PMC:5118429 / 24185-36700 JSONTXT

{"project":"2_test","denotations":[{"id":"27920797-24755649-33226468","span":{"begin":1493,"end":1497},"obj":"24755649"},{"id":"27920797-22387270-33226469","span":{"begin":2290,"end":2294},"obj":"22387270"},{"id":"27920797-22349700-33226470","span":{"begin":2497,"end":2501},"obj":"22349700"},{"id":"27920797-16760430-33226471","span":{"begin":2626,"end":2630},"obj":"16760430"},{"id":"27920797-25009257-33226472","span":{"begin":2793,"end":2797},"obj":"25009257"},{"id":"27920797-25463516-33226473","span":{"begin":2900,"end":2904},"obj":"25463516"},{"id":"27920797-11567635-33226474","span":{"begin":5590,"end":5594},"obj":"11567635"},{"id":"27920797-16365426-33226475","span":{"begin":5612,"end":5616},"obj":"16365426"},{"id":"27920797-25772501-33226476","span":{"begin":5631,"end":5635},"obj":"25772501"},{"id":"27920797-16403448-33226477","span":{"begin":5926,"end":5930},"obj":"16403448"},{"id":"27920797-20525320-33226479","span":{"begin":7692,"end":7696},"obj":"20525320"},{"id":"27920797-25757012-33226480","span":{"begin":7722,"end":7726},"obj":"25757012"},{"id":"27920797-26582102-33226481","span":{"begin":7741,"end":7745},"obj":"26582102"},{"id":"27920797-12920098-33226482","span":{"begin":7786,"end":7790},"obj":"12920098"},{"id":"27920797-15653562-33226483","span":{"begin":7806,"end":7810},"obj":"15653562"},{"id":"27920797-20609225-33226484","span":{"begin":7827,"end":7831},"obj":"20609225"},{"id":"27920797-20525320-33226485","span":{"begin":8354,"end":8358},"obj":"20525320"},{"id":"27920797-20609225-33226486","span":{"begin":8375,"end":8379},"obj":"20609225"},{"id":"27920797-26582102-33226487","span":{"begin":8394,"end":8398},"obj":"26582102"},{"id":"27920797-19223591-33226488","span":{"begin":8807,"end":8811},"obj":"19223591"},{"id":"27920797-25655896-33226489","span":{"begin":8825,"end":8829},"obj":"25655896"},{"id":"27920797-26582102-33226490","span":{"begin":8844,"end":8848},"obj":"26582102"},{"id":"27920797-26582102-33226491","span":{"begin":9053,"end":9057},"obj":"26582102"},{"id":"27920797-24755649-33226492","span":{"begin":9261,"end":9265},"obj":"24755649"}],"text":"GWAS\nThe Manhattan plots from GWAS results at iteration 5 for FY, FW, BW10, BW13, and CAR are shown in Figures 1–5, respectively. In total, 1906 non-overlapping, non-repetitive windows of 20 successive SNPs were used. Of these windows, two windows located on chromosome Omy9 explained 1.5 and 1.0% of the genetic variance for FY. The same windows explained 1.2 and 1.1% of the genetic variance for FW. Only one window, located on Omy5, was responsible for 1.38 and 0.95% of the genetic variance for BW10 and BW13, respectively. Three windows located on Omy27, Omy17, and Omy9 were responsible for 1.7, 1.7, and 1.0%, of the genetic variance in CAR, respectively.\nFigure 1 The proportion of genetic variance explained by 20-SNP regions for fillet yield.\nFigure 2 The proportion of genetic variance explained by 20-SNP regions for fillet weight.\nFigure 3 The proportion of genetic variance explained by 20-SNP regions for 10-month body weight.\nFigure 4 The proportion of genetic variance explained by 20-SNP regions for 13-month body weight.