1
|
Zhao H, Guo X, Wang W, Wang Z, Rawson P, Wilbur A, Hare M. Consequences of domestication in eastern oyster: Insights from whole genomic analyses. Evol Appl 2024; 17:e13710. [PMID: 38817396 PMCID: PMC11134191 DOI: 10.1111/eva.13710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/02/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024] Open
Abstract
Selective breeding for production traits has yielded relatively rapid successes with high-fecundity aquaculture species. Discovering the genetic changes associated with selection is an important goal for understanding adaptation and can also facilitate better predictions about the likely fitness of selected strains if they escape aquaculture farms. Here, we hypothesize domestication as a genetic change induced by inadvertent selection in culture. Our premise is that standardized culture protocols generate parallel domestication effects across independent strains. Using eastern oyster as a model and a newly developed 600K SNP array, this study tested for parallel domestication effects in multiple independent selection lines compared with their progenitor wild populations. A single contrast was made between pooled selected strains (1-17 generations in culture) and all wild progenitor samples combined. Population structure analysis indicated rank order levels of differentiation as [wild - wild] < [wild - cultured] < [cultured - cultured]. A genome scan for parallel adaptation to the captive environment applied two methodologically distinct outlier tests to the wild versus selected strain contrast and identified a total of 1174 candidate SNPs. Contrasting wild versus selected strains revealed the early evolutionary consequences of domestication in terms of genomic differentiation, standing genetic diversity, effective population size, relatedness, runs of homozygosity profiles, and genome-wide linkage disequilibrium patterns. Random Forest was used to identify 37 outlier SNPs that had the greatest discriminatory power between bulked wild and selected oysters. The outlier SNPs were in genes enriched for cytoskeletal functions, hinting at possible traits under inadvertent selection during larval culture or pediveliger setting at high density. This study documents rapid genomic changes stemming from hatchery-based cultivation of eastern oysters, identifies candidate loci responding to domestication in parallel among independent aquaculture strains, and provides potentially useful genomic resources for monitoring interbreeding between farm and wild oysters.
Collapse
Affiliation(s)
- Honggang Zhao
- Department of Natural Resources & the EnvironmentCornell UniversityIthacaNew YorkUSA
- Present address:
Center for Aquaculture TechnologySan DiegoCaliforniaUSA
| | - Ximing Guo
- Haskin Shellfish Research LaboratoryRutgers UniversityPort NorrisNew JerseyUSA
| | - Wenlu Wang
- Department of Computer SciencesTexas A&M University‐Corpus ChristiCorpus ChristiTexasUSA
| | - Zhenwei Wang
- Haskin Shellfish Research LaboratoryRutgers UniversityPort NorrisNew JerseyUSA
| | - Paul Rawson
- School of Marine SciencesUniversity of MaineOronoMaineUSA
| | - Ami Wilbur
- Shellfish Research Hatchery, Center for Marine ScienceUniversity of North Carolina WilmingtonWilmingtonNorth CarolinaUSA
| | - Matthew Hare
- Department of Natural Resources & the EnvironmentCornell UniversityIthacaNew YorkUSA
| |
Collapse
|
2
|
Paul K, Restoux G, Phocas F. Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss). Genet Sel Evol 2024; 56:13. [PMID: 38389056 PMCID: PMC10882880 DOI: 10.1186/s12711-024-00884-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Evolutionary processes leave footprints along the genome over time. Highly homozygous regions may correspond to positive selection of favorable alleles, while maintenance of heterozygous regions may be due to balancing selection phenomena. We analyzed data from 176 fish from four disconnected domestic rainbow trout populations that were genotyped using a high-density Axiom Trout genotyping 665K single nucleotide polymorphism array, including 20 from the US and 156 from three French lines. Using methods based on runs of homozygosity and extended haplotype homozygosity, we detected signatures of selection in these four populations. RESULTS Nine genomic regions that included 253 genes were identified as being under positive selection in all four populations Most were located on chromosome 2 but also on chromosomes 12, 15, 16, and 20. In addition, four heterozygous regions that contain 29 genes that are putatively under balancing selection were also shared by the four populations. These were located on chromosomes 10, 13, and 19. Regardless of the homozygous or heterozygous nature of the regions, in each region, we detected several genes that are highly conserved among vertebrates due to their critical roles in cellular and nuclear organization, embryonic development, or immunity. We identified new candidate genes involved in rainbow trout fitness, as well as 17 genes that were previously identified to be under positive selection, 10 of which in other fishes (auts2, atp1b3, zp4, znf135, igf-1α, brd2, col9a2, mrap2, pbx1, and emilin-3). CONCLUSIONS Using material from disconnected populations of different origins allowed us to draw a genome-wide map of signatures of positive selection that are shared between these rainbow trout populations, and to identify several regions that are putatively under balancing selection. These results provide a valuable resource for future investigations of the dynamics of genetic diversity and genome evolution during domestication.
Collapse
Affiliation(s)
- Katy Paul
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Gwendal Restoux
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
| |
Collapse
|
3
|
Howe NS, Hale MC, Waters CD, Schaal SM, Shedd KR, Larson WA. Genomic evidence for domestication selection in three hatchery populations of Chinook salmon, Oncorhynchus tshawytscha. Evol Appl 2024; 17:e13656. [PMID: 38357359 PMCID: PMC10866082 DOI: 10.1111/eva.13656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
Fish hatcheries are widely used to enhance fisheries and supplement declining wild populations. However, substantial evidence suggests that hatchery fish are subject to differential selection pressures compared to their wild counterparts. Domestication selection, or adaptation to the hatchery environment, poses a risk to wild populations if traits specific to success in the hatchery environment have a genetic component and there is subsequent introgression between hatchery and wild fish. Few studies have investigated domestication selection in hatcheries on a genomic level, and even fewer have done so in parallel across multiple hatchery-wild population pairs. In this study, we used low-coverage whole-genome sequencing to investigate signals of domestication selection in three separate hatchery populations of Chinook salmon, Oncorhynchus tshawytscha, after approximately seven generations of divergence from their corresponding wild progenitor populations. We sequenced 192 individuals from populations across Southeast Alaska and estimated genotype likelihoods at over six million loci. We discovered a total of 14 outlier peaks displaying high genetic differentiation (F ST) between hatchery-wild pairs, although no peaks were shared across the three comparisons. Peaks were small (53 kb on average) and often displayed elevated absolute genetic divergence (D xy) and linkage disequilibrium, suggesting some level of domestication selection has occurred. Our study provides evidence that domestication selection can lead to genetic differences between hatchery and wild populations in only a few generations. Additionally, our data suggest that population-specific adaptation to hatchery environments likely occurs through different genetic pathways, even for populations with similar standing genetic variation. These results highlight the need to collect paired genotype-phenotype data to understand how domestication may be affecting fitness and to identify potential management practices that may mitigate genetic risks despite multiple pathways of domestication.
