Genome-Wide Association Study for Identifying Loci that Affect Fillet Yield, Carcass, and Body Weight Traits in Rainbow Trout (Oncorhynchus mykiss)

Gonzalez-Pena, Dianelys; Gao, Guangtu; Baranski, Matthew; Moen, Thomas; Cleveland, Beth M.; Kenney, P. Brett; Vallejo, Roger L.; Palti, Yniv; Leeds, Timothy D.

doi:10.3389/fgene.2016.00203

Title: Genome-Wide Association Study for Identifying Loci that Affect Fillet Yield, Carcass, and Body Weight Traits in Rainbow Trout (Oncorhynchus mykiss)

Journal Article · Tue Nov 22 00:00:00 EST 2016 · Frontiers in Genetics

DOI:https://doi.org/10.3389/fgene.2016.00203· OSTI ID:1628040

Gonzalez-Pena, Dianelys ^[1]; Gao, Guangtu ^[1]; Baranski, Matthew ^[2]; Moen, Thomas ^[3]; Cleveland, Beth M. ^[1]; Kenney, P. Brett ^[4]; Vallejo, Roger L. ^[1]; Palti, Yniv ^[1]; Leeds, Timothy D. ^[1]

US Dept. of Agriculture (USDA), National Center for Cool and Cold Water Aquaculture, Kearneysville, WV (United States).
Nofima, Ås (Norway)
Aquagen, Ås (Norway)
West Virginia Univ., Morgantown, WV (United States)

Fillet yield (FY, %) is an economically-important trait in rainbow trout aquaculture that affects production efficiency. Despite that, FY has received little attention in breeding programs because it is difficult to measure on a large number of fish and cannot be directly measured on breeding candidates. The recent development of a high-density SNP array for rainbow trout has provided the needed tool for studying the underlying genetic architecture of this trait. A genome-wide association study (GWAS) was conducted for FY, body weight at 10 (BW10) and 13 (BW13) months post-hatching, head-off carcass weight (CAR), and fillet weight (FW) in a pedigreed rainbow trout population selectively bred for improved growth performance. The GWAS analysis was performed using the weighted single-step GBLUP method (wssGWAS). Phenotypic records of 1447 fish (1.5 kg at harvest) from 299 full-sib families in three successive generations, of which 875 fish from 196 full-sib families were genotyped, were used in the GWAS analysis. A total of 38,107 polymorphic SNPs were analyzed in a univariate model with hatch year and harvest group as fixed effects, harvest weight as a continuous covariate, and animal and common environment as random effects. A new linkage map was developed to create windows of 20 adjacent SNPs for use in the GWAS. The two windows with largest effect for FY and FW were located on chromosome Omy9 and explained only 1.0–1.5% of genetic variance, thus suggesting a polygenic architecture affected by multiple loci with small effects in this population. One window on Omy5 explained 1.4 and 1.0% of the genetic variance for BW10 and BW13, respectively. Three windows located on Omy27, Omy17, and Omy9 (same window detected for FY) explained 1.7, 1.7, and 1.0%, respectively, of genetic variance for CAR. Among the detected 100 SNPs, 55% were located directly in genes (intron and exons). Nucleotide sequences of intragenic SNPs were blasted to the Mus musculus genome to create a putative gene network. The network suggests that differences in the ability to maintain a proliferative and renewable population of myogenic precursor cells may affect variation in growth and fillet yield in rainbow trout.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Oak Ridge Associated Univ., Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-06OR23100; CRIS Project 8082-31000-012

OSTI ID:: 1628040

Journal Information:: Frontiers in Genetics, Vol. 7; ISSN 1664-8021

Publisher:: FrontiersCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 91 works

Citation information provided by
Web of Science

References (106)

