A Genetic Linkage Map of Sole (Solea Solea): a Tool for Evolutionary and Comparative Analyses of Exploited (flat)fishes

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2014 Dec 27

PMID 25541971

Citations 6

Authors

Eveline Diopere

Gregory E Maes

Hans Komen

Filip A M Volckaert

Martien A M Groenen

Affiliations

Soon will be listed here.

Abstract

Linkage maps based on markers derived from genes are essential evolutionary tools for commercial marine fish to help identify genomic regions associated with complex traits and subject to selective forces at play during exploitation or selective breeding. Additionally, they allow the use of genomic information from other related species for which more detailed information is available. Sole (solea solea L.) is a commercially important flatfish species in the North Sea, subject to overexploitation and showing evidence of fisheries-induced evolutionary changes in growth- and maturation-related traits. Sole would definitely benefit from a linkage map to better understand how evolution has shaped its genome structure. This study presents a linkage map of sole based on 423 single nucleotide polymorphisms derived from expressed sequence tags and 8 neutral microsatellite markers. The total map length is 1233.8 cM and consists of 38 linkage groups with a size varying between 0 to 92.1 cM. Being derived from expressed sequence tags allowed us to align the map with the genome of four model fish species, namely medaka (Oryzias latipes), Nile tilapia (Oreochromis niloticus), three-spined stickleback (Gasterosteus aculeatus) and green spotted pufferfish (Tetraodon nigroviridis). This comparison revealed multiple conserved syntenic regions with all four species, and suggested that the linkage groups represent 21 putative sole chromosomes. The map was also compared to the linkage map of turbot (Scophthalmus maximus), another commercially important flatfish species and closely related to sole. For all putative sole chromosomes (except one) a turbot homolog was detected, confirming the even higher degree of synteny between these two flatfish species.

Citing Articles

Genomic Characterization of Genes in Senegalese Sole (, Kaup 1858): Clues to Evolutionary Path in Pleuronectiformes.

Mendizabal-Castillero M, Merlo M, Cross I, Rodriguez M, Rebordinos L Animals (Basel). 2022; 12(24).

PMID: 36552509 PMC: 9774920. DOI: 10.3390/ani12243586.

A Comprehensive Integrated Genetic Map of the Complete Karyotype of (Kaup 1858).

Merlo M, Portela-Bens S, Rodriguez M, Garcia-Angulo A, Cross I, Arias-Perez A Genes (Basel). 2021; 12(1).

PMID: 33396249 PMC: 7824234. DOI: 10.3390/genes12010049.

Genome and Phylogenetic Analysis of Genes Involved in the Immune System of - Potential Applications in Aquaculture.

Garcia-Angulo A, Merlo M, Rodriguez M, Portela-Bens S, Liehr T, Rebordinos L Front Genet. 2019; 10:529.

PMID: 31244883 PMC: 6579814. DOI: 10.3389/fgene.2019.00529.

Genetic load in marine animals: a review.

Plough L Curr Zool. 2018; 62(6):567-579.

PMID: 29491946 PMC: 5804265. DOI: 10.1093/cz/zow096.

Construction of a high-density linkage map and fine mapping of QTLs for growth and gonad related traits in blunt snout bream.

Wan S, Liu H, Zhao B, Nie C, Wang W, Gao Z Sci Rep. 2017; 7:46509.

PMID: 28422147 PMC: 5395971. DOI: 10.1038/srep46509.

References

Betancur-R R, Li C, Munroe T, Ballesteros J, Orti G . Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes). Syst Biol. 2013; 62(5):763-85. DOI: 10.1093/sysbio/syt039. View

Liao X, Ma H, Xu G, Shao C, Tian Y, Ji X . Construction of a genetic linkage map and mapping of a female-specific DNA marker in half-smooth tongue sole (Cynoglossus semilaevis). Mar Biotechnol (NY). 2009; 11(6):699-709. DOI: 10.1007/s10126-009-9184-3. View

Mabuchi K, Miya M, Azuma Y, Nishida M . Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes. BMC Evol Biol. 2007; 7:10. PMC: 1797158. DOI: 10.1186/1471-2148-7-10. View