Collapse
Affiliation(s)
- Natasha S. Howe
- Department of BiologyTexas Christian UniversityFort WorthTexasUSA
| | - Matthew C. Hale
- Department of BiologyTexas Christian UniversityFort WorthTexasUSA
| | - Charles D. Waters
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
| | - Sara M. Schaal
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
| | - Kyle R. Shedd
- Alaska Department of Fish and Game, Division of Commercial FisheriesGene Conservation LaboratoryAnchorageAlaskaUSA
| | - Wesley A. Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
| |
Collapse
|
4
|
Åsheim ER, Debes PV, House A, Liljeström P, Niemelä PT, Siren JP, Erkinaro J, Primmer CR. Atlantic salmon ( Salmo salar) age at maturity is strongly affected by temperature, population and age-at-maturity genotype. CONSERVATION PHYSIOLOGY 2023; 11:coac086. [PMID: 36726866 PMCID: PMC9871436 DOI: 10.1093/conphys/coac086] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/10/2022] [Accepted: 01/05/2023] [Indexed: 06/18/2023]
Abstract
Age at maturity is a key life history trait involving a trade-off between survival risk and reproductive investment, and is an important factor for population structures. In ectotherms, a warming environment may have a dramatic influence on development and life history, but this influence may differ between populations. While an increasing number of studies have examined population-dependent reactions with temperature, few have investigated this in the context of maturation timing. Atlantic salmon, a species of high conservation relevance, is a good study species for this topic as it displays considerable variation in age at maturity, of which a large proportion has been associated with a genomic region including the strong candidate gene vgll3. Until now, the effect of this gene in the context of different environments and populations has not been studied. Using a large-scale common-garden experiment, we find strong effects of temperature, population-of-origin, and vgll3 genotype on maturation in 2-year-old male Atlantic salmon (Salmo salar). With a temperature difference of 1.8°C, maturation probability was 4.8 times higher in the warm treatment than the cold treatment. This temperature effect was population-specific and was higher in the southern (60.48°N) compared to the northern (65.01°N) population. The early maturation vgll3*E allele was associated with a significantly higher maturation probability, but there was no vgll3 interaction with temperature or population. Both body condition and body mass associated with maturation. The body mass association was only present in the warm treatment. Our findings demonstrate that (i) populations can vary in their response to temperature change in terms of age at maturity, (ii) high intrinsic growth could be associated with higher thermal sensitivity for life history variation and (iii) vgll3 effects on age at maturity might be similar between populations and different thermal environments.
Collapse
Affiliation(s)
- Eirik R Åsheim
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
- Lammi Biological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, 16900 Lammi, Finland
| | - Paul V Debes
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur 550, Iceland
| | - Andrew House
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
- Lammi Biological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, 16900 Lammi, Finland
| | - Petra Liljeström
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
- Lammi Biological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, 16900 Lammi, Finland
| | - Petri T Niemelä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Jukka P Siren
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
| | - Jaakko Erkinaro
- Natural Resources Institute Finland (LUKE), 90014 Oulu, Finland
| | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
5
|
Sun CF, Zhang XH, Dong JJ, You XX, Tian YY, Gao FY, Zhang HT, Shi Q, Ye X, Shi Q, Ye X. Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass ( Micropterus salmoides). Zool Res 2023; 44:78-89. [PMID: 36349358 PMCID: PMC9841193 DOI: 10.24272/j.issn.2095-8137.2022.274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Largemouth bass ( Micropterus salmoides) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study, we sequenced 149 largemouth bass fish, including protospecies (imported from the US) and improved breeds (four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection, including several associated with growth (p sst1 and grb10), early development ( klf9, sp4, and sp8), and immune traits ( pkn2, sept2, bcl6, and ripk2). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.
Collapse
Affiliation(s)
- Cheng-Fei Sun
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Xin-Hui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun-Jian Dong
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Xin-Xin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan-Yuan Tian
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Feng-Ying Gao
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - He-Tong Zhang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China,E-mail:
| | - Xing Ye
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China,
| | | | | | | | | | | | | |
Collapse
|
6
|
Sui J, Luan S, Cao J, Dai P, Meng X, Luo K, Chen B, Tan J, Fu Q, Kong J. Genomic signatures of artificial selection in fecundity of Pacific white shrimp, Penaeus vannamei. Front Genet 2022; 13:929889. [PMID: 36105098 PMCID: PMC9465174 DOI: 10.3389/fgene.2022.929889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/14/2022] [Indexed: 12/04/2022] Open
Abstract
Penaeusvannamei is the most important economic shrimp in the world. Many selective breeding programs are carried out to improve its production and performance traits. Although significant differences in the reproductive ability of female P. vannamei under artificial breeding conditions have been reported, the genome-wide adaption of the reproductive ability of domesticated female P. vannamei is less investigated. In this study, whole-genome analysis was performed along with pooled DNA sequencing on two fecundity separated bulks, high fecundity bulk (HB), and low fecundity bulk (LB). Each bulk contained 30 individuals from 3 commercial populations. A sequencing depth of >30× was achieved for each bulk, leading to the identification of 625,181 and 629,748 single nucleotide polymorphisms (SNPs) in HB and LB, respectively. Fixation index (Fst) combined with p ratio allowed for the identification of 145 selective sweep regions, with a sequence length of 14.5 Mb, accounting for 0.59% of the genome. Among the 145 selective sweep regions, a total of 64,046 SNPs were identified, and further verification was performed by genotyping 50 candidate SNPs on 60 samples from the offspring of the three populations. Furthermore, 121 genes were screened from the sweep regions. GO annotation and KEGG enrichment analyses showed that partial genes were essential for fecundity regulation. This study provides important information for in-depth investigation of genomic characteristics for long-term selective breeding on the fecundity of female P. vannamei and will also be important for genome-assisted breeding of P. vannamei in the future.
Collapse
Affiliation(s)
- Juan Sui
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Sheng Luan
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jiawang Cao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ping Dai
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xianhong Meng
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Kun Luo
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Baolong Chen
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jian Tan
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qiang Fu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jie Kong
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Jie Kong,
| |
Collapse
|
7
|
Gabián M, Morán P, Saura M, Carvajal-Rodríguez A. Detecting Local Adaptation between North and South European Atlantic Salmon Populations. BIOLOGY 2022; 11:933. [PMID: 35741456 PMCID: PMC9219887 DOI: 10.3390/biology11060933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Pollution and other anthropogenic effects have driven a decrease in Atlantic salmon (Salmo salar) in the Iberian Peninsula. The restocking effort carried out in the 1980s, with salmon from northern latitudes with the aim of mitigating the decline of native populations, failed, probably due to the deficiency in adaptation of foreign salmon from northern Europe to the warm waters of the Iberian Peninsula. This result would imply that the Iberian populations of Atlantic salmon have experienced local adaptation in their past evolutionary history, as has been described for other populations of this species and other salmonids. Local adaptation can occur by divergent selections between environments, favoring the fixation of alleles that increase the fitness of a population in the environment it inhabits relative to other alleles favored in another population. In this work, we compared the genomes of different populations from the Iberian Peninsula (Atlantic and Cantabric basins) and Scotland in order to provide tentative evidence of candidate SNPs responsible for the adaptive differences between populations, which may explain the failures of restocking carried out during the 1980s. For this purpose, the samples were genotyped with a 220,000 high-density SNP array (Affymetrix) specific to Atlantic salmon. Our results revealed potential evidence of local adaptation for North Spanish and Scottish populations. As expected, most differences concerned the comparison of the Iberian Peninsula with Scotland, although there were also differences between Atlantic and Cantabric populations. A high proportion of the genes identified are related to development and cellular metabolism, DNA transcription and anatomical structure. A particular SNP was identified within the NADP-dependent malic enzyme-2 (mMEP-2*), previously reported by independent studies as a candidate for local adaptation in salmon from the Iberian Peninsula. Interestingly, the corresponding SNP within the mMEP-2* region was consistent with a genomic pattern of divergent selection.
