècnica de València. The high response of selection in intramuscular fat content, after nine generations of selection, and a multidimensional scaling analysis showed a high degree of genomic differentiation between the two divergent populations. Therefore, local genomic differences could link genomic regions, encompassing selective sweeps, to the trait used as selection criterion. In this sense, the aim of this study was to identify genomic regions related to intramuscular fat through three methods for detection of selection signatures and to generate a list of candidate genes. The methods implemented in this study were Wright's fixation index, cross population composite likelihood ratio and cross population - extended haplotype homozygosity. Genomic data came from the 9th generation of the two populations divergently selected, 237 from Low line and 240 from High line. A high single nucleotide polymorphism (SNP) density array, Affymetrix Axiom OrcunSNP Array (around 200k SNPs), was used for genotyping samples. Several genomic regions distributed along rabbit chromosomes (OCU) were identified as signatures of selection (SNPs having a value above cut-off of 1%) within each method. In contrast, 8 genomic regions, harbouring 80 SNPs (OCU1, OCU3, OCU6, OCU7, OCU16 and OCU17), were identified by at least 2 methods and none by the 3 methods. In general, our results suggest that intramuscular fat selection influenced multiple genomic regions which can be a consequence of either only selection effect or the combined effect of selection and genetic drift. In addition, 73 genes were retrieved from the 8 selection signatures. After functional and enrichment analyses, the main genes into the selection signatures linked to energy, fatty acids, carbohydrates and lipid metabolic processes were ACER2, PLIN2, DENND4C, RPS6, RRAGA (OCU1), ST8SIA6, VIM (OCU16), RORA, GANC and PLA2G4B (OCU17). This genomic scan is the first study using rabbits from a divergent selection experiment. Our results pointed out a large polygenic component of the intramuscular fat content. Besides, promising positional candidate genes would be analysed in further studies in order to bear out their contributions to this trait and their feasible implications for rabbit breeding programmes.
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58
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VolcanoFinder: Genomic scans for adaptive introgression. PLoS Genet 2020; 16:e1008867. [PMID: 32555579 PMCID: PMC7326285 DOI: 10.1371/journal.pgen.1008867] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 06/30/2020] [Accepted: 05/18/2020] [Indexed: 12/16/2022] Open
Abstract
Recent research shows that introgression between closely-related species is an important source of adaptive alleles for a wide range of taxa. Typically, detection of adaptive introgression from genomic data relies on comparative analyses that require sequence data from both the recipient and the donor species. However, in many cases, the donor is unknown or the data is not currently available. Here, we introduce a genome-scan method—VolcanoFinder—to detect recent events of adaptive introgression using polymorphism data from the recipient species only. VolcanoFinder detects adaptive introgression sweeps from the pattern of excess intermediate-frequency polymorphism they produce in the flanking region of the genome, a pattern which appears as a volcano-shape in pairwise genetic diversity. Using coalescent theory, we derive analytical predictions for these patterns. Based on these results, we develop a composite-likelihood test to detect signatures of adaptive introgression relative to the genomic background. Simulation results show that VolcanoFinder has high statistical power to detect these signatures, even for older sweeps and for soft sweeps initiated by multiple migrant haplotypes. Finally, we implement VolcanoFinder to detect archaic introgression in European and sub-Saharan African human populations, and uncovered interesting candidates in both populations, such as TSHR in Europeans and TCHH-RPTN in Africans. We discuss their biological implications and provide guidelines for identifying and circumventing artifactual signals during empirical applications of VolcanoFinder. The process by which beneficial alleles are introduced into a species from a closely-related species is termed adaptive introgression. We present an analytically-tractable model for the effects of adaptive introgression on non-adaptive genetic variation in the genomic region surrounding the beneficial allele. The result we describe is a characteristic volcano-shaped pattern of increased variability that arises around the positively-selected site, and we introduce an open-source method VolcanoFinder to detect this signal in genomic data. Importantly, VolcanoFinder is a population-genetic likelihood-based approach, rather than a comparative-genomic approach, and can therefore probe genomic variation data from a single population for footprints of adaptive introgression, even from a priori unknown and possibly extinct donor species.
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Abied A, Bagadi A, Bordbar F, Pu Y, Augustino SM, Xue X, Xing F, Gebreselassie G, Han JL, Mwacharo JM, Ma Y, Zhao Q. Genomic Diversity, Population Structure, and Signature of Selection in Five Chinese Native Sheep Breeds Adapted to Extreme Environments. Genes (Basel) 2020; 11:genes11050494. [PMID: 32365888 PMCID: PMC7290715 DOI: 10.3390/genes11050494] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 11/30/2022] Open
Abstract
Through long term natural and artificial selection, domestic sheep (Ovis aries) have become adapted to a diverse range of agro-ecological environments and display multiple phenotypic traits. Characterization of diversity and selection signature is essential for genetic improvement, understanding of environmental adaptation, as well as utilization and conservation of sheep genetic resources. Here, we aimed to assess genomic diversity, population structure, and genomic selection among five Chinese native sheep breeds using 600K high density SNP genotypes. A total of 96 animals of the five breeds were selected from different geographical locations with extremely dry or humid conditions. We found a high proportion of informative SNPs, ranging from 93.3% in Yabuyi to 95.5% in Wadi, Hu, and Hetian sheep. The average pairwise population differentiation (FST) between the breeds was 0.048%, ranging from 0.022% to 0.054%, indicating their low to moderate differentiation. PCA, ADMIXTURE, and phylogenetic tree analyses revealed a clustering pattern of the five Chinese sheep breeds according to their geographical distribution, tail type, coat color, body size, and breeding history. The genomic regions under putative selection identified by FST and XP-EHH approaches frequently overlapped across the breeds, and spanned genes associated with adaptation to extremely dry or humid environments, innate and adaptive immune responses, and growth, wool, milk, and reproduction traits. The present study offers novel insight into genomic adaptation to dry and humid climates in sheep among other domestic animals and provides a valuable resource for further investigation. Moreover, it contributes useful information to sustainable utilization and conservation of sheep genetic resources.
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Affiliation(s)
- Adam Abied
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
- Dry Land Research Center (DLRC) and Animal Production, Agricultural Research Corporation (ARC), Wad Madani 511, Sudan;
| | - Alnoor Bagadi
- Dry Land Research Center (DLRC) and Animal Production, Agricultural Research Corporation (ARC), Wad Madani 511, Sudan;
| | - Farhad Bordbar
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Yabin Pu
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Serafino M.A. Augustino
- College of Animal Science and Technology, China Agricultural University (CAU), Beijing 100193, China;
| | - Xianglan Xue
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Feng Xing
- College of Animal Science, Talimu University (TU), Xinjiang, Alar 843300, China;
| | - Gebremedhin Gebreselassie
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China;
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Joram M. Mwacharo
- International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa 1108-2010, Ethiopia;
| | - Yuehui Ma
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Qianjun Zhao
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
- Correspondence:
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Abstract
Of all the big cats, or perhaps of all the endangered wildlife, the tiger may be both the most charismatic and most well-recognized flagship species in the world. The rapidly changing field of molecular genetics, particularly advances in genome sequencing technologies, has provided new tools to reconstruct what characterizes a tiger. Here we review how applications of molecular genomic tools have been used to depict the tiger's ancestral roots, phylogenetic hierarchy, demographic history, morphological diversity, and genetic patterns of diversification on both temporal and geographical scales. Tiger conservation, stabilization, and management are important areas that benefit from use of these genome resources for developing survival strategies for this charismatic megafauna both in situ and ex situ.
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Affiliation(s)
- Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China;
| | - Yue-Chen Liu
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China;
| | - Xiao Xu
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China;
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61
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Shen J, Hanif Q, Cao Y, Yu Y, Lei C, Zhang G, Zhao Y. Whole Genome Scan and Selection Signatures for Climate Adaption in Yanbian Cattle. Front Genet 2020; 11:94. [PMID: 32180793 PMCID: PMC7059643 DOI: 10.3389/fgene.2020.00094] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 01/28/2020] [Indexed: 12/15/2022] Open
Abstract
Yanbian cattle is inhabitant of North of China, exhibiting many phenotypic features, such as long, dense body hair, and abundant intramuscular fat, designed to combat the extreme cold climate adaption. In the current study, we studied the cold tolerance of nine Yanbian cattle by whole genome resequencing and compared with African tropical cattle, N’Dama, as a control group. Yanbian cattle was aligned to the Bos taurus reference genome (ARS-UCD1.2) yielding an average of 10.8 fold coverage. The positive selective sweep analysis for the cold adaption in Yanbian cattle were analyzed using composite likelihood ratio (CLR) and nucleotide diversity (θπ), resulting in 292 overlapped genes. The strongest selective signal was found on BTA16 with potential mutation in CORT gene, a regulatory gene of primary hormone in the hypothalamic-pituitary-adrenal (HPA) axis, is reported to be associated with the cold stress, representedfour missense mutations (c.269C > T, p.Lys90Ile; c.251A > G, p.Glu84Gly; c.112C > T, p.Pro38Ser; c.86G > A, p.Pro29His). Meanwhile another gene on BTA6, showed significantly higher selective sweep signals for a cold adapted trait for hair follicle and length development, FGF5 (fibroblast growth factor 5) with a missense mutation (c.191C > T, p.Ser64Phe). Moreover, cold adapted Yanbian cattle was statistically compared with the hot adapted N’Dama cattle, a taurine cattle reported to show superior heat tolerance than zebu cattle, making them better adapted to the hot regions of Africa. XP-CLR, Fst, and θπ ratio were used to compare both breeds, yielding 487, 924, and 346 genes respectively. Among the 12 overlapped genes, (CD36) (c.638A > G, p.Lys 213Arg) involved in fat digestion and absorption plays an important role in membrane transport of long-chain fatty acid and its expression could increase in cold exposure. Henceforth, our study provides a novel genetic insights into the cold climate adaptation of Yanbian cattle and identified three candidate genes (CORT, FGF5, and CD36), which can add to an understanding of the cold climate adaptation of Yanbian cattle.
