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- Author:
- Guangtu Gao, et al. ; Beth M. Cleveland; Lisa M. Radler; Matthew J. Picklo; Show all 4 Authors
- Source:
- Lipids 2021 v.56 no.2 pp. 189-200
- ISSN:
- 0024-4201
- Subject:
- Oncorhynchus mykiss; acyl coenzyme A; cholesterol; diet; extracellular matrix; fatty acid composition; feed deprivation; finishing; fish feeding; fish feeds; fish oils; gene expression regulation; homeostasis; lipid metabolism; liver; long chain unsaturated fatty acids; omega-3 fatty acids; redox reactions; transcriptome; transcriptomics; trout; vegetable oil
- Abstract:
- ... A finishing diet strategy is effective at increasing fillet long‐chain n‐3 fatty acid content in fish consuming sustainable plant oil‐based diets. This study investigates the outcomes of a fish oil finishing diet upon the hepatic fatty acid and transcriptome profile in rainbow trout (Oncorhynchus mykiss). Fish were placed on one of three feeding treatments: (1) FO: a fish oil (FO) diet for 20 week ...
- Handle:
- 10113/7175943
- DOI:
- 10.1002/lipd.12287
- https://doi.org/10.1002/lipd.12287
- Author:
- Guangtu Gao, et al. ; Susana Magadan; Stanislas Mondot; Yniv Palti; Marie Paule Lefranc; Pierre Boudinot; Show all 6 Authors
- Source:
- Developmental and comparative immunology 2021 v.118 pp. 103998
- ISSN:
- 0145-305X
- Subject:
- B-lymphocytes; Oncorhynchus mykiss; Salmo salar; fish; genes; genomics; immunology; vaccination
- Abstract:
- ... High-throughput sequencing technologies brought a renewed interest for immune repertoires. Fish Ab and B cell repertoires are no exception, and their comprehensive analysis can both provide new insights into poorly understood immune mechanisms, and identify markers of protection after vaccination. However, the lack of genomic description and standardized nomenclature of IG genes hampers accurate a ...
- DOI:
- 10.1016/j.dci.2021.103998
- CHORUS:
- 10.1016/j.dci.2021.103998
- https://doi.org/10.1016/j.dci.2021.103998
- Author:
- Guangtu Gao, et al. ; Hao Ma; Yueh-Chiang Han; Yniv Palti; Sixin Liu; Debra E. Palmquist; Gregory D. Wiens; Brian S. Shepherd; Show all 8 Authors
- Source:
- Developmental and comparative immunology 2021 v.116 no. pp. 103961
- ISSN:
- 0145-305X
- Subject:
- Flavobacterium psychrophilum; Oncorhynchus mykiss; amino acid sequences; antimicrobial peptides; aquaculture; brain; cytotoxicity; exons; gene expression; innate immunity; intestines; introns; juveniles; kidneys; oocytes; pathogens; phylogeny; pineal body; salinity; sequence homology; spleen; temperature; trout
- Abstract:
- ... Nk-lysin (Nkl), an antimicrobial peptide (AMP) product of natural killer cells and cytotoxic T cells in mammals, has recently been characterized in a number of finfish species. In this study, we identified six genes with sequence homology to Nkl and characterized their patterns of mRNA expression and abundances in rainbow trout (Oncorhynchus mykiss). The cDNA sequences for the six Nkls encoded pre ...
- DOI:
- 10.1016/j.dci.2020.103961
- CHORUS:
- 10.1016/j.dci.2020.103961
- https://doi.org/10.1016/j.dci.2020.103961
4. Transcriptomic Response to Selective Breeding for Fast Growth in Rainbow Trout (Oncorhynchus mykiss)
- Author:
- Guangtu Gao, et al. ; Beth M. Cleveland; Timothy D. Leeds; Show all 3 Authors
- Source:
- Marine biotechnology 2020 v.22 no.4 pp. 539-550
- ISSN:
- 1436-2228
- Subject:
- Oncorhynchus mykiss; aquaculture; biochemical pathways; body weight; breeding programs; complement; cyclic AMP; eggs; fish; gene expression; gene expression regulation; genes; genetic improvement; genetic lines; genetic variation; growth performance; innate immunity; insulin-like growth factor I; liver; mitogen-activated protein kinase; muscles; phenotype; selective breeding; signal transduction; somatotropin; transcriptome; transcriptomics
- Abstract:
- ... Genetic improvement for faster growth is a conventional approach to increase growth rates in aquaculture species; however, the genetic and physiological factors regulating growth performance in fish are not fully characterized. The objective of this study was to identify physiological mechanisms associated with faster growth rates by comparing the liver and muscle transcriptome of a rainbow trout ...
