1
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Lichilín N, Salzburger W, Böhne A. No evidence for sex chromosomes in natural populations of the cichlid fish Astatotilapia burtoni. G3 (BETHESDA, MD.) 2023; 13:6989787. [PMID: 36649174 PMCID: PMC9997565 DOI: 10.1093/g3journal/jkad011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/14/2022] [Accepted: 12/16/2022] [Indexed: 01/18/2023]
Abstract
Sex determination (SD) is not conserved among teleost fishes and can even differ between populations of the same species. Across the outstandingly species-rich fish family Cichlidae, more and more SD systems are being discovered. Still, the picture of SD evolution in this group is far from being complete. Lake Tanganyika and its affluent rivers are home to Astatotilapia burtoni, which belongs to the extremely successful East African cichlid lineage Haplochromini. Previously, in different families of an A. burtoni laboratory strain, an XYW system and an XY system have been described. The latter was also found in a second laboratory strain. In a laboratory-reared family descending from a population of the species' southern distribution, a second XY system was discovered. Yet, an analysis of sex chromosomes for the whole species distribution is missing. Here, we examined the genomes of 11 natural populations of A. burtoni, encompassing a wide range of its distribution, for sex-linked regions. We did not detect signs of differentiated sex chromosomes and also not the previously described sex chromosomal systems present in laboratory lines, suggesting different SD systems in the same species under natural and (long-term) artificial conditions. We suggest that SD in A. burtoni is more labile than previously assumed and consists of a combination of non-genetic, polygenic, or poorly differentiated sex chromosomes.
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Affiliation(s)
- Nicolás Lichilín
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland.,Department of Neuroscience and Developmental Biology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Astrid Böhne
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland.,Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113 Bonn, Germany
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2
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Etherington GJ, Nash W, Ciezarek A, Mehta TK, Barria A, Peñaloza C, Khan MGQ, Durrant A, Forrester N, Fraser F, Irish N, Kaithakottil GG, Lipscombe J, Trong T, Watkins C, Swarbreck D, Angiolini E, Cnaani A, Gharbi K, Houston RD, Benzie JAH, Haerty W. Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus. BMC Genomics 2022; 23:832. [PMID: 36522771 PMCID: PMC9756657 DOI: 10.1186/s12864-022-09065-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Nile tilapia (Oreochromis niloticus) is the third most important freshwater fish for aquaculture. Its success is directly linked to continuous breeding efforts focusing on production traits such as growth rate and weight. Among those elite strains, the Genetically Improved Farmed Tilapia (GIFT) programme initiated by WorldFish is now distributed worldwide. To accelerate the development of the GIFT strain through genomic selection, a high-quality reference genome is necessary. RESULTS Using a combination of short (10X Genomics) and long read (PacBio HiFi, PacBio CLR) sequencing and a genetic map for the GIFT strain, we generated a chromosome level genome assembly for the GIFT. Using genomes of two closely related species (O. mossambicus, O. aureus), we characterised the extent of introgression between these species and O. niloticus that has occurred during the breeding process. Over 11 Mb of O. mossambicus genomic material could be identified within the GIFT genome, including genes associated with immunity but also with traits of interest such as growth rate. CONCLUSION Because of the breeding history of elite strains, current reference genomes might not be the most suitable to support further studies into the GIFT strain. We generated a chromosome level assembly of the GIFT strain, characterising its mixed origins, and the potential contributions of introgressed regions to selected traits.