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Affiliation(s)
- Jiafei Shen
- Key Laboratory of Beef Cattle Genetics and Breeding in Ministry of Agriculture and Rural Agriculture, Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, China.,College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Quratulain Hanif
- Computational Biology Laboratory, Department of Agricutural Biotechnology, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Pakistan
| | - Yang Cao
- Key Laboratory of Beef Cattle Genetics and Breeding in Ministry of Agriculture and Rural Agriculture, Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yongsheng Yu
- Key Laboratory of Beef Cattle Genetics and Breeding in Ministry of Agriculture and Rural Agriculture, Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Guoliang Zhang
- Key Laboratory of Beef Cattle Genetics and Breeding in Ministry of Agriculture and Rural Agriculture, Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yumin Zhao
- Key Laboratory of Beef Cattle Genetics and Breeding in Ministry of Agriculture and Rural Agriculture, Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, China
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62
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Sard NM, Smith SR, Homola JJ, Kanefsky J, Bravener G, Adams JV, Holbrook CM, Hrodey PJ, Tallon K, Scribner KT. RAPTURE (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics. Ecol Evol 2020; 10:1469-1488. [PMID: 32076528 PMCID: PMC7029094 DOI: 10.1002/ece3.6001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 12/18/2022] Open
Abstract
Genomic tools are lacking for invasive and native populations of sea lamprey (Petromyzon marinus). Our objective was to discover single nucleotide polymorphism (SNP) loci to conduct pedigree analyses to quantify reproductive contributions of adult sea lampreys and dispersion of sibling larval sea lampreys of different ages in Great Lakes tributaries. Additional applications of data were explored using additional geographically expansive samples. We used restriction site-associated DNA sequencing (RAD-Seq) to discover genetic variation in Duffins Creek (DC), Ontario, Canada, and the St. Clair River (SCR), Michigan, USA. We subsequently developed RAD capture baits to genotype 3,446 RAD loci that contained 11,970 SNPs. Based on RAD capture assays, estimates of variance in SNP allele frequency among five Great Lakes tributary populations (mean F ST 0.008; range 0.00-0.018) were concordant with previous microsatellite-based studies; however, outlier loci were identified that contributed substantially to spatial population genetic structure. At finer scales within streams, simulations indicated that accuracy in genetic pedigree reconstruction was high when 200 or 500 independent loci were used, even in situations of high spawner abundance (e.g., 1,000 adults). Based on empirical collections of larval sea lamprey genotypes, we found that age-1 and age-2 families of full and half-siblings were widely but nonrandomly distributed within stream reaches sampled. Using the genomic scale set of SNP loci developed in this study, biologists can rapidly genotype sea lamprey in non-native and native ranges to investigate questions pertaining to population structuring and reproductive ecology at previously unattainable scales.
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Affiliation(s)
- Nicholas M. Sard
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
- Biology DepartmentSUNY OswegoOswegoNew York
| | - Seth R. Smith
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
| | - Jared J. Homola
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
| | - Jeannette Kanefsky
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
| | | | - Jean V. Adams
- Great Lakes Science CenterU.S. Geological SurveyAnn ArborMichigan
| | - Christopher M. Holbrook
- Great Lakes Science CenterHammond Bay Biological StationU.S. Geological SurveyMillersburgMichigan
| | | | - Kevin Tallon
- Fisheries and Oceans CanadaSault Ste. MarieONCanada
| | - Kim T. Scribner
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
- Department of Integrative BiologyState UniversityEast LansingMichigan
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63
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Oh KP, Aldridge CL, Forbey JS, Dadabay CY, Oyler-McCance SJ. Conservation Genomics in the Sagebrush Sea: Population Divergence, Demographic History, and Local Adaptation in Sage-Grouse (Centrocercus spp.). Genome Biol Evol 2020; 11:2023-2034. [PMID: 31135036 DOI: 10.1093/gbe/evz112] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2019] [Indexed: 02/06/2023] Open
Abstract
Sage-grouse are two closely related iconic species of the North American West, with historically broad distributions across sagebrush-steppe habitat. Both species are dietary specialists on sagebrush during winter, with presumed adaptations to tolerate the high concentrations of toxic secondary metabolites that function as plant chemical defenses. Marked range contraction and declining population sizes since European settlement have motivated efforts to identify distinct population genetic variation, particularly that which might be associated with local genetic adaptation and dietary specialization of sage-grouse. We assembled a reference genome and performed whole-genome sequencing across sage-grouse from six populations, encompassing both species and including several populations on the periphery of the species ranges. Population genomic analyses reaffirmed genome-wide differentiation between greater and Gunnison sage-grouse, revealed pronounced intraspecific population structure, and highlighted important differentiation of a small isolated population of greater sage-grouse in the northwest of the range. Patterns of genome-wide differentiation were largely consistent with a hypothesized role of genetic drift due to limited gene flow among populations. Inferred ancient population demography suggested persistent declines in effective population sizes that have likely contributed to differentiation within and among species. Several genomic regions with single-nucleotide polymorphisms exhibiting extreme population differentiation were associated with candidate genes linked to metabolism of xenobiotic compounds. In vitro activity of enzymes isolated from sage-grouse livers supported a role for these genes in detoxification of sagebrush, suggesting that the observed interpopulation variation may underlie important local dietary adaptations, warranting close consideration for conservation strategies that link sage-grouse to the chemistry of local sagebrush.
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Affiliation(s)
- Kevin P Oh
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado
| | - Cameron L Aldridge
- Natural Resource Ecology Laboratory and Department of Ecosystem Sciences, Colorado State University in cooperation with U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado
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64
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Mekonnen YA, Gültas M, Effa K, Hanotte O, Schmitt AO. Identification of Candidate Signature Genes and Key Regulators Associated With Trypanotolerance in the Sheko Breed. Front Genet 2019; 10:1095. [PMID: 31803229 PMCID: PMC6872528 DOI: 10.3389/fgene.2019.01095] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/11/2019] [Indexed: 12/23/2022] Open
Abstract
African animal trypanosomiasis (AAT) is caused by a protozoan parasite that affects the health of livestock. Livestock production in Ethiopia is severely hampered by AAT and various controlling measures were not successful to eradicate the disease. AAT affects the indigenous breeds in varying degrees. However, the Sheko breed shows better trypanotolerance than other breeds. The tolerance attributes of Sheko are believed to be associated with its taurine genetic background but the genetic controls of these tolerance attributes of Sheko are not well understood. In order to investigate the level of taurine background in the genome, we compare the genome of Sheko with that of 11 other African breeds. We find that Sheko has an admixed genome composed of taurine and indicine ancestries. We apply three methods: (i) The integrated haplotype score (iHS), (ii) the standardized log ratio of integrated site specific extended haplotype homozygosity between populations (Rsb), and (iii) the composite likelihood ratio (CLR) method to discover selective sweeps in the Sheko genome. We identify 99 genomic regions harboring 364 signature genes in Sheko. Out of the signature genes, 15 genes are selected based on their biological importance described in the literature. We also identify 13 overrepresented pathways and 10 master regulators in Sheko using the TRANSPATH database in the geneXplain platform. Most of the pathways are related with oxidative stress responses indicating a possible selection response against the induction of oxidative stress following trypanosomiasis infection in Sheko. Furthermore, we present for the first time the importance of master regulators involved in trypanotolerance not only for the Sheko breed but also in the context of cattle genomics. Our finding shows that the master regulator Caspase is a key protease which plays a major role for the emergence of adaptive immunity in harmony with the other master regulators. These results suggest that designing and implementing genetic intervention strategies is necessary to improve the performance of susceptible animals. Moreover, the master regulatory analysis suggests potential candidate therapeutic targets for the development of new drugs for trypanosomiasis treatment.
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Affiliation(s)
- Yonatan Ayalew Mekonnen
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, Göttingen, Germany
| | - Mehmet Gültas
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, Göttingen, Germany.,Center for Integrated Breeding Research (CiBreed), University of Göttingen, Göttingen, Germany
| | - Kefena Effa
- Animal Biosciences, National Program Coordinator for African Dairy Genetic Gain, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Cells, Organisms amd Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.,LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Armin O Schmitt
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, Göttingen, Germany.,Center for Integrated Breeding Research (CiBreed), University of Göttingen, Göttingen, Germany
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65
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Brandt JR, van Coeverden de Groot PJ, Witt KE, Engelbrektsson PK, Helgen KM, Malhi RS, Ryder OA, Roca AL. Genetic Structure and Diversity Among Historic and Modern Populations of the Sumatran Rhinoceros (Dicerorhinus sumatrensis). J Hered 2019; 109:553-565. [PMID: 29684146 DOI: 10.1093/jhered/esy019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/14/2018] [Indexed: 11/13/2022] Open
Abstract
The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control region mitochondrial (mt) DNA, identifying 17 distinct mitochondrial haplotypes across modern (N = 13) and museum (N = 26) samples. Museum specimens from Laos and Myanmar had divergent mtDNA, consistent with the placement of western mainland rhinos into the distinct subspecies D. s. lasiotis (presumed extinct). Haplotypes from Bornean rhinos were highly diverse, but dissimilar from those of other regions, supporting the distinctiveness of the subspecies D. s. harrissoni. Rhinos from Sumatra and Peninsular Malaysia shared mtDNA haplotypes, consistent with their traditional placement into a single subspecies D. s sumatrensis. Modern samples of D. s. sumatrensis were genotyped at 18 microsatellite loci. Rhinos within Sumatra formed 2 sub-populations, likely separated by the Barisan Mountains, though with only modest genetic differentiation between them. There are so few remaining Sumatran rhinoceros that separate management strategies for subspecies or subpopulations may not be viable, while each surviving rhino pedigree is likely to retain alleles found in no other individuals. Given the low population size and low reproductive potential of Sumatran rhinos, rapid genetic erosion is inevitable, though an under-appreciated concern is the potential for fixation of harmful genetic variants. Both concerns underscore 2 overriding priorities for the species: 1) translocation of wild rhinos to ex situ facilities, and 2) collection and storage of gametes and cell lines from every surviving captive and wild individual.
