Special Issue: Genotyping by Sequencing
Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing
Abstract
Caviar‐producing sturgeons belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued overfishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production have led to the collapse of wild stocks across Europe and Asia. The evolutionary relationships among Adriatic, Russian, Persian and Siberian sturgeons are complex because of past introgression events and remain poorly understood. Conservation management, traceability and enforcement suffer a lack of appropriate DNA markers for the genetic identification of sturgeon at the species, population and individual level. This study employed RAD sequencing to discover and characterize single nucleotide polymorphism (SNP) DNA markers for use in sturgeon conservation in these four tetraploid species over three biological levels, using a single sequencing lane. Four population meta‐samples and eight individual samples from one family were barcoded separately before sequencing. Analysis of 14.4 Gb of paired‐end RAD data focused on the identification of SNPs in the paired‐end contig, with subsequent in silico and empirical validation of candidate markers. Thousands of putatively informative markers were identified including, for the first time, SNPs that show population‐wide differentiation between Russian and Persian sturgeons, representing an important advance in our ability to manage these cryptic species. The results highlight the challenges of genotyping‐by‐sequencing in polyploid taxa, while establishing the potential genetic resources for developing a new range of caviar traceability and enforcement tools.
Citing Literature
Number of times cited: 37
- Connor Seamus Stobie, Carel J. Oosthuizen, Michael J. Cunningham and Paulette Bloomer, Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing, Ecology and Evolution, 8, 4, (2326-2342), (2018).
- Roman Wenne, Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations, Aquatic Living Resources, 10.1051/alr/2017043, 31, (2), (2017).
- Diego Robledo, Christos Palaiokostas, Luca Bargelloni, Paulino Martínez and Ross Houston, Applications of genotyping by sequencing in aquaculture breeding and genetics, Reviews in Aquaculture, 10, 3, (670-682), (2017).
- Mallory Van Wyngaarden, Paul V. R. Snelgrove, Claudio DiBacco, Lorraine C. Hamilton, Naiara Rodríguez‐Ezpeleta, Nicholas W. Jeffery, Ryan R. E. Stanley and Ian R. Bradbury, Identifying patterns of dispersal, connectivity and selection in the sea scallop, Placopecten magellanicus, using RADseq‐derived SNPs, Evolutionary Applications, 10, 1, (102-117), (2016).
- Andrew N. Black, Heidi A. Seears, Christopher M. Hollenbeck and Paul B. Samollow, Rapid genetic and morphologic divergence between captive and wild populations of the endangered Leon Springs pupfish, Cyprinodon bovinus, Molecular Ecology, 26, 8, (2237-2256), (2017).
- Laura Benestan, Jean‐Sébastien Moore, Ben J. G. Sutherland, Jérémy Le Luyer, Halim Maaroufi, Clément Rougeux, Eric Normandeau, Nathan Rycroft, Jelle Atema, Les N. Harris, Ross F. Tallman, Spencer J. Greenwood, Fraser K. Clark and Louis Bernatchez, Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems, Molecular Ecology, 26, 24, (6767-6783), (2017).
- Carlos Carreras, Víctor Ordóñez, Lorenzo Zane, Claudia Kruschel, Ina Nasto, Enrique Macpherson and Marta Pascual, Population genomics of an endemic Mediterranean fish: differentiation by fine scale dispersal and adaptation, Scientific Reports, 7, (43417), (2017).
- Yan-He Li and Han-Ping Wang, Advances of genotyping-by-sequencing in fisheries and aquaculture, Reviews in Fish Biology and Fisheries, 10.1007/s11160-017-9473-2, 27, 3, (535-559), (2017).
- Yong Suk Chung, Sang Chul Choi, Tae-Hwan Jun and Changsoo Kim, Genotyping-by-sequencing: a promising tool for plant genetics research and breeding, Horticulture, Environment, and Biotechnology, 58, 5, (425), (2017).
- Miloš Havelka, Takafumi Fujimoto, Seishi Hagihara, Shinji Adachi and Katsutoshi Arai, Nuclear DNA markers for identification of Beluga and Sterlet sturgeons and their interspecific Bester hybrid, Scientific Reports, 7, 1, (2017).