- DOI:
- 10.1007/s10126-020-09974-3
- https://doi.org/10.1007/s10126-020-09974-3
- Author:
- Guangtu Gao, et al. ; Roger L. Vallejo; Jason P. Evenhuis; Hao Cheng; Breno O. Fragomeni; Sixin Liu; Roseanna L. Long; Kristy L. Shewbridge; Rafael M.O. Silva; Gregory D. Wiens; Timothy D. Leeds; Kyle E. Martin; Yniv Palti; Show all 13 Authors
- Source:
- Aquaculture 2022 v.560 pp. 738574
- ISSN:
- 0044-8486
- Subject:
- Flavobacterium psychrophilum; Oncorhynchus mykiss; bacterial cold-water disease; genetic drift; genetic resistance; genetic variance; marker-assisted selection; quantitative traits
- Abstract:
- ... Bacterial cold water disease (BCWD), caused by Flavobacterium psychrophilum, is a frequent and problematic disease in rainbow trout (Oncorhynchus mykiss) aquaculture. A focus of our research is to improve genetic resistance against this disease in commercial populations. Commercial rainbow trout breeding is complicated by multiple populations that spawn naturally at different times of the year and ...
- DOI:
- 10.1016/j.aquaculture.2022.738574
- CHORUS:
- 10.1016/j.aquaculture.2022.738574
- https://doi.org/10.1016/j.aquaculture.2022.738574
- Author:
- Guangtu Gao, et al. ; Cassidy H. Shaw; Gregory D. Wiens; Show all 3 Authors
- Source:
- Developmental and comparative immunology 2018 v.87 pp. 193-203
- ISSN:
- 0145-305X
- Subject:
- Oncorhynchus kisutch; Oncorhynchus mykiss; Salmo salar; adults; amino acid sequences; birds; chromosomes; disease resistance; gene expression; gene expression regulation; genome assembly; genomics; homeostasis; immune response; inflammation; interleukin-1; mammals; messenger RNA; nucleotide sequences; phylogeny; pseudogenes; quantitative polymerase chain reaction; sequence homology; tissues
- Abstract:
- ... Interleukin-1 receptor-like 1 (Il1rl1 or ST2), a member of the interleukin-1 receptor family, has pleiotropic roles including tissue homeostasis, inflammation, immune polarization, and disease resistance in mammals. A single orthologue was previously described in salmonid fish; however, a recently improved genome assembly of rainbow trout (Oncorhynchus mykiss) revealed three adjacent, tandem il1rl ...
- DOI:
- 10.1016/j.dci.2018.06.003
- CHORUS:
- 10.1016/j.dci.2018.06.003
- https://doi.org/10.1016/j.dci.2018.06.003
- Author:
- Guangtu Gao, et al. ; Roger L. Vallejo; Hao Cheng; Breno O. Fragomeni; Rafael M.O. Silva; Kyle E. Martin; Jason P. Evenhuis; Gregory D. Wiens; Timothy D. Leeds; Yniv Palti; Show all 10 Authors
- Source:
- Aquaculture 2021 v.545 no. pp. -
- ISSN:
- 0044-8486
- Subject:
- Bayesian theory; Oncorhynchus mykiss; bacterial cold-water disease; disease resistance; genomics; genotyping; linkage disequilibrium; marker-assisted selection; models; mortality; phenotype; prediction; regression analysis; single nucleotide polymorphism arrays
- Abstract:
- ... Bacterial cold water disease (BCWD) causes significant mortality and economic losses in salmonid aquaculture. Previously, we reported high genomic prediction accuracy of 0.72 for BCWD resistance in rainbow trout using the 57 K Axiom SNP array. Due to the high cost of phenotyping and genotyping in rainbow trout breeding programs, it is paramount to know if acceptable genomic prediction accuracy can ...
- Handle:
- 10113/7443038
- DOI:
- 10.1016/j.aquaculture.2021.737164
- CHORUS:
- 10.1016/j.aquaculture.2021.737164
- https://doi.org/10.1016/j.aquaculture.2021.737164
- Author:
- Guangtu Gao, et al. ; Roger L. Vallejo; Hao Cheng; Breno O. Fragomeni; Kristy L. Shewbridge; John R. MacMillan; Richard Towner; Yniv Palti; Show all 8 Authors
- Source:
- Genetics, selection, evolution 2019 v.51 no.1 pp. 47
- ISSN:
- 0999-193X
- Subject:
- Bayesian theory; Infectious hematopoietic necrosis virus; Oncorhynchus mykiss; accuracy; aquaculture; architecture; breeding programs; breeding value; cost effectiveness; evolution; financial economics; foods; genetic merit; genetic resistance; genetic variance; genome-wide association study; loci; marker-assisted selection; models; mortality; necrosis; objectives; population; prediction; quantitative trait loci; regression analysis; selective breeding; viruses
- Abstract:
- ... BACKGROUND: Infectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV). Under intensive aquaculture conditions, IHNV can cause significant mortality and economic losses. Currently, there is no proven and cost-effective method for IHNV control. Clear Springs Foods, Inc. has been applying selective breeding to improve genetic resistance to IHNV in th ...