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Affiliation(s)
- G. J. Etherington
- grid.421605.40000 0004 0447 4123Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ UK
| | - W. Nash
- grid.421605.40000 0004 0447 4123Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ UK
| | - A. Ciezarek
- grid.421605.40000 0004 0447 4123Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ UK
| | - T. K. Mehta
- grid.421605.40000 0004 0447 4123Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ UK
| | - A. Barria
- grid.4305.20000 0004 1936 7988The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG UK
| | - C. Peñaloza
- grid.4305.20000 0004 1936 7988The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG UK
| | - M. G. Q. Khan
- grid.4305.20000 0004 1936 7988The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG UK ,grid.411511.10000 0001 2179 3896Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh, 2202 Bangladesh
| | - A. Durrant
- grid.421605.40000 0004 0447 4123Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ UK
| | - N. Forrester
- grid.421605.40000 0004 0447 4123Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ UK
| | - F. Fraser
- grid.421605.40000 0004 0447 4123Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ UK
| | - N. Irish
- grid.421605.40000 0004 0447 4123Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ UK
| | - G. G. Kaithakottil
- grid.421605.40000 0004 0447 4123Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ UK
| | - J. Lipscombe
- grid.421605.40000 0004 0447 4123Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ UK
| | - T. Trong
- grid.425190.bWorldFish, 10670 Penang, Malaysia
| | - C. Watkins
- grid.421605.40000 0004 0447 4123Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ UK
| | - D. Swarbreck
- grid.421605.40000 0004 0447 4123Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ UK
| | - E. Angiolini
- grid.421605.40000 0004 0447 4123Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ UK
| | - A. Cnaani
- grid.410498.00000 0001 0465 9329Department of Poultry and Aquaculture, Institute of Animal Science, Agricultural Research Organization - Volcani Institute, Rishon LeTsiyon, Israel
| | - K. Gharbi
- grid.421605.40000 0004 0447 4123Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ UK
| | - R. D. Houston
- grid.4305.20000 0004 1936 7988The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG UK ,Benchmark Genetics, 1 Pioneer Building, Edinburgh Technopole, Penicuik, EH26 0GB UK
| | | | - W. Haerty
- grid.421605.40000 0004 0447 4123Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ UK ,grid.8273.e0000 0001 1092 7967School of Biological Sciences, University of East Anglia, Norwich, UK
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3
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Triay C, Courcelle M, Caminade P, Bezault E, Baroiller JF, Kocher TD, D'Cotta H. Polymorphism of Sex Determination Amongst Wild Populations Suggests its Rapid Turnover Within the Nile Tilapia Species. Front Genet 2022; 13:820772. [PMID: 35656328 PMCID: PMC9152217 DOI: 10.3389/fgene.2022.820772] [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] [Received: 11/23/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Sex-determining regions have been identified in the Nile tilapia on linkage groups (LG) 1, 20 and 23, depending on the domesticated strains used. Sex determining studies on wild populations of this species are scarce. Previous work on two wild populations, from Lake Volta (Ghana) and from Lake Koka (Ethiopia), found the sex-determining region on LG23. These populations have a Y-specific tandem duplication containing two copies of the Anti-Müllerian Hormone amh gene (named amhY and amhΔY). Here, we performed a whole-genome short-reads analysis using male and female pools on a third wild population from Lake Hora (Ethiopia). We found no association of sex with LG23, and no duplication of the amh gene. Furthermore, we found no evidence of sex linkage on LG1 or on any other LGs. Long read whole genome sequencing of a male from each population confirmed the absence of a duplicated region on LG23 in the Lake Hora male. In contrast, long reads established the structure of the Y haplotype in Koka and Kpandu males and the order of the genes in the duplicated region. Phylogenies constructed on the nuclear and mitochondrial genomes, showed a closer relationship between the two Ethiopian populations compared to the Ghanaian population, implying an absence of the LG23Y sex-determination region in Lake Hora males. Our study supports the hypothesis that the amh region is not the sex-determining region in Hora males. The absence of the Y amh duplication in the Lake Hora population reflects a rapid change in sex determination within Nile tilapia populations. The genetic basis of sex determination in the Lake Hora population remains unknown.
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Affiliation(s)
- Cécile Triay
- UMR116-Institut des Sciences de l'Evolution de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International Baillarguet, Montpellier, France.,UMR-Institut des Sciences de l'Evolution de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche Pour le Développement, Ecole Pratique des Hautes Etudes, University of Montpellier, Montpellier, France
| | - Maxime Courcelle
- UMR-Institut des Sciences de l'Evolution de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche Pour le Développement, Ecole Pratique des Hautes Etudes, University of Montpellier, Montpellier, France
| | - Pierre Caminade
- UMR-Institut des Sciences de l'Evolution de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche Pour le Développement, Ecole Pratique des Hautes Etudes, University of Montpellier, Montpellier, France
| | - Etienne Bezault
- UMR BOREA, CNRS-7208/MNHN/UPMC/IRD-207/UCN/UA, Université des Antilles, Guadeloupe, France
| | - Jean-François Baroiller