- Elisa Boscari, Nicola Vitulo, Arne Ludwig, Chiara Caruso, Nikolai S. Mugue, Radu Suciu, Dalia F. Onara, Chiara Papetti, Ilaria A.M. Marino, Lorenzo Zane and Leonardo Congiu, Fast genetic identification of the Beluga sturgeon and its sought-after caviar to stem illegal trade, Food Control, 75, (145), (2017).
- Christoph Hahn, Martin J Genner, George F Turner and Domino A Joyce, The genomic basis of cichlid fish adaptation within the deepwater “twilight zone” of Lake Malawi, Evolution Letters, 1, 4, (184-198), (2017).
- T. Aykanat, M. Lindqvist, V. L. Pritchard and C. R. Primmer, From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome‐wide approaches in Atlantic salmon Salmo salar, Journal of Fish Biology, 89, 6, (2658-2679), (2016).
- Paul D. Blischak, Laura S. Kubatko and Andrea D. Wolfe, Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids, Molecular Ecology Resources, 16, 3, (742-754), (2015).
- Vladimir A. Trifonov, Svetlana S. Romanenko, Violetta R. Beklemisheva, Larisa S. Biltueva, Alexey I. Makunin, Natalia A. Lemskaya, Anastasia I. Kulemzina, Roscoe Stanyon and Alexander S. Graphodatsky, Evolutionary plasticity of acipenseriform genomes, Chromosoma, 125, 4, (661), (2016).
- Sajad Nazari, Valiolah Jafari, Mohammad Pourkazemi, Hamed Kolangi Miandare and Hossein Ali Abdolhay, Association between myostatin gene ( MSTN-1 ) polymorphism and growth traits in domesticated rainbow trout ( Oncorhynchus mykiss ), Agri Gene, 1, (109), (2016).
- Richard P. Brown, Steve Paterson and Judith Risse, Genomic Signatures of Historical Allopatry and Ecological Divergence in an Island Lizard, Genome Biology and Evolution, 8, 11, (3618), (2016).
- Emily Humble, Michael A. S. Thorne, Jaume Forcada and Joseph I. Hoffman, Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success, BMC Research Notes, 9, 1, (2016).
- Yuezhi Pan, Xueqin Wang, Guiling Sun, Fusheng Li, Xun Gong and Tzen-Yuh Chiang, Application of RAD Sequencing for Evaluating the Genetic Diversity of Domesticated Panax notoginseng (Araliaceae), PLOS ONE, 11, 11, (e0166419), (2016).
- Fausto Valenzuela-Quiñonez, How fisheries management can benefit from genomics?, Briefings in Functional Genomics, 15, 5, (352), (2016).
- Jean-Baptiste Ledoux, Agostinho Antunes, Anne Haguenauer, Marine Pratlong, Federica Costantini, Marco Abbiati and Didier Aurelle, Molecular Forensics into the Sea: How Molecular Markers Can Help to Struggle Against Poaching and Illegal Trade in Precious Corals?, The Cnidaria, Past, Present and Future, 10.1007/978-3-319-31305-4_45, (729-745), (2016).
- Laura Benestan, Thierry Gosselin, Charles Perrier, Bernard Sainte‐Marie, Rémy Rochette and Louis Bernatchez, RAD genotyping reveals fine‐scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (omarus americanus), Molecular Ecology, 24, 13, (3299-3315), (2015).
- Lilian Pukk, Freed Ahmad, Shihab Hasan, Veljo Kisand, Riho Gross and Anti Vasemägi, Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology, Molecular Ecology Resources, 15, 5, (1145-1152), (2015).
- Carly F. Graham, Travis C. Glenn, Andrew G. McArthur, Douglas R. Boreham, Troy Kieran, Stacey Lance, Richard G. Manzon, Jessica A. Martino, Todd Pierson, Sean M. Rogers, Joanna Y. Wilson and Christopher M. Somers, Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq), Molecular Ecology Resources, 15, 6, (1304-1315), (2015).
- ShiGang Yu, WeiWei Chu, LiFan Zhang, HouMing Han, RongXue Zhao, Wei Wu, JiangNing Zhu, Michael V. Dodson, Wei Wei, HongLin Liu, Jie Chen and Gen Hua Yue, Identification of Laying-Related SNP Markers in Geese Using RAD Sequencing, PLOS ONE, 10, 7, (e0131572), (2015).
