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Waldbieser GC, Bosworth BG. A standardized microsatellite marker panel for parentage and kinship analyses in channel catfish, Ictalurus punctatus. Anim Genet 2012; 44:476-9. [PMID: 23216371 DOI: 10.1111/age.12017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2012] [Indexed: 11/28/2022]
Abstract
This research was designed to produce a standardized set of microsatellite loci for parentage and kinship analyses in channel catfish, the leading species of US aquaculture. Three panels of five to six markers each were developed that contained a total of two dinucleotide-, eight trinucleotide- and seven tetranucleotide-microsatellite loci respectively. The loci had a range of nine to 31 alleles per locus in an outbred population. Based on the allele frequencies measured in commercial randomly bred broodstock, the combined probability of non-exclusion of an unrelated candidate parent pair was 5.36e-18. The combined probability of non-exclusion of unrelated identical genotypes was 2.58e-08. The microsatellite panels were validated by parentage and kinship evaluation in three populations. A total of 697 spawns were collected from matings of outbred broodstock over three spawning seasons, and parents were determined unambiguously for all but three spawns. Genotype analysis also enabled the identification of half-sibling and full-sibling families produced by pond spawning. In a second experiment, parentage was unambiguously determined in nine spawns from a population consisting of broodstock derived from only four families. A third experiment demonstrated that all but one of 374 individuals from 10 full-sibling families could be assigned to a family after coculture in an earthen pond for 1 year. The standardized microsatellite panels enable the development of pedigreed catfish populations and large-scale performance evaluations in common environments to support the genetic improvement of cultured catfish through selective breeding.
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Affiliation(s)
- G C Waldbieser
- U.S. Department of Agriculture, Agricultural Research Service, Catfish Genetics Research Unit, Stoneville, MS, 38776, USA.
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102
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Provan J, Glendinning K, Kelly R, Maggs CA. Levels and patterns of population genetic diversity in the red seaweedChondrus crispus(Florideophyceae): a direct comparison of single nucleotide polymorphisms and microsatellites. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.02010.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Jim Provan
- School of Biological Sciences; Queen's University Belfast; 97 Lisburn Road; Belfast; BT9 7BL; UK
| | - Keith Glendinning
- School of Biological Sciences; Queen's University Belfast; 97 Lisburn Road; Belfast; BT9 7BL; UK
| | - Ruth Kelly
- School of Biological Sciences; Queen's University Belfast; 97 Lisburn Road; Belfast; BT9 7BL; UK
| | - Christine A. Maggs
- School of Biological Sciences; Queen's University Belfast; 97 Lisburn Road; Belfast; BT9 7BL; UK
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103
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Loridon K, Burgarella C, Chantret N, Martins F, Gouzy J, Prospéri JM, Ronfort J. Single-nucleotide polymorphism discovery and diversity in the model legume Medicago truncatula. Mol Ecol Resour 2012; 13:84-95. [PMID: 23017123 DOI: 10.1111/1755-0998.12021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 08/16/2012] [Accepted: 08/20/2012] [Indexed: 01/09/2023]
Abstract
Extensive genomic resources are available in the model legume Medicago truncatula. Here, we present the discovery and design of the first array of single-nucleotide polymorphism (SNP) markers in M. truncatula through large-scale Sanger resequencing of genomic fragments spanning the genome, in a diverse panel of 16 M. truncatula accessions. Both anonymous fragments and fragments targeting candidate genes for flowering phenology and symbiosis were surveyed for nucleotide variation in almost 230 kb of unique genomic regions. A set of 384 SNP markers was designed for an Illumina's GoldenGate assay, genotyped on a collection of 192 inbred lines (CC192) representing the geographical range of the species and used to survey the diversity of two natural populations. Finally, 86% of the tested SNPs were of high quality and exhibited polymorphism in the CC192 collection. Even at the population level, we detected polymorphism for more than 50% of the selected SNPs. Analysis of the allele frequency spectrum in the CC192 showed a reduced ascertainment bias, mostly limited to very rare alleles (frequency <0.01). The substantial polymorphism detected at the species and population levels, the high marker quality and the potential to survey large samples of individuals make this set of SNP markers a valuable tool to improve our understanding of the effect of demographic and selective factors that shape the natural genetic diversity within the selfing species Medicago truncatula.
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Affiliation(s)
- Karine Loridon
- INRA, UMR AGAP, 2 place Pierre Viala, F-34060, Montpellier Cedex 1, France.