- DOI:
- 10.1186/s12711-019-0489-z
- PubMed:
- 31455244
- PubMed Central:
- PMC6712688
- https://doi.org/10.1186/s12711-019-0489-z
- Author:
- Guangtu Gao, et al. ; Sixin Liu; Yniv Palti; Caird E. Rexroad; Show all 4 Authors
- Source:
- Aquaculture 2016 v.452 pp. 178-182
- ISSN:
- 0044-8486
- Subject:
- Oncorhynchus mykiss; USDA; aquaculture; chromosomes; cold; fish; genetic markers; genome; genotype; genotyping; microsatellite repeats; parentage; pedigree; selection methods; single nucleotide polymorphism; transponders
- Abstract:
- ... In salmonid aquaculture, family-based selective breeding programs rely on accurate pedigree information for estimating genetic merits. The pedigree information can be tracked through the use of Passive Integrated Transponder (PIT) tags. However, PIT tags can be expensive, and cannot be used with small fish. DNA markers offer an alternative approach for pedigree tracking and microsatellites have be ...
- DOI:
- 10.1016/j.aquaculture.2015.11.001
- https://doi.org/10.1016/j.aquaculture.2015.11.001
- Author:
- Guangtu Gao, et al. ; Rafael M. O. Silva; Jason P. Evenhuis; Roger L. Vallejo; Kyle E. Martin; Tim D. Leeds; Yniv Palti; Daniela A. L. Lourenco; Show all 8 Authors
- Source:
- Genetics, selection, evolution 2019 v.51 no.1 pp. 42
- ISSN:
- 0999-193X
- Subject:
- Oncorhynchus mykiss; aquaculture; aquaculture industry; breeding; breeding value; chromosomes; columnaris disease; disease resistance; fish; genetic traits; genetic variance; genomics; genotype; models; phenotype; prediction; quantitative trait loci; regression analysis; single nucleotide polymorphism; water; United States
- Abstract:
- ... BACKGROUND: Columnaris disease (CD) is an emerging problem for the rainbow trout aquaculture industry in the US. The objectives of this study were to: (1) identify common genomic regions that explain a large proportion of the additive genetic variance for resistance to CD in two rainbow trout (Oncorhynchus mykiss) populations; and (2) estimate the gains in prediction accuracy when genomic informat ...
- DOI:
- 10.1186/s12711-019-0484-4
- PubMed:
- 31387519
- PubMed Central:
- PMC6683352
- https://doi.org/10.1186/s12711-019-0484-4
- Author:
- Guangtu Gao, et al. ; Roger L. Vallejo; Timothy D. Leeds; James E. Parsons; Kyle E. Martin; Jason P. Evenhuis; Breno O. Fragomeni; Gregory D. Wiens; Yniv Palti; Show all 9 Authors
- Source:
- Genetics, selection, evolution 2017 v.49 no.1 pp. 17
- ISSN:
- 0999-193X
- Subject:
- Oncorhynchus mykiss; accuracy; aquaculture; bacterial cold-water disease; breeding value; disease resistance; fish; genetic improvement; genetic variation; genotype; genotyping; livestock; marker-assisted selection; models; parents; phenotype; prediction; progeny; progeny testing; sampling; siblings; single nucleotide polymorphism
- Abstract:
- ... BACKGROUND: Previously, we have shown that bacterial cold water disease (BCWD) resistance in rainbow trout can be improved using traditional family-based selection, but progress has been limited to exploiting only between-family genetic variation. Genomic selection (GS) is a new alternative that enables exploitation of within-family genetic variation. METHODS: We compared three GS models [single-s ...