\nFigure 5 The proportion of genetic variance explained by 20-SNP regions for carcass weight. No major QTL was detected for FY, suggesting that this trait has a polygenic architecture affected by multiple loci with small effects in this rainbow trout population. The SNP markers from the two windows that explained at least 1.0% of the proportion of variance for FY and harboring or neighboring genes from the same genome scaffold (Berthelot et al., 2014) are listed in Table 3. An extended list of all the SNPs markers is provided in Table S2. Only 13 of the 40 SNPs identified by the wssGWAS on Omy9 explained a proportion of the genetic variance equal to or greater than 0.1%. Of them, nine were located within a gene (exon or intron) and the other four had known neighboring genes in the same genome scaffold. Four of those 13 SNPs were located in scaffold_516, of which one SNP was mapped to exon 6 of Properdin, another to exon 3 of Transmembrane protein 201-like, and two SNPs were mapped in the intron regions of Calsyntenin-1-like isoform x2 (Table 3). Briefly, Properdin is one of the proteins that participates in the complement system, which also may interfere with fatty acid uptake and esterification in adipocytes (Gauvreau et al., 2012). Transmembrane protein 201-like is a component of transmembrane actin-associated nuclear lines with a role in centrosome orientation and nuclear movement prior to cell migration (Borrego-Pinto et al., 2012). Calsyntenin-1 is associated with kinesin-1-mediated transport of vesicles and tubulovesicular organelles (Konecna et al., 2006), appears to participate in intracellular transport and endosomal trafficking, and is necessary for the formation of peripheral sensory axons (Ponomareva et al., 2014). However, the biological functions of calsyntenins are not well understood yet (Ortiz-Medina et al., 2015).\nTable 3 The SNP markers that explained the largest proportion of variance for fillet yield using 20-SNP windows.\nMarker Chr Position (cM) Alleles VE (%) Scaffold Scaffold position Scaffold size Loc Description\nWINDOW 1 TOTAL PROPORTION 1.5%\nAX-89976492 9 125.19 T/C 0.13 Scaffold_8612 10,780 26,627 Intron Beta-catenin-interacting protein 1 isoform x1\nAX-89970327 9 125.19 A/C 0.11 Scaffold_516 399,414 728,099 Intron Calsyntenin-1-like isoform x2\nAX-89940136 9 125.19 A/G 0.12 Scaffold_516 407,663 728,099 Intron Calsyntenin-1-like isoform x2\nAX-89936139 9 125.67 A/C 0.13 Near* None\nAX-89944669 9 125.67 G/T 0.13 Scaffold_32707 921 3946 Exon 1 Nudix hydrolase chloroplastic-like\nAX-89940514 9 125.67 T/C 0.12 Scaffold_10308 15,430 21,663 Near* None\nAX-89937961 9 125.67 G/T 0.13 Scaffold_516 586,177 728,099 Exon 6 Properdin\nAX-89951506 9 125.67 G/A 0.12 Scaffold_516 555,991 728,099 Exon 3 Transmembrane protein 201-like\nAX-89938525 9 125.86 G/A 0.10 Scaffold_52 1,795,215 2,128,772 Intron Atpase family aaa domain-containing protein 3-like\nAX-89957923 9 126.04 A/G 0.13 Scaffold_19674 6079 8261 Near* None\nWINDOW 2 TOTAL PROPORTION 1.0%\nAX-89951447 9 117.12 G/A 0.10 Scaffold_43535 864 3113 Near* None\nAX-89940159 9 117.12 T/C 0.11 Scaffold_347 148,757 935,129 Intron Serine threonine-protein kinase sbk1-like\nAX-89924961 9 117.91 C/T 0.10 Scaffold_347 414,782 935,129 Exon 6 Phd finger protein 20-like isoform x3\nChr, chromosome; VE, percentage of the genetic variance explained by the SNP; Loc, location in the scaffold with three possibilities: intron, exon, or near an exon. The same two windows found in the FY GWAS were also associated with FW. However, from the 40 SNPs markers identified by the wssGWAS, only 12 explained a proportion equal to or greater than 0.1% and of them, nine were in a gene (exon or intron, Table 4). An extended list of all the SNP markers is provided in Table S3. Similar to FY, no major QTL was detected for FW which supports the polygenic architecture of FW. Three of the 12 SNPs were also located in scaffold_516 within the