Defining desired genetic gains for rainbow trout breeding objective using analytic hierarchy process1 Sae-Lim, P.; Komen, H.; Kause, A. Journal of Animal Science, Vol. 90, Issue 6 https://doi.org/10.2527/jas.2011-4267	journal	June 2012
Samp1 is a component of TAN lines and is required for nuclear movement Borrego-Pinto, J.; Jegou, T.; Osorio, D. S. Journal of Cell Science, Vol. 125, Issue 5 https://doi.org/10.1242/jcs.087049	journal	February 2012
Myoblast Fusion Requires Fibronectin Degradation by Exteriorized m-Calpain Dourdin, Nathalie; Brustis, Jean-Jacques; Balcerzak, Denis Experimental Cell Research, Vol. 235, Issue 2 https://doi.org/10.1006/excr.1997.3684	journal	September 1997
Flesh Quality in Large Rainbow Trout with high or low Fillet Yield: Fillet Yield and Flesh Quality in Large Rainbow Trout Bugeon, Jerome; Lefevre, Florence; Cardinal, Mireille Journal of Muscle Foods, Vol. 21, Issue 4 https://doi.org/10.1111/j.1745-4573.2010.00214.x	journal	September 2010
Regulation of Cell Migration by the Calcium-dependent Protease Calpain Huttenlocher, Anna; Palecek, Sean P.; Lu, Qin Journal of Biological Chemistry, Vol. 272, Issue 52 https://doi.org/10.1074/jbc.272.52.32719	journal	December 1997
The Mouse Genome Brown, S. D. M.; Hancock, J. M. Vertebrate Genomes https://doi.org/10.1159/000095091	book	January 2006
Asymmetric Chromatid Segregation in Cardiac Progenitor Cells Is Enhanced by Pim-1 Kinase Sundararaman, Balaji; Avitabile, Daniele; Konstandin, Mathias H. Circulation Research, Vol. 110, Issue 9 https://doi.org/10.1161/circresaha.112.267716	journal	April 2012
Growth and the regulation of myotomal muscle mass in teleost fish Johnston, I. A.; Bower, N. I.; Macqueen, D. J. Journal of Experimental Biology, Vol. 214, Issue 10 https://doi.org/10.1242/jeb.038620	journal	April 2011
A Poised Chromatin Platform for TGF-β Access to Master Regulators Xi, Qiaoran; Wang, Zhanxin; Zaromytidou, Alexia-Ileana Cell, Vol. 147, Issue 7 https://doi.org/10.1016/j.cell.2011.11.032	journal	December 2011
Genomics to systems biology in animal and veterinary sciences: Progress, lessons and opportunities Kadarmideen, Haja N. Livestock Science, Vol. 166 https://doi.org/10.1016/j.livsci.2014.04.028	journal	August 2014
Mitotic Clonal Expansion during Preadipocyte Differentiation: Calpain-mediated Turnover of p27 Patel, Yashomati M.; Lane, M. Daniel Journal of Biological Chemistry, Vol. 275, Issue 23 https://doi.org/10.1074/jbc.m910445199	journal	April 2000
Studies on carcass quality traits in two populations of Coho salmon (Oncorhynchus kisutch): phenotypic and genetic parameters Neira, Roberto; Lhorente, Jean Paul; Araneda, Cristian Aquaculture, Vol. 241, Issue 1-4 https://doi.org/10.1016/j.aquaculture.2004.08.009	journal	November 2004
Reduction in fragile X related 1 protein causes cardiomyopathy and muscular dystrophy in zebrafish van't Padje, S.; Chaudhry, B.; Severijnen, L. -A. Journal of Experimental Biology, Vol. 212, Issue 16 https://doi.org/10.1242/jeb.032532	journal	July 2009
Growth-related quantitative trait loci in domestic and wild rainbow trout (Oncorhynchus mykiss) Wringe, Brendan F.; Devlin, Robert H.; Ferguson, Moira M. BMC Genetics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2156-11-63	journal	January 2010
Genomic prediction in an admixed population of Atlantic salmon (Salmo salar) Ã˜degÃ¥rd, JÃ¸rgen; Moen, Thomas; Santi, Nina Frontiers in Genetics, Vol. 5 https://doi.org/10.3389/fgene.2014.00402	journal	November 2014
Genomic prediction when some animals are not genotyped Christensen, Ole F.; Lund, Mogens S. Genetics Selection Evolution, Vol. 42, Issue 1 https://doi.org/10.1186/1297-9686-42-2	journal	January 2010
Identification and molecular characterization of the rainbow trout calpains (Capn1 and Capn2): their expression in muscle wasting during starvation Salem, Mohamed; Nath, Joginder; Rexroad, Caird E. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, Vol. 140, Issue 1 https://doi.org/10.1016/j.cbpc.2004.09.007	journal	January 2005
Extension of the bayesian alphabet for genomic selection Habier, David; Fernando, Rohan L.; Kizilkaya, Kadir BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-186	journal	May 2011
Genetic parameters of production traits in Atlantic salmon (Salmo salar) Powell, Joseph; White, Ian; Guy, Derrick Aquaculture, Vol. 274, Issue 2-4 https://doi.org/10.1016/j.aquaculture.2007.11.036	journal	February 2008
Role of SRC-like adaptor protein (SLAP) in immune and malignant cell signaling Kazi, Julhash U.; Kabir, Nuzhat N.; Rönnstrand, Lars Cellular and Molecular Life Sciences, Vol. 72, Issue 13 https://doi.org/10.1007/s00018-015-1882-6	journal	March 2015
Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors Takahashi, Kazutoshi; Yamanaka, Shinya Cell, Vol. 126, Issue 4 https://doi.org/10.1016/j.cell.2006.07.024	journal	August 2006
TGF-β signaling to chromatin: How Smads regulate transcription during self-renewal and differentiation Gaarenstroom, Tessa; Hill, Caroline S. Seminars in Cell & Developmental Biology, Vol. 32 https://doi.org/10.1016/j.semcdb.2014.01.009	journal	August 2014