- Derek D. Houston, Kevin S. Mitchell, Jared W. Clouse, Peter J. Maughan, J. Curtis Creighton, Ashlee N. Smith, Seth M. Bybee and Mark C. Belk, SNP development in North American burying beetles (Coleoptera: Silphidae): a tool to inform conservation decisions, Conservation Genetics Resources, 7, 2, (349), (2015).
- Mari Hagenlund, Kjartan Østbye, Kjell Langdal, Marius Hassve, Ruben A. Pettersen, Eric Anderson, Finn Gregersen and Kim Præbel, Fauna crime: elucidating the potential source and introduction history of European smelt (Osmerus eperlanus L.) into Lake Storsjøen, Norway, Conservation Genetics, 16, 5, (1085), (2015).
- E. Boscari, M. Vidotto, D. Martini, C. Papetti, R. Ogden and L. Congiu, Microsatellites from the genome and the transcriptome of the tetraploid Adriatic sturgeon, Acipenser naccarii (Bonaparte, 1836) and cross‐species applicability to the diploid beluga sturgeon, Huso huso (Linnaeus, 1758), Journal of Applied Ichthyology, 31, 6, (977-983), (2015).
- Andrea Benazzo, Alex Panziera and Giorgio Bertorelle, 4P: fast computing of population genetics statistics from large DNA polymorphism panels, Ecology and Evolution, 5, 1, (172-175), (2014).
- France Dufresne, Marc Stift, Roland Vergilino and Barbara K. Mable, Recent progress and challenges in population genetics of polyploid organisms: an overview of current state‐of‐the‐art molecular and statistical tools, Molecular Ecology, 23, 1, (40-69), (2013).
- Loren Rieseberg, Tim Vines, Jennifer Gow and Nolan Kane, Editorial 2014, Molecular Ecology, 23, 1, (1-15), (2013).
- Pei Xu, Shizhong Xu, Xiaohua Wu, Ye Tao, Baogen Wang, Sha Wang, Dehui Qin, Zhongfu Lu and Guojing Li, Population genomic analyses from low‐coverage RAD‐Seq data: a case study on the non‐model cucurbit bottle gourd, The Plant Journal, 77, 3, (430-442), (2013).
- Eric C. Anderson, Hans J. Skaug and Daniel J. Barshis, Next‐generation sequencing for molecular ecology: a caveat regarding pooled samples, Molecular Ecology, 23, 3, (502-512), (2014).
- Shawn R. Narum, C. Alex Buerkle, John W. Davey, Michael R. Miller and Paul A. Hohenlohe, Genotyping‐by‐sequencing in ecological and conservation genomics, Molecular Ecology, 22, 11, (2841-2847), (2013).
- Sergey M. Rastorguev, Artem V. Nedoluzhko, Alexander M. Mazur, Natalia M. Gruzdeva, Alexander A. Volkov, Anna E. Barmintseva, Nikolai S. Mugue and Egor B. Prokhortchouk, High‐throughput SNP‐genotyping analysis of the relationships among Ponto‐Caspian sturgeon species, Ecology and Evolution, 3, 8, (2612-2618), (2013).
- Mathieu Gautier, Julien Foucaud, Karim Gharbi, Timothée Cézard, Maxime Galan, Anne Loiseau, Marian Thomson, Pierre Pudlo, Carole Kerdelhué and Arnaud Estoup, Estimation of population allele frequencies from next‐generation sequencing data: pool‐versus individual‐based genotyping, Molecular Ecology, 22, 14, (3766-3779), (2013).
- Troy C. Nelson, Phaedra Doukakis, Steven T. Lindley, Andrea D. Schreier, Joseph E. Hightower, Larry R. Hildebrand, Rebecca E. Whitlock, Molly A. H. Webb and Athanassios C. Tsikliras, Research Tools to Investigate Movements, Migrations, and Life History of Sturgeons (Acipenseridae), with an Emphasis on Marine-Oriented Populations, PLoS ONE, 8, 8, (e71552), (2013).