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104
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Bernardi G, Beldade R, Holbrook SJ, Schmitt RJ. Full-sibs in cohorts of newly settled coral reef fishes. PLoS One 2012; 7:e44953. [PMID: 23028700 PMCID: PMC3441696 DOI: 10.1371/journal.pone.0044953] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 08/14/2012] [Indexed: 11/23/2022] Open
Abstract
Reef fishes exhibit a bipartite life cycle where a benthic adult stage is preceded by a pelagic dispersal phase during which larvae are presumed to be mixed and transported by oceanic currents. Genetic analyses based on twelve microsatellite loci of 181 three-spot dascyllus (Dascyllus trimaculatus) that settled concurrently on a small reef in French Polynesia revealed 11 groups of siblings (1 full sibs and 10 half-sibs). This is the first evidence that fish siblings can journey together throughout their entire planktonic dispersal phase (nearly a month long for three-spot dascyllus). Our findings have critical implications for the dynamics and genetic structure of fish populations, as well as for the design of marine protected areas and management of fisheries.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America.
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105
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Guyon R, Rakotomanga M, Azzouzi N, Coutanceau JP, Bonillo C, D'Cotta H, Pepey E, Soler L, Rodier-Goud M, D'Hont A, Conte MA, van Bers NEM, Penman DJ, Hitte C, Crooijmans RPMA, Kocher TD, Ozouf-Costaz C, Baroiller JF, Galibert F. A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs. BMC Genomics 2012; 13:222. [PMID: 22672252 PMCID: PMC3441813 DOI: 10.1186/1471-2164-13-222] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 04/23/2012] [Indexed: 12/25/2022] Open
Abstract
Background The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited. Results We have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR3500 and 937,310 kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish. Conclusion The RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia and the other model fishes. These maps represent a valuable resource for organizing the forthcoming genome sequence of Nile tilapia, and provide a foundation for evolutionary studies of East African cichlid fishes.
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Affiliation(s)
- Richard Guyon
- Institut Génétique et Développement (UMR 6061) CNRS/Université de Rennes 1, Rennes, France
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106
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LAMAZE FABIENC, SAUVAGE CHRISTOPHER, MARIE AMANDINE, GARANT DANY, BERNATCHEZ LOUIS. Dynamics of introgressive hybridization assessed by SNP population genomics of coding genes in stocked brook charr (Salvelinus fontinalis). Mol Ecol 2012; 21:2877-95. [DOI: 10.1111/j.1365-294x.2012.05579.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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107
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Van Bers NEM, Crooijmans RPMA, Groenen MAM, Dibbits BW, Komen J. SNP marker detection and genotyping in tilapia. Mol Ecol Resour 2012; 12:932-41. [PMID: 22524158 DOI: 10.1111/j.1755-0998.2012.03144.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We have generated a unique resource consisting of nearly 175 000 short contig sequences and 3569 SNP markers from the widely cultured GIFT (Genetically Improved Farmed Tilapia) strain of Nile tilapia (Oreochromis niloticus). In total, 384 SNPs were selected to monitor the wider applicability of the SNPs by genotyping tilapia individuals from different strains and different geographical locations. In all strains and species tested (O. niloticus, O. aureus and O. mossambicus), the genotyping assay was working for a similar number of SNPs (288-305 SNPs). The actual number of polymorphic SNPs was, as expected, highest for individuals from the GIFT population (255 SNPs). In the individuals from an Egyptian strain and in individuals caught in the wild in the basin of the river Volta, 197 and 163 SNPs were polymorphic, respectively. A pairwise calculation of Nei's genetic distance allowed the discrimination of the individual strains and species based on the genotypes determined with the SNP set. We expect that this set will be widely applicable for use in tilapia aquaculture, e.g. for pedigree reconstruction. In addition, this set is currently used for assaying the genetic diversity of native Nile tilapia in areas where tilapia is, or will be, introduced in aquaculture projects. This allows the tracing of escapees from aquaculture and the monitoring of effects of introgression and hybridization.
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Affiliation(s)
- N E M Van Bers
- Animal Breeding and Genomics Centre, Wageningen University, PO Box 338, Wageningen, 6700 AH, The Netherlands
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108
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Templin WD, Seeb JE, Jasper JR, Barclay AW, Seeb LW. Genetic differentiation of Alaska Chinook salmon: the missing link for migratory studies. Mol Ecol Resour 2011; 11 Suppl 1:226-46. [PMID: 21429177 DOI: 10.1111/j.1755-0998.2010.02968.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Most information about Chinook salmon genetic diversity and life history originates from studies from the West Coast USA, western Canada and southeast Alaska; less is known about Chinook salmon from western and southcentral Alaska drainages. Populations in this large area are genetically distinct from populations to the south and represent an evolutionary legacy of unique genetic, phenotypic and life history diversity. More genetic information is necessary to advance mixed stock analysis applications for studies involving these populations. We assembled a comprehensive, open-access baseline of 45 single nucleotide polymorphisms (SNPs) from 172 populations ranging from Russia to California. We compare SNP data from representative populations throughout the range with particular emphasis on western and southcentral Alaska. We grouped populations into major lineages based upon genetic and geographic characteristics, evaluated the resolution for identifying the composition of admixtures and performed mixed stock analysis on Chinook salmon caught incidentally in the walleye pollock fishery in the Bering Sea. SNP data reveal complex genetic structure within Alaska and can be used in applications to address not only regional issues, but also migration pathways, bycatch studies on the high seas, and potential changes in the range of the species in response to climate change.