- UMR116-Institut des Sciences de l'Evolution de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International Baillarguet, Montpellier, France.,UMR-Institut des Sciences de l'Evolution de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche Pour le Développement, Ecole Pratique des Hautes Etudes, University of Montpellier, Montpellier, France
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, United States
| | - Helena D'Cotta
- UMR116-Institut des Sciences de l'Evolution de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International Baillarguet, Montpellier, France.,UMR-Institut des Sciences de l'Evolution de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche Pour le Développement, Ecole Pratique des Hautes Etudes, University of Montpellier, Montpellier, France
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4
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Dynamics of sexual development in teleosts with a note on Mugil cephalus. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Ciezarek A, Ford AG, Etherington GJ, Kasozi N, Malinsky M, Mehta TK, Penso-Dolfin L, Ngatunga BP, Shechonge A, Tamatamah R, Haerty W, Di Palma F, Genner MJ, Turner GF. Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2022; 548:737637. [PMID: 35177872 PMCID: PMC8655616 DOI: 10.1016/j.aquaculture.2021.737637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 06/14/2023]
Abstract
Cichlid fish of the genus Oreochromis form the basis of the global tilapia aquaculture and fisheries industries. Broodstocks for aquaculture are often collected from wild populations, which in Africa may be from locations containing multiple Oreochromis species. However, many species are difficult to distinguish morphologically, hampering efforts to maintain good quality farmed strains. Additionally, non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native Oreochromis species, which themselves are important for capture fisheries. The morphological identification of these hybrids is particularly unreliable. Here, we describe the development of a single nucleotide polymorphism (SNP) genotyping panel from whole-genome resequencing data that enables targeted species identification in Tanzania. We demonstrate that an optimized panel of 96 genome-wide SNPs based on FST outliers performs comparably to whole genome resequencing in distinguishing species and identifying hybrids. We also show this panel outperforms microsatellite-based and phenotype-based classification methods. Case studies indicate several locations where introduced aquaculture species have become established in the wild, threatening native Oreochromis species. The novel SNP markers identified here represent an important resource for assessing broodstock purity in hatcheries and helping to conserve unique endemic biodiversity.
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Affiliation(s)
- A. Ciezarek
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Antonia G.P. Ford
- Department of Life Sciences, Roehampton University, London SW15 4JD, UK
| | | | - Nasser Kasozi
- National Agricultural Research Organisation, Abi Zonal Agricultural Research and Development Institute, P.O. Box 219, Arua, Uganda
| | - Milan Malinsky
- Zoological Institute, Department of Environmental Sciences, University of Basel, 4051 Basel, Switzerland
| | - Tarang K. Mehta
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Luca Penso-Dolfin
- Silence Therapeutics GmbH, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Benjamin P. Ngatunga
- Tanzania Fisheries Research Institute (TAFIRI), PO. Box 9750, Dar es Salaam. Tanzania
| | - Asilatu Shechonge
- Tanzania Fisheries Research Institute (TAFIRI), PO. Box 9750, Dar es Salaam. Tanzania
| | - Rashid Tamatamah
- Tanzania Fisheries Research Institute (TAFIRI), PO. Box 9750, Dar es Salaam. Tanzania
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Federica Di Palma
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, UK
| | - Martin J. Genner
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - George F. Turner
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
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6
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Varela ES, Bekaert M, Ganeco-Kirschnik LN, Torati LS, Shiotsuki L, de Almeida FL, Villela LCV, Rezende FP, da Silva Barroso A, de Freitas LEL, Taggart JB, Migaud H. A high-density linkage map and sex-linked markers for the Amazon Tambaqui Colossoma macropomum. BMC Genomics 2021; 22:709. [PMID: 34598670 PMCID: PMC8487117 DOI: 10.1186/s12864-021-08037-8] [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: 05/27/2021] [Accepted: 09/15/2021] [Indexed: 11/12/2022] Open
Abstract
Background Tambaqui (Colossoma macropomum, Cuvier, 1818) is the most economically important native freshwater fish species in Brazil. It can reach a total length of over 1 m and a weight of over 40 kg. The species displays a clear sex dimorphism in growth performance, with females reaching larger sizes at harvest. In aquaculture, the production of monosex populations in selective breeding programmes has been therefore identified as a key priority. Results In the present study, a genetic linkage map was generated by double digest restriction-site associated DNA (ddRAD) sequencing from 248 individuals sampled from two F1 families. The map was constructed using 14,805 informative SNPs and spanned 27 linkage groups. From this, the tambaqui draft genome was improved, by ordering the scaffolds into chromosomes, and sex-linked markers were identified. A total of 235 markers on linkage group 26 showed a significant association with the phenotypic sex, supporting an XX/XY sex determination system in the species. The four most informative sex-linked markers were validated on another 206 sexed individuals, demonstrating an accuracy in predicting sex ranging from 90.0 to 96.7%. Conclusions The genetic mapping and novel sex-linked DNA markers identified and validated offer new tools for rapid progeny sexing, thus supporting the development of monosex female production in the industry while also supporting breeding programmes of the species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08037-8.