Calsyntenin-1-like isoform x2, Properdin and Transmembrane protein 201-like genes (Table 4). Three additional SNPs were located in scaffold_347 in the Src-like-adapter 2; Serine/ threonine-protein kinase sbk1-like; and Phd finger protein 20-like isoform x3 genes. Briefly, Src-like-adapter 2 is an adaptor protein that regulates T and B cell maturation and development, and it is a critical component regulating signal transduction in immune and malignant cells (Sosinowski et al., 2001; Dragone et al., 2006; Kazi et al., 2015). Additionally, differentially-expressed transcripts in response to handling and confinement stress in rainbow trout were mapped to a serine/threonine-protein kinase, SBK1, homologous in zebrafish that participates in signal transduction pathways related to brain development (Chou et al., 2006; Liu et al., 2015a).\nTable 4 The SNP markers that explained the largest proportion of variance for fillet weight using 20-SNP windows.\nMarker Chr Position (cM) Alleles VE (%) Scaffold Scaffold position Scaffold size Loc Description\nWINDOW 1 TOTAL PROPORTION 1.2%\nAX-89976492 9 125.19 T/C 0.12 Scaffold_8612 10,780 26,627 Intron Beta-catenin-interacting protein 1 isoform x1\nAX-89970327 9 125.19 A/C 0.10 Scaffold_516 399,414 728,099 Intron Calsyntenin-1-like isoform x2\nAX-89936139 9 125.67 A/C 0.11 Near* None\nAX-89944669 9 125.67 G/T 0.11 Scaffold_32707 921 3946 Exon 1 Nudix hydrolase chloroplastic-like\nAX-89940514 9 125.67 T/C 0.10 Scaffold_10308 15,430 21,663 Near* None\nAX-89937961 9 125.67 G/T 0.11 Scaffold_516 586,177 728,099 Exon 6 Properdin\nAX-89951506 9 125.67 G/A 0.11 Scaffold_516 555,991 728,099 Exon 3 Transmembrane protein 201-like\nWINDOW 2 TOTAL PROPORTION 1.1%\nAX-89953042 9 116.09 G/A 0.10 Scaffold_1609 166,168 200,099 Exon 4 Kelch domain-containing protein 8b\nAX-89951447 9 117.12 G/A 0.13 Scaffold_43535 864 3113 Near* None\nAX-89975284 9 117.12 A/C 0.11 Scaffold_347 348,224 935,129 Exon 7 Src-like-adapter 2\nAX-89940159 9 117.12 T/C 0.12 Scaffold_347 148,757 935,129 Intron Serine threonine-protein kinase sbk1-like\nAX-89924961 9 117.91 C/T 0.13 Scaffold_347 414,782 935,129 Exon 6 Phd finger protein 20-like isoform x3\nChr, chromosome; VE, percentage of the genetic variance explained by the SNP; Loc, location in the scaffold with three possibilities: intron, exon, or near an exon. Genome regions associated with growth have been detected on most of the 29 chromosomes in Atlantic salmon (Baranski et al., 2010; Gutierrez et al., 2012, 2015; Tsai et al., 2015) and in rainbow trout (O'Malley et al., 2003; Perry et al., 2005; Wringe et al., 2010). The heterogeneity in the results makes it hard to compare our results to previous studies. Many factors contribute to this observed heterogeneity between studies including: (1) the highly polygenic architecture of growth and growth-related traits; (2) differences in marker segregation that may be affected by the strain genetic background, and different types and densities of markers used in each study; (3) different algorithms used in the QTL detection analyses; (4) large variation in sample size (Baranski et al., 2010; Wringe et al., 2010; Tsai et al., 2015), and (5) possible false positives. None of the 20 SNPs identified by the wssGWAS for BW10 and BW13 on chromosome Omy5 (Figures 3, 4) were able to surpass the threshold of 0.1%. The complete list of the SNPs is provided in Tables S4, S5 for BW10 and BW13, respectively. Our findings of the polygenic architecture of growth traits in fish is consistent with previous reports in the literature (Devlin et al., 2009; Dai et al., 2015; Tsai et al., 2015), and, congruent with our GWAS results, several markers were associated with weight in a GWAS for Atlantic salmon, but the proportion of variance explained by each marker was less than 0.1% (Tsai et al., 2015).