Coding Gene Single Nucleotide Polymorphism Mapping and Quantitative Trait Loci Detection for Physiological Reproductive Traits in Brook Charr, Salvelinus fontinalis Christopher Sauvage, Marie Vagner, Nicolas Derome, Céline Audet, Louis Bernatchez To cite this version: Christopher Sauvage, Marie Vagner, Nicolas Derome, Céline Audet, Louis Bernatchez. Coding Gene Single Nucleotide Polymorphism Mapping and Quantitative Trait Loci Detection for Physiological Reproductive Traits in Brook Charr, Salvelinus fontinalis. G3, Genetics Society of America, 2012, 2 (3), pp.379-392. 10.1534/g3.111.001867. hal-02107010 HAL Id: hal-02107010 https://hal.archives-ouvertes.fr/hal-02107010 Submitted on 29 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License INVESTIGATION Coding Gene Single Nucleotide Polymorphism Mapping and Quantitative Trait Loci Detection for Physiological Reproductive Traits in Brook Charr, Salvelinus fontinalis Christopher Sauvage,*,†,1,2 Marie Vagner,‡,§,1 Nicolas Derôme,* Céline Audet,‡ and Louis Bernatchez* *Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Québec (Québec) Canada, G1V 0A6, †INRA, UR1052, Unité de Génétique et d’Amélioration des Fruits et Légumes, 84143 Montfavet, France, ‡Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Rimouski (Québec) Canada, G5L 3A1, § and Institut du Littoral et de l’Environnement, LIENSs UMR6250, 2 rue Olympe de Gouges, 17000 La Rochelle, France ABSTRACT A linkage map of 40 linkage groups (LGs) was developed for brook charr, Salvelinus fontinalis, KEYWORDS using an F2 interstrain hybrid progeny (n = 171) and 256 coding gene SNP developed specifically for brook linkage mapping charr and validated from a large (.1000) subset of putative SNP, as well as 81 microsatellite markers. To QTL detection identify quantitative trait loci (QTL) related to reproduction functions, these fish were also phenotyped at six single nucleotide physiological traits, including spermatozoid head diameter, sperm concentration, plasma testosterone, plasma polymorphisms 11-keto-testosterone, egg diameter, and plasma 17b-estradiol. Five significant QTL were detected over four (SNP) LGs for egg diameter and plasma 17b-estradiol concentration in females, and sperm concentration as well as reproduction spermatozoid head diameter in males. In females, two different QTLs located on LG 11 and LG 34 were Salvelinus associated with the egg number, whereas one QTL was associated with plasma 17b-estradiol concentration fontinalis (LG 8). Their total percent variance explained (PVE) was 26.7% and 27.6%, respectively. In males, two QTL were also detected for the sperm concentration, and their PVE were estimated at 18.58% and 14.95%, respectively. ThelowQTLnumber,associatedwiththehighPVE,suggests that the variance in these reproductive physi- ological traits was either under the control of one major gene or a small number of genes. The QTL associated with sperm concentration, plasma 17b-estradiol, and egg diameter appeared to be under a dominance effect, whereas the two others were under a negative additive effect. These results show that genes underlying the phenotypic variance of these traits are under different modes of action (additive vs. dominance) and may be used to predict an increase or a decrease in their phenotypic values in subsequent generations of selective breeding. Moreover, this newly developed panel of mapped SNP located in coding gene regions will be useful for screening wild populations, especially in the context of investigating the genetic impact of massive stocking of domestic brook charr to support the angling industry throughout eastern North America. Copyright © 2012 Sauvage et al. Linkages maps have numerous applications in evolutionary and com- doi: 10.1534/g3.111.001867 parative genomics (Gharbi et al. 2006, Jaari et al. 2009). Namely, one Manuscript received December 19, 2011; accepted for publication January 19, 2012 of the main applications of linkage maps relies on the mapping of This is an open-access article distributed under the terms of the Creative quantitative trait loci (QTL), which allows localizing genomic regions Commons Attribution Unported License (http://creativecommons.org/licenses/ by/3.0/), which permits unrestricted use, distribution, and