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Affiliation(s)
- Eduardo Sousa Varela
- Embrapa Pesca e Aquicultura, Prolongamento da Av. NS 10, Cruzamento com AV. LO 18, Sentido Norte, loteamento Água Fria, CEP, Palmas, TO, 77008-900, Brazil.
| | - Michaël Bekaert
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
| | - Luciana Nakaghi Ganeco-Kirschnik
- Embrapa Pesca e Aquicultura, Prolongamento da Av. NS 10, Cruzamento com AV. LO 18, Sentido Norte, loteamento Água Fria, CEP, Palmas, TO, 77008-900, Brazil
| | - Lucas Simon Torati
- Embrapa Pesca e Aquicultura, Prolongamento da Av. NS 10, Cruzamento com AV. LO 18, Sentido Norte, loteamento Água Fria, CEP, Palmas, TO, 77008-900, Brazil
| | - Luciana Shiotsuki
- Embrapa Pesca e Aquicultura, Prolongamento da Av. NS 10, Cruzamento com AV. LO 18, Sentido Norte, loteamento Água Fria, CEP, Palmas, TO, 77008-900, Brazil
| | | | - Luciana Cristine Vasques Villela
- Embrapa Pesca e Aquicultura, Prolongamento da Av. NS 10, Cruzamento com AV. LO 18, Sentido Norte, loteamento Água Fria, CEP, Palmas, TO, 77008-900, Brazil
| | - Fabrício Pereira Rezende
- Embrapa Pesca e Aquicultura, Prolongamento da Av. NS 10, Cruzamento com AV. LO 18, Sentido Norte, loteamento Água Fria, CEP, Palmas, TO, 77008-900, Brazil
| | - Aurisan da Silva Barroso
- Embrapa Pesca e Aquicultura, Prolongamento da Av. NS 10, Cruzamento com AV. LO 18, Sentido Norte, loteamento Água Fria, CEP, Palmas, TO, 77008-900, Brazil
| | - Luiz Eduardo Lima de Freitas
- Embrapa Pesca e Aquicultura, Prolongamento da Av. NS 10, Cruzamento com AV. LO 18, Sentido Norte, loteamento Água Fria, CEP, Palmas, TO, 77008-900, Brazil
| | - John Bernard Taggart
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
| | - Herve Migaud
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
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7
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Barría A, Benzie JAH, Houston RD, De Koning DJ, de Verdal H. Genomic Selection and Genome-wide Association Study for Feed-Efficiency Traits in a Farmed Nile Tilapia ( Oreochromis niloticus) Population. Front Genet 2021; 12:737906. [PMID: 34616434 PMCID: PMC8488396 DOI: 10.3389/fgene.2021.737906] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/31/2021] [Indexed: 11/24/2022] Open
Abstract
Nile tilapia is a key aquaculture species with one of the highest production volumes globally. Genetic improvement of feed efficiency via selective breeding is an important goal, and genomic selection may expedite this process. The aims of this study were to 1) dissect the genetic architecture of feed-efficiency traits in a Nile tilapia breeding population, 2) map the genomic regions associated with these traits and identify candidate genes, 3) evaluate the accuracy of breeding value prediction using genomic data, and 4) assess the impact of the genetic marker density on genomic prediction accuracies. Using an experimental video recording trial, feed conversion ratio (FCR), body weight gain (BWG), residual feed intake (RFI) and feed intake (FI) traits were recorded in 40 full-sibling families from the GIFT (Genetically Improved Farmed Tilapia) Nile tilapia breeding population. Fish were genotyped with a ThermoFisher Axiom 65 K Nile tilapia SNP array. Significant heritabilities, ranging from 0.12 to 0.22, were estimated for all the assessed traits using the genomic relationship matrix. A negative but favourable genetic correlation was found between BWG and the feed-efficiency related traits; -0.60 and -0.63 for FCR and RFI, respectively. While the genome-wide association analyses suggested a polygenic genetic architecture for all the measured traits, there were significant QTL identified for BWG and FI on chromosomes seven and five respectively. Candidate genes previously found to be associated with feed-efficiency traits were located in these QTL regions, including ntrk3a, ghrh and eif4e3. The accuracy of breeding value prediction using the genomic data was up to 34% higher than using pedigree records. A SNP density of approximately 5,000 SNPs was sufficient to achieve similar prediction accuracy as the full genotype data set. Our results highlight the potential of genomic selection to improve feed efficiency traits in Nile tilapia breeding programmes.