Collapse
Affiliation(s)
- María Gabián
- Centro de Investigación Mariña (CIM), Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain; (M.G.); (P.M.)
| | - Paloma Morán
- Centro de Investigación Mariña (CIM), Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain; (M.G.); (P.M.)
| | - María Saura
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), 28040 Madrid, Spain;
| | - Antonio Carvajal-Rodríguez
- Centro de Investigación Mariña (CIM), Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain; (M.G.); (P.M.)
| |
Collapse
|
8
|
The phylogenetic position of zebrafish (Danio rerio) from south african pet shops. Mol Biol Rep 2022; 49:7327-7336. [PMID: 35596052 DOI: 10.1007/s11033-022-07522-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Zebrafish (Danio rerio), a small freshwater fish that originates from India, Bangladesh, Nepal, Bhutan and northern Myanmar, have been widely used as a model organism for studies of developmental biology and genetics. The current study aimed to determine the origin of South African pet shop stock that are currently being used to establish a laboratory population founded from diverse sources available locally. METHODS AND RESULTS Zebrafish DNA was extracted from 65 specimens housed at the University of the Free State (UFS) Department of Genetics. For phylogenetic analysis, cytb sequences were generated from all samples. A further 178 sequences were downloaded from the GenBank database, including sequences of an outgroup species (Danio kyathit). Five microsatellite markers were used to further assess the genetic diversity of the UFS zebrafish specimens. A maximum likelihood analysis was performed for the cytb data. Results of the phylogenetic analyses divided the sequences into three major genetic groups, which was congruent with a previous study on laboratory zebrafish provenance. The SA pet shop fish grouped with the lines from the northern and north-eastern regions of India. High levels of microsatellite genetic diversity were observed for the pet shop sourced population, correlating to what has previously been observed in zebrafish. CONCLUSION These results can be used to guide the future development of laboratory lines suited to the needs at the UFS.
Collapse
|
9
|
Leitwein M, Wellband K, Cayuela H, Le Luyer J, Mohns K, Withler R, Bernatchez L. Strong parallel differential gene expression induced by hatchery rearing weakly associated with methylation signals in adult Coho Salmon (O. kisutch). Genome Biol Evol 2022; 14:6547269. [PMID: 35276004 PMCID: PMC8995047 DOI: 10.1093/gbe/evac036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2022] [Indexed: 11/14/2022] Open
Abstract
Human activities and resource exploitation led to a massive decline of wild salmonid populations, consequently, numerous conservation programs have been developed to supplement wild populations. However, many studies documented reduced fitness of hatchery-born relative to wild fish. Here, by using both RNA sequencing and Whole Genome Bisulfite Sequencing of hatchery and wild-born adult Coho salmon (Oncorhynchus kisutch) originating from two previously studied river systems, we show that early-life hatchery-rearing environment-induced significant and parallel gene expression differentiation is maintained until Coho come back to their natal river for reproduction. A total of 3,643 genes differentially expressed and 859 coexpressed genes were downregulated in parallel in hatchery-born fish from both rivers relative to their wild congeners. Among those genes, 26 displayed a significant relationship between gene expression and the median gene body methylation and 669 single CpGs displayed a significant correlation between methylation level and the associated gene expression. The link between methylation and gene expression was weak suggesting that DNA methylation is not the only player in mediating hatchery-related expression differences. Yet, significant gene expression differentiation was observed despite 18 months spent in a common environment (i.e., the sea). Finally, the differentiation is observed in parallel in two different river systems, highlighting the fact that early-life environment may account for at least some of the reduced fitness of the hatchery salmon in the wild. These results illustrate the relevance and importance of considering both epigenome and transcriptome to evaluate the costs and benefits of large-scale supplementation programs.
Collapse
Affiliation(s)
- Maeva Leitwein
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada, G1V 0A6.,Centre pour la Biodiversité Marine, l'exploitation et la Conservation, Université de Montpellier, Centre National de la Recherche Scientifique, Ifremer, Institut de Recherche pour le Développement, Palavas-les-Flots, France
| | - Kyle Wellband
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada, G1V 0A6.,Fisheries and Oceans Canada, Pacific Science Enterprise Centre, West Vancouver, British Columbia, Canada, V7V 1N6
| | - Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada, G1V 0A6.,Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-769622, Villeurbanne, France
| | - Jérémy Le Luyer
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens, Centre Ifremer du Pacifique, BP 49, 98719 Tahiti, Polynésie française
| | - Kayla Mohns
- Department of Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada, V9T 6N7
| | - Ruth Withler
- Department of Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada, V9T 6N7
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada, G1V 0A6
| |
Collapse
|
10
|
Islam SS, Xue X, Caballero-Solares A, Bradbury IR, Rise ML, Fleming IA. Distinct early life stage gene expression effects of hybridization among European and North American farmed and wild Atlantic salmon populations. Mol Ecol 2022; 31:2712-2729. [PMID: 35243721 DOI: 10.1111/mec.16418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/29/2022] [Accepted: 02/21/2022] [Indexed: 11/27/2022]
Abstract
Due to multi-generation domestication selection, farmed and wild Atlantic salmon diverge genetically, which raises concerns about potential genetic interactions among escaped farmed and wild populations and disruption of local adaptation through introgression. When farmed strains of distant geographic origin are used, it is unknown whether the genetic consequences posed by escaped farmed fish will be greater than if more locally derived strains are used. Quantifying gene transcript expression differences among divergent farmed, wild and F1 hybrids under controlled conditions is one of the ways to explore the consequences of hybridization. We compared the transcriptomes of fry at the end of yolk sac absorption of a European (EO) farmed ("StofnFiskur", Norwegian strain), a North American (NA) farmed (Saint John River, NB strain), a Newfoundland (NF) wild population with EO ancestry, and related F1 hybrids using 44K microarrays. Our findings indicate that the wild population showed greater transcriptome differences from the EO farmed strain than that of the NA farmed strain. We also found the largest differences in global gene expression between the two farmed strains. We detected the fewest differentially expressed transcripts between F1 hybrids and domesticated/wild maternal strains. We also found that the differentially expressed genes between cross types over-represented GO terms associated with metabolism, development, growth, immune response, and redox homeostasis processes. These findings suggest that the interbreeding of escaped EO/NA farmed and NF wild population would alter gene transcription, and the consequences of hybridization would be greater from escaped EO farmed than NA farmed salmon, resulting in potential effects on the wild populations.