Calsyntenin-1 docks vesicular cargo to kinesin-1. Konecna, A.; Frischknecht, R.; Kinter, J. The American Soc. of Cell Biol. https://doi.org/10.5167/uzh-1134	text	January 2006
Myoblast migration is regulated by calpain through its involvement in cell attachment and cytoskeletal organization Dedieu, Stéphane; Poussard, Sylvie; Mazères, Germain Experimental Cell Research, Vol. 292, Issue 1 https://doi.org/10.1016/j.yexcr.2003.08.014	journal	January 2004
Src-Like Adaptor Protein Regulates B Cell Development and Function Dragone, Leonard L.; Myers, Margaret D.; White, Carmen The Journal of Immunology, Vol. 176, Issue 1 https://doi.org/10.4049/jimmunol.176.1.335	journal	December 2005
Single nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattle Serão, Nick VL; González-Peña, Dianelys; Beever, Jonathan E. BMC Genetics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2156-14-94	journal	January 2013
Genome wide association and genomic prediction for growth traits in juvenile farmed Atlantic salmon using a high density SNP array Tsai, Hsin-Yuan; Hamilton, Alastair; Tinch, Alan E. BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-2117-9	journal	November 2015
Trends in Postmortem Aging in Fish: Understanding of Proteolysis and Disorganization of the Myofibrillar Structure Delbarre-Ladrat, Christine; Chéret, Romuald; Taylor, Richard Critical Reviews in Food Science and Nutrition, Vol. 46, Issue 5 https://doi.org/10.1080/10408390591000929	journal	June 2006
A Novel Role for the RNA–Binding Protein FXR1P in Myoblasts Cell-Cycle Progression by Modulating p21/Cdkn1a/Cip1/Waf1 mRNA Stability Davidovic, Laetitia; Durand, Nelly; Khalfallah, Olfa PLoS Genetics, Vol. 9, Issue 3 https://doi.org/10.1371/journal.pgen.1003367	journal	March 2013
Regulation of muscle growth by multiple ligands signaling through activin type II receptors Lee, S. -J.; Reed, L. A.; Davies, M. V. Proceedings of the National Academy of Sciences, Vol. 102, Issue 50 https://doi.org/10.1073/pnas.0505996102	journal	December 2005
A genome-wide association study in catfish reveals the presence of functional hubs of related genes within QTLs for columnaris disease resistance Geng, Xin; Sha, Jin; Liu, Shikai BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-1409-4	journal	March 2015
Zebrafish calsyntenins mediate homophilic adhesion through their amino-terminal cadherin repeats Ortiz-Medina, H.; Emond, M. R.; Jontes, J. D. Neuroscience, Vol. 286 https://doi.org/10.1016/j.neuroscience.2014.11.030	journal	February 2015
Sex-linked Quantitative Trait Loci for Thermotolerance and Length in the Rainbow Trout Perry, G. M. L.; Ferguson, M. M.; Sakamoto, T. Journal of Heredity, Vol. 96, Issue 2 https://doi.org/10.1093/jhered/esi019	journal	January 2005
Expression and characterization of a brain-specific protein kinase BSK146 from zebrafish Chou, Chih-Ming; Chen, Yi-Chung; Lee, Ming-Ting Biochemical and Biophysical Research Communications, Vol. 340, Issue 3 https://doi.org/10.1016/j.bbrc.2005.12.090	journal	February 2006
Mapping of quantitative trait loci for flesh colour and growth traits in Atlantic salmon (Salmo salar) Baranski, Matthew; Moen, Thomas; Våge, Dag Inge Genetics Selection Evolution, Vol. 42, Issue 1 https://doi.org/10.1186/1297-9686-42-17	journal	June 2010
Sox2, a key factor in the regulation of pluripotency and neural differentiation Zhang, Shuchen World Journal of Stem Cells, Vol. 6, Issue 3 https://doi.org/10.4252/wjsc.v6.i3.305	journal	January 2014
Genome-Wide Association Study (GWAS) for Growth Rate and Age at Sexual Maturation in Atlantic Salmon (Salmo salar) Gutierrez, Alejandro P.; Yáñez, José M.; Fukui, Steve PLOS ONE, Vol. 10, Issue 3 https://doi.org/10.1371/journal.pone.0119730	journal	March 2015
Genomics in aquaculture to better understand species biology and accelerate genetic progress YÃ¡Ã±ez, JosÃ© M.; Newman, Scott; Houston, Ross D. Frontiers in Genetics, Vol. 6 https://doi.org/10.3389/fgene.2015.00128	journal	April 2015
Lep-MAP: fast and accurate linkage map construction for large SNP datasets Rastas, Pasi; Paulin, Lars; Hanski, Ilkka Bioinformatics, Vol. 29, Issue 24 https://doi.org/10.1093/bioinformatics/btt563	journal	September 2013
Hot topic: A unified approach to utilize phenotypic, full pedigree, and genomic information for genetic evaluation of Holstein final score Aguilar, I.; Misztal, I.; Johnson, D. L. Journal of Dairy Science, Vol. 93, Issue 2 https://doi.org/10.3168/jds.2009-2730	journal	February 2010
Identification of single nucleotide polymorphism markers associated with bacterial cold water disease resistance and spleen size in rainbow trout Liu, Sixin; Vallejo, Roger L.; Palti, Yniv Frontiers in Genetics, Vol. 6 https://doi.org/10.3389/fgene.2015.00298	journal	September 2015
Myostatin inhibits myosatellite cell proliferation and consequently activates differentiation: evidence for endocrine-regulated transcript processing Garikipati, Dilip K.; Rodgers, Buel D. Journal of Endocrinology, Vol. 215, Issue 1 https://doi.org/10.1530/joe-12-0260	journal	August 2012