\nLastly, SNP markers that explained more than 0.1% of the proportion of genetic variance for CAR on Omy27, 17, and 9, and harboring or neighboring genes from the same genome scaffold (Berthelot et al., 2014) are listed in Table 5. No major QTL was detected for this trait. An extended list of all the SNP markers is provided in Table S6. From the 60 SNP markers identified by wssGWAS, only 18 explained a proportion equal to or greater than 0.1%, of which 10 were in a gene (exon or intron). Four of the 18 SNPs were located in scaffold_173; one was in the exon of ubiquitin-conjugating enzyme e2 variant 1, and three were near this gene and near the histone h2b 1 2-like gene. One of the SNPs was mapped to the Calsyntenin-1-like isoform x2 intron region in scaffold_516 that also affected FY and FW.\nTable 5 The SNP markers that explained the largest proportion of variance for carcass weight using 20-SNP windows.\nMarker Chr Position (cM) Alleles VE (%) Scaffold Scaffold position Scaffold size Loc Description\nWINDOW 1 TOTAL PROPORTION 1.7%\nAX-89952551 27 75.09 A/G 0.12 Scaffold_1006 143,453 383,627 Near nitric oxide inducible/serine threonine-protein kinase nlk\nAX-89954149 27 75.09 C/A 0.12 Scaffold_147 921,922 1,497,438 Near atp-sensitive inward rectifier potassium channel 1-like/cmp-n-acetylneuraminate-beta-galactosamide-alpha-sialyltransferase 4-like isoform x1\nAX-89938133 27 75.09 A/G 0.13 Scaffold_1006 46,265 383,627 Exon3 nitric oxide inducible\nAX-89948564 27 74.78 G/A 0.12 Scaffold_8798 5532 26,005 Near Undetermined/None\nAX-89974542 27 74.58 G/T 0.11 Scaffold_842 38,757 463,739 Intron kinase suppressor of ras 1-like isoform x2\nAX-89926230 27 74.58 A/G 0.12 Scaffold_1952 116,665 147,230 Near neurofibromin isoform x2/oligodendrocyte-myelin glyco\nAX-89938965 27 74.43 G/T 0.12 Scaffold_842 38,933 463,739 Intron kinase suppressor of ras 1-like isoform x2\nAX-89928353 27 73.96 G/A 0.10 Scaffold_1675 177,158 191,261 Intron vascular endothelial zinc finger 1-like isoform x2\nAX-89968747 27 73.96 A/G 0.11 Scaffold_3611 60,104 62,580 Intron unconventional myosin-xviiia-like isoform x1\nAX-89947091 27 73.96 na 0.10 na Na\nAX-89942611 27 73.42 C/A 0.16 Scaffold_3980 33,385 57,002 Intron unconventional myosin-xviiia-like isoform x2\nWINDOW 2 TOTAL PROPORTION 1.7%\nAX-89973675 17 115.87 G/T 0.10 Scaffold_26752 3396 4948 Intron spectrin beta non-erythrocytic 1-like\nAX-89969602 17 114.85 C/T 0.10 Scaffold_24 197,378 2,579,057 Intron calpain-2 catalytic subunit-like\nAX-89935000 17 114.02 A/G 0.17 Scaffold_173 119,365 1,392,108 Near histone h2b 1 2-like/ubiquitin-conjugating enzyme e2 variant 1\nAX-89918454 17 114.02 C/A 0.12 Scaffold_173 123,912 1,392,108 Near histone h2b 1 2-like/ubiquitin-conjugating enzyme e2 variant 1\nAX-89923840 17 113.51 C/T 0.18 Scaffold_173 195,297 1,392,108 Exon4 ubiquitin-conjugating enzyme e2 variant 1\nAX-89925576 17 113.51 A/G 0.18 Scaffold_173 160,398 1,392,108 Near histone h2b 1 2-like/ubiquitin-conjugating enzyme e2 variant 1\nWINDOW 3 TOTAL PROPORTION 1.0%\nAX-89940136 9 125.19 A/G 0.10 Scaffold_516 407,663 728,099 Intron Calsyntenin-1-like isoform x2\nChr, chromosome; VE, percentage of the genetic variance explained by the SNP; Loc, location in the scaffold with three possibilities: intron, exon, or near an exon."}