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Affiliation(s)
- Jessica R Brandt
- Department of Animal Sciences, University of Illinois Urbana-Champaign (UIUC), Urbana, IL.,Department of Biology, Marian University, Fond du Lac, WI
| | | | | | | | - Kristofer M Helgen
- School of Biological Sciences and Environment Institute, University of Adelaide, Adelaide, SA, Australia
| | - Ripan S Malhi
- Department of Anthropology, UIUC, Urbana, IL.,Carl R. Woese Institute for Genomic Biology, UIUC, Urbana, IL
| | - Oliver A Ryder
- Institute of Conservation Research, San Diego Zoo Global, Escondido, CA
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois Urbana-Champaign (UIUC), Urbana, IL.,Carl R. Woese Institute for Genomic Biology, UIUC, Urbana, IL
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66
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López ME, Linderoth T, Norris A, Lhorente JP, Neira R, Yáñez JM. Multiple Selection Signatures in Farmed Atlantic Salmon Adapted to Different Environments Across Hemispheres. Front Genet 2019; 10:901. [PMID: 31632437 PMCID: PMC6786245 DOI: 10.3389/fgene.2019.00901] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 08/26/2019] [Indexed: 01/08/2023] Open
Abstract
Domestication of Atlantic salmon started approximately 40 years ago, using artificial selection through genetic improvement programs. Selection is likely to have imposed distinctive signatures on the salmon genome, which are often characterized by high genetic differentiation across population and/or reduction in genetic diversity in regions associated to traits under selection. The identification of such selection signatures may give insights into the candidate genomic regions of biological and commercial interest. Here, we used three complementary statistics to detect selection signatures, two haplotype-based (iHS and XP-EHH), and one FST-based method (BayeScan) among four populations of Atlantic salmon with a common genetic origin. Several regions were identified for these techniques that harbored genes, such as kind1 and chp2, which have been associated with growth-related traits or the kcnb2 gene related to immune system in Atlantic salmon, making them particularly relevant in the context of aquaculture. Our results provide candidate genes to inform the evolutionary and biological mechanisms controlling complex selected traits in Atlantic salmon.
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Affiliation(s)
- María Eugenia López
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tyler Linderoth
- Department of Integrative Biology, University of California, Berkeley, CA, United States
| | - Ashie Norris
- Marine Harvest, Kindrum, Fanad, C. Donegal, Ireland
| | | | - Roberto Neira
- Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - José Manuel Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile.,Núcleo Milenio INVASAL, Concepción, Chile
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67
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Bahbahani H, Musa HH, Wragg D, Shuiep ES, Almathen F, Hanotte O. Genome Diversity and Signatures of Selection for Production and Performance Traits in Dromedary Camels. Front Genet 2019; 10:893. [PMID: 31608121 PMCID: PMC6761857 DOI: 10.3389/fgene.2019.00893] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 08/23/2019] [Indexed: 12/20/2022] Open
Abstract
Dromedary camels (Camelus dromedarius) are single-humped animals found throughout the deserts of Africa, the Arabian Peninsula, and the southwest of Asia. This well-adapted species is mainly used for milk and meat production, although some specific types exhibit superior running performance and are used in racing competitions. However, neither performance nor production camels are bred under intensive genomic selection programs with specific aims to improve these traits. In this study, the full genome sequence data of six camels from the Arabian Peninsula and the genotyping-by-sequencing data of 44 camels (29 packing and 15 racing) from Sudan were analyzed to assess their genome diversities, relationships, and candidate signatures of positive selection. Genome ADMIXTURE and principle component analyses indicate clear geographic separation between the Sudanese and the Arabian Peninsula camels, but with no population-specific genetic distinction within populations. Camel samples from the Arabian Peninsula show higher mean heterozygosity (0.560 ± 0.003) than those from Sudan (0.347 ± 0.003). Analyses of signatures of selection, using pooled heterozygosity (Hp) approach, in the Sudanese camels revealed 176, 189, and 308 candidate regions under positive selection in the combined and packing and racing camel populations, respectively. These regions host genes that might be associated with adaptation to arid environment, dairy traits, energy homeostasis, and chondrogenesis. Eight regions show high genetic differentiation, based on Fst analysis, between the Sudanese packing and racing camel types. Genes associated with chondrogenesis, energy balance, and urinary system development were found within these regions. Our results advocate for further detailed investigation of the genome of the dromedary camel to identify and characterize genes and variants associated with their valuable phenotypic traits. The results of which may support the development of breeding programs to improve the production and performance traits of this unique domesticated species.
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Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait City, Kuwait
| | - Hassan H Musa
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum North, Sudan
| | - David Wragg
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, United Kingdom
| | - Eltahir S Shuiep
- Department of Animal Production, Faculty of Agricultural and Environmental Sciences, University of Gadarif, Gadarif State, Sudan
| | - Faisal Almathen
- Department of Public Health, College of Veterinary Medicine, King Faisal University, Al-Hasa, Saudi Arabia
| | - Olivier Hanotte
- LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
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68
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An Evolutionary Perspective on the Impact of Genomic Copy Number Variation on Human Health. J Mol Evol 2019; 88:104-119. [PMID: 31522275 DOI: 10.1007/s00239-019-09911-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Abstract
Copy number variants (CNVs), deletions and duplications of segments of DNA, account for at least five times more variable base pairs in humans than single-nucleotide variants. Several common CNVs were shown to change coding and regulatory sequences and thus dramatically affect adaptive phenotypes involving immunity, perception, metabolism, skin structure, among others. Some of these CNVs were also associated with susceptibility to cancer, infection, and metabolic disorders. These observations raise the possibility that CNVs are a primary contributor to human phenotypic variation and consequently evolve under selective pressures. Indeed, locus-specific haplotype-level analyses revealed signatures of natural selection on several CNVs. However, more traditional tests of selection which are often applied to single-nucleotide variation often have diminished statistical power when applied to CNVs because they often do not show strong linkage disequilibrium with nearby variants. Recombination-based formation mechanisms of CNVs lead to frequent recurrence and gene conversion events, breaking the linkage disequilibrium involving CNVs. Similar methodological challenges also prevent routine genome-wide association studies to adequately investigate the impact of CNVs on heritable human disease. Thus, we argue that the full relevance of CNVs to human health and evolution is yet to be elucidated. We further argue that a holistic investigation of formation mechanisms within an evolutionary framework would provide a powerful framework to understand the functional and biomedical impact of CNVs. In this paper, we review several cases where studies reveal diverse evolutionary histories and unexpected functional consequences of CNVs. We hope that this review will encourage further work on CNVs by both evolutionary and medical geneticists.
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69
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Preite V, Sailer C, Syllwasschy L, Bray S, Ahmadi H, Krämer U, Yant L. Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180243. [PMID: 31154972 PMCID: PMC6560266 DOI: 10.1098/rstb.2018.0243] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2019] [Indexed: 01/09/2023] Open
Abstract
It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, Arabidopsis halleri and Arabidopsis arenosa, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide polymorphisms in several A. halleri genes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Veronica Preite
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Christian Sailer
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Lara Syllwasschy
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Sian Bray
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Hassan Ahmadi
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Ute Krämer
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Levi Yant
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
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70
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Preite V, Sailer C, Syllwasschy L, Bray S, Ahmadi H, Krämer U, Yant L. Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180243. [PMID: 31154972 DOI: 10.5061/dryad.jg30j4v] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, Arabidopsis halleri and Arabidopsis arenosa, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide polymorphisms in several A. halleri genes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Veronica Preite
- 1 Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum , 44801 Bochum , Germany
| | - Christian Sailer
- 2 Cell and Developmental Biology, John Innes Centre , Norwich NR4 7UH , UK
| | - Lara Syllwasschy
- 1 Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum , 44801 Bochum , Germany
| | - Sian Bray
- 2 Cell and Developmental Biology, John Innes Centre , Norwich NR4 7UH , UK
| | - Hassan Ahmadi
- 1 Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum , 44801 Bochum , Germany
| | - Ute Krämer
- 1 Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum , 44801 Bochum , Germany
| | - Levi Yant
- 2 Cell and Developmental Biology, John Innes Centre , Norwich NR4 7UH , UK
- 3 School of Life Sciences, University of Nottingham , Nottingham NG7 2RD , UK
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71
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Preite V, Sailer C, Syllwasschy L, Bray S, Ahmadi H, Krämer U, Yant L. Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils. Philos Trans R Soc Lond B Biol Sci 2019. [PMID: 31154972 DOI: 10.1101/459362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, Arabidopsis halleri and Arabidopsis arenosa, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide polymorphisms in several A. halleri genes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Veronica Preite
- 1 Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum , 44801 Bochum , Germany
| | - Christian Sailer
- 2 Cell and Developmental Biology, John Innes Centre , Norwich NR4 7UH , UK
| | - Lara Syllwasschy
- 1 Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum , 44801 Bochum , Germany
| | - Sian Bray
- 2 Cell and Developmental Biology, John Innes Centre , Norwich NR4 7UH , UK
| | - Hassan Ahmadi
- 1 Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum , 44801 Bochum , Germany
| | - Ute Krämer
- 1 Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum , 44801 Bochum , Germany
| | - Levi Yant
- 2 Cell and Developmental Biology, John Innes Centre , Norwich NR4 7UH , UK
- 3 School of Life Sciences, University of Nottingham , Nottingham NG7 2RD , UK
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72
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Borelli G, Fiamenghi MB, dos Santos LV, Carazzolle MF, Pereira GAG, José J. Positive Selection Evidence in Xylose-Related Genes Suggests Methylglyoxal Reductase as a Target for the Improvement of Yeasts' Fermentation in Industry. Genome Biol Evol 2019; 11:1923-1938. [PMID: 31070742 PMCID: PMC6637916 DOI: 10.1093/gbe/evz036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2019] [Indexed: 12/12/2022] Open
Abstract
Xylose assimilation and fermentation are important traits for second generation ethanol production. However, some genomic features associated with this pentose sugar's metabolism remain unknown in yeasts. Comparative genomics studies have led to important insights in this field, but we are still far from completely understanding endogenous yeasts' xylose metabolism. In this work, we carried out a deep evolutionary analysis suited for comparative genomics of xylose-consuming yeasts, searching for of positive selection on genes associated with glucose and xylose metabolism in the xylose-fermenters' clade. Our investigation detected positive selection fingerprints at this clade not only among sequences of important genes for xylose metabolism, such as xylose reductase and xylitol dehydrogenase, but also in genes expected to undergo neutral evolution, such as the glycolytic gene phosphoglycerate mutase. In addition, we present expansion, positive selection marks, and convergence as evidence supporting the hypothesis that natural selection is shaping the evolution of the little studied methylglyoxal reductases. We propose a metabolic model suggesting that selected codons among these proteins caused a putative change in cofactor preference from NADPH to NADH that alleviates cellular redox imbalance. These findings provide a wider look into pentose metabolism of yeasts and add this previously overlooked piece into the intricate puzzle of oxidative imbalance. Although being extensively discussed in evolutionary works the awareness of selection patterns is recent in biotechnology researches, rendering insights to surpass the reached status quo in many of its subareas.
