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Ivanova P, Dzhembekova N, Atanassov I, Rusanov K, Raykov V, Zlateva I, Yankova M, Raev Y, Nikolov G. Genetic diversity and morphological characterisation of three turbot (Scophthalmus maximus L., 1758) populations along the Bulgarian Black Sea coast. NATURE CONSERVATION 2021. [DOI: 10.3897/natureconservation.43.64195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Turbot (Scophthalmus maximusL., 1758) is a valuable commercial fish species classified as endangered. The conservation and sustainability of the turbot populations require knowledge of the population’s genetic structure and constant monitoring of its biodiversity. The present study was performed to evaluate the population structure of turbot along the Bulgarian Black Sea coast using seven pairs of microsatellites, two mitochondrial DNA (COIII and CR) and 23 morphological (15 morphometric and 8 meristic) markers. A total of 72 specimens at three locations were genotyped and 59 alleles were identified. The observed number of alleles of microsatellites was more than the effective number of alleles. The overall mean values of observed (Ho) and expected heterogeneity (He) were 0.638 and 0.685. A high rate of migration between turbot populations (overall mean of Nm = 17.484), with the maximum value (19.498) between Shabla and Nesebar locations, was observed. This result corresponded to the low level of genetic differentiation amongst these populations (overall mean Fst = 0.014), but there was no correlation between genetic and geographical distance. A high level of genetic diversity in the populations was also observed. The average Garza-Williamson M index value for all populations was low (0.359), suggesting a reduction in genetic variation due to a founder effect or a genetic bottleneck. Concerning mitochondrial DNA, a total number of 17 haplotypes for COIII and 41 haplotypes for CR were identified. The mitochondrial DNA control region showed patterns with high haplotype diversity and very low nucleotide diversity, indicating a significant number of closely-related haplotypes and suggesting that this population may have undergone a recent expansion. Tajima’s D test and Fu’s FS test suggested recent population growth. Pairwise Fst values were very low. The admixture and lack of genetic structuring found pointed to the populations analysed probably belonging to the same genetic unit. Therefore, a proper understanding and a sound knowledge of the level and distribution of genetic diversity in turbot is an important prerequisite for successful sustainable development and conservation strategies to preserve their evolutionary potential.
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Song X, Shen F, Huang J, Huang Y, Du L, Wang C, Fan Z, Hou R, Yue B, Zhang X. Transcriptome-Derived Tetranucleotide Microsatellites and Their Associated Genes from the Giant Panda (Ailuropoda melanoleuca). J Hered 2016; 107:423-30. [PMID: 27112165 DOI: 10.1093/jhered/esw024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/18/2016] [Indexed: 01/19/2023] Open
Abstract
Recently, an increasing number of microsatellites or simple sequence repeats (SSRs) have been found and characterized from transcriptomes. Such SSRs can be employed as putative functional markers to easily tag corresponding genes, which play an important role in biomedical studies and genetic analysis. However, the transcriptome-derived SSRs for giant panda (Ailuropoda melanoleuca) are not yet available. In this work, we identified and characterized 20 tetranucleotide microsatellite loci from a transcript database generated from the blood of giant panda. Furthermore, we assigned their predicted transcriptome locations: 16 loci were assigned to untranslated regions (UTRs) and 4 loci were assigned to coding regions (CDSs). Gene identities of 14 transcripts contained corresponding microsatellites were determined, which provide useful information to study the potential contribution of SSRs to gene regulation in giant panda. The polymorphic information content (PIC) values ranged from 0.293 to 0.789 with an average of 0.603 for the 16 UTRs-derived SSRs. Interestingly, 4 CDS-derived microsatellites developed in our study were also polymorphic, and the instability of these 4 CDS-derived SSRs was further validated by re-genotyping and sequencing. The genes containing these 4 CDS-derived SSRs were embedded with various types of repeat motifs. The interaction of all the length-changing SSRs might provide a way against coding region frameshift caused by microsatellite instability. We hope these newly gene-associated biomarkers will pave the way for genetic and biomedical studies for giant panda in the future. In sum, this set of transcriptome-derived markers complements the genetic resources available for giant panda.
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Affiliation(s)
- Xuhao Song
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Fujun Shen
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Jie Huang
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Yan Huang
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Lianming Du
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Chengdong Wang
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Zhenxin Fan
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Rong Hou
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Bisong Yue
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang)
| | - Xiuyue Zhang
- From the Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China (Song, Huang, Du, Fan, Yue, and Zhang); The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081, China (Shen, Wang, and Hou); and China Research and Conservation Center for the Giant Panda, Wenchuan 623006, China (Huang).