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Affiliation(s)
- Agustin Barría
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, United Kingdom
| | - John A. H. Benzie
- WorldFish, Bayan Lepas, Malaysia
- School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, United Kingdom
| | - Dirk-Jan De Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hugues de Verdal
- CIRAD, UMR ISEM, Montpellier, France
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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8
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Palaiokostas C, Anjum A, Jeuthe H, Kurta K, Lopes Pinto F, Koning DJ. A genomic‐based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (
Salvelinus alpinus
). Evol Appl 2021; 15:565-577. [PMID: 35505879 PMCID: PMC9046918 DOI: 10.1111/eva.13261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/19/2021] [Accepted: 05/29/2021] [Indexed: 12/25/2022] Open
Abstract
Routine implementation of genomic information for guiding selection decisions is not yet common in the majority of aquaculture species. Reduced representation sequencing approaches offer a cost‐effective solution for obtaining genome‐wide information in species with a limited availability of genomic resources. In the current study, we implemented double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq) on an Arctic charr strain with the longest known history of selection (approximately 40 years) aiming to improve selection decisions. In total, 1730 animals reared at four different farms in Sweden and spanning from year classes 2013–2017 were genotyped using ddRAD‐seq. Approximately 5000 single nucleotide polymorphisms (SNPs) were identified, genetic diversity‐related metrics were estimated, and genome‐wide association studies (GWAS) for body length at different time points and age of sexual maturation were conducted. Low genetic differentiation amongst animals from the different farms was observed based on both the results from pairwise Fst values and principal component analysis (PCA). The existence of associations was investigated between the mean genome‐wide heterozygosity of each full‐sib family (year class 2017) and the corresponding inbreeding coefficient or survival to the eyed stage. A moderate correlation (−0.33) was estimated between the mean observed heterozygosity of each full‐sib family and the corresponding inbreeding coefficient, while no linear association was obtained with the survival to the eyed stage. GWAS did not detect loci with major effect for any of the studied traits. However, genomic regions explaining more than 1% of the additive genetic variance for either studied traits were suggested across 14 different chromosomes. Overall, key insights valuable for future selection decisions of Arctic charr have been obtained, suggesting ddRAD as an attractive genotyping platform for obtaining genome‐wide information in a cost‐effective manner.
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Affiliation(s)
- Christos Palaiokostas
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Anam Anjum
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Henrik Jeuthe
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
- Aquaculture Center North Kälarne Sweden
| | - Khrystyna Kurta
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Fernando Lopes Pinto
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Dirk Jan Koning
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
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9
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Curzon AY, Shirak A, Benet-Perlberg A, Naor A, Low-Tanne SI, Sharkawi H, Ron M, Seroussi E. Gene Variant of Barrier to Autointegration Factor 2 ( Banf2w) Is Concordant with Female Determination in Cichlids. Int J Mol Sci 2021; 22:7073. [PMID: 34209244 PMCID: PMC8268354 DOI: 10.3390/ijms22137073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/23/2021] [Accepted: 06/27/2021] [Indexed: 11/15/2022] Open
Abstract
Oreochromis fishes exhibit variability of sex-determination (SD) genes whose characterization contributes to understanding of the sex differentiation network, and to effective tilapia farming, which requires all-male culture. However, O. niloticus (On) amh is the only master-key regulator (MKR) of SD that has been mapped (XY/XX SD-system on LG23). In O. aureus (Oa), LG3 controls a WZ/ZZ SD-system that has recently been delimited to 9.2 Mbp, with an embedded interval rich with female-specific variation, harboring two paics genes and banf2. Developing genetic markers within this interval and using a hybrid Oa stock that demonstrates no recombination repression in LG3, we mapped the critical SD region to 235 Kbp on the orthologous On physical map (p < 1.5 × 10-26). DNA-seq assembly and peak-proportion analysis of variation based on Sanger chromatograms allowed the characterization of copy-number variation (CNV) of banf2. Oa males had three exons capable of encoding 90-amino-acid polypeptides, yet in Oa females, we found an extra copy with an 89-amino-acid polypeptide and three non-conservative amino acid substitutions, designated as banf2w. CNV analysis suggested the existence of two to five copies of banf2 in diploidic Cichlidae. Disrupting the Hardy-Weinberg equilibrium (p < 4.2 × 10-3), banf2w was concordant with female determination in Oa and in three cichlids with LG3 WZ/ZZ SD-systems (O. tanganicae, O. hornorum and Pelmatolapia mariae). Furthermore, exclusive RNA-seq expression in Oa females strengthened the candidacy of banf2w as the long-sought LG3 SD MKR. As banf genes mediate nuclear assembly, chromatin organization, gene expression and gonad development, banf2w may play a fundamental role inducing female nucleus formation that is essential for WZ/ZZ SD.
