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Hasan MM, Thomson PC, Raadsma HW, Khatkar MS. Genetic analysis of digital image derived morphometric traits of black tiger shrimp (Penaeus monodon) by incorporating G × E investigations. Front Genet 2022; 13:1007123. [PMID: 36338959 PMCID: PMC9632751 DOI: 10.3389/fgene.2022.1007123] [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: 07/29/2022] [Accepted: 09/27/2022] [Indexed: 11/15/2022] Open
Abstract
The black tiger shrimp, Penaeus monodon, is the second most economically important aquaculture shrimp species in the world, and in Australia it is one of the most commonly farmed shrimp species. Despite its economic significance, very few studies have reported the genetic evaluation of economically important morphological size and shape traits of shrimp grown in commercial grow-out environments. In this study we obtained genetic parameter estimates and evaluated genotype-by-environment interaction (GxE) for nine body morphological traits of shrimp derived from images. The data set contained image and body weight (BW) records of 5,308 shrimp, from 64 sires and 54 dams, reared in eight grow-out ponds for an average of 133 days. From the images, landmark based morphological distances were computed from which novel morphological traits associated with size and shape were derived for genetic evaluation. These traits included body weight (BW), body length (BL), body size (BS), head size (HS), Abdominal size (AS), abdominal percentage (AP), tail tip (TT), front by back ratio (FBR), condition factor (CF) and condition factor length (CFL). We also evaluated G×E interaction effects of these traits for shrimp reared in different ponds. The heritability estimates for growth related morphological and body weight traits were moderately high (BW: h2 = 0.32 ± 0.05; BL: h2 = 0.36 ± 0.06; BS: h2 = 0.32 ± 0.05; HS: h2 = 0.31 ± 0.05; AS: h2 = 0.32 ± 0.05; and TT: h2 = 0.28 ± 0.05) and low for abdominal percentage and body shape traits (AP: h2 = 0.09 ± 0.02; FBR: h2 = 0.08 ± 0.02; CF: h2 = 0.06 ± 0.02; and CFL: h2 = 0.003 ± 0.004). G × E interaction were negligible for all traits for shrimp reared in different ponds, suggesting re-ranking is not prevalent for this population. Genetic correlations among growth related morphological traits were high ranging from 0.36 to 0.99, suggesting these traits can be simultaneously improved through indirect genetic selection. However, negative genetic correlations were observed for FBR & CF shape traits with major growth traits (ranged −0.08 to −0.95), suggesting genetic selection for rapid growth will likely result in thick/fatty shrimp over generations. Our study showed image-based landmark data can be successfully employed for genetic evaluation of complex morphological traits of shrimp and is potentially amenable to machine-learning derived parameters in semi-automated high volume phenotyping systems needed under commercial conditions.
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Affiliation(s)
- Md. Mehedi Hasan
- The University of Sydney, Faculty of Science, Sydney School of Veterinary Science, Camden, NSW, Australia
- ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, Australia
- *Correspondence: Md. Mehedi Hasan,
| | - Peter C. Thomson
- The University of Sydney, Faculty of Science, Sydney School of Veterinary Science, Camden, NSW, Australia
- ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, Australia
| | - Herman W. Raadsma
- The University of Sydney, Faculty of Science, Sydney School of Veterinary Science, Camden, NSW, Australia
- ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, Australia
| | - Mehar S. Khatkar
- The University of Sydney, Faculty of Science, Sydney School of Veterinary Science, Camden, NSW, Australia
- ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, Australia
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2
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Stepaniak MD, Square TA, Miller CT. Evolved Bmp6 enhancer alleles drive spatial shifts in gene expression during tooth development in sticklebacks. Genetics 2021; 219:6374454. [PMID: 34849839 PMCID: PMC8664583 DOI: 10.1093/genetics/iyab151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
Mutations in enhancers have been shown to often underlie natural variation but the evolved differences in enhancer activity can be difficult to identify in vivo. Threespine sticklebacks (Gasterosteus aculeatus) are a robust system for studying enhancer evolution due to abundant natural genetic variation, a diversity of evolved phenotypes between ancestral marine and derived freshwater forms, and the tractability of transgenic techniques. Previous work identified a series of polymorphisms within an intronic enhancer of the Bone morphogenetic protein 6 (Bmp6) gene that are associated with evolved tooth gain, a derived increase in freshwater tooth number that arises late in development. Here, we use a bicistronic reporter construct containing a genetic insulator and a pair of reciprocal two-color transgenic reporter lines to compare enhancer activity of marine and freshwater alleles of this enhancer. In older fish, the two alleles drive partially overlapping expression in both mesenchyme and epithelium of developing teeth, but the freshwater enhancer drives a reduced mesenchymal domain and a larger epithelial domain relative to the marine enhancer. In younger fish, these spatial shifts in enhancer activity are less pronounced. Comparing Bmp6 expression by in situ hybridization in developing teeth of marine and freshwater fish reveals similar evolved spatial shifts in gene expression. Together, these data support a model in which the polymorphisms within this enhancer underlie evolved tooth gain by shifting the spatial expression of Bmp6 during tooth development, and provide a general strategy to identify spatial differences in enhancer activity in vivo.