{"project":"MyTest","denotations":[{"id":"27920797-24755649-33226468","span":{"begin":1493,"end":1497},"obj":"24755649"},{"id":"27920797-22387270-33226469","span":{"begin":2290,"end":2294},"obj":"22387270"},{"id":"27920797-22349700-33226470","span":{"begin":2497,"end":2501},"obj":"22349700"},{"id":"27920797-16760430-33226471","span":{"begin":2626,"end":2630},"obj":"16760430"},{"id":"27920797-25009257-33226472","span":{"begin":2793,"end":2797},"obj":"25009257"},{"id":"27920797-25463516-33226473","span":{"begin":2900,"end":2904},"obj":"25463516"},{"id":"27920797-11567635-33226474","span":{"begin":5590,"end":5594},"obj":"11567635"},{"id":"27920797-16365426-33226475","span":{"begin":5612,"end":5616},"obj":"16365426"},{"id":"27920797-25772501-33226476","span":{"begin":5631,"end":5635},"obj":"25772501"},{"id":"27920797-16403448-33226477","span":{"begin":5926,"end":5930},"obj":"16403448"},{"id":"27920797-20525320-33226479","span":{"begin":7692,"end":7696},"obj":"20525320"},{"id":"27920797-25757012-33226480","span":{"begin":7722,"end":7726},"obj":"25757012"},{"id":"27920797-26582102-33226481","span":{"begin":7741,"end":7745},"obj":"26582102"},{"id":"27920797-12920098-33226482","span":{"begin":7786,"end":7790},"obj":"12920098"},{"id":"27920797-15653562-33226483","span":{"begin":7806,"end":7810},"obj":"15653562"},{"id":"27920797-20609225-33226484","span":{"begin":7827,"end":7831},"obj":"20609225"},{"id":"27920797-20525320-33226485","span":{"begin":8354,"end":8358},"obj":"20525320"},{"id":"27920797-20609225-33226486","span":{"begin":8375,"end":8379},"obj":"20609225"},{"id":"27920797-26582102-33226487","span":{"begin":8394,"end":8398},"obj":"26582102"},{"id":"27920797-19223591-33226488","span":{"begin":8807,"end":8811},"obj":"19223591"},{"id":"27920797-25655896-33226489","span":{"begin":8825,"end":8829},"obj":"25655896"},{"id":"27920797-26582102-33226490","span":{"begin":8844,"end":8848},"obj":"26582102"},{"id":"27920797-26582102-33226491","span":{"begin":9053,"end":9057},"obj":"26582102"},{"id":"27920797-24755649-33226492","span":{"begin":9261,"end":9265},"obj":"24755649"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"GWAS\nThe Manhattan plots from GWAS results at iteration 5 for FY, FW, BW10, BW13, and CAR are shown in Figures 1–5, respectively. In total, 1906 non-overlapping, non-repetitive windows of 20 successive SNPs were used. Of these windows, two windows located on chromosome Omy9 explained 1.5 and 1.0% of the genetic variance for FY. The same windows explained 1.2 and 1.1% of the genetic variance for FW. Only one window, located on Omy5, was responsible for 1.38 and 0.95% of the genetic variance for BW10 and BW13, respectively. Three windows located on Omy27, Omy17, and Omy9 were responsible for 1.7, 1.7, and 1.0%, of the genetic variance in CAR, respectively.\nFigure 1 The proportion of genetic variance explained by 20-SNP regions for fillet yield.\nFigure 2 The proportion of genetic variance explained by 20-SNP regions for fillet weight.\nFigure 3 The proportion of genetic variance explained by 20-SNP regions for 10-month body weight.\nFigure 4 The proportion of genetic variance explained by 20-SNP regions for 13-month body weight.