Collapse
Affiliation(s)
- Shahinur S Islam
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Xi Xue
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Albert Caballero-Solares
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Ian R Bradbury
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada.,Salmonids Section, Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 East White Hills Road, St. John's, NL, A1C 5X, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Ian A Fleming
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| |
Collapse
|
11
|
Agudelo JFG, Mastrochirico‐Filho VA, de Souza Borges CH, Ariede RB, Lira LVG, de Oliveira Neto RR, de Freitas MV, Sucerquia GAL, Vera M, Berrocal MHM, Hashimoto DT. Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South America. Evol Appl 2022; 15:679-693. [PMID: 35505878 PMCID: PMC9046916 DOI: 10.1111/eva.13351] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 12/21/2021] [Accepted: 01/21/2022] [Indexed: 11/26/2022] Open
Abstract
Tambaqui or cachama (Colossoma macropomum) is one of the most important neotropical freshwater fish used for aquaculture in South America, and its production is concentrated at low latitudes (close to the Equator, 0°), where the water temperature is warm. Therefore, understanding how selection shapes genetic variations and structure in farmed populations is of paramount importance in evolutionary biology. High‐throughput sequencing to generate genome‐wide data for fish species allows for elucidating the genomic basis of adaptation to local or farmed conditions and uncovering genes that control the phenotypes of interest. The present study aimed to detect genomic selection signatures and analyze the genetic variability in farmed populations of tambaqui in South America using single‐nucleotide polymorphism (SNP) markers obtained with double‐digest restriction site‐associated DNA sequencing. Initially, 199 samples of tambaqui farmed populations from different locations (located in Brazil, Colombia, and Peru), a wild population (Amazon River, Brazil), and the base population of a breeding program (Aquaculture Center, CAUNESP, Jaboticabal, SP, Brazil) were genotyped. Observed and expected heterozygosity was 0.231–0.350 and 0.288–0.360, respectively. Significant genetic differentiation was observed using global FST analyses of SNP loci (FST = 0.064, p < 0.050). Farmed populations from Colombia and Peru that differentiated from the Brazilian populations formed distinct groups. Several regions, particularly those harboring the genes of significance to aquaculture, were identified to be under positive selection, suggesting local adaptation to stress under different farming conditions and management practices. Studies aimed at improving the knowledge of genomics of tambaqui farmed populations are essential for aquaculture to gain deeper insights into the evolutionary history of these fish and provide resources for the establishment of breeding programs.
Collapse
Affiliation(s)
| | | | | | - Raquel Belini Ariede
- São Paulo State University (Unesp) Aquaculture Center of Unesp 14884‐900 Jaboticabal SP Brazil
| | | | | | | | | | - Manuel Vera
- Facultad de Veterinaria Universidad de Santiago de Compostela (USC) ES27002 Lugo Spain
| | | | - Diogo Teruo Hashimoto
- São Paulo State University (Unesp) Aquaculture Center of Unesp 14884‐900 Jaboticabal SP Brazil
| |
Collapse
|
12
|
Lu Y, Shi C, Jin X, He J, Yin Z. Domestication of farmed fish via the attenuation of stress responses mediated by the hypothalamus-pituitary-inter-renal endocrine axis. Front Endocrinol (Lausanne) 2022; 13:923475. [PMID: 35937837 PMCID: PMC9353172 DOI: 10.3389/fendo.2022.923475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/29/2022] [Indexed: 12/13/2022] Open
Abstract
Human-directed domestication of terrestrial animals traditionally requires thousands of years for breeding. The most prominent behavioral features of domesticated animals include reduced aggression and enhanced tameness relative to their wild forebears, and such behaviors improve the social tolerance of domestic animals toward both humans and crowds of their own species. These behavioral responses are primarily mediated by the hypothalamic-pituitary-adrenal (inter-renal in fish) (HPA/I) endocrine axis, which is involved in the rapid conversion of neuronal-derived perceptual information into hormonal signals. Over recent decades, growing evidence implicating the attenuation of the HPA/I axis during the domestication of animals have been identified through comprehensive genomic analyses of the paleogenomic datasets of wild progenitors and their domestic congeners. Compared with that of terrestrial animals, domestication of most farmed fish species remains at early stages. The present review focuses on the application of HPI signaling attenuation to accelerate the domestication and genetic breeding of farmed fish. We anticipate that deeper understanding of HPI signaling and its implementation in the domestication of farmed fish will benefit genetic breeding to meet the global demands of the aquaculture industry.
Collapse
Affiliation(s)
- Yao Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chuang Shi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xia Jin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jiangyan He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zhan Yin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
- *Correspondence: Zhan Yin,
| |
Collapse
|
13
|
Cádiz MI, López ME, Díaz-Domínguez D, Cáceres G, Marin-Nahuelpi R, Gomez-Uchida D, Canales-Aguirre CB, Orozco-terWengel P, Yáñez JM. Detection of selection signatures in the genome of a farmed population of anadromous rainbow trout (Oncorhynchus mykiss). Genomics 2021; 113:3395-3404. [PMID: 34339816 DOI: 10.1016/j.ygeno.2021.07.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 07/06/2021] [Accepted: 07/28/2021] [Indexed: 11/26/2022]
Abstract
Domestication processes and artificial selection are likely to leave signatures that can be detected at a molecular level in farmed rainbow trout (Oncorhynchus mykiss). These signatures of selection are genomic regions that contain functional genetic variants conferring a higher fitness to their bearers. We genotyped 749 rainbow trout from a commercial population using a rainbow trout Axiom 57 K SNP array panel and identified putative genomic regions under selection using the pcadapt, Composite Likelihood Ratio (CLR) and Integrated Haplotype Score (iHS) methods. After applying quality-control pipelines and statistical analyses, we detected 12, 96 and 16 SNPs putatively under selection, associated with 96, 781 and 115 candidate genes, respectively. Several of these candidate genes were associated with growth, early development, reproduction, behavior and immune system traits. In addition, some of the SNPs were found in interesting regions located in autosomal inversions on Omy05 and Omy20. These findings could represent a genome-wide map of selection signatures in farmed rainbow trout and could be important in explaining domestication and selection for genetic traits of commercial interest.
Collapse
Affiliation(s)
- María I Cádiz
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago 8820808, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - María E López
- Department of Aquatic Resources, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| | | | - Giovanna Cáceres
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago 8820808, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile
| | - Rodrigo Marin-Nahuelpi
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Daniel Gomez-Uchida
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Cristian B Canales-Aguirre
- Centro i~Mar, Universidad de Los Lagos, Camino Chinquihue 6 km, Puerto Montt, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | | | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile.
| |
Collapse
|
14
|
López ME, Cádiz MI, Rondeau EB, Koop BF, Yáñez JM. Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information. Sci Rep 2021; 11:9685. [PMID: 33958603 PMCID: PMC8102513 DOI: 10.1038/s41598-021-86154-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/08/2021] [Indexed: 01/01/2023] Open
Abstract
Animal domestication and artificial selection give rise to gradual changes at the genomic level in populations. Subsequent footprints of selection, known as selection signatures or selective sweeps, have been traced in the genomes of many animal livestock species by exploiting variation in linkage disequilibrium patterns and/or reduction of genetic diversity. Domestication of most aquatic species is recent in comparison with land animals, and salmonids are one of the most important fish species in aquaculture. Coho salmon (Oncorhynchus kisutch), cultivated primarily in Chile, has been subjected to breeding programs to improve growth, disease resistance traits, and flesh color. This study aimed to identify selection signatures that may be involved in adaptation to culture conditions and traits of productive interest. To do so, individuals of two domestic populations cultured in Chile were genotyped with 200 thousand SNPs, and analyses were conducted using iHS, XP-EHH and CLR. Several signatures of selection on different chromosomal regions were detected across both populations. Some of the identified regions under selection contained genes such anapc2, alad, chp2 and myn, which have been previously associated with body weight in Atlantic salmon, or sec24d and robo1, which have been associated with resistance to Piscirickettsia salmonis in coho salmon. Findings in our study can contribute to an integrated genome-wide map of selection signatures, to help identify the genetic mechanisms of phenotypic diversity in coho salmon.