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Affiliation(s)
- Mark D Stepaniak
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Tyler A Square
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Craig T Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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3
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Kong S, Zhou Z, Zhou T, Zhao J, Chen L, Lin H, Pu F, Ke Q, Bai H, Xu P. Genome-Wide Association Study of Body Shape-Related Traits in Large Yellow Croaker (Larimichthys crocea). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:631-643. [PMID: 32666363 DOI: 10.1007/s10126-020-09983-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
Large yellow croaker (Larimichthys crocea) is one of the most important cultured marine fish on the southeast coast of China. Its body shape is important for the aquaculture industry since it affects the behavior such as swimming, ingesting, and evading, as well as customer preference. Due to the greater consumer demand of small head, slender body large yellow croaker, selecting and breeding of slender individuals with the assistance of genetic markers will benefit the industry quickly. In this study, several traits were employed to represent body shape, including body depth/body length (BD/BL), body thickness/body length (BT/BL), caudal peduncle depth/caudal peduncle length (CPDLR), tail length/body length (TL/BL), and body area/head area (BA/HA). Genome-wide association study was conducted with a panmictic population of 280 individuals to identify SNP and genes potentially associated with body shape. A set of 20 SNPs on 12 chromosomes were identified to be significantly associated with body shape-related traits. Besides, 5 SNPs were identified to be suggestive associated with CPDLR and BT/BL. Surrounding these SNPs, we found some body shape-related candidate genes, including fabp1, acrv1, bcor, mstn, bambi, and neo1, which involved in lipid metabolism, TGF-β signaling, and BMP pathway and other important regulatory pathways. These results will be useful for the understanding of the genetic basis of body shape formation and helpful for body shape controlling of large yellow croaker by using marker-assisted selection.
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Affiliation(s)
- Shengnan Kong
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Zhixiong Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Ji Zhao
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Lin Chen
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Huanling Lin
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Fei Pu
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
| | - Qiaozhen Ke
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Huaqiang Bai
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Peng Xu
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
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4
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Dong L, Han Z, Fang M, Xiao S, Wang Z. Genome-wide association study identifies loci for body shape in the large yellow croaker (Larimichthys crocea). AQUACULTURE AND FISHERIES 2019. [DOI: 10.1016/j.aaf.2018.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Bolotovskiy AA, Levina MA, DeFaveri J, Merilä J, Levin BA. Heterochronic development of lateral plates in the three-spined stickleback induced by thyroid hormone level alterations. PLoS One 2018. [PMID: 29522555 PMCID: PMC5844557 DOI: 10.1371/journal.pone.0194040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The three-spined stickleback Gasterosteus aculeatus is an important model for studying microevolution and parallel adaptation to freshwater environments. Marine and freshwater forms differ markedly in their phenotype, especially in the number of lateral plates, which are serially repeated elements of the exoskeleton. In fishes, thyroid hormones are involved in adaptation to salinity, as well as the developmental regulation of serially repeated elements. To study how thyroid hormones influence lateral plate development, we manipulated levels of triiodothyronine and thiourea during early ontogeny in a marine and freshwater population with complete and low plate phenotypes, respectively. The development of lateral plates along the body and keel was heterochronic among experimental groups. Fish with a low dosage of exogenous triiodothyronine and those treated with thiourea exhibited retarded development of bony plates compared to both control fish and those treated with higher a triiodothyronine dosage. Several triiodothyronine-treated individuals of the marine form expressed the partial lateral plate phenotype. Some individuals with delayed development of lateral plates manifested 1–2 extra bony plates located above the main row of lateral plates.