\nFigure 5 The proportion of genetic variance explained by 20-SNP regions for carcass weight. No major QTL was detected for FY, suggesting that this trait has a polygenic architecture affected by multiple loci with small effects in this rainbow trout population. The SNP markers from the two windows that explained at least 1.0% of the proportion of variance for FY and harboring or neighboring genes from the same genome scaffold (Berthelot et al., 2014) are listed in Table 3. An extended list of all the SNPs markers is provided in Table S2. Only 13 of the 40 SNPs identified by the wssGWAS on Omy9 explained a proportion of the genetic variance equal to or greater than 0.1%. Of them, nine were located within a gene (exon or intron) and the other four had known neighboring genes in the same genome scaffold. Four of those 13 SNPs were located in scaffold_516, of which one SNP was mapped to exon 6 of Properdin, another to exon 3 of Transmembrane protein 201-like, and two SNPs were mapped in the intron regions of Calsyntenin-1-like isoform x2 (Table 3). Briefly, Properdin is one of the proteins that participates in the complement system, which also may interfere with fatty acid uptake and esterification in adipocytes (Gauvreau et al., 2012). Transmembrane protein 201-like is a component of transmembrane actin-associated nuclear lines with a role in centrosome orientation and nuclear movement prior to cell migration (Borrego-Pinto et al., 2012). Calsyntenin-1 is associated with kinesin-1-mediated transport of vesicles and tubulovesicular organelles (Konecna et al., 2006), appears to participate in intracellular transport and endosomal trafficking, and is necessary for the formation of peripheral sensory axons (Ponomareva et al., 2014). However, the biological functions of calsyntenins are not well understood yet (Ortiz-Medina et al., 2015).\nTable 3 The SNP markers that explained the largest proportion of variance for fillet yield using 20-SNP windows.\nMarker Chr Position (cM) Alleles VE (%) Scaffold Scaffold position Scaffold size Loc Description\nWINDOW 1 TOTAL PROPORTION 1.5%\nAX-89976492 9 125.19 T/C 0.13 Scaffold_8612 10,780 26,627 Intron Beta-catenin-interacting protein 1 isoform x1\nAX-89970327 9 125.19 A/C 0.11 Scaffold_516 399,414 728,099 Intron Calsyntenin-1-like isoform x2\nAX-89940136 9 125.19 A/G 0.12 Scaffold_516 407,663 728,099 Intron Calsyntenin-1-like isoform x2\nAX-89936139 9 125.67 A/C 0.13 Near* None\nAX-89944669 9 125.67 G/T 0.13 Scaffold_32707 921 3946 Exon 1 Nudix hydrolase chloroplastic-like\nAX-89940514 9 125.67 T/C 0.12 Scaffold_10308 15,430 21,663 Near* None\nAX-89937961 9 125.67 G/T 0.13 Scaffold_516 586,177 728,099 Exon 6 Properdin\nAX-89951506 9 125.67 G/A 0.12 Scaffold_516 555,991 728,099 Exon 3 Transmembrane protein 201-like\nAX-89938525 9 125.86 G/A 0.10 Scaffold_52 1,795,215 2,128,772 Intron Atpase family aaa domain-containing protein 3-like\nAX-89957923 9 126.04 A/G 0.13 Scaffold_19674 6079 8261 Near* None\nWINDOW 2 TOTAL PROPORTION 1.0%\nAX-89951447 9 117.12 G/A 0.10 Scaffold_43535 864 3113 Near* None\nAX-89940159 9 117.12 T/C 0.11 Scaffold_347 148,757 935,129 Intron Serine threonine-protein kinase sbk1-like\nAX-89924961 9 117.91 C/T 0.10 Scaffold_347 414,782 935,129 Exon 6 Phd finger protein 20-like isoform x3\nChr, chromosome; VE, percentage of the genetic variance explained by the SNP; Loc, location in the scaffold with three possibilities: intron, exon, or near an exon. The same two windows found in the FY GWAS were also associated with FW. However, from the 40 SNPs markers identified by the wssGWAS, only 12 explained a proportion equal to or greater than 0.1% and of them, nine were in a gene (exon or intron, Table 4). An extended list of all the SNP markers is provided in Table S3. Similar to FY, no major QTL was detected for FW which supports the polygenic architecture of FW. Three of the 12 SNPs were also located in scaffold_516 within the