Neuroendocrine regulation of somatic growth in fishes Dai, XiangYan; Zhang, Wei; Zhuo, ZiJian Science China Life Sciences, Vol. 58, Issue 2 https://doi.org/10.1007/s11427-015-4805-8	journal	February 2015
The development and characterization of a 57K single nucleotide polymorphism array for rainbow trout Palti, Y.; Gao, G.; Liu, S. Molecular Ecology Resources, Vol. 15, Issue 3 https://doi.org/10.1111/1755-0998.12337	journal	October 2014
Two members of the Fxr gene family, Fmr1 and Fxr1, are differentially expressed in Xenopus tropicalis Blonden, Lau; van 't Padje, Sandra; Severijnen, Lies-anne The International Journal of Developmental Biology, Vol. 49, Issue 4 https://doi.org/10.1387/ijdb.051974lb	journal	January 2005
Ca2+-SPECIFIC REMOVAL OF Z LINES FROM RABBIT SKELETAL MUSCLE Busch, Wayne A.; Stromer, M. H.; Goll, Darrel E. The Journal of Cell Biology, Vol. 52, Issue 2 https://doi.org/10.1083/jcb.52.2.367	journal	February 1972
Genome-wide marker-assisted selection combining all pedigree phenotypic information with genotypic data in one step: An example using broiler chickens Chen, C. Y.; Misztal, I.; Aguilar, I. Journal of Animal Science, Vol. 89, Issue 1 https://doi.org/10.2527/jas.2010-3071	journal	January 2011
Genetic mapping of quantitative trait loci (QTL) for body-weight in Atlantic salmon (Salmo salar) using a 6.5K SNP array Gutierrez, Alejandro P.; Lubieniecki, Krzysztof P.; Davidson, Evelyn A. Aquaculture, Vol. 358-359 https://doi.org/10.1016/j.aquaculture.2012.06.017	journal	August 2012
The mouse genome Guenet, J. L. Genome Research, Vol. 15, Issue 12 https://doi.org/10.1101/gr.3728305	journal	December 2005
Protein Phosphatase 2A Positively Regulates Ras Signaling by Dephosphorylating KSR1 and Raf-1 on Critical 14-3-3 Binding Sites Ory, Stéphane; Zhou, Ming; Conrads, Thomas P. Current Biology, Vol. 13, Issue 16 https://doi.org/10.1016/s0960-9822(03)00535-9	journal	August 2003
The role of Ca2+-dependent proteases (calpains) in post mortem proteolysis and meat tenderness Koohmaraie, M. Biochimie, Vol. 74, Issue 3 https://doi.org/10.1016/0300-9084(92)90122-u	journal	March 1992
Computing procedures for genetic evaluation including phenotypic, full pedigree, and genomic information Misztal, I.; Legarra, A.; Aguilar, I. Journal of Dairy Science, Vol. 92, Issue 9 https://doi.org/10.3168/jds.2009-2064	journal	September 2009
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Huang, Da Wei; Sherman, Brad T.; Lempicki, Richard A. Nature Protocols, Vol. 4, Issue 1 https://doi.org/10.1038/nprot.2008.211	journal	December 2008
The Mouse Genome Adams, M. The Mouse in Biomedical Research https://doi.org/10.1016/b978-012369454-6/50018-2	book	January 2007
Negative genetic correlations between production traits and head or bony tissues in large all-female rainbow trout (Oncorhynchus mykiss) Haffray, Pierrick; Bugeon, Jérôme; Pincent, Cédric Aquaculture, Vol. 368-369 https://doi.org/10.1016/j.aquaculture.2012.09.023	journal	November 2012
Changes in variance explained by top SNP windows over generations for three traits in broiler chicken Fragomeni, Breno de Oliveira; Misztal, Ignacy; Lourenco, Daniela Lino Frontiers in Genetics, Vol. 5 https://doi.org/10.3389/fgene.2014.00332	journal	October 2014
Detection and Validation of QTL Affecting Bacterial Cold Water Disease Resistance in Rainbow Trout Using Restriction-Site Associated DNA Sequencing Palti, Yniv; Vallejo, Roger L.; Gao, Guangtu PLOS ONE, Vol. 10, Issue 9 https://doi.org/10.1371/journal.pone.0138435	journal	September 2015
Regulation of calpain and calpastatin in differentiating myoblasts: mRNA levels, protein synthesis and stability Barnoy, Sivia; Supino-Rosin, Lia; Kosower, Nechama S. Biochemical Journal, Vol. 351, Issue 2 https://doi.org/10.1042/0264-6021:3510413	journal	October 2000
Genome-Wide Association Mapping for Identification of Quantitative Trait Loci for Rectal Temperature during Heat Stress in Holstein Cattle Dikmen, Serdal; Cole, John B.; Null, Daniel J. PLoS ONE, Vol. 8, Issue 7 https://doi.org/10.1371/journal.pone.0069202	journal	July 2013
Regulation of calpain and calpastatin in differentiating myoblasts: mRNA levels, protein synthesis and stability Barnoy, Sivia; Supino-Rosin, Lia; Kosower, Nechama S. Biochemical Journal, Vol. 351, Issue 2 https://doi.org/10.1042/bj3510413	journal	October 2000
Membrane Proximal ERK Signaling Is Required for M-calpain Activation Downstream of Epidermal Growth Factor Receptor Signaling Glading, Angela; Überall, Florian; Keyse, Stephen M. Journal of Biological Chemistry, Vol. 276, Issue 26 https://doi.org/10.1074/jbc.m008847200	journal	April 2001
Identification of Single-Nucleotide Polymorphism Markers Associated with Cortisol Response to Crowding in Rainbow Trout Liu, Sixin; Vallejo, Roger L.; Gao, Guangtu Marine Biotechnology, Vol. 17, Issue 3 https://doi.org/10.1007/s10126-015-9621-4	journal	February 2015
The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates Berthelot, Camille; Brunet, Frédéric; Chalopin, Domitille Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms4657	journal	April 2014