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Affiliation(s)
- Aleksey A. Bolotovskiy
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Prov., Russia
| | - Marina A. Levina
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Prov., Russia
| | - Jacquelin DeFaveri
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Boris A. Levin
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Prov., Russia
- Cherepovets State University, Cherepovets, Russia
- * E-mail:
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6
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Zheng X, Kuang Y, Lv W, Cao D, Sun Z, Jin W, Sun X. Quantitative trait loci for morphometric traits in multiple families of common carp (Cyprinus carpio). SCIENCE CHINA-LIFE SCIENCES 2016; 60:287-297. [PMID: 27826895 DOI: 10.1007/s11427-016-0182-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 10/08/2016] [Indexed: 11/27/2022]
Abstract
Quantitative trait locus (QTL) mapping is frequently used to understand the genetic architecture of quantitative traits. Herein, we performed a genome scan for QTL affecting the morphometric characters in eight full-sib families containing 522 individuals using different statistical methods (Sib-pair and half-sib model). A total of 194 QTLs were detected in 25 different regions on 10 linkage groups (LGs). Among them, 37 QTLs on five LGs (eight, 13, 24, 40 and 45) were significant (5% genome-wide level), while the remaining 40 (1% chromosome-wide level) and 117 (5% chromosome-wide level) indicated suggestive effect on those traits. Heritabilities for most morphometric traits were moderate to high, ranging from 0.21 to 0.66, with generally strong phenotypic and genetic correlations between the traits. A large number of QTLs for morphometric traits were co-located, consistent with their high correlations, and may reflect pleiotropic effect on the same genes. Biological pathways were mapped for possible candidate genes on QTL regions. One significantly enriched pathway was identified on LG45, which had a P-value of 0.04 and corresponded to the "regulation of actin cytoskeleton pathway". The results are expected to be useful in marker-assisted selection (MAS) and provide valuable information for the study of gene pathway for morphometric and growth traits of the common carp.
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Affiliation(s)
- Xianhu Zheng
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
| | - Youyi Kuang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
| | - Weihua Lv
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Dingchen Cao
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
| | - Zhipeng Sun
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
| | - Wu Jin
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Xiaowen Sun
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China.
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7
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Magalhaes IS, D'Agostino D, Hohenlohe PA, MacColl ADC. The ecology of an adaptive radiation of three-spined stickleback from North Uist, Scotland. Mol Ecol 2016; 25:4319-36. [PMID: 27374399 PMCID: PMC5031221 DOI: 10.1111/mec.13746] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 06/16/2016] [Accepted: 06/22/2016] [Indexed: 01/15/2023]
Abstract
There has been a large focus on the genetics of traits involved in adaptation, but knowledge of the environmental variables leading to adaptive changes is surprisingly poor. Combined use of environmental data with morphological and genomic data should allow us to understand the extent to which patterns of phenotypic and genetic diversity within a species can be explained by the structure of the environment. Here, we analyse the variation of populations of three‐spined stickleback from 27 freshwater lakes on North Uist, Scotland, that vary greatly in their environment, to understand how environmental and genetic constraints contribute to phenotypic divergence. We collected 35 individuals per population and 30 abiotic and biotic environmental parameters to characterize variation across lakes and analyse phenotype–environment associations. Additionally, we used RAD sequencing to estimate the genetic relationships among a subset of these populations. We found a large amount of phenotypic variation among populations, most prominently in armour and spine traits. Despite large variation in the abiotic environment, namely in ion composition, depth and dissolved organic Carbon, more phenotypic variation was explained by the biotic variables (presence of predators and density of predator and competitors), than by associated abiotic variables. Genetic structure among populations was partly geographic, with closer populations being more similar. Altogether, our results suggest that differences in body shape among stickleback populations are the result of both canalized genetic and plastic responses to environmental factors, which shape fish morphology in a predictable direction regardless of their genetic starting point.