Calsyntenin-1-like isoform x2, Properdin and Transmembrane protein 201-like genes (Table 4). Three additional SNPs were located in scaffold_347 in the Src-like-adapter 2; Serine/ threonine-protein kinase sbk1-like; and Phd finger protein 20-like isoform x3 genes. Briefly, Src-like-adapter 2 is an adaptor protein that regulates T and B cell maturation and development, and it is a critical component regulating signal transduction in immune and malignant cells (Sosinowski et al., 2001; Dragone et al., 2006; Kazi et al., 2015). Additionally, differentially-expressed transcripts in response to handling and confinement stress in rainbow trout were mapped to a serine/threonine-protein kinase, SBK1, homologous in zebrafish that participates in signal transduction pathways related to brain development (Chou et al., 2006; Liu et al., 2015a).\nTable 4 The SNP markers that explained the largest proportion of variance for fillet weight using 20-SNP windows.\nMarker Chr Position (cM) Alleles VE (%) Scaffold Scaffold position Scaffold size Loc Description\nWINDOW 1 TOTAL PROPORTION 1.2%\nAX-89976492 9 125.19 T/C 0.12 Scaffold_8612 10,780 26,627 Intron Beta-catenin-interacting protein 1 isoform x1\nAX-89970327 9 125.19 A/C 0.10 Scaffold_516 399,414 728,099 Intron Calsyntenin-1-like isoform x2\nAX-89936139 9 125.67 A/C 0.11 Near* None\nAX-89944669 9 125.67 G/T 0.11 Scaffold_32707 921 3946 Exon 1 Nudix hydrolase chloroplastic-like\nAX-89940514 9 125.67 T/C 0.10 Scaffold_10308 15,430 21,663 Near* None\nAX-89937961 9 125.67 G/T 0.11 Scaffold_516 586,177 728,099 Exon 6 Properdin\nAX-89951506 9 125.67 G/A 0.11 Scaffold_516 555,991 728,099 Exon 3 Transmembrane protein 201-like\nWINDOW 2 TOTAL PROPORTION 1.1%\nAX-89953042 9 116.09 G/A 0.10 Scaffold_1609 166,168 200,099 Exon 4 Kelch domain-containing protein 8b\nAX-89951447 9 117.12 G/A 0.13 Scaffold_43535 864 3113 Near* None\nAX-89975284 9 117.12 A/C 0.11 Scaffold_347 348,224 935,129 Exon 7 Src-like-adapter 2\nAX-89940159 9 117.12 T/C 0.12 Scaffold_347 148,757 935,129 Intron Serine threonine-protein kinase sbk1-like\nAX-89924961 9 117.91 C/T 0.13 Scaffold_347 414,782 935,129 Exon 6 Phd finger protein 20-like isoform x3\nChr, chromosome; VE, percentage of the genetic variance explained by the SNP; Loc, location in the scaffold with three possibilities: intron, exon, or near an exon. Genome regions associated with growth have been detected on most of the 29 chromosomes in Atlantic salmon (Baranski et al., 2010; Gutierrez et al., 2012, 2015; Tsai et al., 2015) and in rainbow trout (O'Malley et al., 2003; Perry et al., 2005; Wringe et al., 2010). The heterogeneity in the results makes it hard to compare our results to previous studies. Many factors contribute to this observed heterogeneity between studies including: (1) the highly polygenic architecture of growth and growth-related traits; (2) differences in marker segregation that may be affected by the strain genetic background, and different types and densities of markers used in each study; (3) different algorithms used in the QTL detection analyses; (4) large variation in sample size (Baranski et al., 2010; Wringe et al., 2010; Tsai et al., 2015), and (5) possible false positives. None of the 20 SNPs identified by the wssGWAS for BW10 and BW13 on chromosome Omy5 (Figures 3, 4) were able to surpass the threshold of 0.1%. The complete list of the SNPs is provided in Tables S4, S5 for BW10 and BW13, respectively. Our findings of the polygenic architecture of growth traits in fish is consistent with previous reports in the literature (Devlin et al., 2009; Dai et al., 2015; Tsai et al., 2015), and, congruent with our GWAS results, several markers were associated with weight in a GWAS for Atlantic salmon, but the proportion of variance explained by each marker was less than 0.1% (Tsai et al., 2015).