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Affiliation(s)
- Arie Yehuda Curzon
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 7528809, Israel; (A.Y.C.); (A.S.); (M.R.)
- Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Andrey Shirak
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 7528809, Israel; (A.Y.C.); (A.S.); (M.R.)
| | - Ayana Benet-Perlberg
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Alon Naor
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Shai Israel Low-Tanne
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Haled Sharkawi
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Micha Ron
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 7528809, Israel; (A.Y.C.); (A.S.); (M.R.)
| | - Eyal Seroussi
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 7528809, Israel; (A.Y.C.); (A.S.); (M.R.)
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10
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Wan ZY, Lin VCL, Hua YG. Pomc Plays an Important Role in Sexual Size Dimorphism in Tilapia. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:201-214. [PMID: 33580373 DOI: 10.1007/s10126-020-10015-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/27/2020] [Indexed: 06/12/2023]
Abstract
Sexual dimorphism is common across the animal kingdom. Knowledge of the mechanisms of sexual size dimorphism is limited although it is important in biology and aquaculture. Tilapia is the common name for ~ 100 species of cichlid fish. Some are important aquaculture species and males outgrow females. To gain novel insights into the mechanisms underlying sexual size dimorphism, we analyzed the differences of brain transcriptomes between males and females in Mozambique tilapia and studied the function of the pro-opiomelanocortin (Pomc) gene in tilapia and zebrafish. The transcriptome analysis identified 123, 55, and 2706 sex-biased genes at 5, 30, and 90 dph (days post-hatch), respectively, indicating sexual dimorphism of gene expressions in the brain. The expression of Pomc in the tilapia brain was a female-biased at 30, 90, and 120 dph. An analysis of the DNA sequence located upstream of the tilapia Pomc transcriptional start site identified two estrogenic response elements. In vitro luciferase assay of the two elements revealed that β-estradiol significantly enhanced the expression of luciferase activity, suggesting that the expression of Pomc is mediated by estrogen. We knocked out Pomc in zebrafish using Crispr/Cas-9. The Pomc-knockout zebrafish showed faster growth and higher sensitivity to feeding as compared to the wild-type fish. Taken together, our results indicate that Pomc contributes to sexual size dimorphism and suggest that the high estrogen level in females promotes the expression of Pomc and suppresses feeding in female tilapias, which leads to the slower growth of female tilapias.
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Affiliation(s)
- Z Y Wan
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - V C L Lin
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
| | - Yue Gen Hua
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
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11
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Pappas F, Palaiokostas C. Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr ( Salvelinus alpinus). Animals (Basel) 2021; 11:899. [PMID: 33801139 PMCID: PMC8004150 DOI: 10.3390/ani11030899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/13/2021] [Accepted: 03/16/2021] [Indexed: 12/17/2022] Open
Abstract
Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.
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Affiliation(s)
| | - Christos Palaiokostas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7090, 750 07 Uppsala, Sweden;
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12
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Maroso F, Gkagkavouzis K, De Innocentiis S, Hillen J, do Prado F, Karaiskou N, Taggart JB, Carr A, Nielsen E, Triantafyllidis A, Bargelloni L. Genome-wide analysis clarifies the population genetic structure of wild gilthead sea bream (Sparus aurata). PLoS One 2021; 16:e0236230. [PMID: 33428622 PMCID: PMC7799848 DOI: 10.1371/journal.pone.0236230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/22/2020] [Indexed: 11/30/2022] Open
Abstract
Gilthead sea bream is an important target for both recreational and commercial fishing in Europe, where it is also one of the most important cultured fish. Its distribution ranges from the Mediterranean to the African and European coasts of the North-East Atlantic. Until now, the population genetic structure of this species in the wild has largely been studied using microsatellite DNA markers, with minimal genetic differentiation being detected. In this geographically widespread study, 958 wild gilthead sea bream from 23 locations within the Mediterranean Sea and Atlantic Ocean were genotyped at 1159 genome-wide SNP markers by RAD sequencing. Outlier analyses identified 18 loci potentially under selection. Neutral marker analyses identified weak subdivision into three genetic clusters: Atlantic, West, and East Mediterranean. The latter group could be further subdivided into an Ionian/Adriatic and an Aegean group using the outlier markers alone. Seascape analysis suggested that this differentiation was mainly due to difference in salinity, this being also supported by preliminary genomic functional analysis. These results are of fundamental importance for the development of proper management of this species in the wild and are a first step toward the study of the potential genetic impact of the sea bream aquaculture industry.