Collapse
Affiliation(s)
- M E López
- Department of Aquatic Resources, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| | - M I Cádiz
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - E B Rondeau
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - B F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - J M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile. .,Núcleo Milenio INVASAL, Concepción, Chile.
| |
Collapse
|
15
|
Farm Animals Are Long Away from Natural Behavior: Open Questions and Operative Consequences on Animal Welfare. Animals (Basel) 2021; 11:ani11030724. [PMID: 33800925 PMCID: PMC8001272 DOI: 10.3390/ani11030724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Animal welfare is a very important issue. One of the tasks of researchers is to provide explanations and possible solutions to questions arising from non-experts. This work analyzes part of the extensive literature on relationships between selection and domestic, mainly farm, animals’ behavior and deals with some very important themes, such as the role of regulations, domestication, and selection. Abstract The concept of welfare applied to farm animals has undergone a remarkable evolution. The growing awareness of citizens pushes farmers to guarantee the highest possible level of welfare to their animals. New perspectives could be opened for animal welfare reasoning around the concept of domestic, especially farm, animals as partial human artifacts. Therefore, it is important to understand how much a particular behavior of a farm animal is far from the natural one of its ancestors. This paper is a contribution to better understand the role of genetics of the farm animals on their behavior. This means that the naïve approach to animal welfare regarding returning animals to their natural state should be challenged and that welfare assessment should be considered.
Collapse
|
16
|
Konstantinidis I, Sætrom P, Mjelle R, Nedoluzhko AV, Robledo D, Fernandes JMO. Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication. Epigenetics 2020; 15:1052-1067. [PMID: 32264748 PMCID: PMC7116051 DOI: 10.1080/15592294.2020.1748914] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/23/2020] [Accepted: 03/25/2020] [Indexed: 12/29/2022] Open
Abstract
The historically recent domestication of fishes has been essential to meet the protein demands of a growing human population. Selection for traits of interest during domestication is a complex process whose epigenetic basis is poorly understood. Cytosine hydroxymethylation is increasingly recognized as an important DNA modification involved in epigenetic regulation. In the present study, we investigated if hydroxymethylation plays a role in fish domestication and demonstrated for the first time at a genome-wide level and single nucleotide resolution that the muscle hydroxymethylome changes after a single generation of Nile tilapia (Oreochromis niloticus, Linnaeus) domestication. The overall decrease in hydroxymethylcytosine levels was accompanied by the downregulation of 2015 genes in fish reared in captivity compared to their wild progenitors. In contrast, several myogenic and metabolic genes that can affect growth potential were upregulated. There were 126 differentially hydroxymethylated cytosines between groups, which were not due to genetic variation; they were associated with genes involved in immune-, growth- and neuronal-related pathways. Taken together, our data unveil a new role for DNA hydroxymethylation in epigenetic regulation of fish domestication with impact in aquaculture and implications in artificial selection, environmental adaptation and genome evolution.
Collapse
Affiliation(s)
| | - Pål Sætrom
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Computer Science, Norwegian University of Science and Technology, Trondheim, Norway
- Bioinformatics Core facility-BioCore, Norwegian University of Science and Technology, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Robin Mjelle
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | | |
Collapse
|
17
|
Naval-Sanchez M, McWilliam S, Evans B, Yáñez JM, Houston RD, Kijas JW. Changed Patterns of Genomic Variation Following Recent Domestication: Selection Sweeps in Farmed Atlantic Salmon. Front Genet 2020; 11:264. [PMID: 32318091 PMCID: PMC7147387 DOI: 10.3389/fgene.2020.00264] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/05/2020] [Indexed: 12/30/2022] Open
Abstract
The introduction of wild Atlantic salmon into captivity, and their subsequent artificial selection for production traits, has caused phenotypic differences between domesticated fish and their wild counterparts. Identification of regions of the genome underling these changes offers the promise of characterizing the early biological consequences of domestication. In the current study, we sequenced a population of farmed European Atlantic salmon and compared the observed patterns of SNP variation to those found in conspecific wild populations. This identified 139 genomic regions that contained significantly elevated SNP homozygosity in farmed fish when compared to their wild counterparts. The most extreme was adjacent to versican, a gene involved in control of neural crest cell migration. To control for false positive signals, a second and independent dataset of farmed and wild European Atlantic salmon was assessed using the same methodology. A total of 81 outlier regions detected in the first dataset showed significantly reduced homozygosity within the second one, strongly suggesting the genomic regions identified are enriched for true selection sweeps. Examination of the associated genes identified a number previously characterized as targets of selection in other domestic species and that have roles in development, behavior and olfactory system. These include arcvf, sema6, errb4, id2-like, and 6n1-like genes. Finally, we searched for evidence of parallel sweeps using a farmed population of North American origin. This failed to detect a convincing overlap to the putative sweeps present in European populations, suggesting the factors that drive patterns of variation under domestication and early artificial selection were largely independent. This is the first analysis on domestication of aquaculture species exploiting whole-genome sequence data and resulted in the identification of sweeps common to multiple independent populations of farmed European Atlantic salmon.
Collapse
Affiliation(s)
| | | | - Bradley Evans
- Salmon Enterprises of Tasmania Pty. Limited, Wayatinah, TAS, Australia
| | - José M Yáñez
- Faculty of Veterinary and Animal Sciences, University of Chile, Santiago, Chile
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - James W Kijas
- CSIRO Agriculture and Food, Brisbane, QLD, Australia
| |
Collapse
|
18
|
Rodriguez Barreto D, Garcia de Leaniz C, Verspoor E, Sobolewska H, Coulson M, Consuegra S. DNA Methylation Changes in the Sperm of Captive-Reared Fish: A Route to Epigenetic Introgression in Wild Populations. Mol Biol Evol 2020; 36:2205-2211. [PMID: 31180510 PMCID: PMC6759066 DOI: 10.1093/molbev/msz135] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interbreeding between hatchery-reared and wild fish, through deliberate stocking or escapes from fish farms, can result in rapid phenotypic and gene expression changes in hybrids, but the underlying mechanisms are unknown. We assessed if one generation of captive breeding was sufficient to generate inter- and/or transgenerational epigenetic modifications in Atlantic salmon. We found that the sperm of wild and captive-reared males differed in methylated regions consistent with early epigenetic signatures of domestication. Some of the epigenetic marks that differed between hatchery and wild males affected genes related to transcription, neural development, olfaction, and aggression, and were maintained in the offspring beyond developmental reprogramming. Our findings suggest that rearing in captivity may trigger epigenetic modifications in the sperm of hatchery fish that could explain the rapid phenotypic and genetic changes observed among hybrid fish. Epigenetic introgression via fish sperm represents a previously unappreciated mechanism that could compromise locally adapted fish populations.