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Affiliation(s)
- Isabel S Magalhaes
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Daniele D'Agostino
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Andrew D C MacColl
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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8
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Calboli FCF, Byström P, Merilä J. A test for within-lake niche differentiation in the nine-spined sticklebacks (Pungitius pungitius). Ecol Evol 2016; 6:4753-60. [PMID: 27547310 PMCID: PMC4979704 DOI: 10.1002/ece3.2182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/12/2016] [Accepted: 04/26/2016] [Indexed: 12/19/2022] Open
Abstract
Specialization for the use of different resources can lead to ecological speciation. Accordingly, there are numerous examples of ecologically specialized pairs of fish "species" in postglacial lakes. Using a polymorphic panel of single nucleotide variants, we tested for genetic footprints of within-lake population stratification in nine-spined sticklebacks (Pungitius pungitius) collected from three habitats (viz. littoral, benthic, and pelagic) within a northern Swedish lake. Analyses of admixture, population structure, and relatedness all supported the conclusion that the fish from this lake form a single interbreeding unit.
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Affiliation(s)
- Federico C. F. Calboli
- Ecological Genetics Research UnitDepartment of BiosciencesUniversity of HelsinkiHelsinkiFinland
| | - Pär Byström
- Department of Ecology and Environmental SciencesUmeå UniversityUmeåSweden
| | - Juha Merilä
- Ecological Genetics Research UnitDepartment of BiosciencesUniversity of HelsinkiHelsinkiFinland
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9
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Lucek K, Kristjánsson BK, Skúlason S, Seehausen O. Ecosystem size matters: the dimensionality of intralacustrine diversification in Icelandic stickleback is predicted by lake size. Ecol Evol 2016; 6:5256-72. [PMID: 27551381 PMCID: PMC4984502 DOI: 10.1002/ece3.2239] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/10/2016] [Accepted: 05/16/2016] [Indexed: 02/03/2023] Open
Abstract
Cases of evolutionary diversification can be characterized along a continuum from weak to strong genetic and phenotypic differentiation. Several factors may facilitate or constrain the differentiation process. Comparative analyses of replicates of the same taxon at different stages of differentiation can be useful to identify these factors. We estimated the number of distinct phenotypic groups in three‐spine stickleback populations from nine lakes in Iceland and in one marine population. Using the inferred number of phenotypic groups in each lake, genetic divergence from the marine population, and physical lake and landscape variables, we tested whether ecosystem size, approximated by lake size and depth, or isolation from the ancestral marine gene pool predicts the occurrence and the extent of phenotypic and genetic diversification within lakes. We find intralacustrine phenotypic diversification to be the rule rather than the exception, occurring in all but the youngest lake population and being manifest in ecologically important phenotypic traits. Neutral genetic data further indicate nonrandom mating in four of nine studied lakes, and restricted gene flow between sympatric phenotypic groups in two. Although neither the phenotypic variation nor the number of intralacustrine phenotypic groups was associated with any of our environmental variables, the number of phenotypic traits that were differentiated was significantly positively related to lake size, and evidence for restricted gene flow between sympatric phenotypic groups was only found in the largest lakes where trait specific phenotypic differentiation was highest.