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Affiliation(s)
- Francesco Maroso
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro (PD), Italy
| | - Konstantinos Gkagkavouzis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece
| | | | - Jasmien Hillen
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Leuven, Belgium
| | - Fernanda do Prado
- Department of Biological Sciences, São Paulo State University, Bauru, Brazil
| | - Nikoleta Karaiskou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece
| | | | - Adrian Carr
- Fios Genomics Ltd, Edinburgh, United Kingdom
| | - Einar Nielsen
- Section for Population Ecology and Genetics, National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Alexandros Triantafyllidis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro (PD), Italy
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13
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Curzon AY, Shirak A, Dor L, Zak T, Perelberg A, Seroussi E, Ron M. A duplication of the Anti-Müllerian hormone gene is associated with genetic sex determination of different Oreochromis niloticus strains. Heredity (Edinb) 2020; 125:317-327. [PMID: 32647338 PMCID: PMC7555829 DOI: 10.1038/s41437-020-0340-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 06/25/2020] [Indexed: 11/08/2022] Open
Abstract
Sex determination (SD) mechanisms are ancient and conserved, yet much diversity is exhibited in primary sex-determining signals that trigger male or female development. In O. niloticus, SD is associated with a male-specific locus on linkage group (LG) 23 which harbors the Y-linked Anti-Müllerian hormone (amh) gene, and a truncated duplication, denoted amhΔy. We have evaluated the possible role of identified indels and SNPs in the amh gene on SD, based on conservation in different O. niloticus strains. A fluorescent assay for the detection of a 5 bp insertion in amhΔy exon VI, efficiently discriminated between XX, XY, and YY genotypes. Concordance rate between amhΔy and sex varied in six Oreochromis strains, from 100% (Ghana) through 90% (Swansea) to 85% (Thai-Chitralada). The association of amhΔy with sex was found to be conserved in all tested O. niloticus strains, and thus supports its key role in SD. However, the previously identified missense SNP (C/T) in amh exon II was found only in the Swansea strain, thus excluding its candidacy for the causal variation of SD across all strains. Effects of markers on LGs 1, 3, and 23 (amhΔy) fully explained sex distribution in one Thai-Chitralada family (R2 = 1.0), whereas in another family only the major effect of LG23 (amhΔy) was significant (R2 = 0.37). Thus, amhΔy on LG23 is associated with genetic SD, either as a single causal gene in different O. niloticus strains, or in combination with segregating genes on LGs 1 and 3 in the Thai-Chitralada hybrid strain.
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Affiliation(s)
- A Y Curzon
- Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, 76100, Rehovot, Israel
- Institute of Animal Science, Agricultural Research Organization, 50250, Bet Dagan, Israel
| | - A Shirak
- Institute of Animal Science, Agricultural Research Organization, 50250, Bet Dagan, Israel
| | - L Dor
- Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, 76100, Rehovot, Israel
- Institute of Animal Science, Agricultural Research Organization, 50250, Bet Dagan, Israel
| | - T Zak
- Dor Research Station, Fisheries and Aquaculture Department, Ministry of Agriculture and Rural Development, Bet Dagan, Israel
| | - A Perelberg
- Dor Research Station, Fisheries and Aquaculture Department, Ministry of Agriculture and Rural Development, Bet Dagan, Israel
| | - E Seroussi
- Institute of Animal Science, Agricultural Research Organization, 50250, Bet Dagan, Israel
| | - M Ron
- Institute of Animal Science, Agricultural Research Organization, 50250, Bet Dagan, Israel.
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14
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Local ancestry inference provides insight into Tilapia breeding programmes. Sci Rep 2020; 10:18613. [PMID: 33122794 PMCID: PMC7596482 DOI: 10.1038/s41598-020-75744-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/12/2020] [Indexed: 11/30/2022] Open
Abstract
Tilapia is one of the most commercially valuable species in aquaculture with over 5 million tonnes of Nile tilapia, Oreochromis niloticus, produced worldwide every year. It has become increasingly important to keep track of the inheritance of the selected traits under continuous improvement (e.g. growth rate, size at maturity or genetic gender), as selective breeding has also resulted in genes that can hitchhike as part of the process. The goal of this study was to generate a Local Ancestry Interence workflow that harnessed existing tilapia genotyping-by-sequencing studies, such as Double Digest RAD-seq derived Single-Nucleotide Polymorphism markers. We developed a workflow and implemented a suite of tools to resolve the local ancestry of each chromosomal locus based on reference panels of tilapia species of known origin. We used tilapia species, wild populations and breeding programmes to validate our methods. The precision of the pipeline was evaluated on the basis of its ability to identify the genetic makeup of samples of known ancestry. The easy and inexpensive application of local ancestry inference in breeding programmes will facilitate the monitoring of the genetic profile of individuals of interest, the tracking of the movement of genes from parents to offspring and the detection of hybrids and their origin.