Collapse
Affiliation(s)
| | | | - Eric Verspoor
- Rivers and Lochs Institute, University of the Highlands and Islands, Inverness College, Inverness, United Kingdom
| | - Halina Sobolewska
- Noahgene Ltd, The e-Centre, Cooperage Way Business Village, Alloa, United Kingdom
| | - Mark Coulson
- Rivers and Lochs Institute, University of the Highlands and Islands, Inverness College, Inverness, United Kingdom
| | - Sofia Consuegra
- Biosciences Department, College of Science, Swansea University, Swansea, United Kingdom
| |
Collapse
|
19
|
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: 22] [Impact Index Per Article: 4.4] [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.
Collapse
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
| |
Collapse
|
20
|
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: 34] [Impact Index Per Article: 6.8] [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.
Collapse
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
| |
Collapse
|
21
|
Barria A, López ME, Yoshida G, Carvalheiro R, Lhorente JP, Yáñez JM. Population Genomic Structure and Genome-Wide Linkage Disequilibrium in Farmed Atlantic Salmon ( Salmo salar L.) Using Dense SNP Genotypes. Front Genet 2018; 9:649. [PMID: 30619473 PMCID: PMC6302115 DOI: 10.3389/fgene.2018.00649] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 11/30/2018] [Indexed: 01/15/2023] Open
Abstract
Chilean Farmed Atlantic salmon (Salmo salar) populations were established with individuals of both European and North American origins. These populations are expected to be highly genetically differentiated due to evolutionary history and poor gene flow between ancestral populations from different continents. The extent and decay of linkage disequilibrium (LD) among single nucleotide polymorphism (SNP) impacts the implementation of genome-wide association studies and genomic selection and provides relevant information about demographic processes of fish populations. We assessed the population structure and characterized the extent and decay of LD in three Chilean commercial populations of Atlantic salmon with North American (NAM), Scottish (SCO), and Norwegian (NOR) origin. A total of 123 animals were genotyped using a 159 K SNP Axiom® myDesignTM Genotyping Array. A total of 32 K SNP markers, representing the common SNPs along the three populations after quality control were used. The principal component analysis explained 78.9% of the genetic diversity between populations, clearly discriminating between populations of North American and European origin, and also between European populations. NAM had the lowest effective population size, followed by SCO and NOR. Large differences in the LD decay were observed between populations of North American and European origin. An r 2 threshold of 0.2 was estimated for marker pairs separated by 7,800, 64, and 50 kb in the NAM, SCO, and NOR populations, respectively. In this study we show that this SNP panel can be used to detect association between markers and traits of interests and also to capture high-resolution information for genome-enabled predictions. Also, we suggest the feasibility to achieve similar prediction accuracies using a smaller SNP data set for the NAM population, compared with samples with European origin which would need a higher density SNP array.
Collapse
Affiliation(s)
- Agustin Barria
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, La Pintana, Chile
| | - Maria E. López
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, La Pintana, Chile
| | - Grazyella Yoshida
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, Brazil
| | - Roberto Carvalheiro
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, Brazil
| | | | - José M. Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, La Pintana, Chile
- Benchmark Genetic S.A., Puerto Montt, Chile
- Nucleo Milenio INVASAL, Concepción, Chile
| |
Collapse
|
22
|
Henriques D, Wallberg A, Chávez-Galarza J, Johnston JS, Webster MT, Pinto MA. Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula. Sci Rep 2018; 8:11145. [PMID: 30042407 PMCID: PMC6057950 DOI: 10.1038/s41598-018-29469-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/06/2018] [Indexed: 12/25/2022] Open
Abstract
The availability of powerful high-throughput genomic tools, combined with genome scans, has helped identifying genes and genetic changes responsible for environmental adaptation in many organisms, including the honeybee. Here, we resequenced 87 whole genomes of the honeybee native to Iberia and used conceptually different selection methods (Samβada, LFMM, PCAdapt, iHs) together with in sillico protein modelling to search for selection footprints along environmental gradients. We found 670 outlier SNPs, most of which associated with precipitation, longitude and latitude. Over 88.7% SNPs laid outside exons and there was a significant enrichment in regions adjacent to exons and UTRs. Enrichment was also detected in exonic regions. Furthermore, in silico protein modelling suggests that several non-synonymous SNPs are likely direct targets of selection, as they lead to amino acid replacements in functionally important sites of proteins. We identified genomic signatures of local adaptation in 140 genes, many of which are putatively implicated in fitness-related functions such as reproduction, immunity, olfaction, lipid biosynthesis and circadian clock. Our genome scan suggests that local adaptation in the Iberian honeybee involves variations in regions that might alter patterns of gene expression and in protein-coding genes, which are promising candidates to underpin adaptive change in the honeybee.
Collapse
Affiliation(s)
- Dora Henriques
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE -751 23, Uppsala, Sweden
| | - Julio Chávez-Galarza
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal
- Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, La Molina, Lima, Peru
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE -751 23, Uppsala, Sweden
| | - M Alice Pinto
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal.
| |
Collapse
|
23
|
Pritchard VL, Mäkinen H, Vähä JP, Erkinaro J, Orell P, Primmer CR. Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes. Mol Ecol 2018; 27:2560-2575. [DOI: 10.1111/mec.14705] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | - Hannu Mäkinen
- Department of Biology; University of Turku; Turku Finland
- Department of Biosciences; University of Helsinki; Helsinki Finland
| | - Juha-Pekka Vähä
- Kevo Subarctic Research Institute; University of Turku; Turku Finland
| | | | - Panu Orell
- Natural Resources Institute Finland (LUKE); Oulu Finland
| | - Craig R. Primmer
- Department of Biology; University of Turku; Turku Finland
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Institute of Biotechnology; University of Helsinki; Helsinki Finland
| |
Collapse
|
24
|
Horreo JL, Valiente AG, Ardura A, Blanco A, Garcia-Gonzalez C, Garcia-Vazquez E. Nature versus nurture? Consequences of short captivity in early stages. Ecol Evol 2017; 8:521-529. [PMID: 29321890 PMCID: PMC5756874 DOI: 10.1002/ece3.3555] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 01/10/2023] Open
Abstract
Biological changes occurring as a consequence of domestication and/or captivity are not still deeply known. In Atlantic salmon (Salmo salar), endangered (Southern Europe) populations are enhanced by supportive breeding, which involves only 6 months of captive rearing following artificial spawning of wild-collected adults. In this work, we assess whether several fitness-correlated life-history traits (migratory behavior, straying rate, age at maturity, and growth) are affected by early exposure to the captive environment within a generation, before reproduction thus before genetic selection. Results showed significant differences in growth and migratory behavior (including straying), associated with this very short period of captivity in natural fish populations, changing even genetic variability (decreased in hatchery-reared adults) and the native population structure within and between rivers of the species. These changes appeared within a single generation, suggesting very short time of captivity is enough for initiating changes normally attributed to domestication. These results may have potential implications for the long-term population stability/viability of species subjected to restoration and enhancement processes and could be also considered for the management of zoo populations.