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Ma D, Ma A, Huang Z, Wang G, Wang T, Xia D, Ma B. Transcriptome Analysis for Identification of Genes Related to Gonad Differentiation, Growth, Immune Response and Marker Discovery in The Turbot (Scophthalmus maximus). PLoS One 2016; 11:e0149414. [PMID: 26925843 PMCID: PMC4771204 DOI: 10.1371/journal.pone.0149414] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/01/2016] [Indexed: 11/18/2022] Open
Abstract
Background Turbot Scophthalmus maximus is an economically important species extensively aquacultured in China. The genetic selection program is necessary and urgent for the sustainable development of this industry, requiring more and more genome background knowledge. Transcriptome sequencing is an excellent alternative way to identify transcripts involved in specific biological processes and exploit a considerable quantity of molecular makers when no genome sequences are available. In this study, a comprehensive transcript dataset for major tissues of S. maximus was produced on basis of an Illumina platform. Results Total RNA was isolated from liver, spleen, kidney, cerebrum, gonad (testis and ovary) and muscle. Equal quantities of RNA from each type of tissues were pooled to construct two cDNA libraries (male and female). Using the Illumina paired-end sequencing technology, nearly 44.22 million clean reads in length of 100 bp were generated and then assembled into 106,643 contigs, of which 71,107 were named unigenes with an average length of 892 bp after the elimination of redundancies. Of these, 24,052 unigenes (33.83% of the total) were successfully annotated. GO, KEGG pathway mapping and COG analysis were performed to predict potential genes and their functions. Based on our sequence analysis and published documents, many candidate genes with fundamental roles in sex determination and gonad differentiation (dmrt1), growth (ghrh, myf5, prl/prlr) and immune response (TLR1/TLR21/TLR22, IL-15/IL-34), were identified for the first time in this species. In addition, a large number of credible genetic markers, including 21,192 SSRs and 8,642 SNPs, were identified in the present dataset. Conclusion This informative transcriptome provides valuable new data to increase genomic resources of Scophthalmus maximus. The future studies of corresponding gene functions will be very useful for the management of reproduction, growth and disease control in turbot aquaculture breeding programs. The molecular markers identified in this database will aid in genetic linkage analyses, mapping of quantitative trait loci, and acceleration of marker assisted selection programs.
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Affiliation(s)
- Deyou Ma
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- Dalian Ocean University, Dalian, 116023, China
| | - Aijun Ma
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- * E-mail:
| | - Zhihui Huang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Guangning Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Ting Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Dandan Xia
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Benhe Ma
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
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Lin Y, Chen Y, Xiong W, Zhan A. Genomewide gene-associated microsatellite markers for the model invasive ascidian, Ciona intestinalis species complex. Mol Ecol Resour 2015; 16:784-93. [PMID: 26505988 DOI: 10.1111/1755-0998.12481] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 09/23/2015] [Accepted: 10/21/2015] [Indexed: 11/29/2022]
Abstract
The vase tunicate, Ciona intestinalis species complex, has become a good model for ecological and evolutionary studies, especially those focusing on microevolution associated with rapidly changing environments. However, genomewide genetic markers are still lacking. Here, we characterized a large set of genomewide gene-associated microsatellite markers for C. intestinalis spA (=C. robusta). Bioinformatic analysis identified 4654 microsatellites from expressed sequence tags (ESTs), 2126 of which successfully assigned to chromosomes were selected for further analysis. Based on the distribution evenness on chromosomes, function annotation and suitability for primer design, we chose 545 candidate microsatellites for further characterization. After amplification validation and variation assessment, 218 loci were polymorphic in at least one of the two populations collected from the coast of Arenys de Mar, Spain (N = 24-48), and Cape Town, South Africa (N = 24-33). The number of alleles, observed heterozygosity and expected heterozygosity ranged from 2 to 11, 0 to 0.833 and 0.021 to 0.818, and from 2 to 10, 0 to 0.879 and 0.031 to 0.845 for the Spanish and African populations, respectively. When all microsatellites were tested for cross-species utility, only 60 loci (25.8%) could be successfully amplified and all loci were polymorphic in C. intestinalis spB. A high level of genomewide polymorphism is likely responsible for the low transferability. The large set of microsatellite markers characterized here is expected to provide a useful genomewide resource for ecological and evolutionary studies using C. intestinalis as a model.