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Affiliation(s)
- Guilherme Borelli
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
| | - Mateus Bernabe Fiamenghi
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
| | - Leandro Vieira dos Santos
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Marcelo Falsarella Carazzolle
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Juliana José
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
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Szpak M, Xue Y, Ayub Q, Tyler‐Smith C. How well do we understand the basis of classic selective sweeps in humans? FEBS Lett 2019; 593:1431-1448. [DOI: 10.1002/1873-3468.13447] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/29/2019] [Accepted: 05/17/2019] [Indexed: 12/14/2022]
Affiliation(s)
| | - Yali Xue
- The Wellcome Sanger Institute Hinxton UK
| | - Qasim Ayub
- School of Science Monash University Malaysia Bandar Sunway Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform Monash University Malaysia Genomics Facility Bandar Sunway Malaysia
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74
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Montes DE, Braz CU, Ribeiro AMF, Cavani L, Barbero MMD, Albuquerque LG, Curi RA, Oliveira HN. Selection signatures in candidate genes and QTL for reproductive traits in Nellore heifers. Anim Reprod Sci 2019; 207:1-8. [PMID: 31266598 DOI: 10.1016/j.anireprosci.2019.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/18/2019] [Accepted: 06/04/2019] [Indexed: 12/19/2022]
Abstract
The identification of selection signature genes may help to detect genomic regions that underwent artificial selection and contributed to phenotypic diversity. The aim of this study, therefore, was to detect selection signatures in candidate genes and quantitative trait locus (QTL) for reproductive traits in a Nellore population being selected for sexual precocity. A total of 2035 Nellore heifers, sourced from breeding programs focused on sexual precocity, were used. Candidate genes and some specific QTL related to reproductive traits were chosen based on published literature and Animal QTL databases, respectively, for investigation whether these regions were affected by selection. Selection signature DNA sequences were detected in the selected regions using the extended haplotype homozygosity (EHH) and relative extended haplotype homozygosity (REHH) methods. From 22,241 single nucleotide polymorphisms (SNPs) located in the candidate genes and QTL, 17,312 SNPs generated 2756 haplotype blocks. A total of 7518 EHH tests were analyzed using haplotypes with a frequency of more than 25%, for which there were 39 tests that were significant for REHH (P<0.01). Selection signature DNA sequences were detected that contained several QTLs for important reproductive traits in cattle, suggesting that reproductive traits may have been affected by selection for sexual precocity in this population. Forty-six genes were located in the selection signature regions, whereas 24 genes participated in important biological processes or pathways that may underlie sexual precocity. These results indicate there are possible molecular mechanisms related to sexual precocity in the Nellore breed.
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Affiliation(s)
- Donicer E Montes
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil; Universidad de Sucre, Facultad de Ciencias Agropecuarias, Departamento de Zootecnia, Sincelejo, Colombia
| | - Camila U Braz
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil
| | - André M F Ribeiro
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil
| | - Lígia Cavani
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil
| | - Marina M D Barbero
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil
| | - Lucia G Albuquerque
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil
| | - Rogério A Curi
- São Paulo State University (UNESP), School of Veterinary Medicine and Animal Science, Campus (Botucatu), Department of Animal Improvement and Nutrition, Brazil
| | - Henrique N Oliveira
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil.
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75
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Manzari Z, Mehrabani-Yeganeh H, Nejati-Javaremi A, Moradi MH, Gholizadeh M. Detecting selection signatures in three Iranian sheep breeds. Anim Genet 2019; 50:298-302. [PMID: 30883840 DOI: 10.1111/age.12772] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2018] [Indexed: 12/26/2022]
Abstract
The objective of genome mapping is to achieve valuable insight into the connection between gene variants (genotype) and observed traits (phenotype). Part of that objective is to understand the selective forces that have operated on a population. Finding links between genotype-phenotype changes makes it possible to identify selective sweeps by patterns of genetic variation and linkage disequilibrium. Based on Illumina 50KSNP chip data, two approaches, XP-EHH (cross-population extend haplotype homozygosity) and FST (fixation index), were carried out in this research to identify selective sweeps in the genome of three Iranian local sheep breeds: Baluchi (n = 86), Lori-Bakhtiari (n = 45) and Zel (n = 45). Using both methods, 93 candidate genomic regions were identified as harboring putative selective sweeps. Bioinformatics analysis of the genomic regions showed that signatures of selection related to multiple candidate genes, such as HOXB9, HOXB13, ACAN, NPR2, TRIL, AOX1, CSF2, GHR, TNS2, SPAG8, HINT2, ALS2, AAAS, RARG, SYCP2, CAV1, PPP1R3D, PLA2G7, TTLL7 and C20orf10, that play a role in skeletal system and tail, sugar and energy metabolisms, growth, reproduction, immune and nervous system traits. Our findings indicated diverse genomic selection during the domestication of Iranian sheep breeds.
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Affiliation(s)
- Z Manzari
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, 3158711167-4111, Iran
| | - H Mehrabani-Yeganeh
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, 3158711167-4111, Iran
| | - A Nejati-Javaremi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, 3158711167-4111, Iran
| | - M H Moradi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, 38156-8-8349, Iran
| | - M Gholizadeh
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, Sari, 4818168984, Iran
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76
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Feulner PGD, Seehausen O. Genomic insights into the vulnerability of sympatric whitefish species flocks. Mol Ecol 2019; 28:615-629. [PMID: 30554444 DOI: 10.1111/mec.14977] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 12/24/2022]
Abstract
The erosion of habitat heterogeneity can reduce species diversity directly but can also lead to the loss of distinctiveness of sympatric species through speciation reversal. We know little about changes in genomic differentiation during the early stages of these processes, which can be mediated by anthropogenic perturbation. Here, we analyse three sympatric whitefish species (Coregonus spp) sampled across two neighbouring and connected Swiss pre-alpine lakes, which have been differentially affected by anthropogenic eutrophication. Our data set comprises 16,173 loci genotyped across 138 whitefish using restriction-site associated DNA sequencing (RADseq). Our analysis suggests that in each of the two lakes, the population of a different, but ecologically similar, whitefish species declined following a recent period of eutrophication. Genomic signatures consistent with hybridization are more pronounced in the more severely impacted lake. Comparisons between sympatric pairs of whitefish species with contrasting ecology, where one is shallow benthic and the other one more profundal pelagic, reveal genomic differentiation that is largely correlated along the genome, while differentiation is uncorrelated between pairs of allopatric provenance with similar ecology. We identify four genomic loci that provide evidence of parallel divergent adaptation between the shallow benthic species and the two different more profundal species. Functional annotations available for two of those loci are consistent with divergent ecological adaptation. Our genomic analysis indicates the action of divergent natural selection between sympatric whitefish species in pre-alpine lakes and reveals the vulnerability of these species to anthropogenic alterations of the environment and associated adaptive landscape.