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Affiliation(s)
- Kay Lucek
- Aquatic Ecology and Evolution Institute of Ecology and Evolution University of Bern Baltzerstrasse 6CH-3012 Bern Switzerland; Department of Fish Ecology and Evolution EAWAG Swiss Federal Institute of Aquatic Science and Technology Center for Ecology, Evolution and Biogeochemistry CH-6047 Kastanienbaum Switzerland; Department of Animal and Plant Sciences University of Sheffield Sheffield UK
| | - Bjarni K Kristjánsson
- Department of Aquaculture and Fish Biology Hólar University College 550 Saudárkrókur Iceland
| | - Skúli Skúlason
- Department of Aquaculture and Fish Biology Hólar University College 550 Saudárkrókur Iceland
| | - Ole Seehausen
- Aquatic Ecology and Evolution Institute of Ecology and Evolution University of Bern Baltzerstrasse 6CH-3012 Bern Switzerland; Department of Fish Ecology and Evolution EAWAG Swiss Federal Institute of Aquatic Science and Technology Center for Ecology, Evolution and Biogeochemistry CH-6047 Kastanienbaum Switzerland
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10
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Quantitative trait locus analysis of body shape divergence in nine-spined sticklebacks based on high-density SNP-panel. Sci Rep 2016; 6:26632. [PMID: 27226078 PMCID: PMC4880927 DOI: 10.1038/srep26632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 05/06/2016] [Indexed: 12/26/2022] Open
Abstract
Heritable phenotypic differences between populations, caused by the selective effects of distinct environmental conditions, are of commonplace occurrence in nature. However, the actual genomic targets of this kind of selection are still poorly understood. We conducted a quantitative trait locus (QTL) mapping study to identify genomic regions responsible for morphometric differentiation between genetically and phenotypically divergent marine and freshwater nine-spined stickleback (Pungitius pungitius) populations. Using a dense panel of SNP-markers obtained by restriction site associated DNA sequencing of an F2 recombinant cross, we found 22 QTL that explained 3.5-12.9% of phenotypic variance in the traits under investigation. We detected one fairly large-effect (PVE = 9.6%) QTL for caudal peduncle length-a trait with a well-established adaptive function showing clear differentiation among marine and freshwater populations. We also identified two large-effect QTL for lateral plate numbers, which are different from the lateral plate QTL reported in earlier studies of this and related species. Hence, apart from identifying several large-effect QTL in shape traits showing adaptive differentiation in response to different environmental conditions, the results suggest intra- and interspecific heterogeneity in the genomic basis of lateral plate number variation.
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11
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Aykanat T, Johnston SE, Orell P, Niemelä E, Erkinaro J, Primmer CR. Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population. Mol Ecol 2015; 24:5158-74. [DOI: 10.1111/mec.13383] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 09/04/2015] [Accepted: 09/09/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Tutku Aykanat
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FI-20520 Finland
| | - Susan E. Johnston
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FI-20520 Finland
- Institute of Evolutionary Biology; University of Edinburgh; Charlotte Auerbach Road Edinburgh EH9 3FL UK
| | - Panu Orell
- Natural Resources Institute Finland; Utsjoki FI-99980 Finland
| | - Eero Niemelä
- Natural Resources Institute Finland; Utsjoki FI-99980 Finland
| | - Jaakko Erkinaro
- Natural Resources Institute Finland; Utsjoki FI-99980 Finland
| | - Craig R. Primmer
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FI-20520 Finland
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12
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Brodersen J, Howeth JG, Post DM. Emergence of a novel prey life history promotes contemporary sympatric diversification in a top predator. Nat Commun 2015; 6:8115. [DOI: 10.1038/ncomms9115] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 07/21/2015] [Indexed: 11/09/2022] Open
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13
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Kakioka R, Kokita T, Kumada H, Watanabe K, Okuda N. Genomic architecture of habitat-related divergence and signature of directional selection in the body shapes of Gnathopogon fishes. Mol Ecol 2015; 24:4159-74. [PMID: 26179373 DOI: 10.1111/mec.13309] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 06/19/2015] [Accepted: 07/03/2015] [Indexed: 01/19/2023]
Abstract
Evolution of ecomorphologically relevant traits such as body shapes is important to colonize and persist in a novel environment. Habitat-related adaptive divergence of these traits is therefore common among animals. We studied the genomic architecture of habitat-related divergence in the body shape of Gnathopogon fishes, a novel example of lake-stream ecomorphological divergence, and tested for the action of directional selection on body shape differentiation. Compared to stream-dwelling Gnathopogon elongatus, the sister species Gnathopogon caerulescens, exclusively inhabiting a large ancient lake, had an elongated body, increased proportion of the caudal region and small head, which would be advantageous in the limnetic environment. Using an F2 interspecific cross between the two Gnathopogon species (195 individuals), quantitative trait locus (QTL) analysis with geometric morphometric quantification of body shape and restriction-site associated DNA sequencing-derived markers (1622 loci) identified 26 significant QTLs associated with the interspecific differences of body shape-related traits. These QTLs had small to moderate effects, supporting polygenic inheritance of the body shape-related traits. Each QTL was mostly located on different genomic regions, while colocalized QTLs were detected for some ecomorphologically relevant traits that are proxy of body and caudal peduncle depths, suggesting different degree of modularity among traits. The directions of the body shape QTLs were mostly consistent with the interspecific difference, and QTL sign test suggested a genetic signature of directional selection in the body shape divergence. Thus, we successfully elucidated the genomic architecture underlying the adaptive changes of the quantitative and complex morphological trait in a novel system.