Sharpe D, Hendry A . Life history change in commercially exploited fish stocks: an analysis of trends across studies. Evol Appl. 2015; 2(3):260-75. PMC: 3352497. DOI: 10.1111/j.1752-4571.2009.00080.x. View

Iyengar , Piyapattanakorn , Stone , Heipel , Howell , Baynes . Identification of Microsatellite Repeats in Turbot (Scophthalmus maximus) and Dover Sole (Solea solea) using a RAPD-Based Technique: Characterization of Microsatellite Markers in Dover Sole. Mar Biotechnol (NY). 2000; 2(1):49-56. DOI: 10.1007/s101269900007. View

Kai W, Kikuchi K, Tohari S, Chew A, Tay A, Fujiwara A . Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals. Genome Biol Evol. 2011; 3:424-42. PMC: 5654407. DOI: 10.1093/gbe/evr041. View

Cerda J, Manchado M . Advances in genomics for flatfish aquaculture. Genes Nutr. 2012; 8(1):5-17. PMC: 3534989. DOI: 10.1007/s12263-012-0312-8. View

Betancur-R R, Broughton R, Wiley E, Carpenter K, Lopez J, Li C . The tree of life and a new classification of bony fishes. PLoS Curr. 2013; 5. PMC: 3644299. DOI: 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288. View

Blonk R, Komen H, Kamstra A, van Arendonk J . Estimating breeding values with molecular relatedness and reconstructed pedigrees in natural mating populations of common sole, Solea solea. Genetics. 2009; 184(1):213-9. PMC: 2804404. DOI: 10.1534/genetics.109.110536. View

10.

Storz J . Using genome scans of DNA polymorphism to infer adaptive population divergence. Mol Ecol. 2005; 14(3):671-88. DOI: 10.1111/j.1365-294X.2005.02437.x. View

11.

Kang J, Kim W, Lee W . Genetic linkage map of olive flounder, Paralichthys olivaceus. Int J Biol Sci. 2008; 4(3):143-9. PMC: 2387059. DOI: 10.7150/ijbs.4.143. View

12.

Brunet F, Crollius H, Paris M, Aury J, Gibert P, Jaillon O . Gene loss and evolutionary rates following whole-genome duplication in teleost fishes. Mol Biol Evol. 2006; 23(9):1808-16. DOI: 10.1093/molbev/msl049. View

13.

Walsh M, Munch S, Chiba S, Conover D . Maladaptive changes in multiple traits caused by fishing: impediments to population recovery. Ecol Lett. 2006; 9(2):142-8. DOI: 10.1111/j.1461-0248.2005.00858.x. View

14.

Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B . The medaka draft genome and insights into vertebrate genome evolution. Nature. 2007; 447(7145):714-9. DOI: 10.1038/nature05846. View

15.

Fishman L, Kelly A, Morgan E, Willis J . A genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions. Genetics. 2002; 159(4):1701-16. PMC: 1461909. DOI: 10.1093/genetics/159.4.1701. View

16.

Sarropoulou E, Nousdili D, Magoulas A, Kotoulas G . Linking the genomes of nonmodel teleosts through comparative genomics. Mar Biotechnol (NY). 2008; 10(3):227-33. DOI: 10.1007/s10126-007-9066-5. View

17.

Moen T, Delghandi M, Wesmajervi M, Westgaard J, Fjalestad K . A SNP/microsatellite genetic linkage map of the Atlantic cod (Gadus morhua). Anim Genet. 2009; 40(6):993-6. DOI: 10.1111/j.1365-2052.2009.01938.x. View

18.

Yu J, La Rota M, Kantety R, Sorrells M . EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genomics. 2004; 271(6):742-51. DOI: 10.1007/s00438-004-1027-3. View

19.

Myers R, Worm B . Rapid worldwide depletion of predatory fish communities. Nature. 2003; 423(6937):280-3. DOI: 10.1038/nature01610. View

20.

Li X, Li J . An almost linear time algorithm for a general haplotype solution on tree pedigrees with no recombination and its extensions. J Bioinform Comput Biol. 2009; 7(3):521-45. PMC: 3326668. DOI: 10.1142/s0219720009004217. View