Calpain Regulates Actin Remodeling during Cell Spreading Potter, David A.; Tirnauer, Jennifer S.; Janssen, Richard Journal of Cell Biology, Vol. 141, Issue 3 https://doi.org/10.1083/jcb.141.3.647	journal	May 1998
Quantitative Trait Loci for Spawning Date and Body Weight in Rainbow Trout: Testing for Conserved Effects Across Ancestrally Duplicated Chromosomes O'Malley, K. G. Journal of Heredity, Vol. 94, Issue 4 https://doi.org/10.1093/jhered/esg067	journal	July 2003
Muscle growth in teleost fish is regulated by factors utilizing the activin II B receptor Phelps, M. P.; Jaffe, I. M.; Bradley, T. M. Journal of Experimental Biology, Vol. 216, Issue 19 https://doi.org/10.1242/jeb.086660	journal	June 2013
Genetic and environmental components of variation in body traits of rainbow trout (Oncorhynchus mykiss) in relation to age Elvingson, Pontus; Johansson, Kjell Aquaculture, Vol. 118, Issue 3-4 https://doi.org/10.1016/0044-8486(93)90456-9	journal	December 1993
Microglia Transcriptome Changes in a Model of Depressive Behavior after Immune Challenge Gonzalez-Pena, Dianelys; Nixon, Scott E.; O’Connor, Jason C. PLOS ONE, Vol. 11, Issue 3 https://doi.org/10.1371/journal.pone.0150858	journal	March 2016
Efficient Methods to Compute Genomic Predictions VanRaden, P. M. Journal of Dairy Science, Vol. 91, Issue 11 https://doi.org/10.3168/jds.2007-0980	journal	November 2008
Stories and Challenges of Genome Wide Association Studies in Livestock — A Review Sharma, Aditi; Lee, Jun Seop; Dang, Chang Gwon Asian-Australasian Journal of Animal Sciences, Vol. 28, Issue 10 https://doi.org/10.5713/ajas.14.0715	journal	March 2015
Response to five generations of selection for growth performance traits in rainbow trout (Oncorhynchus mykiss) Leeds, Timothy D.; Vallejo, Roger L.; Weber, Gregory M. Aquaculture, Vol. 465 https://doi.org/10.1016/j.aquaculture.2016.08.036	journal	December 2016
Transcriptional background of beef marbling — Novel genes implicated in intramuscular fat deposition Sadkowski, T.; Ciecierska, A.; Majewska, A. Meat Science, Vol. 97, Issue 1 https://doi.org/10.1016/j.meatsci.2013.12.017	journal	May 2014
Direct and indirect selection of visceral lipid weight, fillet weight, and fillet percentage in a rainbow trout breeding program1 Kause, A.; Paananen, T.; Ritola, O. Journal of Animal Science, Vol. 85, Issue 12 https://doi.org/10.2527/jas.2007-0332	journal	December 2007
Calpain Function in the Modulation of Signal Transduction Molecules Sato, Kaori; Kawashima, Seiichi Biological Chemistry, Vol. 382, Issue 5 https://doi.org/10.1515/bchm.2001.382.5.743	journal	January 2001
Coupling body weight and its composition: a quantitative genetic analysis in rainbow trout Kause, Antti; Ritola, Ossi; Paananen, Tuija Aquaculture, Vol. 211, Issue 1-4 https://doi.org/10.1016/s0044-8486(01)00884-5	journal	August 2002
Domestication and growth hormone transgenesis cause similar changes in gene expression in coho salmon (Oncorhynchus kisutch) Devlin, R. H.; Sakhrani, D.; Tymchuk, W. E. Proceedings of the National Academy of Sciences, Vol. 106, Issue 9 https://doi.org/10.1073/pnas.0809798106	journal	February 2009
A new effector of lipid metabolism: Complement factor properdin Gauvreau, Danny; Roy, Christian; Tom, Fun-Qun Molecular Immunology, Vol. 51, Issue 1 https://doi.org/10.1016/j.molimm.2012.02.110	journal	May 2012
Comparison of accuracy of genome-wide and BLUP breeding value estimates in sib based aquaculture breeding schemes Nielsen, Hanne M.; Sonesson, Anna K.; Yazdi, Hossein Aquaculture, Vol. 289, Issue 3-4 https://doi.org/10.1016/j.aquaculture.2009.01.027	journal	April 2009
Genome-wide association mapping including phenotypes from relatives without genotypes in a single-step (ssGWAS) for 6-week body weight in broiler chickens Wang, Huiyu; Misztal, Ignacy; Aguilar, Ignacio Frontiers in Genetics, Vol. 5 https://doi.org/10.3389/fgene.2014.00134	journal	May 2014
Calsyntenin-1 Docks Vesicular Cargo to Kinesin-1 Konecna, Anetta; Frischknecht, Renato; Kinter, Jochen Molecular Biology of the Cell, Vol. 17, Issue 8 https://doi.org/10.1091/mbc.e06-02-0112	journal	August 2006
Application of Genomics Tools to Animal Breeding C. M. Dekkers, Jack Current Genomics, Vol. 13, Issue 3 https://doi.org/10.2174/138920212800543057	journal	April 2012
Adipose-derived mesenchymal stem cells differentiate into heterogeneous cancer-associated fibroblasts in a stroma-rich xenograft model Miyazaki, Yoshihiro; Oda, Tatsuya; Inagaki, Yuki Scientific Reports, Vol. 11, Issue 1 https://doi.org/10.1038/s41598-021-84058-3	journal	February 2021
Paradigms of growth in fish Mommsen, Thomas P. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, Vol. 129, Issue 2-3 https://doi.org/10.1016/S1096-4959(01)00312-8	journal	June 2001
Co-localization of growth QTL with differentially expressed candidate genes in rainbow trout Kocmarek, Andrea L.; Ferguson, Moira M.; Danzmann, Roy G. Genome, Vol. 58, Issue 9 https://doi.org/10.1139/gen-2015-0047	journal	September 2015