\nLastly, SNP markers that explained more than 0.1% of the proportion of genetic variance for CAR on Omy27, 17, and 9, and harboring or neighboring genes from the same genome scaffold (Berthelot et al., 2014) are listed in Table 5. No major QTL was detected for this trait. An extended list of all the SNP markers is provided in Table S6. From the 60 SNP markers identified by wssGWAS, only 18 explained a proportion equal to or greater than 0.1%, of which 10 were in a gene (exon or intron). Four of the 18 SNPs were located in scaffold_173; one was in the exon of ubiquitin-conjugating enzyme e2 variant 1, and three were near this gene and near the histone h2b 1 2-like gene. One of the SNPs was mapped to the Calsyntenin-1-like isoform x2 intron region in scaffold_516 that also affected FY and FW.\nTable 5 The SNP markers that explained the largest proportion of variance for carcass weight using 20-SNP windows.\nMarker Chr Position (cM) Alleles VE (%) Scaffold Scaffold position Scaffold size Loc Description\nWINDOW 1 TOTAL PROPORTION 1.7%\nAX-89952551 27 75.09 A/G 0.12 Scaffold_1006 143,453 383,627 Near nitric oxide inducible/serine threonine-protein kinase nlk\nAX-89954149 27 75.09 C/A 0.12 Scaffold_147 921,922 1,497,438 Near atp-sensitive inward rectifier potassium channel 1-like/cmp-n-acetylneuraminate-beta-galactosamide-alpha-sialyltransferase 4-like isoform x1\nAX-89938133 27 75.09 A/G 0.13 Scaffold_1006 46,265 383,627 Exon3 nitric oxide inducible\nAX-89948564 27 74.78 G/A 0.12 Scaffold_8798 5532 26,005 Near Undetermined/None\nAX-89974542 27 74.58 G/T 0.11 Scaffold_842 38,757 463,739 Intron kinase suppressor of ras 1-like isoform x2\nAX-89926230 27 74.58 A/G 0.12 Scaffold_1952 116,665 147,230 Near neurofibromin isoform x2/oligodendrocyte-myelin glyco\nAX-89938965 27 74.43 G/T 0.12 Scaffold_842 38,933 463,739 Intron kinase suppressor of ras 1-like isoform x2\nAX-89928353 27 73.96 G/A 0.10 Scaffold_1675 177,158 191,261 Intron vascular endothelial zinc finger 1-like isoform x2\nAX-89968747 27 73.96 A/G 0.11 Scaffold_3611 60,104 62,580 Intron unconventional myosin-xviiia-like isoform x1\nAX-89947091 27 73.96 na 0.10 na Na\nAX-89942611 27 73.42 C/A 0.16 Scaffold_3980 33,385 57,002 Intron unconventional myosin-xviiia-like isoform x2\nWINDOW 2 TOTAL PROPORTION 1.7%\nAX-89973675 17 115.87 G/T 0.10 Scaffold_26752 3396 4948 Intron spectrin beta non-erythrocytic 1-like\nAX-89969602 17 114.85 C/T 0.10 Scaffold_24 197,378 2,579,057 Intron calpain-2 catalytic subunit-like\nAX-89935000 17 114.02 A/G 0.17 Scaffold_173 119,365 1,392,108 Near histone h2b 1 2-like/ubiquitin-conjugating enzyme e2 variant 1\nAX-89918454 17 114.02 C/A 0.12 Scaffold_173 123,912 1,392,108 Near histone h2b 1 2-like/ubiquitin-conjugating enzyme e2 variant 1\nAX-89923840 17 113.51 C/T 0.18 Scaffold_173 195,297 1,392,108 Exon4 ubiquitin-conjugating enzyme e2 variant 1\nAX-89925576 17 113.51 A/G 0.18 Scaffold_173 160,398 1,392,108 Near histone h2b 1 2-like/ubiquitin-conjugating enzyme e2 variant 1\nWINDOW 3 TOTAL PROPORTION 1.0%\nAX-89940136 9 125.19 A/G 0.10 Scaffold_516 407,663 728,099 Intron Calsyntenin-1-like isoform x2\nChr, chromosome; VE, percentage of the genetic variance explained by the SNP; Loc, location in the scaffold with three possibilities: intron, exon, or near an exon."}