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Affiliation(s)
- Yaping Lin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Wei Xiong
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
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Wang G, Li EF, Mao ZC, Xie BY. Development of polymorphic microsatellites for Meloidogyne incognita, through screening predicted microsatellite loci based on genome sequence. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415010135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Molina-Luzón MJ, Hermida M, Navajas-Pérez R, Robles F, Navas JI, Ruiz-Rejón C, Bouza C, Martínez P, de la Herrán R. First haploid genetic map based on microsatellite markers in Senegalese sole (Solea senegalensis, Kaup 1858). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:8-22. [PMID: 25107689 DOI: 10.1007/s10126-014-9589-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 07/12/2014] [Indexed: 06/03/2023]
Abstract
The Senegalese sole (Solea senegalensis, Kaup 1858) is a flatfish species of great value for aquaculture. In this study, we develop the first linkage map in this species based on microsatellite markers characterized from genomic DNA libraries and EST databases of Senegalese sole and from other flatfish species. Three reference gynogenetic families were obtained by chromosome-manipulation techniques: two haploid gynogenetics, used to assign and order microsatellites to linkage groups and another diploid gynogenetic family, used for estimating marker-centromere distances. The consensus map consists of 129 microsatellites distributed in 27 linkage groups (LG), with an average density of 4.7 markers per LG and comprising 1,004 centimorgans (cM). Additionally, 15 markers remained unlinked. Through half-tetrad analysis, we were able to estimate the centromere distance for 81 markers belonging to 24 LG, representing an average of 3 markers per LG. Comparative mapping was performed between flatfish species LG and model fish species chromosomes (stickleback, Tetraodon, medaka, fugu and zebrafish). The usefulness of microsatellite markers and the genetic map as tools for comparative mapping and evolution studies is discussed.
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Affiliation(s)
- Ma Jesús Molina-Luzón
- Facultad de Ciencias, Departamento de Genética, Universidad de Granada, 18071, Granada, Spain
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Ribas L, Pardo BG, Fernández C, Alvarez-Diós JA, Gómez-Tato A, Quiroga MI, Planas JV, Sitjà-Bobadilla A, Martínez P, Piferrer F. A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus). BMC Genomics 2013; 14:180. [PMID: 23497389 PMCID: PMC3700835 DOI: 10.1186/1471-2164-14-180] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 02/27/2013] [Indexed: 02/02/2023] Open
Abstract
Background Genomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for establishing adequate genetic selection programs. Current available techniques for high-throughput sequencing have been implemented in a number of species, including fish, to obtain a proper description of the transcriptome. The objective of this study was to generate a comprehensive transcriptomic database in turbot, a highly priced farmed fish species in Europe, with potential expansion to other areas of the world, for which there are unsolved production bottlenecks, to understand better reproductive- and immune-related functions. This information is essential to implement marker assisted selection programs useful for the turbot industry. Results Expressed sequence tags were generated by Sanger sequencing of cDNA libraries from different immune-related tissues after several parasitic challenges. The resulting database (“Turbot 2 database”) was enlarged with sequences generated from a 454 sequencing run of brain-hypophysis-gonadal axis-derived RNA obtained from turbot at different development stages. The assembly of Sanger and 454 sequences generated 52,427 consensus sequences (“Turbot 3 database”), of which 23,661 were successfully annotated. A total of 1,410 sequences were confirmed to be related to reproduction and key genes involved in sex differentiation and maturation were identified for the first time in turbot (AR, AMH, SRY-related genes, CYP19A, ZPGs, STAR FSHR, etc.). Similarly, 2,241 sequences were related to the immune system and several novel key immune genes were identified (BCL, TRAF, NCK, CD28 and TOLLIP, among others). The number of genes of many relevant reproduction- and immune-related pathways present in the database was 50–90% of the total gene count of each pathway. In addition, 1,237 microsatellites and 7,362 single nucleotide polymorphisms (SNPs) were also compiled. Further, 2,976 putative natural antisense transcripts (NATs) including microRNAs were also identified. Conclusions The combined sequencing strategies employed here significantly increased the turbot genomic resources available, including 34,400 novel sequences. The generated database contains a larger number of genes relevant for reproduction- and immune-associated studies, with an excellent coverage of most genes present in many relevant physiological pathways. This database also allowed the identification of many microsatellites and SNP markers that will be very useful for population and genome screening and a valuable aid in marker assisted selection programs.
