An Expressed Sequence Tag (EST)-enriched genetic map of turbot (Scophthalmus maximus): a useful framework for comparative genomics across model and farmed teleosts

被引:40
作者
Bouza, Carmen [1 ]
Hermida, Miguel [1 ]
Pardo, Belen G. [1 ]
Vera, Manuel [1 ]
Fernandez, Carlos [1 ]
de la Herran, Roberto [2 ]
Navajas-Perez, Rafael [2 ]
Antonio Alvarez-Dios, Jose [3 ]
Gomez-Tato, Antonio [4 ]
Martinez, Paulino [1 ]
机构
[1] Univ Santiago de Compostela, Fac Vet, Dept Genet, Lugo 27002, Spain
[2] Univ Granada, Fac Ciencias, Dept Genet, E-18071 Granada, Spain
[3] Univ Santiago de Compostela, Fac Matemat, Dept Matemat Aplicada, Santiago De Compostela 15782, Spain
[4] Univ Santiago de Compostela, Fac Matemat, Dept Geometria & Topol, Santiago De Compostela 15782, Spain
来源
BMC GENETICS | 2012年 / 13卷
关键词
Turbot; Scopththalmus maximus; Pleuronectiformes; Genetic map; Recombination frequency; Comparative mapping; LINKAGE MAP; MICROSATELLITE MARKERS; SEA-BASS; EVOLUTION; PATTERNS; FISH; QTL; RESISTANCE; CHROMOSOME; INSIGHTS;
D O I
10.1186/1471-2156-13-54
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
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; similar to 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.
引用
收藏
页数:10
相关论文
共 68 条
[31]   A second-generation genetic linkage map of tilapia (Oreochromis spp.) [J].
Lee, BY ;
Lee, WJ ;
Streelman, JT ;
Carleton, KL ;
Howe, AE ;
Hulata, G ;
Slettan, A ;
Stern, JE ;
Terai, Y ;
Kocher, TD .
GENETICS, 2005, 170 (01) :237-244
[32]   Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci [J].
Li, Chenhong ;
Lu, Guoqing ;
Orti, Guillermo .
SYSTEMATIC BIOLOGY, 2008, 57 (04) :519-539
[33]   Comparative Genomics Identifies Candidate Genes for Infectious Salmon Anemia (ISA) Resistance in Atlantic Salmon (Salmo salar) [J].
Li, Jieying ;
Boroevich, Keith A. ;
Koop, Ben F. ;
Davidson, William S. .
MARINE BIOTECHNOLOGY, 2011, 13 (02) :232-241
[34]   Identification of polymorphic microsatellite markers from RAPD product in turbot (Scophthalmus maximus) and a test of cross-species amplification [J].
Liu, Y. G. ;
Liu, L. X. ;
Lei, Z. W. ;
Gao, A. Y. ;
Li, B. F. .
MOLECULAR ECOLOGY NOTES, 2006, 6 (03) :867-869
[35]   Quantitative Trait Loci Involved in Sex Determination and Body Growth in the Gilthead Sea Bream (Sparus aurata L.) through Targeted Genome Scan [J].
Loukovitis, Dimitrios ;
Sarropoulou, Elena ;
Tsigenopoulos, Costas S. ;
Batargias, Costas ;
Magoulas, Antonios ;
Apostolidis, Apostolos P. ;
Chatziplis, Dimitrios ;
Kotoulas, Georgios .
PLOS ONE, 2011, 6 (01)
[36]   Recombinational landscape of porcine X chromosome and individual variation in female meiotic recombination associated with haplotypes of Chinese pigs [J].
Ma, Junwu ;
Iannuccelli, Nathalie ;
Duan, Yanyu ;
Huang, Weibing ;
Guo, Beili ;
Riquet, Juliette ;
Huang, Lusheng ;
Milan, Denis .
BMC GENOMICS, 2010, 11
[37]   Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes [J].
Mabuchi, Kohji ;
Miya, Masaki ;
Azuma, Yoichiro ;
Nishida, Mutsumi .
BMC EVOLUTIONARY BIOLOGY, 2007, 7
[38]   Centromere-linkage in the turbot (Scophthalmus maximus) through half-tetrad analysis in diploid meiogynogenetics [J].
Martinez, Paulino ;
Hermida, Miguel ;
Pardo, Belen G. ;
Fernandez, Carlos ;
Castro, Jaime ;
Cal, Rosa M. ;
Alvarez-Dios, Jose A. ;
Gomez-Tato, Antonio ;
Bouza, Carmen .
AQUACULTURE, 2008, 280 (1-4) :81-88
[39]   Identification of the Major Sex-Determining Region of Turbot (Scophthalmus maximus) [J].
Martinez, Paulino ;
Bouza, Carmen ;
Hermida, Miguel ;
Fernandez, Jesus ;
Angel Toro, Miguel ;
Vera, Manuel ;
Pardo, Belen ;
Millan, Adrian ;
Fernandez, Carlos ;
Vilas, Roman ;
Vinas, Ana ;
Sanchez, Laura ;
Felip, Alicia ;
Piferrer, Francesc ;
Ferreiro, Isabel ;
Cabaleiro, Santiago .
GENETICS, 2009, 183 (04) :1443-1452
[40]   Gene Expression Profiles of the Spleen, Liver, and Head Kidney in Turbot (Scophthalmus maximus) Along the Infection Process with Aeromonas salmonicida Using an Immune-Enriched Oligo-microarray [J].
Millan, Adrian ;
Gomez-Tato, Antonio ;
Pardo, Belen G. ;
Fernandez, Carlos ;
Bouza, Carmen ;
Vera, Manuel ;
Antonio Alvarez-Dios, Jose ;
Cabaleiro, Santiago ;
Lamas, Jesus ;
Lemos, Manuel L. ;
Martinez, Paulino .
MARINE BIOTECHNOLOGY, 2011, 13 (06) :1099-1114