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Affiliation(s)
- Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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77
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Ahbara A, Bahbahani H, Almathen F, Al Abri M, Agoub MO, Abeba A, Kebede A, Musa HH, Mastrangelo S, Pilla F, Ciani E, Hanotte O, Mwacharo JM. Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep. Front Genet 2019; 9:699. [PMID: 30687385 PMCID: PMC6334744 DOI: 10.3389/fgene.2018.00699] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 12/13/2018] [Indexed: 12/03/2022] Open
Abstract
Variations in body weight and in the distribution of body fat are associated with feed availability, thermoregulation, and energy reserve. Ethiopia is characterized by distinct agro-ecological and human ethnic farmer diversity of ancient origin, which have impacted on the variation of its indigenous livestock. Here, we investigate autosomal genome-wide profiles of 11 Ethiopian indigenous sheep populations using the Illumina Ovine 50 K SNP BeadChip assay. Sheep from the Caribbean, Europe, Middle East, China, and western, northern and southern Africa were included to address globally, the genetic variation and history of Ethiopian populations. Population relationship and structure analysis separated Ethiopian indigenous fat-tail sheep from their North African and Middle Eastern counterparts. It indicates two main genetic backgrounds and supports two distinct genetic histories for African fat-tail sheep. Within Ethiopian sheep, our results show that the short fat-tail sheep do not represent a monophyletic group. Four genetic backgrounds are present in Ethiopian indigenous sheep but at different proportions among the fat-rump and the long fat-tail sheep from western and southern Ethiopia. The Ethiopian fat-rump sheep share a genetic background with Sudanese thin-tail sheep. Genome-wide selection signature analysis identified eight putative candidate regions spanning genes influencing growth traits and fat deposition (NPR2, HINT2, SPAG8, INSR), development of limbs and skeleton, and tail formation (ALX4, HOXB13, BMP4), embryonic development of tendons, bones and cartilages (EYA2, SULF2), regulation of body temperature (TRPM8), body weight and height variation (DIS3L2), control of lipogenesis and intracellular transport of long-chain fatty acids (FABP3), the occurrence and morphology of horns (RXFP2), and response to heat stress (DNAJC18). Our findings suggest that Ethiopian fat-tail sheep represent a uniquely admixed but distinct genepool that presents an important resource for understanding the genetic control of skeletal growth, fat metabolism and associated physiological processes.
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Affiliation(s)
- Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya
| | - Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Mohammed Al Abri
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | | | - Ayelle Abeba
- Debre Berhan Research Centre, Debre Berhan, Ethiopia
| | - Adebabay Kebede
- Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Hassan Hussein Musa
- Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie e Forestali, Viale delle Scienze, Università Palermo, Palermo, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari “Aldo Moro ”, Bari, Italy
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M. Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
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78
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López ME, Benestan L, Moore J, Perrier C, Gilbey J, Di Genova A, Maass A, Diaz D, Lhorente J, Correa K, Neira R, Bernatchez L, Yáñez JM. Comparing genomic signatures of domestication in two Atlantic salmon ( Salmo salar L.) populations with different geographical origins. Evol Appl 2019; 12:137-156. [PMID: 30622641 PMCID: PMC6304691 DOI: 10.1111/eva.12689] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 06/29/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022] Open
Abstract
Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In this study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins, respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins, respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population-specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point toward a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps.
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Affiliation(s)
- Maria E. López
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileSantiagoChile
- Facultad de Ciencias AgronómicasUniversidad de ChileSantiagoChile
| | - Laura Benestan
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - Jean‐Sebastien Moore
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - Charles Perrier
- Centre d’Écologie Fonctionnelle et ÉvolutiveUnité Mixte de Recherche CNRS 5175MontpellierFrance
| | - John Gilbey
- Marine Scotland ScienceFreshwater Fisheries LaboratoryFaskallyPitlochryUK
| | - Alex Di Genova
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | - Alejandro Maass
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | - Diego Diaz
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | | | | | - Roberto Neira
- Facultad de Ciencias AgronómicasUniversidad de ChileSantiagoChile
| | - Louis Bernatchez
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - José M. Yáñez
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileSantiagoChile
- AquainnovoPuerto MonttChile
- Núcleo Milenio INVASALConcepciónChile
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79
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Bamba M, Kawaguchi YW, Tsuchimatsu T. Plant adaptation and speciation studied by population genomic approaches. Dev Growth Differ 2018; 61:12-24. [DOI: 10.1111/dgd.12578] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/22/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Masaru Bamba
- Department of Biology (Frontier Science Program); Graduate School of Science and Engineering; Chiba University; Chiba Japan
| | - Yawako W. Kawaguchi
- Department of Biology (Frontier Science Program); Graduate School of Science and Engineering; Chiba University; Chiba Japan
| | - Takashi Tsuchimatsu
- Department of Biology; Graduate School of Science; Chiba University; Chiba Japan
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80
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Sailer C, Babst-Kostecka A, Fischer MC, Zoller S, Widmer A, Vollenweider P, Gugerli F, Rellstab C. Transmembrane transport and stress response genes play an important role in adaptation of Arabidopsis halleri to metalliferous soils. Sci Rep 2018; 8:16085. [PMID: 30382172 PMCID: PMC6208402 DOI: 10.1038/s41598-018-33938-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/09/2018] [Indexed: 12/17/2022] Open
Abstract
When plants adapt to local environments, strong signatures of selection are expected in the genome, particularly in high-stress environments such as trace metal element enriched (metalliferous) soils. Using Arabidopsis halleri, a model species for metal homeostasis and adaptation to extreme environments, we identifid genes, gene variants, and pathways that are associated with soil properties and may thus contribute to adaptation to high concentrations of trace metal elements. We analysed whole-genome Pool-seq data from two metallicolous (from metalliferous soils) and two non-metallicolous populations (in total 119 individuals) and associated allele frequencies of the identified single-nucleotide polymorphisms (SNPs) with soil variables measured on site. Additionally, we accounted for polygenic adaptation by searching for gene pathways showing enrichment of signatures of selection. Out of >2.5 million SNPs, we identified 57 SNPs in 19 genes that were significantly associated with soil variables and are members of three enriched pathways. At least three of these candidate genes and pathways are involved in transmembrane transport and/or associated with responses to various stresses such as oxidative stress. We conclude that both allocation and detoxification processes play a crucial role in A. halleri for coping with these unfavourable conditions.
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Affiliation(s)
- Christian Sailer
- WSL Swiss Federal Research Institute, Birmensdorf, 8903, Switzerland.
- ETH Zürich, Institute of Integrative Biology, Zürich, 8092, Switzerland.
| | | | - Martin C Fischer
- ETH Zürich, Institute of Integrative Biology, Zürich, 8092, Switzerland
| | - Stefan Zoller
- ETH Zürich, Genetic Diversity Centre, Zürich, 8092, Switzerland
| | - Alex Widmer
- ETH Zürich, Institute of Integrative Biology, Zürich, 8092, Switzerland
| | | | - Felix Gugerli
- WSL Swiss Federal Research Institute, Birmensdorf, 8903, Switzerland
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81
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Goodswen SJ, Kennedy PJ, Ellis JT. A Gene-Based Positive Selection Detection Approach to Identify Vaccine Candidates Using Toxoplasma gondii as a Test Case Protozoan Pathogen. Front Genet 2018; 9:332. [PMID: 30177953 PMCID: PMC6109633 DOI: 10.3389/fgene.2018.00332] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/02/2018] [Indexed: 11/22/2022] Open
Abstract
Over the last two decades, various in silico approaches have been developed and refined that attempt to identify protein and/or peptide vaccines candidates from informative signals encoded in protein sequences of a target pathogen. As to date, no signal has been identified that clearly indicates a protein will effectively contribute to a protective immune response in a host. The premise for this study is that proteins under positive selection from the immune system are more likely suitable vaccine candidates than proteins exposed to other selection pressures. Furthermore, our expectation is that protein sequence regions encoding major histocompatibility complexes (MHC) binding peptides will contain consecutive positive selection sites. Using freely available data and bioinformatic tools, we present a high-throughput approach through a pipeline that predicts positive selection sites, protein subcellular locations, and sequence locations of medium to high T-Cell MHC class I binding peptides. Positive selection sites are estimated from a sequence alignment by comparing rates of synonymous (dS) and non-synonymous (dN) substitutions among protein coding sequences of orthologous genes in a phylogeny. The main pipeline output is a list of protein vaccine candidates predicted to be naturally exposed to the immune system and containing sites under positive selection. Candidates are ranked with respect to the number of consecutive sites located on protein sequence regions encoding MHCI-binding peptides. Results are constrained by the reliability of prediction programs and quality of input data. Protein sequences from Toxoplasma gondii ME49 strain (TGME49) were used as a case study. Surface antigen (SAG), dense granules (GRA), microneme (MIC), and rhoptry (ROP) proteins are considered worthy T. gondii candidates. Given 8263 TGME49 protein sequences processed anonymously, the top 10 predicted candidates were all worthy candidates. In particular, the top ten included ROP5 and ROP18, which are T. gondii virulence determinants. The chance of randomly selecting a ROP protein was 0.2% given 8263 sequences. We conclude that the approach described is a valuable addition to other in silico approaches to identify vaccines candidates worthy of laboratory validation and could be adapted for other apicomplexan parasite species (with appropriate data).
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Affiliation(s)
- Stephen J Goodswen
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Paul J Kennedy
- School of Software, Faculty of Engineering and Information Technology, Centre for Artificial Intelligence, University of Technology Sydney, Ultimo, NSW, Australia
| | - John T Ellis
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
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82
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Early selection of bZIP73 facilitated adaptation of japonica rice to cold climates. Nat Commun 2018; 9:3302. [PMID: 30120236 PMCID: PMC6098049 DOI: 10.1038/s41467-018-05753-w] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 06/08/2018] [Indexed: 12/17/2022] Open
Abstract
Cold stress is a major factor limiting production and geographic distribution of rice (Oryza sativa). Although the growth range of japonica subspecies has expanded northward compared to modern wild rice (O. rufipogon), the molecular basis of the adaptation remains unclear. Here we report bZIP73, a bZIP transcription factor-coding gene with only one functional polymorphism (+511 G>A) between the two subspecies japonica and indica, may have facilitated japonica adaptation to cold climates. We show the japonica version of bZIP73 (bZIP73Jap) interacts with bZIP71 and modulates ABA levels and ROS homeostasis. Evolutionary and population genetic analyses suggest bZIP73 has undergone balancing selection; the bZIP73Jap allele has firstly selected from standing variations in wild rice and likely facilitated cold climate adaptation during initial japonica domestication, while the indica allele bZIP73Ind was subsequently selected for reasons that remain unclear. Our findings reveal early selection of bZIP73Jap may have facilitated climate adaptation of primitive rice germplasms. Japonica rice can grow further north than wild or indica rice and is more tolerant of cold climates. Here, the authors show that bZIP73 likely underwent selection in the early phase of rice domestication to facilitate cold tolerance in japonica by modulating ABA and ROS homeostasis.