Collapse
Affiliation(s)
- Jose L Horreo
- Department of Biodiversity and Evolutionary Biology National Museum of Natural Sciences (CSIC) Madrid Spain
| | | | - Alba Ardura
- Department of Functional Biology University of Oviedo Oviedo Spain
| | - Aida Blanco
- Department of Functional Biology University of Oviedo Oviedo Spain
| | | | | |
Collapse
|
25
|
Parallel epigenetic modifications induced by hatchery rearing in a Pacific salmon. Proc Natl Acad Sci U S A 2017; 114:12964-12969. [PMID: 29162695 DOI: 10.1073/pnas.1711229114] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Wild stocks of Pacific salmonids have experienced sharp declines in abundance over the past century. Consequently, billions of fish are released each year for enhancing abundance and sustaining fisheries. However, the beneficial role of this widely used management practice is highly debated since fitness decrease of hatchery-origin fish in the wild has been documented. Artificial selection in hatcheries has often been invoked as the most likely explanation for reduced fitness, and most studies to date have focused on finding signatures of hatchery-induced selection at the DNA level. We tested an alternative hypothesis, that captive rearing induces epigenetic reprogramming, by comparing genome-wide patterns of methylation and variation at the DNA level in hatchery-reared coho salmon (Oncorhynchus kisutch) with those of their wild counterparts in two geographically distant rivers. We found a highly significant proportion of epigenetic variation explained by the rearing environment that was as high as the one explained by the river of origin. The differentially methylated regions show enrichment for biological functions that may affect the capacity of hatchery-born smolts to migrate successfully in the ocean. Shared epigenetic variation between hatchery-reared salmon provides evidence for parallel epigenetic modifications induced by hatchery rearing in the absence of genetic differentiation between hatchery and natural-origin fish for each river. This study highlights epigenetic modifications induced by captive rearing as a potential explanatory mechanism for reduced fitness in hatchery-reared salmon.
Collapse
|
26
|
Liu L, Ang KP, Elliott JAK, Kent MP, Lien S, MacDonald D, Boulding EG. A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits. Evol Appl 2016; 10:276-296. [PMID: 28250812 PMCID: PMC5322405 DOI: 10.1111/eva.12450] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 11/16/2016] [Indexed: 01/08/2023] Open
Abstract
Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset. Outlier loci were then identified as those showing extreme differentiation between the aquaculture population and the founder population. All Arlequin methods identified an overlapping subset of 17 outlier loci, three of which were also identified by BayeScan. Many outlier loci were near candidate genes and some were near published quantitative trait loci (QTLs) for growth, appetite, maturity, or disease resistance. Parallel comparisons using a wild, nonfounder population (Stewiacke River) yielded only one overlapping outlier locus as well as a known maturity QTL. We conclude that genome scans comparing a recently domesticated strain with its wild founder population can facilitate identification of candidate genes for traits known to have been under strong artificial selection.
Collapse
Affiliation(s)
- Lei Liu
- Department of Integrative Biology University of Guelph Guelph ON Canada; Present address: School of Marine Sciences Ningbo University Ningbo China
| | | | | | - Matthew Peter Kent
- Department of Animal and Aquacultural Sciences (IHA) Center for Integrative Genetics (CIGENE) Norwegian University of Life Sciences Ås Norway
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences (IHA) Center for Integrative Genetics (CIGENE) Norwegian University of Life Sciences Ås Norway
| | - Danielle MacDonald
- Saint Andrews Biological Station Department of Fisheries and Oceans Canada Saint Andrews NB Canada
| | | |
Collapse
|
27
|
Bernatchez L. On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes. JOURNAL OF FISH BIOLOGY 2016; 89:2519-2556. [PMID: 27687146 DOI: 10.1111/jfb.13145] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 08/23/2016] [Indexed: 05/18/2023]
Abstract
The first goal of this paper was to overview modern approaches to local adaptation, with a focus on the use of population genomics data to detect signals of natural selection in fishes. Several mechanisms are discussed that may enhance the maintenance of genetic variation and evolutionary potential, which have been overlooked and should be considered in future theoretical development and predictive models: the prevalence of soft sweeps, polygenic basis of adaptation, balancing selection and transient polymorphisms, parallel evolution, as well as epigenetic variation. Research on fish population genomics has provided ample evidence for local adaptation at the genome level. Pervasive adaptive evolution, however, seems to almost never involve the fixation of beneficial alleles. Instead, adaptation apparently proceeds most commonly by soft sweeps entailing shifts in frequencies of alleles being shared between differentially adapted populations. One obvious factor contributing to the maintenance of standing genetic variation in the face of selective pressures is that adaptive phenotypic traits are most often highly polygenic, and consequently the response to selection should derive mostly from allelic co-variances among causative loci rather than pronounced allele frequency changes. Balancing selection in its various forms may also play an important role in maintaining adaptive genetic variation and the evolutionary potential of species to cope with environmental change. A large body of literature on fishes also shows that repeated evolution of adaptive phenotypes is a ubiquitous evolutionary phenomenon that seems to occur most often via different genetic solutions, further adding to the potential options of species to cope with a changing environment. Moreover, a paradox is emerging from recent fish studies whereby populations of highly reduced effective population sizes and impoverished genetic diversity can apparently retain their adaptive potential in some circumstances. Although more empirical support is needed, several recent studies suggest that epigenetic variation could account for this apparent paradox. Therefore, epigenetic variation should be fully integrated with considerations pertaining to role of soft sweeps, polygenic and balancing selection, as well as repeated adaptation involving different genetic basis towards improving models predicting the evolutionary potential of species to cope with a changing world.
Collapse
Affiliation(s)
- L Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1Y 2T8, Canada
| |
Collapse
|
28
|
Evidence of recent signatures of selection during domestication in an Atlantic salmon population. Mar Genomics 2016; 26:41-50. [DOI: 10.1016/j.margen.2015.12.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 11/25/2015] [Accepted: 12/16/2015] [Indexed: 11/17/2022]
|
29
|
Yáñez JM, Naswa S, López ME, Bassini L, Correa K, Gilbey J, Bernatchez L, Norris A, Neira R, Lhorente JP, Schnable PS, Newman S, Mileham A, Deeb N, Di Genova A, Maass A. Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar): validation in wild and farmed American and European populations. Mol Ecol Resour 2016; 16:1002-11. [PMID: 26849107 DOI: 10.1111/1755-0998.12503] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 01/11/2016] [Accepted: 01/16/2016] [Indexed: 11/29/2022]
Abstract
A considerable number of single nucleotide polymorphisms (SNPs) are required to elucidate genotype-phenotype associations and determine the molecular basis of important traits. In this work, we carried out de novo SNP discovery accounting for both genome duplication and genetic variation from American and European salmon populations. A total of 9 736 473 nonredundant SNPs were identified across a set of 20 fish by whole-genome sequencing. After applying six bioinformatic filtering steps, 200 K SNPs were selected to develop an Affymetrix Axiom(®) myDesign Custom Array. This array was used to genotype 480 fish representing wild and farmed salmon from Europe, North America and Chile. A total of 159 099 (79.6%) SNPs were validated as high quality based on clustering properties. A total of 151 509 validated SNPs showed a unique position in the genome. When comparing these SNPs against 238 572 markers currently available in two other Atlantic salmon arrays, only 4.6% of the SNP overlapped with the panel developed in this study. This novel high-density SNP panel will be very useful for the dissection of economically and ecologically relevant traits, enhancing breeding programmes through genomic selection as well as supporting genetic studies in both wild and farmed populations of Atlantic salmon using high-resolution genomewide information.