Genome-wide association analysis reveals loci associated with resistance against Piscirickettsia salmonis in two Atlantic salmon (Salmo salar L.) chromosomes Correa, Katharina; Lhorente, Jean P.; López, María E. BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-2038-7	journal	October 2015
Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants Julca, Irene; Ferrari, Camilla; Flores-Tornero, María Nature Plants, Vol. 7, Issue 8 https://doi.org/10.1038/s41477-021-00958-2	journal	July 2021
Sarcopenia and piscines: the case for indeterminate-growing fish as unique genetic model organisms in aging and longevity research Froehlich, Jacob M.; Fowler, Zachary G.; Galt, Nicholas J. Frontiers in Genetics, Vol. 4 https://doi.org/10.3389/fgene.2013.00159	journal	January 2013
Self-assembly of embryonic and two extra-embryonic stem cell types into gastrulating embryo-like structures. Sozen, Berna; Amadei, Gianluca; Cox, Andy Springer Science and Business Media LLC https://doi.org/10.17863/cam.41771	journalarticle	January 2018
BisoGenet: a new tool for gene network building, visualization and analysis Martin, Alexander; Ochagavia, Maria E.; Rabasa, Laya C. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-91	journal	January 2010
The myogenic kinome: protein kinases critical to mammalian skeletal myogenesis Knight, James DR; Kothary, Rashmi Skeletal Muscle, Vol. 1, Issue 1 https://doi.org/10.1186/2044-5040-1-29	journal	January 2011
Characterisation and expression analysis of cathepsins and ubiquitin-proteasome genes in gilthead sea bream (Sparus aurata) skeletal muscle Salmerón, Cristina; Navarro, Isabel; Johnston, Ian A. BMC Research Notes, Vol. 8, Issue 1 https://doi.org/10.1186/s13104-015-1121-0	journal	April 2015
Genomic breeding value prediction and QTL mapping of QTLMAS2010 data using Bayesian Methods Sun, Xiaochen; Habier, David; Fernando, Rohan L. BMC Proceedings, Vol. 5, Issue Suppl 3 https://doi.org/10.1186/1753-6561-5-s3-s13	journal	January 2011
Myostatin inhibits proliferation but not differentiation of trout myoblasts Seiliez, Iban; Sabin, Nathalie; Gabillard, Jean-Charles Molecular and Cellular Endocrinology, Vol. 351, Issue 2 https://doi.org/10.1016/j.mce.2011.12.011	journal	April 2012
qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots D. Turner, Stephen Journal of Open Source Software, Vol. 3, Issue 25 https://doi.org/10.21105/joss.00731	journal	May 2018
Enhancing the Potential of Cardiac Progenitor Cells: Pushing Forward With Pim-1 Del Re, Dominic P.; Sadoshima, Junichi Circulation Research, Vol. 110, Issue 9 https://doi.org/10.1161/CIRCRESAHA.112.269183	journal	April 2012
Genome-wide association mapping including phenotypes from relatives without genotypes Wang, H.; Misztal, I.; Aguilar, I. Genetics Research, Vol. 94, Issue 2 https://doi.org/10.1017/S0016672312000274	journal	April 2012
Calpain Function in the Modulation of Signal Transduction Molecules Sato, K.; Kawashima, S. Biological Chemistry, Vol. 382, Issue 5 https://doi.org/10.1515/BC.2001.090	journal	January 2001
Calsyntenin-1 Regulates Axon Branching and Endosomal Trafficking during Sensory Neuron Development In Vivo Ponomareva, O. Y.; Holmen, I. C.; Sperry, A. J. Journal of Neuroscience, Vol. 34, Issue 28 https://doi.org/10.1523/jneurosci.0561-14.2014	journal	July 2014
The Src-like Adaptor Protein Downregulates the T Cell Receptor on CD4+CD8+ Thymocytes and Regulates Positive Selection Sosinowski, Tomasz; Killeen, Nigel; Weiss, Arthur Immunity, Vol. 15, Issue 3 https://doi.org/10.1016/s1074-7613(01)00195-9	journal	September 2001
Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps Meuwissen, T. H. E.; Hayes, B. J.; Goddard, M. E. Genetics, Vol. 157, Issue 4 https://doi.org/10.1093/genetics/157.4.1819	journal	April 2001
Prohibitin 2 deficiency impairs cardiac fatty acid oxidation and causes heart failure Wu, Dechao; Jian, Chongshu; Peng, Qi Cell Death & Disease, Vol. 11, Issue 3 https://doi.org/10.1038/s41419-020-2374-7	journal	March 2020
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks Shannon, P. Genome Research, Vol. 13, Issue 11 https://doi.org/10.1101/gr.1239303	journal	November 2003
Weighting Strategies for Single-Step Genomic BLUP: An Iterative Approach for Accurate Calculation of GEBV and GWAS Zhang, Xinyue; Lourenco, Daniela; Aguilar, Ignacio Frontiers in Genetics, Vol. 7 https://doi.org/10.3389/fgene.2016.00151	journal	August 2016
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists Huang, Da Wei; Sherman, Brad T.; Lempicki, Richard A. Nucleic Acids Research, Vol. 37, Issue 1 https://doi.org/10.1093/nar/gkn923	journal	November 2008
Expression of the Dermatomyositis Autoantigen Transcription Intermediary Factor 1γ in Regenerating Muscle: TIF1γ Expression in Regenerating Muscle Mohassel, Payam; Rosen, Paul; Casciola-Rosen, Livia Arthritis & Rheumatology, Vol. 67, Issue 1 https://doi.org/10.1002/art.38863	journal	December 2014
Transactivation of capn2 by Myogenic Regulatory Factors During Myogenesis Dedieu, Stéphane; Mazères, Germain; Dourdin, Nathalie Journal of Molecular Biology, Vol. 326, Issue 2 https://doi.org/10.1016/s0022-2836(02)01310-4	journal	February 2003