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Affiliation(s)
- Laia Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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Bouza C, Hermida M, Pardo BG, Vera M, Fernández C, de la Herrán R, Navajas-Pérez R, Álvarez-Dios JA, Gómez-Tato A, Martínez P. An Expressed Sequence Tag (EST)-enriched genetic map of turbot (Scophthalmus maximus): a useful framework for comparative genomics across model and farmed teleosts. BMC Genet 2012; 13:54. [PMID: 22747677 PMCID: PMC3464660 DOI: 10.1186/1471-2156-13-54] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 07/02/2012] [Indexed: 12/18/2022] Open
Abstract
Background The turbot (Scophthalmus maximus) is a relevant species in European aquaculture. The small turbot genome provides a source for genomics strategies to use in order to understand the genetic basis of productive traits, particularly those related to sex, growth and pathogen resistance. Genetic maps represent essential genomic screening tools allowing to localize quantitative trait loci (QTL) and to identify candidate genes through comparative mapping. This information is the backbone to develop marker-assisted selection (MAS) programs in aquaculture. Expressed sequenced tag (EST) resources have largely increased in turbot, thus supplying numerous type I markers suitable for extending the previous linkage map, which was mostly based on anonymous loci. The aim of this study was to construct a higher-resolution turbot genetic map using EST-linked markers, which will turn out to be useful for comparative mapping studies. Results A consensus gene-enriched genetic map of the turbot was constructed using 463 SNP and microsatellite markers in nine reference families. This map contains 438 markers, 180 EST-linked, clustered at 24 linkage groups. Linkage and comparative genomics evidences suggested additional linkage group fusions toward the consolidation of turbot map according to karyotype information. The linkage map showed a total length of 1402.7 cM with low average intermarker distance (3.7 cM; ~2 Mb). A global 1.6:1 female-to-male recombination frequency (RF) ratio was observed, although largely variable among linkage groups and chromosome regions. Comparative sequence analysis revealed large macrosyntenic patterns against model teleost genomes, significant hits decreasing from stickleback (54%) to zebrafish (20%). Comparative mapping supported particular chromosome rearrangements within Acanthopterygii and aided to assign unallocated markers to specific turbot linkage groups. Conclusions The new gene-enriched high-resolution turbot map represents a useful genomic tool for QTL identification, positional cloning strategies, and future genome assembling. This map showed large synteny conservation against model teleost genomes. Comparative genomics and data mining from landmarks will provide straightforward access to candidate genes, which will be the basis for genetic breeding programs and evolutionary studies in this species.
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Affiliation(s)
- Carmen Bouza
- Departamento de Genética, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Campus de Lugo, 27002, Lugo, Spain
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Molina-Luzón MJ, López JR, Navajas-Pérez R, Robles F, Ruiz-Rejón C, De La Herrán R. Validation and comparison of microsatellite markers derived from Senegalese sole (Solea senegalensis, Kaup) genomic and expressed sequence tags libraries. Mol Ecol Resour 2012; 12:956-66. [PMID: 22734446 DOI: 10.1111/j.1755-0998.2012.03163.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this work, we tested 100 potential new microsatellites (SSRs) equally derived from expressed sequence tag (EST) and enriched genomic-DNA libraries from Senegalese sole (Solea senegalensis, Kaup), a valuable cultured flatfish species. A final set of 69 new polymorphic microsatellites were validated after a population analysis, 37 of which corresponded to the first EST library constructed for Senegalese sole (EST-SSR). Although differences were not significant, EST sequences provided a higher proportion of quality markers (74%) than anonymous ones (64%). Most of the rejected anonymous SSRs (17 loci) were discarded because they did not generate PCR products; only one was monomorphic. On the contrary, all EST-SSRs gave PCR products, although monomorphism was more frequent (26%). Altogether, the number of alleles per locus was fairly similar in both SSR types, ranging from 2 to 19. The observed and expected heterozygosities varied from 0.105 to 1 and from 0.108 to 0.937, respectively. The main difference between the two sets was the percentage of annotated loci, being higher in EST-SSRs, as expected. Within the EST-SSRs, 46% of them showed flanking regions that significantly matched with EST sequences from other three flatfish species; however, the microsatellite itself was present only on half of these cases. These two new SSR sets constitute a suitable tool for fingerprinting, gene flow, genetic diversity, genome mapping studies and molecular-assisted breeding in this species.
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Affiliation(s)
- M J Molina-Luzón
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
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