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Affiliation(s)
- Ryo Kakioka
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tomoyuki Kokita
- Department of Marine Bioscience, Fukui Prefectural University, 1-1 Gakuen-cho, Obama, 917-0003, Japan
| | - Hiroki Kumada
- Department of Marine Bioscience, Fukui Prefectural University, 1-1 Gakuen-cho, Obama, 917-0003, Japan
| | - Katsutoshi Watanabe
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Noboru Okuda
- Center for Ecological Research, Kyoto University, 509-3 Hirano 2-chome, Otsu, 520-2113, Japan
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14
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Laghari MY, Lashari P, Zhang X, Xu P, Narejo NT, Liu Y, Mehboob S, Al-Ghanim K, Zhang Y, Sun X. Mapping QTLs for swimming ability related traits in Cyprinus carpio L. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:629-637. [PMID: 24985693 DOI: 10.1007/s10126-014-9578-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 05/30/2014] [Indexed: 06/03/2023]
Abstract
Body height (BH), head length (HL), snout length (SL), and tail length (TL) are important traits related with swimming ability of fish. Therefore, improving these traits will increase the production which is the basic goal of aquaculture breeding. To understand the genetic basis of swimming ability related traits in Cyprinus carpio L., a high-density linkage map spanning 3,301 cM in 50 linkage groups was utilized for quantitative trait locus (QTL) mapping. Mapping family comprised 190 offspring and 627 molecular markers were genotyped with average distance of 5.6 cM. A total of 15 QTLs including four (qBH13, qBH30, qBH33, qBH48) for BH, four (qHL10, qHL18, qHL29, qHL48) for HL, three (qSL24, qSL27, qSL45) for SL, and four (qTL15, qTL17, qTL18, qTL44) for TL were detected on 13 linkage groups LG10, LG13, LG15, LG17, LG18, LG24, LG27, LG29, LG30, LG33, LG44, LG45, and LG48. Each LG consisted on single QTL except LG18 and LG48. LG18 was found with two QTLs associated with HL and TL. While LG48 was comprised, the QTLs related with BH and HL. The phenotype variance was recorded from 12.6 to 40.6 %. Five QTLs, qHL48, qSL45, qTL15, qTL18, and qTL44, explained phenotype variance of >20 % with a significant levels of 0.047, 0.049, 0.037, 0.025, and 0.023, respectively. The neighbored loci of these QTLs were considered as main region of chromosomes controlling the traits. These identified genetic regions will be the main source of discovering gene(s) associated with swimming ability related traits in C. carpio L.
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Colihueque N, Araneda C. Appearance traits in fish farming: progress from classical genetics to genomics, providing insight into current and potential genetic improvement. Front Genet 2014; 5:251. [PMID: 25140172 PMCID: PMC4121539 DOI: 10.3389/fgene.2014.00251] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/10/2014] [Indexed: 11/13/2022] Open
Abstract
Appearance traits in fish, those external body characteristics that influence consumer acceptance at point of sale, have come to the forefront of commercial fish farming, as culture profitability is closely linked to management of these traits. Appearance traits comprise mainly body shape and skin pigmentation. Analysis of the genetic basis of these traits in different fish reveals significant genetic variation within populations, indicating potential for their genetic improvement. Work into ascertaining the minor or major genes underlying appearance traits for commercial fish is emerging, with substantial progress in model fish in terms of identifying genes that control body shape and skin colors. In this review, we describe research progress to date, especially with regard to commercial fish, and discuss genomic findings in model fish in order to better address the genetic basis of the traits. Given that appearance traits are important in commercial fish, the genomic information related to this issue promises to accelerate the selection process in coming years.