Cited By (34)

Association and Functional Analyses Revealed That PPP1R3B Plays an Important Role in the Regulation of Glycogen Content in the Pacific Oyster Crassostrea gigas Liu, Sheng; Li, Li; Meng, Jie Frontiers in Genetics, Vol. 10 https://doi.org/10.3389/fgene.2019.00106	journal	February 2019
Advances in genetic improvement for salmon and trout aquaculture: the Chilean situation and prospects Lhorente, Jean P.; Araneda, Marcelo; Neira, Roberto Reviews in Aquaculture, Vol. 11, Issue 2 https://doi.org/10.1111/raq.12335	journal	March 2019
Single-Step Genome-Wide Association Study for Resistance to Piscirickettsia salmonis in Rainbow Trout ( Oncorhynchus mykiss ) Barria, Agustin; Marín-Nahuelpi, Rodrigo; Cáceres, Pablo G3: Genes\|Genomes\|Genetics, Vol. 9, Issue 11 https://doi.org/10.1534/g3.119.400204	journal	September 2019
Weighted single-step GWAS and gene network analysis reveal new candidate genes for semen traits in pigs Marques, Daniele B. D.; Bastiaansen, John W. M.; Broekhuijse, Marleen L. W. J. Genetics Selection Evolution, Vol. 50, Issue 1 https://doi.org/10.1186/s12711-018-0412-z	journal	August 2018
A genome-wide association study on growth traits in orange-spotted grouper (Epinephelus coioides) with RAD-seq genotyping Yu, Hui; You, Xinxin; Li, Jia Science China Life Sciences, Vol. 61, Issue 8 https://doi.org/10.1007/s11427-017-9161-4	journal	March 2018
Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations Wenne, Roman Aquatic Living Resources, Vol. 31 https://doi.org/10.1051/alr/2017043	journal	November 2017
Genome-wide identification of loci associated with growth in rainbow trout Ali, Ali; Al-Tobasei, Rafet; Lourenco, Daniela BMC Genomics https://doi.org/10.21203/rs.2.17035/v1	journal	March 2020
Genome-wide identification of loci associated with growth in rainbow trout Ali, Ali; Al-Tobasei, Rafat; Lourenco, Daniela BMC Genomics https://doi.org/10.21203/rs.2.17035/v4	journal	March 2020
First High-Density Linkage Map and Single Nucleotide Polymorphisms Significantly Associated With Traits of Economic Importance in Yellowtail Kingfish Seriola lalandi Nguyen, Nguyen H.; Rastas, Pasi M. A.; Premachandra, H. K. A. Frontiers in Genetics, Vol. 9 https://doi.org/10.3389/fgene.2018.00127	journal	April 2018
Genome-wide association analysis with a 50K transcribed gene SNP-chip identifies QTL affecting muscle yield in rainbow trout Salem, Mohamed; Al-Tobasei, Rafet; Ali, Ali Frontiers In Genetics https://doi.org/10.1101/355792	journal	June 2018
Development and Validation of 58K SNP-Array and High-Density Linkage Map in Nile Tilapia (O. niloticus) Joshi, Rajesh; Árnyasi, Mariann; Lien, Sigbjørn Frontiers in Genetics, Vol. 9 https://doi.org/10.3389/fgene.2018.00472	journal	October 2018
Whole Genome Sequencing of Greater Amberjack ( Seriola dumerili ) for SNP Identification on Aligned Scaffolds and Genome Structural Variation Analysis Using Parallel Resequencing Araki, Kazuo; Aokic, Jun-ya; Kawase, Junya International Journal of Genomics, Vol. 2018 https://doi.org/10.1155/2018/7984292	journal	January 2018
Genome-wide identification of loci associated with growth in rainbow trout Ali, Ali; Al-Tobasei, Rafet; Lourenco, Daniela BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-6617-x	journal	March 2020
Development of genomic predictions for harvest and carcass weight in channel catfish Garcia, Andre L. S.; Bosworth, Brian; Waldbieser, Geoffrey Genetics Selection Evolution, Vol. 50, Issue 1 https://doi.org/10.1186/s12711-018-0435-5	journal	December 2018
Functional Partitioning of Genomic Variance and Genome-Wide Association Study for Carcass Traits in Korean Hanwoo Cattle Using Imputed Sequence Level SNP Data Bhuiyan, Mohammad S. A.; Lim, Dajeong; Park, Mina Frontiers in Genetics, Vol. 9 https://doi.org/10.3389/fgene.2018.00217	journal	June 2018
Genetic (co)variation in skin pigmentation patterns and growth in rainbow trout Rodríguez, F. H.; Cáceres, G.; Lhorente, J. P. Animal, Vol. 13, Issue 4 https://doi.org/10.1017/S175173111800188X	journal	January 2019
Accurate genomic predictions for BCWD resistance in rainbow trout are achieved using low-density SNP panels: Evidence that long-range LD is a major contributing factor Vallejo, Roger L.; Silva, Rafael M. O.; Evenhuis, Jason P. Journal of Animal Breeding and Genetics, Vol. 135, Issue 4 https://doi.org/10.1111/jbg.12335	journal	June 2018
Genome-wide association analysis and accuracy of genome-enabled breeding value predictions for resistance to infectious hematopoietic necrosis virus in a commercial rainbow trout breeding population Vallejo, Roger L.; Cheng, Hao; Fragomeni, Breno O. Genetics Selection Evolution, Vol. 51, Issue 1 https://doi.org/10.1186/s12711-019-0489-z	journal	August 2019
Weighted single-step GWAS identified candidate genes associated with semen traits in a Duroc boar population Gao, Ning; Chen, Yilong; Liu, Xiaohong BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-6164-5	journal	October 2019
Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding D’Ambrosio, Jonathan; Phocas, Florence; Haffray, Pierrick Genetics Selection Evolution, Vol. 51, Issue 1 https://doi.org/10.1186/s12711-019-0468-4	journal	June 2019
Genome-wide association analysis for body weight identifies candidate genes related to development and metabolism in rainbow trout (Oncorhynchus mykiss) Reis Neto, Rafael Vilhena; Yoshida, Grazyella Massako; Lhorente, Jean Paul Molecular Genetics and Genomics, Vol. 294, Issue 3 https://doi.org/10.1007/s00438-018-1518-2	journal	January 2019
Genome-Wide Association Study and Cost-Efficient Genomic Predictions for Growth and Fillet Yield in Nile Tilapia ( Oreochromis niloticus ) Yoshida, Grazyella M.; Lhorente, Jean P.; Correa, Katharina G3: Genes\|Genomes\|Genetics, Vol. 9, Issue 8 https://doi.org/10.1534/g3.119.400116	journal	June 2019
Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analyses of pooled RNA-Seq samples in rainbow trout Al-Tobasei, Rafet; Ali, Ali; Leeds, Timothy D. BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-017-3992-z	journal	August 2017
Transcriptomics in aquaculture: current status and applications Chandhini, Sathyajith; Rejish Kumar, Vattiringal Jayadradhan Reviews in Aquaculture, Vol. 11, Issue 4 https://doi.org/10.1111/raq.12298	journal	August 2018
Integrated analysis of lncRNA and mRNA expression in rainbow trout families showing variation in muscle growth and fillet quality traits Ali, Ali; Al-Tobasei, Rafet; Kenney, Brett Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-30655-8	journal	August 2018
Development and validation of 58K SNP-array and high-density linkage map in Nile tilapia ( O. niloticus ) Joshi, Rajesh; Árnyasi, Mariann; Lien, Sigbjørn Frontiers in Genetics https://doi.org/10.1101/322826	journal	May 2018
Genome-Wide Association Study of Growth and Body-Shape-Related Traits in Large Yellow Croaker (Larimichthys crocea) Using ddRAD Sequencing Zhou, Zhixiong; Han, Kunhuang; Wu, Yidi Marine Biotechnology, Vol. 21, Issue 5 https://doi.org/10.1007/s10126-019-09910-0	journal	July 2019
Population genetic analysis of aquaculture salmonid populations in China using a 57K rainbow trout SNP array Zhang, Han-Yuan; Zhao, Zi-Xia; Xu, Jian PLOS ONE, Vol. 13, Issue 8 https://doi.org/10.1371/journal.pone.0202582	journal	August 2018
Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research Abdelrahman, Hisham; ElHady, Mohamed; Alcivar-Warren, Acacia BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-017-3557-1	journal	February 2017
Genome-Wide Association Analysis With a 50K Transcribed Gene SNP-Chip Identifies QTL Affecting Muscle Yield in Rainbow Trout Salem, Mohamed; Al-Tobasei, Rafet; Ali, Ali Frontiers in Genetics, Vol. 9 https://doi.org/10.3389/fgene.2018.00387	journal	September 2018
A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing Gao, Guangtu; Nome, Torfinn; Pearse, Devon E. Frontiers in Genetics, Vol. 9 https://doi.org/10.3389/fgene.2018.00147	journal	April 2018
Genome-Wide Association Study Identifies Genomic Loci Affecting Filet Firmness and Protein Content in Rainbow Trout Ali, Ali; Al-Tobasei, Rafet; Lourenco, Daniela Frontiers in Genetics, Vol. 10 https://doi.org/10.3389/fgene.2019.00386	journal	May 2019
Genome Scan for Genomic Regions and Genes Associated with Growth Trait in Pacific White Shrimp Litopeneaus vannamei Yu, Yang; Wang, Quanchao; Zhang, Qian Marine Biotechnology, Vol. 21, Issue 3 https://doi.org/10.1007/s10126-019-09887-w	journal	March 2019
Genomic Selection for Growth Traits in Pacific Oyster (Crassostrea gigas): Potential of Low-Density Marker Panels for Breeding Value Prediction Gutierrez, Alejandro P.; Matika, Oswald; Bean, Tim P. Frontiers in Genetics, Vol. 9 https://doi.org/10.3389/fgene.2018.00391	journal	September 2018

Figures / Tables (11)

Similar Records

Whole-genome mapping of quantitative trait loci and accuracy of genomic predictions for resistance to columnaris disease in two rainbow trout breeding populations

Journal Article · Tue Aug 06 00:00:00 EDT 2019 · Genetics Selection Evolution (Online) · OSTI ID:1628040

Silva, Rafael M. O.; Evenhuis, Jason P.; Vallejo, Roger L.; +5 more

Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa

Journal Article · Wed Sep 09 00:00:00 EDT 2020 · Frontiers in Plant Science · OSTI ID:1628040

Chhetri, Hari B.; Furches, Anna; Macaya-Sanz, David; +8 more

Exploiting Genetic Variation of Fiber Components and Morphology in Juvenile Loblolly Pine

Technical Report · Thu Jun 30 00:00:00 EDT 2005 · OSTI ID:1628040

Chang, Hou-Min; Kadia, John F.; Li, Bailian; +1 more

Related Subjects

54 ENVIRONMENTAL SCIENCES
Genetics & Heredity
fillet yield
gene network
genome-wide association study
genomic selection
linkage map
rainbow trout
single-step GBLUP