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Affiliation(s)
- William D Templin
- Alaska Department of Fish and Game, Division of Commercial Fisheries, Anchorage, 99518, USA.
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109
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Seeb JE, Carvalho G, Hauser L, Naish K, Roberts S, Seeb LW. Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Mol Ecol Resour 2011; 11 Suppl 1:1-8. [PMID: 21429158 DOI: 10.1111/j.1755-0998.2010.02979.x] [Citation(s) in RCA: 232] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- J E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, 98195, USA.
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110
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Brieuc MSO, Naish KA. Detecting signatures of positive selection in partial sequences generated on a large scale: pitfalls, procedures and resources. Mol Ecol Resour 2011; 11 Suppl 1:172-83. [PMID: 21429173 DOI: 10.1111/j.1755-0998.2010.02948.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Studying the actions of selection provides insight into adaptation, population divergence and gene function. Next-generation sequencing produces large amounts of partial sequences, potentially facilitating efforts to detect signatures of selection based on comparisons between synonymous (d(S)) and nonsynonymous (d(N)) substitutions, and single nucleotide polymorphism assays placed in selected genes would improve the ability to study adaptation in population surveys. However, sequences generated by these technologies are typically short. In nonmodel organisms that are a focus of evolutionary studies, the lack of a reference genome that facilitates the assembly of short sequences has limited surveys of positive selection in large numbers of genes. Here, we describe a series of steps to facilitate these surveys. We provide PERL scripts to assist data analysis, and describe the use of commonly available programs. We demonstrate these approaches in six salmon species, which have partially duplicated genomes. We recommend using multiway blast to optimize the number of alignments between partial coding sequences. Reading frames should be manually detected after alignment with sequences in Genbank using the BLASTX program. We encourage the use of a phylogenetic approach to separate orthologs from paralogs in duplicated genomes. Simple simulations on a gene known to have undergone selection in salmon species, transferrin, showed that the ability to detect selection in short sequences (<600 bp) depended on the proportion of codons under selection (1-2%) within that sequence. This relationship was less relevant in longer sequences. In this exploratory study, we detected 11 genes showing evidence of positive selection.
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Affiliation(s)
- Marine S O Brieuc
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, 98195, USA.
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111
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Smith MJ, Pascal CE, Grauvogel Z, Habicht C, Seeb JE, Seeb LW. Multiplex preamplification PCR and microsatellite validation enables accurate single nucleotide polymorphism genotyping of historical fish scales. Mol Ecol Resour 2011; 11 Suppl 1:268-77. [PMID: 21429180 DOI: 10.1111/j.1755-0998.2010.02965.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Incorporating historical tissues into the study of ecological, conservation and management questions can broaden the scope of population genetic research by enhancing our understanding of evolutionary processes and anthropogenic influences on natural populations. Genotyping historical and low-quality samples has been plagued by challenges associated with low amounts of template DNA and the potential for pre-existing DNA contamination among samples. We describe a two-step process designed to (i) accurately genotype large numbers of historical low-quality scale samples in a high-throughput format and (ii) screen samples for pre-existing DNA contamination. First, we describe how an efficient multiplex preamplification PCR of 45 single nucleotide polymorphisms (SNPs) can generate highly accurate genotypes with low failure and error rates in subsequent SNP genotyping reactions of individual historical scales from sockeye salmon (Oncorhynchus nerka). Second, we demonstrate how the method can be modified for the amplification of microsatellite loci to detect pre-existing DNA contamination. A total of 760 individual historical scale and 182 contemporary fin clip samples were genotyped and screened for contamination. Genotyping failure and error rates were exceedingly low and similar for both historical and contemporary samples. Pre-existing contamination in 21% of the historical samples was successfully identified by screening the amplified microsatellite loci. The advantages of automation, low failure and error rates, and ability to multiplex both the preamplification and subsequent genotyping reactions combine to make the protocol ideally suited for efficiently genotyping large numbers of potentially contaminated low-quality sources of DNA.
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Affiliation(s)
- Matt J Smith
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, 98195, USA
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112
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SEEB LW, TEMPLIN WD, SATO S, ABE S, WARHEIT K, PARK JY, SEEB JE. Single nucleotide polymorphisms across a species’ range: implications for conservation studies of Pacific salmon. Mol Ecol Resour 2011; 11 Suppl 1:195-217. [DOI: 10.1111/j.1755-0998.2010.02966.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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113
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HELYAR SJ, HEMMER-HANSEN J, BEKKEVOLD D, TAYLOR MI, OGDEN R, LIMBORG MT, CARIANI A, MAES GE, DIOPERE E, CARVALHO GR, NIELSEN EE. Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Mol Ecol Resour 2011; 11 Suppl 1:123-36. [DOI: 10.1111/j.1755-0998.2010.02943.x] [Citation(s) in RCA: 315] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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