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15
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Nyinondi CS, Mtolera MSP, Mmochi AJ, Lopes Pinto FA, Houston RD, de Koning DJ, Palaiokostas C. Assessing the genetic diversity of farmed and wild Rufiji tilapia ( Oreochromis urolepis urolepis) populations using ddRAD sequencing. Ecol Evol 2020; 10:10044-10056. [PMID: 33005362 PMCID: PMC7520224 DOI: 10.1002/ece3.6664] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 12/21/2022] Open
Abstract
Rufiji tilapia (Oreochromis urolepis urolepis) is an endemic cichlid in Tanzania. In addition to its importance for biodiversity conservation, Rufiji tilapia is also attractive for farming due to its high growth rate, salinity tolerance, and the production of all-male hybrids when crossed with Nile tilapia (Oreochromis niloticus). The aim of the current study was to assess the genetic diversity and population structure of both wild and farmed Rufiji tilapia populations in order to inform conservation and aquaculture practices. Double-digest restriction-site-associated DNA (ddRAD) libraries were constructed from 195 animals originating from eight wild (Nyamisati, Utete, Mansi, Mindu, Wami, Ruaha, Kibasira, and Kilola) and two farmed (Bwawani and Chemchem) populations. The identified single nucleotide polymorphisms (SNPs; n = 2,182) were used to investigate the genetic variation within and among the studied populations. Genetic distance estimates (F st) were low among populations from neighboring locations, with the exception of Utete and Chemchem populations (F st = 0.34). Isolation-by-distance (IBD) analysis among the wild populations did not detect any significant correlation signal (r = .05; p-value = .4) between the genetic distance and the sampling (Euclidean distance) locations. Population structure and putative ancestry were further investigated using both Bayesian (Structure) and multivariate approaches (discriminant analysis of principal components). Both analysis indicated the existence of three distinct genetic clusters. Two cross-validation scenarios were conducted in order to test the efficiency of the SNP dataset for discriminating between farmed and wild animals or predicting the population of origin. Approximately 95% of the test dataset was correctly classified in the first scenario, while in the case of predicting for the population of origin 68% of the test dataset was correctly classified. Overall, our results provide novel insights regarding the population structure of Rufiji tilapia and a new database of informative SNP markers for both conservation management and aquaculture activities.
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Affiliation(s)
- Christer S. Nyinondi
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
- Institute of Marine SciencesUniversity of Dar es SalaamZanzibarTanzania
| | | | - Aviti J. Mmochi
- Institute of Marine SciencesUniversity of Dar es SalaamZanzibarTanzania
| | - Fernando A. Lopes Pinto
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUK
| | - Dirk J. de Koning
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
| | - Christos Palaiokostas
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUK
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16
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Structure and Sequence of the Sex Determining Locus in Two Wild Populations of Nile Tilapia. Genes (Basel) 2020; 11:genes11091017. [PMID: 32872430 PMCID: PMC7563666 DOI: 10.3390/genes11091017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/15/2020] [Accepted: 08/27/2020] [Indexed: 12/30/2022] Open
Abstract
In domesticated strains of the Nile tilapia, phenotypic sex has been linked to genetic variants on linkage groups 1, 20 and 23. This diversity of sex-loci might reflect a naturally polymorphic sex determination system in Nile tilapia, or it might be an artefact arising from the process of domestication. Here, we searched for sex-determiners in wild populations from Kpandu, Lake Volta (Ghana-West Africa), and from Lake Koka (Ethiopia-East Africa) that have not been subjected to any genetic manipulation. We analysed lab-reared families using double-digest Restriction Associated DNA sequencing (ddRAD) and analysed wild-caught males and females with pooled whole-genome sequencing (WGS). Strong sex-linked signals were found on LG23 in both populations, and sex-linked signals with LG3 were observed in Kpandu samples. WGS uncovered blocks of high sequence coverage, suggesting the presence of B chromosomes. We confirmed the existence of a tandem amh duplication in LG23 in both populations and determined its breakpoints between the oaz1 and dot1l genes. We found two common deletions of ~5 kb in males and confirmed the presence of both amhY and amh∆Y genes. Males from Lake Koka lack both the previously reported 234 bp deletion and the 5 bp frameshift-insertion that creates a premature stop codon in amh∆Y.
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