reproduction in any responsible for the variations in continuous phenotypic traits of in- medium, provided the original work is properly cited. terest. To this end, the number and the variety of molecular markers Supporting information is available online at http://www.g3journal.org/lookup/ developed for linkage-mapping have been associated with technological suppl/doi:10.1534/g3.111.001867/-/DC1 advances, namely new marker development such as microsatellites and 1These authors contributed equally to this work. 2Corresponding author: INRA, UR1052, Unité de Génétique et d’Amélioration single nucleotide polymorphisms (SNPs). Also, compared with previ- des Fruits et Légumes, Domaine Saint-Maurice BP94, 84143 Montfavet, France. ous methods based on cloning and Sanger sequencing, next-generation E-mail: [email protected] sequencing technologies now allow the more rapid development of in Volume 2 | March 2012 | 379 n Table 1 Description of the 40 LGs with the number and size of markers composing each LG (in cM) obtained for the consensus (sex-average) linkage map in brook charr Average Spacing, LG Size of the LG, in cM No. Markers in the LG No. SNP No. SSR in cM LG1 132.2 16 11 5 8.26 LG2 130.2 16 11 5 8.14 LG3 95.7 15 10 5 6.38 LG4 73.2 8 6 2 9.15 LG5 95.2 11 6 5 8.65 LG6 77.5 11 9 2 7.04 LG7 46.6 9 6 3 5.17 LG8 81.2 11 8 3 7.38 LG9 82.3 10 9 1 8.23 LG10 63.6 9 8 1 7.06 LG11 70.1 8 4 4 8.76 LG12 78.4 6 4 2 13.06 LG13 74 7 5 2 10.57 LG14 68.5 6 4 2 11.41 LG15 52.6 6 5 1 8.76 LG16 42.8 4 1 3 10.70 LG17 30.3 6 4 2 5.05 LG18 24.9 5 2 3 4.98 LG19 61.1 4 3 1 15.27 LG20 67.2 5 3 2 13.44 LG21 60.7 6 5 1 10.11 LG22 45.8 5 2 3 9.16 LG23 29.2 4 3 1 7.30 LG24 49.3 5 4 1 9.86 LG25 29.8 4 4 0 7.45 LG26 11.5 3 2 1 3.83 LG27 27.8 3 2 1 9.26 LG28 3.9 4 4 0 0.97 LG29 42.3 2 1 1 21.15 LG30 63.9 3 2 1 21.30 LG31 72.3 17 13 4 4.25 LG32 59.1 3 2 1 19.70 LG33 1.4 2 2 0 0.70 LG34 41.8 3 3 0 13.93 LG35 2.4 3 3 0 0.80 LG36 29.1 3 2 1 9.70 LG37 6.5 3 3 0 2.16 LG38 12.9 11 5 6 1.17 LG39 4.5 5 5 0 0.90 LG40 5.6 4 4 0 1.40 Max 132.25 17 13 6 21.3 Min 1.40 2 1 0 0.70 Average 51.18 6.65 4.75 1.90 8.31 Total 2047.45 266.00 190.00 76.00 - LG, linkage group; SNP, single nucleotide-polymorphism; SSR, simple sequence repeat. silico SNP markers (Hudson 2008). Yet, SNP marker development and include up to 5650 markers (Danzmann et al. 2008; Moen et al. 2008; in silico validation remain particularly challenging in polyploid species Lorenz et al. 2010, Lien et al. 2011). In rainbow trout (Onchorynchus as the result of recent whole-genome duplication events, such as in mykiss), multiple generations of linkage maps have been developed salmonids (Seeb et al. 2011). using various types of molecular markers, including amplified frag- Salmonids are of considerable economic, social, and conservation ment length polymorphisms (Young et al. 1998; Nichols et al. 2003), value (Davidson et al. 2010). The salmonidae family contains 11 gen- single-sequence repeats, or SSR (Rexroad et al. 2008), and SNP (Miller era and 68 species, including salmon, trout, charr, freshwater white- et al. 2011; Lien et al. 2011). Lower resolution linkage maps have also fishes, ciscos, and graylings (for review, see Davidson et al. 2010) and been developed in Arctic charr Salvelinus alpinus (Woram et al. has experienced a whole-genome duplication approximately 25 to 100 2004, Moghadam et al. 2007), coho salmon Oncorhynchus kisutch million years ago (e.g., Phillips and Rab 2001). More is known about (McClelland and Naish 2008), brown trout Salmo trutta (Gharbi et al. the biology and genetics of salmonids than in any other groups of fish 2006), lake whitefish Coregonus clupeaformis (Rogers et al. 2007), and (Koop and Davidson 2008), which has led to the development of recently, in brook charr, Salvelinus fontinalis (Timusk et al. 2011). important genomic tools in recent years. For example, linkage maps All these maps exhibit a large number of linkage groups, or LG have been successively developed in the Atlantic salmon Salmo salar to (.28), because the diploid ancestor of salmonids possessed a karyotype 380 | C. Sauvage et al. with 48 acrocentric chromosomes (Phillips and Rab 2001) and a span of 390 to 5548 cM with a genome size estimated at 3.3 · 109 bp (Davidson et al.