Collapse
Affiliation(s)
- J M Yáñez
- Faculty of Veterinary and Animal Sciences, University of Chile, Av. Santa Rosa 11735, Santiago, Chile.,Aquainnovo, Talca 60, Puerto Montt, Chile
| | - S Naswa
- Genus plc, 100 Bluegrass Commons Blvd. Suite 2200, Hendersonville, TN 37075, USA
| | - M E López
- Aquainnovo, Talca 60, Puerto Montt, Chile.,Faculty of Agricultural Sciences, University of Chile, Av. Santa Rosa 11315, Santiago, Chile
| | - L Bassini
- Aquainnovo, Talca 60, Puerto Montt, Chile.,Faculty of Agricultural Sciences, University of Chile, Av. Santa Rosa 11315, Santiago, Chile
| | - K Correa
- Faculty of Veterinary and Animal Sciences, University of Chile, Av. Santa Rosa 11735, Santiago, Chile.,Aquainnovo, Talca 60, Puerto Montt, Chile
| | - J Gilbey
- Marine Scotland Science, Freshwater Fisheries Laboratory, Faskally, Pitlochry, PH16 5LB, Scotland, UK
| | - L Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
| | - A Norris
- Marine Harvest, Kindrum, Fanad, C. Donegal, Ireland
| | - R Neira
- Aquainnovo, Talca 60, Puerto Montt, Chile.,Faculty of Agricultural Sciences, University of Chile, Av. Santa Rosa 11315, Santiago, Chile
| | | | - P S Schnable
- Data2Bio LLC, Ames, IA 50011, USA.,Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - S Newman
- Genus plc, 100 Bluegrass Commons Blvd. Suite 2200, Hendersonville, TN 37075, USA
| | - A Mileham
- Genus plc, 1525 River Road, DeForest, WI 53532, USA
| | - N Deeb
- Genus plc, 100 Bluegrass Commons Blvd. Suite 2200, Hendersonville, TN 37075, USA
| | - A Di Genova
- Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile.,Mathomics Bioinformatics Laboratory, Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile
| | - A Maass
- Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile.,Mathomics Bioinformatics Laboratory, Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile.,Department of Mathematical Engineering, University of Chile, Av. Blanco Encalada 2120, 5th floor, Santiago, Chile
| |
Collapse
|
30
|
Christie MR, Marine ML, Fox SE, French RA, Blouin MS. A single generation of domestication heritably alters the expression of hundreds of genes. Nat Commun 2016; 7:10676. [PMID: 26883375 PMCID: PMC4757788 DOI: 10.1038/ncomms10676] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 01/07/2016] [Indexed: 12/19/2022] Open
Abstract
The genetic underpinnings associated with the earliest stages of plant and animal domestication have remained elusive. Because a genome-wide response to selection can take many generations, the earliest detectable changes associated with domestication may first manifest as heritable changes to global patterns of gene expression. Here, to test this hypothesis, we measured differential gene expression in the offspring of wild and first-generation hatchery steelhead trout (Oncorhynchus mykiss) reared in a common environment. Remarkably, we find that there were 723 genes differentially expressed between the two groups of offspring. Reciprocal crosses reveal that the differentially expressed genes could not be explained by maternal effects or by chance differences in the background levels of gene expression among unrelated families. Gene-enrichment analyses reveal that adaptation to the novel hatchery environment involved responses in wound healing, immunity and metabolism. These findings suggest that the earliest stages of domestication may involve adaptation to highly crowded conditions.
Collapse
Affiliation(s)
- Mark R. Christie
- Department of Biological Sciences, Purdue University, West Lafayette, 47907-2054 IN, USA
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, 47907-2054 IN, USA
- Department of Integrative Biology, Oregon State University, Corvallis, 97331-2914 Oregon, USA
| | - Melanie L. Marine
- Department of Integrative Biology, Oregon State University, Corvallis, 97331-2914 Oregon, USA
| | - Samuel E. Fox
- Department of Integrative Biology, Oregon State University, Corvallis, 97331-2914 Oregon, USA
- Department of Biology, Saint Martin's University, Lacey, 98503-7500 WA, USA
| | - Rod A. French
- Oregon Department of Fish and Wildlife, The Dalles, 97058-4364 Oregon, USA
| | - Michael S. Blouin
- Department of Integrative Biology, Oregon State University, Corvallis, 97331-2914 Oregon, USA
| |
Collapse
|
31
|
Waters CD, Hard JJ, Brieuc MSO, Fast DE, Warheit KI, Waples RS, Knudsen CM, Bosch WJ, Naish KA. Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding. Evol Appl 2015; 8:956-71. [PMID: 26640521 PMCID: PMC4662342 DOI: 10.1111/eva.12331] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/02/2015] [Indexed: 12/28/2022] Open
Abstract
Captive breeding has the potential to rebuild depressed populations. However, associated genetic changes may decrease restoration success and negatively affect the adaptive potential of the entire population. Thus, approaches that minimize genetic risks should be tested in a comparative framework over multiple generations. Genetic diversity in two captive-reared lines of a species of conservation interest, Chinook salmon (Oncorhynchus tshawytscha), was surveyed across three generations using genome-wide approaches. Genetic divergence from the source population was minimal in an integrated line, which implemented managed gene flow by using only naturally-born adults as captive broodstock, but significant in a segregated line, which bred only captive-origin individuals. Estimates of effective number of breeders revealed that the rapid divergence observed in the latter was largely attributable to genetic drift. Three independent tests for signatures of adaptive divergence also identified temporal change within the segregated line, possibly indicating domestication selection. The results empirically demonstrate that using managed gene flow for propagating a captive-reared population reduces genetic divergence over the short term compared to one that relies solely on captive-origin parents. These findings complement existing studies of captive breeding, which typically focus on a single management strategy and examine the fitness of one or two generations.
Collapse
Affiliation(s)
- Charles D Waters
- School of Aquatic and Fishery Sciences, University of WashingtonSeattle, WA, USA
| | - Jeffrey J Hard
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric AdministrationSeattle, WA, USA
| | - Marine S O Brieuc
- School of Aquatic and Fishery Sciences, University of WashingtonSeattle, WA, USA
| | | | | | - Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric AdministrationSeattle, WA, USA
| | | | | | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of WashingtonSeattle, WA, USA
| |
Collapse
|
32
|
Signatures of selection in tilapia revealed by whole genome resequencing. Sci Rep 2015; 5:14168. [PMID: 26373374 PMCID: PMC4570987 DOI: 10.1038/srep14168] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 08/18/2015] [Indexed: 02/06/2023] Open
Abstract
Natural selection and selective breeding for genetic improvement have left detectable signatures within the genome of a species. Identification of selection signatures is important in evolutionary biology and for detecting genes that facilitate to accelerate genetic improvement. However, selection signatures, including artificial selection and natural selection, have only been identified at the whole genome level in several genetically improved fish species. Tilapia is one of the most important genetically improved fish species in the world. Using next-generation sequencing, we sequenced the genomes of 47 tilapia individuals. We identified a total of 1.43 million high-quality SNPs and found that the LD block sizes ranged from 10–100 kb in tilapia. We detected over a hundred putative selective sweep regions in each line of tilapia. Most selection signatures were located in non-coding regions of the tilapia genome. The Wnt signaling, gonadotropin-releasing hormone receptor and integrin signaling pathways were under positive selection in all improved tilapia lines. Our study provides a genome-wide map of genetic variation and selection footprints in tilapia, which could be important for genetic studies and accelerating genetic improvement of tilapia.
Collapse
|