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Affiliation(s)
- Nelson Colihueque
- Laboratorio de Biología Molecular y Citogenética, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, OsornoChile
| | - Cristian Araneda
- Laboratorio de Biotecnología y Genética Aplicada a la Acuicultura, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, SantiagoChile
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16
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Lucek K, Sivasundar A, Kristjánsson BK, Skúlason S, Seehausen O. Quick divergence but slow convergence during ecotype formation in lake and stream stickleback pairs of variable age. J Evol Biol 2014; 27:1878-92. [DOI: 10.1111/jeb.12439] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 05/08/2014] [Accepted: 05/25/2014] [Indexed: 01/27/2023]
Affiliation(s)
- K. Lucek
- Aquatic Ecology and Evolution; Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Department of Fish Ecology and Evolution; EAWAG Swiss Federal Institute of Aquatic Science and Technology; Center for Ecology, Evolution and Biogeochemistry; Kastanienbaum Switzerland
| | - A. Sivasundar
- Aquatic Ecology and Evolution; Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Department of Fish Ecology and Evolution; EAWAG Swiss Federal Institute of Aquatic Science and Technology; Center for Ecology, Evolution and Biogeochemistry; Kastanienbaum Switzerland
| | - B. K. Kristjánsson
- Department of Aquaculture and Fish Biology; Hólar University College; Sauðárkrókur Iceland
| | - S. Skúlason
- Department of Aquaculture and Fish Biology; Hólar University College; Sauðárkrókur Iceland
| | - O. Seehausen
- Aquatic Ecology and Evolution; Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Department of Fish Ecology and Evolution; EAWAG Swiss Federal Institute of Aquatic Science and Technology; Center for Ecology, Evolution and Biogeochemistry; Kastanienbaum Switzerland
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17
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Tyler SEB. The Work Surfaces of Morphogenesis: The Role of the Morphogenetic Field. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s13752-014-0177-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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McGee MD, Schluter D, Wainwright PC. Functional basis of ecological divergence in sympatric stickleback. BMC Evol Biol 2013; 13:277. [PMID: 24380474 PMCID: PMC3890603 DOI: 10.1186/1471-2148-13-277] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 12/04/2013] [Indexed: 11/10/2022] Open
Abstract
Background The evolution of ecological divergence in closely related species is a key component of adaptive radiation. However, in most examples of adaptive radiation the mechanistic basis of ecological divergence remains unclear. A classic example is seen in the young benthic and limnetic stickleback species pairs of British Columbia. In each pair the benthic species feeds on littoral macroinvertebrates whereas the limnetic feeds on pelagic zooplankton. Previous studies indicate that in both short-term feeding trials and long-term enclosure studies, benthics and limnetics exhibit enhanced performance on their own resource but fare more poorly on the other species’ resource. We examined the functional basis of ecological divergence in the stickleback species pair from Paxton Lake, BC, using biomechanical models of fish feeding applied to morphological traits. We examined the consequences of morphological differences using high speed video of feeding fish. Results Benthic stickleback possess morphological traits that predict high suction generation capacity, including greatly hypertrophied epaxial musculature. In contrast, limnetic stickleback possess traits thought to enhance capture of evasive planktonic prey, including greater jaw protrusion than benthics and greater displacement advantage in both the lower jaw-opening lever system and the opercular four-bar linkage. Kinematic data support the expectations from the morphological analysis that limnetic stickleback exhibit faster strikes and greater jaw protrusion than benthic fish, whereas benthics exert greater suction force on attached prey. Conclusions We reveal a previously unknown suite of complex morphological traits that affect rapid ecological divergence in sympatric stickleback. These results indicate that postglacial divergence in stickleback involves many functional systems and shows the value of investigating the functional consequences of phenotypic divergence in adaptive radiation.