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83
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Bahbahani H, Afana A, Wragg D. Genomic signatures of adaptive introgression and environmental adaptation in the Sheko cattle of southwest Ethiopia. PLoS One 2018; 13:e0202479. [PMID: 30114214 PMCID: PMC6095569 DOI: 10.1371/journal.pone.0202479] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 08/04/2018] [Indexed: 11/23/2022] Open
Abstract
Although classified as an African taurine breed, the genomes of Sheko cattle are an admixture of Asian zebu and African taurine ancestries. They populate the humid Bench Maji zone in Sheko and Bench districts in the south-western part of Ethiopia and are considered as a trypanotolerant breed with high potential for dairy production. Here, we investigate the genome of Sheko cattle for candidate signatures of adaptive introgression and positive selection using medium density genome-wide SNP data. Following locus-ancestry deviation analysis, 15 and 72 genome regions show substantial excess and deficiency in Asian zebu ancestry, respectively. Nine and 23 regions show candidate signatures of positive selection following extended haplotype homozygosity (EHH)-based analyses (iHS and Rsb), respectively. The results support natural selection before admixture for one iHS, one Rsb and three zebu ancestry-deficient regions. Genes and/or QTL associated with bovine immunity, fertility, heat tolerance, trypanotolerance and lactation are present within candidate selected regions. The identification of candidate regions under selection in Sheko cattle warrants further investigation of a larger sample size using full genome sequence data to better characterise the underlying haplotypes. The results can then support informative genomic breeding programmes to sustainably enhance livestock productivity in East African trypanosomosis infested areas.
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Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait City, Kuwait
- * E-mail: ,
| | - Arwa Afana
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait City, Kuwait
| | - David Wragg
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, United Kingdom
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84
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Lawal RA, Al-Atiyat RM, Aljumaah RS, Silva P, Mwacharo JM, Hanotte O. Whole-Genome Resequencing of Red Junglefowl and Indigenous Village Chicken Reveal New Insights on the Genome Dynamics of the Species. Front Genet 2018; 9:264. [PMID: 30079080 PMCID: PMC6062655 DOI: 10.3389/fgene.2018.00264] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/29/2018] [Indexed: 12/13/2022] Open
Abstract
The red junglefowl Gallus gallus is the main progenitor of domestic chicken, the commonest livestock species, outnumbering humans by an approximate ratio of six to one. The genetic control for production traits have been well studied in commercial chicken, but the selection pressures underlying unique adaptation and production to local environments remain largely unknown in indigenous village chicken. Likewise, the genome regions under positive selection in the wild red junglefowl remain untapped. Here, using the pool heterozygosity approach, we analyzed indigenous village chicken populations from Ethiopia, Saudi Arabia, and Sri Lanka, alongside six red junglefowl, for signatures of positive selection across the autosomes. Two red junglefowl candidate selected regions were shared with all domestic chicken populations. Four candidates sweep regions, unique to and shared among all indigenous domestic chicken, were detected. Only one region includes annotated genes (TSHR and GTF2A1). Candidate regions that were unique to each domestic chicken population with functions relating to adaptation to temperature gradient, production, reproduction and immunity were identified. Our results provide new insights on the consequence of the selection pressures that followed domestication on the genome landscape of the domestic village chicken.
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Affiliation(s)
- Raman A. Lawal
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Raed M. Al-Atiyat
- Genetics and Biotechnology, Animal Science Department, Agriculture Faculty, Mutah University, Karak, Jordan
- Animal Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Riyadh S. Aljumaah
- Animal Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Pradeepa Silva
- Department of Animal Sciences, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - Joram M. Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- LiveGene – CTLGH, International Livestock Research Institute, Addis Ababa, Ethiopia
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85
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Nouhaud P, Gautier M, Gouin A, Jaquiéry J, Peccoud J, Legeai F, Mieuzet L, Smadja CM, Lemaitre C, Vitalis R, Simon JC. Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races. Mol Ecol 2018; 27:3287-3300. [PMID: 30010213 DOI: 10.1111/mec.14799] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 06/01/2018] [Accepted: 06/11/2018] [Indexed: 01/01/2023]
Abstract
Identifying the genomic bases of adaptation to novel environments is a long-term objective in evolutionary biology. Because genetic differentiation is expected to increase between locally adapted populations at the genes targeted by selection, scanning the genome for elevated levels of differentiation is a first step towards deciphering the genomic architecture underlying adaptive divergence. The pea aphid Acyrthosiphon pisum is a model of choice to address this question, as it forms a large complex of plant-specialized races and cryptic species, resulting from recent adaptive radiation. Here, we characterized genomewide polymorphisms in three pea aphid races specialized on alfalfa, clover and pea crops, respectively, which we sequenced in pools (poolseq). Using a model-based approach that explicitly accounts for selection, we identified 392 genomic hotspots of differentiation spanning 47.3 Mb and 2,484 genes (respectively, 9.12% of the genome size and 8.10% of its genes). Most of these highly differentiated regions were located on the autosomes, and overall differentiation was weaker on the X chromosome. Within these hotspots, high levels of absolute divergence between races suggest that these regions experienced less gene flow than the rest of the genome, most likely by contributing to reproductive isolation. Moreover, population-specific analyses showed evidence of selection in every host race, depending on the hotspot considered. These hotspots were significantly enriched for candidate gene categories that control host-plant selection and use. These genes encode 48 salivary proteins, 14 gustatory receptors, 10 odorant receptors, five P450 cytochromes and one chemosensory protein, which represent promising candidates for the genetic basis of host-plant specialization and ecological isolation in the pea aphid complex. Altogether, our findings open new research directions towards functional studies, for validating the role of these genes on adaptive phenotypes.
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Affiliation(s)
| | - Mathieu Gautier
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- Institut de Biologie Computationnelle, Univ Montpellier, Montpellier, France
| | - Anaïs Gouin
- INRA, UMR 1349 IGEPP, Le Rheu, France
- Inria/IRISA GenScale, Rennes, France
| | | | - Jean Peccoud
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, Poitiers, France
| | - Fabrice Legeai
- INRA, UMR 1349 IGEPP, Le Rheu, France
- Inria/IRISA GenScale, Rennes, France
| | | | - Carole M Smadja
- Institut des Sciences de l'Evolution (UMR 5554) - CNRS - IRD - EPHE - CIRAD -Université de Montpellier, Montpellier, France
| | | | - Renaud Vitalis
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- Institut de Biologie Computationnelle, Univ Montpellier, Montpellier, France
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86
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A genome scan for selection signatures in Taihu pig breeds using next-generation sequencing. Animal 2018; 13:683-693. [PMID: 29987993 DOI: 10.1017/s1751731118001714] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Taihu pig breeds are the most prolific breeds of swine in the world, and they also have superior economic traits, including high resistance to disease, superior meat quality, high resistance to crude feed and a docile temperament. The formation of these phenotypic characteristics is largely a result of long-term artificial or natural selection. Therefore, exploring selection signatures in the genomes of the Taihu pigs will help us to identify porcine genes related to productivity traits, disease and behaviour. In this study, we used both intra-population (Relative Extend Haplotype Homozygosity Test (REHH)) and inter-population (the Cross-Population Extend Haplotype Homozygosity Test (XPEHH); F-STATISTICS, F ST ) methods to detect genomic regions that might be under selection process in Taihu pig breeds. As a result, we found 282 (REHH) and 112 (XPEHH) selection signature candidate regions corresponding to 159.78 Mb (6.15%) and 62.29 Mb (2.40%) genomic regions, respectively. Further investigations of the selection candidate regions revealed that many genes under these genomic regions were related to reproductive traits (such as the TLR9 gene), coat colour (such as the KIT gene) and fat metabolism (such as the CPT1A and MAML3 genes). Furthermore, gene enrichment analyses showed that genes under the selection candidate regions were significantly over-represented in pathways related to diseases, such as autoimmune thyroid and asthma diseases. In conclusion, several candidate genes potentially under positive selection were involved in characteristics of Taihu pig. These results will further allow us to better understand the mechanisms of selection in pig breeding.
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87
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Abstract
Signatures of recent historical admixture are ubiquitous in human populations. We present a mechanistic model of admixture with two source populations, encompassing recurrent admixture periods and study the distribution of admixture fractions for finite but arbitrary genome size. We provide simulation-based methods to estimate the introgression parameters and discuss the implications of reaching stationarity on estimability of parameters when there are recurrent admixture events with different rates.