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Affiliation(s)
- Matthew D McGee
- Department of Evolution and Ecology, University of California Davis, 1 Shields Avenue, Davis, CA 95616, USA.
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19
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Head ML, Kozak GM, Boughman JW. Female mate preferences for male body size and shape promote sexual isolation in threespine sticklebacks. Ecol Evol 2013; 3:2183-96. [PMID: 23919161 PMCID: PMC3728956 DOI: 10.1002/ece3.631] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/09/2013] [Accepted: 05/10/2013] [Indexed: 12/22/2022] Open
Abstract
Female mate preferences for ecologically relevant traits may enhance natural selection, leading to rapid divergence. They may also forge a link between mate choice within species and sexual isolation between species. Here, we examine female mate preference for two ecologically important traits: body size and body shape. We measured female preferences within and between species of benthic, limnetic, and anadromous threespine sticklebacks (Gasterosteus aculeatus species complex). We found that mate preferences differed between species and between contexts (i.e., within vs. between species). Within species, anadromous females preferred males that were deep bodied for their size, benthic females preferred larger males (as measured by centroid size), and limnetic females preferred males that were more limnetic shaped. In heterospecific mating trials between benthics and limnetics, limnetic females continued to prefer males that were more limnetic like in shape when presented with benthic males. Benthic females showed no preferences for size when presented with limnetic males. These results show that females use ecologically relevant traits to select mates in all three species and that female preference has diverged between species. These results suggest that sexual selection may act in concert with natural selection on stickleback size and shape. Further, our results suggest that female preferences may track adaptation to local environments and contribute to sexual isolation between benthic and limnetic sticklebacks.
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Affiliation(s)
- Megan L Head
- Centre for Ecology and Conservation, School of Biosciences, University of Exeter Cornwall Campus, Penryn, TR10 9EZ, UK
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20
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Zhang Y, Wang S, Li J, Zhang X, Jiang L, Xu P, Lu C, Wan Y, Sun X. Primary genome scan for complex body shape-related traits in the common carp Cyprinus carpio. JOURNAL OF FISH BIOLOGY 2013; 82:125-140. [PMID: 23331142 DOI: 10.1111/j.1095-8649.2012.03469.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
To identify quantitative trait loci (QTL) that affect body shape in common carp Cyprinus carpio, a linkage map, 2159·23 cM long, was constructed with a total of 307 markers covering 51 linkage groups (LG). The map included 167 new single nucleotide polymorphism (SNP) markers derived from expressed sequence tags (EST) together with 140 microsatellite markers reported earlier. A primary genome scan was conducted for QTL for standard length (L(S)), head length (L(H)), body height (H(B)), body width (W(B)) and tail length (L(TAIL)) in an F1 line containing 92 offspring. A total of 15 suggestive QTL on six LGs were found to associate with L(S), L(H), H(B), W(B) and L(TAIL) which explained 10·7-17·4% of the variance. Five significant QTL were detected for body-shape related traits and located for LGs (lg1, 12 and 20). These QTL included: one associated with L(S) (21·1% variance explained), three for H(B) (almost 20% variance explained) and one for W(B) (20·7% variance explained).
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Affiliation(s)
- Y Zhang
- The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China
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McCAIRNS RJS, BERNATCHEZ L. Plasticity and heritability of morphological variation within and between parapatric stickleback demes. J Evol Biol 2012; 25:1097-112. [DOI: 10.1111/j.1420-9101.2012.02496.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Dalziel AC, Vines TH, Schulte PM. REDUCTIONS IN PROLONGED SWIMMING CAPACITY FOLLOWING FRESHWATER COLONIZATION IN MULTIPLE THREESPINE STICKLEBACK POPULATIONS. Evolution 2011; 66:1226-39. [PMID: 22486700 DOI: 10.1111/j.1558-5646.2011.01498.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Anne C Dalziel
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada.
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