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Affiliation(s)
- Erkan Ozge Buzbas
- Department of Statistical Science, University of Idaho, United States.
| | - Paul Verdu
- CNRS/MNHN/Université Paris Diderot/Sorbonne Paris Cité, France
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88
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Mokhber M, Moradi-Shahrbabak M, Sadeghi M, Moradi-Shahrbabak H, Stella A, Nicolzzi E, Rahmaninia J, Williams JL. A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds. BMC Genomics 2018; 19:449. [PMID: 29890939 PMCID: PMC5996463 DOI: 10.1186/s12864-018-4759-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 05/04/2018] [Indexed: 01/25/2023] Open
Abstract
Background Identification of genomic regions that have been targets of selection may shed light on the genetic history of livestock populations and help to identify variation controlling commercially important phenotypes. The Azeri and Kuzestani buffalos are the most common indigenous Iranian breeds which have been subjected to divergent selection and are well adapted to completely different regions. Examining the genetic structure of these populations may identify genomic regions associated with adaptation to the different environments and production goals. Results A set of 385 water buffalo samples from Azeri (N = 262) and Khuzestani (N = 123) breeds were genotyped using the Axiom® Buffalo Genotyping 90 K Array. The unbiased fixation index method (FST) was used to detect signatures of selection. In total, 13 regions with outlier FST values (0.1%) were identified. Annotation of these regions using the UMD3.1 Bos taurus Genome Assembly was performed to find putative candidate genes and QTLs within the selected regions. Putative candidate genes identified include FBXO9, NDFIP1, ACTR3, ARHGAP26, SERPINF2, BOLA-DRB3, BOLA-DQB, CLN8, and MYOM2. Conclusions Candidate genes identified in regions potentially under selection were associated with physiological pathways including milk production, cytoskeleton organization, growth, metabolic function, apoptosis and domestication-related changes include immune and nervous system development. The QTL identified are involved in economically important traits in buffalo related to milk composition, udder structure, somatic cell count, meat quality, and carcass and body weight. Electronic supplementary material The online version of this article (10.1186/s12864-018-4759-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mahdi Mokhber
- Department of Animal Science, Faculty of Agriculture, Urmia University, 11Km Sero Road, P. O. Box: 165, Urmia, 5756151818, Iran.
| | - Mohammad Moradi-Shahrbabak
- Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, P. O. Box: 4111, Karaj, 1417614418, Iran
| | - Mostafa Sadeghi
- Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, P. O. Box: 4111, Karaj, 1417614418, Iran
| | - Hossein Moradi-Shahrbabak
- Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, P. O. Box: 4111, Karaj, 1417614418, Iran
| | - Alessandra Stella
- Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, 26900, Lodi, Italy
| | - Ezequiel Nicolzzi
- Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, 26900, Lodi, Italy
| | - Javad Rahmaninia
- Department of Animal Breeding and Genetics, Animal Science Research Institute of Iran (ASRI), Karaj, 3146618361, Iran
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
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89
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Genomic signatures of parasite-driven natural selection in north European Atlantic salmon (Salmo salar). Mar Genomics 2018; 39:26-38. [DOI: 10.1016/j.margen.2018.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 12/16/2017] [Accepted: 01/08/2018] [Indexed: 02/06/2023]
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90
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Grigorev K, Kliver S, Dobrynin P, Komissarov A, Wolfsberger W, Krasheninnikova K, Afanador-Hernández YM, Brandt AL, Paulino LA, Carreras R, Rodríguez LE, Núñez A, Brandt JR, Silva F, Hernández-Martich JD, Majeske AJ, Antunes A, Roca AL, O'Brien SJ, Martínez-Cruzado JC, Oleksyk TK. Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola. Gigascience 2018; 7:4931057. [PMID: 29718205 PMCID: PMC6009670 DOI: 10.1093/gigascience/giy025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 01/26/2018] [Accepted: 03/07/2018] [Indexed: 11/25/2022] Open
Abstract
Solenodons are insectivores that live in Hispaniola and Cuba. They form an isolated branch in the tree of placental mammals that are highly divergent from other eulipothyplan insectivores The history, unique biology, and adaptations of these enigmatic venomous species could be illuminated by the availability of genome data. However, a whole genome assembly for solenodons has not been previously performed, partially due to the difficulty in obtaining samples from the field. Island isolation and reduced numbers have likely resulted in high homozygosity within the Hispaniolan solenodon (Solenodon paradoxus). Thus, we tested the performance of several assembly strategies on the genome of this genetically impoverished species. The string graph-based assembly strategy seemed a better choice compared to the conventional de Bruijn graph approach due to the high levels of homozygosity, which is often a hallmark of endemic or endangered species. A consensus reference genome was assembled from sequences of 5 individuals from the southern subspecies (S. p. woodi). In addition, we obtained an additional sequence from 1 sample of the northern subspecies (S. p. paradoxus). The resulting genome assemblies were compared to each other and annotated for genes, with an emphasis on venom genes, repeats, variable microsatellite loci, and other genomic variants. Phylogenetic positioning and selection signatures were inferred based on 4,416 single-copy orthologs from 10 other mammals. We estimated that solenodons diverged from other extant mammals 73.6 million years ago. Patterns of single-nucleotide polymorphism variation allowed us to infer population demography, which supported a subspecies split within the Hispaniolan solenodon at least 300 thousand years ago.
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Affiliation(s)
- Kirill Grigorev
- Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
| | - Sergey Kliver
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Pavel Dobrynin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Walter Wolfsberger
- Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
- Biology Department, Uzhhorod National University, Uzhhorod, Ukraine
| | - Ksenia Krasheninnikova
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | | | - Adam L Brandt
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Division of Natural Sciences, St. Norbert College, De Pere, Wisconsin, USA
| | - Liz A Paulino
- Instituto Tecnológico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic
| | - Rosanna Carreras
- Instituto Tecnológico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic
| | - Luis E Rodríguez
- Instituto Tecnológico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic
| | - Adrell Núñez
- Department of Conservation and Science, Parque Zoologico Nacional (ZOODOM), Santo Domingo, Dominican Republic
| | - Jessica R Brandt
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biology, Marian University, Fond du Lac, Wisconsin, USA
| | - Filipe Silva
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto. Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - J David Hernández-Martich
- Instituto de Investigaciones Botánicas y Zoológicas, Universidad Autónoma de Santo Domingo, Santo Domingo, Dominican Republic
| | - Audrey J Majeske
- Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto. Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
- Oceanographic Center, Nova Southeastern University, Fort Lauderdale, Florida, USA
| | | | - Taras K Oleksyk
- Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
- Biology Department, Uzhhorod National University, Uzhhorod, Ukraine
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91
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Chen M, Wang J, Wang Y, Wu Y, Fu J, Liu JF. Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle. BMC Genet 2018; 19:31. [PMID: 29776331 PMCID: PMC5960162 DOI: 10.1186/s12863-018-0622-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 04/30/2018] [Indexed: 12/31/2022] Open
Abstract
Background Currently, genome-wide scans for positive selection signatures in commercial breed have been investigated. However, few studies have focused on selection footprints of indigenous breeds. Laiwu pig is an invaluable Chinese indigenous pig breed with extremely high proportion of intramuscular fat (IMF), and an excellent model to detect footprint as the result of natural and artificial selection for fat deposition in muscle. Result In this study, based on GeneSeek Genomic profiler Porcine HD data, three complementary methods, FST, iHS (integrated haplotype homozygosity score) and CLR (composite likelihood ratio), were implemented to detect selection signatures in the whole genome of Laiwu pigs. Totally, 175 candidate selected regions were obtained by at least two of the three methods, which covered 43.75 Mb genomic regions and corresponded to 1.79% of the genome sequence. Gene annotation of the selected regions revealed a list of functionally important genes for feed intake and fat deposition, reproduction, and immune response. Especially, in accordance to the phenotypic features of Laiwu pigs, among the candidate genes, we identified several genes, NPY1R, NPY5R, PIK3R1 and JAKMIP1, involved in the actions of two sets of neurons, which are central regulators in maintaining the balance between food intake and energy expenditure. Conclusions Our results identified a number of regions showing signatures of selection, as well as a list of functionally candidate genes with potential effect on phenotypic traits, especially fat deposition in muscle. Our findings provide insights into the mechanisms of artificial selection of fat deposition and further facilitate follow-up functional studies. Electronic supplementary material The online version of this article (10.1186/s12863-018-0622-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Minhui Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jiying Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Yanping Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Ying Wu
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Jinluan Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Jian-Feng Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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92
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Waterhouse MD, Erb LP, Beever EA, Russello MA. Adaptive population divergence and directional gene flow across steep elevational gradients in a climate-sensitive mammal. Mol Ecol 2018; 27:2512-2528. [DOI: 10.1111/mec.14701] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/29/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Matthew D. Waterhouse
- Department of Biology; University of British Columbia; Kelowna British Columbia Canada
| | - Liesl P. Erb
- Departments of Biology and Environmental Studies; Warren Wilson College; Asheville North Carolina
| | - Erik A. Beever
- U.S. Geological Survey; Northern Rocky Mountain Science Center; Bozeman Montana
- Department of Ecology; Montana State University; Bozeman Montana
| | - Michael A. Russello
- Department of Biology; University of British Columbia; Kelowna British Columbia Canada
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93
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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94
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Garner AG, Goulet BE, Farnitano MC, Molina-Henao YF, Hopkins R. Genomic Signatures of Reinforcement. Genes (Basel) 2018; 9:E191. [PMID: 29614048 PMCID: PMC5924533 DOI: 10.3390/genes9040191] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 12/21/2022] Open
Abstract
Reinforcement is the process by which selection against hybridization increases reproductive isolation between taxa. Much research has focused on demonstrating the existence of reinforcement, yet relatively little is known about the genetic basis of reinforcement or the evolutionary conditions under which reinforcement can occur. Inspired by reinforcement's characteristic phenotypic pattern of reproductive trait divergence in sympatry but not in allopatry, we discuss whether reinforcement also leaves a distinct genomic pattern. First, we describe three patterns of genetic variation we expect as a consequence of reinforcement. Then, we discuss a set of alternative processes and complicating factors that may make the identification of reinforcement at the genomic level difficult. Finally, we consider how genomic analyses can be leveraged to inform if and to what extent reinforcement evolved in the face of gene flow between sympatric lineages and between allopatric and sympatric populations of the same lineage. Our major goals are to understand if genome scans for particular patterns of genetic variation could identify reinforcement, isolate the genetic basis of reinforcement, or infer the conditions under which reinforcement evolved.
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Affiliation(s)
- Austin G Garner
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 021382, USA.
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA.
| | - Benjamin E Goulet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 021382, USA.
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA.
| | - Matthew C Farnitano
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 021382, USA.
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA.
| | - Y Franchesco Molina-Henao
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 021382, USA.
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA.
- Department of Biology, Universidad del Valle, Cali 760032, Colombia.
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 021382, USA.
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA.
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95
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Population genetic evidence for positive and purifying selection acting at the human IFN-γ locus in Africa. Genes Immun 2018; 20:143-157. [PMID: 29599512 DOI: 10.1038/s41435-018-0016-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/22/2018] [Accepted: 01/26/2018] [Indexed: 01/09/2023]
Abstract
Despite its critical role in the defense against microbial infection and tumor development, little is known about the range of nucleotide and haplotype variation at IFN-γ, or the evolutionary forces that have shaped patterns of diversity at this locus. To address this gap in knowledge, we examined sequence data from the IFN-γ gene in 1461 individuals from 15 worldwide populations. Our analyses uncovered novel patterns of variation in distinct African populations, including an excess of high frequency-derived alleles, unusually long haplotype structure surrounding the IFN-γ gene, and a "star-like" genealogy of African-specific haplotypes carrying variants previously associated with infectious disease. We also inferred a deep time to coalescence of variation at IFN-γ (~ 0.8 million years ago) and ancient ages for common polymorphisms predating the evolution of modern humans. Taken together, these results are congruent with a model of positive selection on standing variation in African populations. Furthermore, we inferred that common variants in intron 3 of IFN-γ are the likely targets of selection. In addition, we observed a paucity of non-synonymous substitutions relative to synonymous changes in the exons of IFN-γ in African and non-African populations, suggestive of strong purifying selection. Therefore, we contend that positive and purifying selection have influenced levels of diversity in different regions of IFN-γ, implying that these distinct genic regions are, or have been, functionally important. Overall, this study provides additional insights into the evolutionary events that have contributed to the frequency and distribution of alleles having a role in human health and disease.
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Ruiz-Larrañaga O, Langa J, Rendo F, Manzano C, Iriondo M, Estonba A. Genomic selection signatures in sheep from the Western Pyrenees. Genet Sel Evol 2018; 50:9. [PMID: 29566643 PMCID: PMC5865298 DOI: 10.1186/s12711-018-0378-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 02/12/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The current large spectrum of sheep phenotypic diversity results from the combined product of sheep selection for different production traits such as wool, milk and meat, and its natural adaptation to new environments. In this study, we scanned the genome of 25 Sasi Ardi and 75 Latxa sheep from the Western Pyrenees for three types of regions under selection: (1) regions underlying local adaptation of Sasi Ardi semi-feral sheep, (2) regions related to a long traditional dairy selection pressure in Latxa sheep, and (3) regions experiencing the specific effect of the modern genetic improvement program established for the Latxa breed during the last three decades. RESULTS Thirty-two selected candidate regions including 147 annotated genes were detected by using three statistical parameters: pooled heterozygosity H, Tajima's D, and Wright's fixation index Fst. For Sasi Ardi sheep, chromosomes Ovis aries (OAR)4, 6, and 22 showed the strongest signals and harbored several candidate genes related to energy metabolism and morphology (BBS9, ELOVL3 and LDB1), immunity (NFKB2), and reproduction (H2AFZ). The major genomic difference between Sasi Ardi and Latxa sheep was on OAR6, which is known to affect milk production, with highly selected regions around the ABCG2, SPP1, LAP3, NCAPG, LCORL, and MEPE genes in Latxa sheep. The effect of the modern genetic improvement program on Latxa sheep was also evident on OAR15, on which several olfactory genes are located. We also detected several genes involved in reproduction such as ESR1 and ZNF366 that were affected by this selection program. CONCLUSIONS Natural and artificial selection have shaped the genome of both Sasi Ardi and Latxa sheep. Our results suggest that Sasi Ardi traits related to energy metabolism, morphological, reproductive, and immunological features have been under positive selection to adapt this semi-feral sheep to its particular environment. The highly selected Latxa sheep for dairy production showed clear signatures of selection in genomic regions related to milk production. Furthermore, our data indicate that the selection criteria applied in the modern genetic improvement program affect immunity and reproduction traits.
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Affiliation(s)
- Otsanda Ruiz-Larrañaga
- Genetics, Physical Anthropology and Animal Physiology Department, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Jorge Langa
- Genetics, Physical Anthropology and Animal Physiology Department, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Fernando Rendo
- Genetics, Sequencing and Genotyping Unit, Advanced Research Facilities (SGIker), University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Carmen Manzano
- Genetics, Physical Anthropology and Animal Physiology Department, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Mikel Iriondo
- Genetics, Physical Anthropology and Animal Physiology Department, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Andone Estonba
- Genetics, Physical Anthropology and Animal Physiology Department, University of the Basque Country (UPV/EHU), Leioa, Spain
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Yu J, Miao J, Zhang Z, Xiong H, Zhu X, Sun X, Pan Y, Liang Y, Zhang Q, Abdul Rehman RM, Li J, Zhang H, Li Z. Alternative splicing of OsLG3b controls grain length and yield in japonica rice. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1667-1678. [PMID: 29479793 PMCID: PMC6097128 DOI: 10.1111/pbi.12903] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/31/2017] [Accepted: 02/03/2018] [Indexed: 05/18/2023]
Abstract
Grain size, one of the important components determining grain yield in rice, is controlled by the multiple quantitative trait loci (QTLs). Intensive artificial selection for grain size during domestication is evidenced in modern cultivars compared to their wild relatives. Here, we report the molecular cloning and characterization of OsLG3b, a QTL for grain length in tropical japonica rice that encodes MADS-box transcription factor 1 (OsMADS1). Six SNPs in the OsLG3b region led to alternative splicing, which were associated with grain length in an association analysis of candidate region. Quantitative PCR analysis indicated that OsLG3b expression was higher during the panicle and seed development stages. Analysis of haplotypes and introgression regions revealed that the long-grain allele of OsLG3b might have arisen after domestication of tropical japonica and spread to subspecies indica or temperate japonica by natural crossing and artificial selection. OsLG3b is therefore a target of human selection for adaptation to tropical regions during domestication and/or improvement of rice. Phylogenetic analysis and pedigree records showed that OsLG3b had been employed by breeders, but the gene still has much breeding potential for increasing grain length in indica. These findings will not only aid efforts to elucidate the molecular basis of grain development and domestication, but also facilitate the genetic improvement of rice yield.
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Affiliation(s)
- Jianping Yu
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Jinli Miao
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Zhanying Zhang
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Haiyan Xiong
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Xiaoyang Zhu
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Xingming Sun
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Yinghua Pan
- China/Guangxi Key Laboratory of Rice Genetics and BreedingRice Research InstituteGuangxi Academy of Agricultural SciencesNanningGuangxiChina
| | - Yuntao Liang
- China/Guangxi Key Laboratory of Rice Genetics and BreedingRice Research InstituteGuangxi Academy of Agricultural SciencesNanningGuangxiChina
| | - Qiang Zhang
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Rashid Muhammad Abdul Rehman
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Jinjie Li
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Hongliang Zhang
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Zichao Li
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
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Szpak M, Mezzavilla M, Ayub Q, Chen Y, Xue Y, Tyler-Smith C. FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations. Genome Biol 2018; 19:5. [PMID: 29343290 PMCID: PMC5771147 DOI: 10.1186/s13059-017-1380-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 12/12/2017] [Indexed: 12/30/2022] Open
Abstract
We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated "gold standard" positively selected variants and simulations. FineMAV has good sensitivity and a low false discovery rate. Applying FineMAV to the 1000 Genomes Project Phase 3 SNP dataset, we report many novel selected variants, including ones in TGM3 and PRSS53 associated with hair phenotypes that we validate using available independent data. FineMAV is widely applicable to sequence data from both human and other species.
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Affiliation(s)
- Michał Szpak
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Massimo Mezzavilla
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
- Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - Qasim Ayub
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
- Present Address: Genomics Facility, School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Darul Ehsan Malaysia
| | - Yuan Chen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
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Bahbahani H, Salim B, Almathen F, Al Enezi F, Mwacharo JM, Hanotte O. Signatures of positive selection in African Butana and Kenana dairy zebu cattle. PLoS One 2018; 13:e0190446. [PMID: 29300786 PMCID: PMC5754058 DOI: 10.1371/journal.pone.0190446] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 12/14/2017] [Indexed: 02/02/2023] Open
Abstract
Butana and Kenana are two types of zebu cattle found in Sudan. They are unique amongst African indigenous zebu cattle because of their high milk production. Aiming to understand their genome structure, we genotyped 25 individuals from each breed using the Illumina BovineHD Genotyping BeadChip. Genetic structure analysis shows that both breeds have an admixed genome composed of an even proportion of indicine (0.75 ± 0.03 in Butana, 0.76 ± 0.006 in Kenana) and taurine (0.23 ± 0.009 in Butana, 0.24 ± 0.006 in Kenana) ancestries. We also observe a proportion of 0.02 to 0.12 of European taurine ancestry in ten individuals of Butana that were sampled from cattle herds in Tamboul area suggesting local crossbreeding with exotic breeds. Signatures of selection analyses (iHS and Rsb) reveal 87 and 61 candidate positive selection regions in Butana and Kenana, respectively. These regions span genes and quantitative trait loci (QTL) associated with biological pathways that are important for adaptation to marginal environments (e.g., immunity, reproduction and heat tolerance). Trypanotolerance QTL are intersecting candidate regions in Kenana cattle indicating selection pressure acting on them, which might be associated with an unexplored level of trypanotolerance in this cattle breed. Several dairy traits QTL are overlapping the identified candidate regions in these two zebu cattle breeds. Our findings underline the potential to improve dairy production in the semi-arid pastoral areas of Africa through breeding improvement strategy of indigenous local breeds.
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Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait city, Kuwait
- * E-mail: ,
| | - Bashir Salim
- Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum Khartoum North, Sudan
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Al-Hasa, Kingdom of Saudi Arabia
| | - Fahad Al Enezi
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait city, Kuwait
| | - Joram M. Mwacharo
- Small Ruminant Genomics Group, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
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