- Handle:
- 10113/5695429
- DOI:
- 10.1186/s12711-017-0293-6
- PubMed:
- 28148220
- PubMed Central:
- PMC5289005
- https://doi.org/10.1186/s12711-017-0293-6
- Author:
- Guangtu Gao, et al. ; Sixin Liu; Roger L. Vallejo; Yniv Palti; Gregory M. Weber; Alvaro Hernandez; Caird E. Rexroad III; Show all 7 Authors
- Source:
- Marine biotechnology 2015 v.17 no.3 pp. 328-337
- ISSN:
- 1436-2228
- Subject:
- Danio rerio; Oncorhynchus mykiss; animal welfare; chromosomes; cortisol; gene expression regulation; genes; genetic markers; genome assembly; liver; nonsteroidal anti-inflammatory agents; protein-serine-threonine kinases; quantitative trait loci; single nucleotide polymorphism; stress response
- Abstract:
- ... Understanding stress responses is essential for improving animal welfare and increasing agriculture production efficiency. Previously, we reported microsatellite markers associated with quantitative trait loci (QTL) affecting plasma cortisol response to crowding in rainbow trout. In this study, our main objectives were to identify single-nucleotide polymorphism (SNP) markers associated with cortis ...
- DOI:
- 10.1007/s10126-015-9621-4
- https://doi.org/10.1007/s10126-015-9621-4
- Author:
- Guangtu Gao, et al. ; Dianelys Gonzalez-Pena; Matthew Baranski; Thomas Moen; Beth M. Cleveland; P. Brett Kenney; Roger L. Vallejo; Yniv Palti; Timothy D. Leeds; Show all 9 Authors
- Source:
- Frontiers in genetics 2016 v.7 no. pp. -
- ISSN:
- 1664-8021
- Subject:
- carcass weight; fish; carcass yield; Mus musculus; phenotype; genome-wide association study; genotyping; introns; body weight; models; chromosome mapping; growth performance; genetic variance; exons; single nucleotide polymorphism; fish culture; loci; breeding; Oncorhynchus mykiss; fish fillets; pedigree
- Abstract:
- ... Fillet yield (FY, %) is an economically important trait in rainbow trout aquaculture that affects production efficiency. Despite that, FY has not received much attention in breeding programs because it is difficult to measure on a large number of fish and it cannot be directly measured on breeding candidates. The recent development of a high-density SNP array for rainbow trout has provided the nee ...
- Handle:
- 10113/63324
- DOI:
- 10.3389/fgene.2016.00203
- PubMed:
- 27920797
- PubMed Central:
- PMC5118429
- https://doi.org/10.3389/fgene.2016.00203
- Author:
- Guangtu Gao, et al. ; Roger L. Vallejo; Sixin Liu; Breno O. Fragomeni; Alvaro G. Hernandez; Timothy D. Leeds; James E. Parsons; Kyle E. Martin; Jason P. Evenhuis; Timothy J. Welch; Yniv Palti; Show all 11 Authors
- Source:
- Frontiers in genetics 2017 v.8 no. pp. 156
- ISSN:
- 1664-8021
- Subject:
- DNA; Oncorhynchus mykiss; aquaculture; bacterial cold-water disease; breeding; disease resistance; financial economics; genetic variance; genome; genome-wide association study; genotyping; inheritance (genetics); loci; models; mortality; quantitative trait loci; sequence analysis; single nucleotide polymorphism; variance
- Abstract:
- ... Bacterial cold water disease (BCWD) causes significant mortality and economic losses in salmonid aquaculture. In previous studies, we identified moderate-large effect QTL for BCWD resistance in rainbow trout (Oncorhynchus mykiss). However, the recent availability of a 57K SNP array and a genome physical map have enabled us to conduct genome-wide association studies (GWAS) that overcome several exp ...
- Handle:
- 10113/5859841
- DOI:
- 10.3389/fgene.2017.00156
- PubMed:
- 29109734
- PubMed Central:
- PMC5660510
- https://doi.org/10.3389/fgene.2017.00156
- Author:
- Guangtu Gao, et al. ; Roger L. Vallejo; Rafael M. O. Silva; Jason P. Evenhuis; Sixin Liu; James E. Parsons; Kyle E. Martin; Gregory D. Wiens; Daniela A. L. Lourenco; Timothy D. Leeds; Yniv Palti; Show all 11 Authors
- Source:
- Journal of animal breeding and genetics 2018 v.135 no.4 pp. 263-274
- ISSN:
- 0931-2668
- Subject:
- Bayesian theory; Oncorhynchus mykiss; bacterial cold-water disease; breeding programs; breeding value; disease resistance; genome; genomics; linkage disequilibrium; marker-assisted selection; population structure; prediction; progeny; quantitative trait loci; single nucleotide polymorphism
- Abstract:
- ... Previously accurate genomic predictions for Bacterial cold water disease (BCWD) resistance in rainbow trout were obtained using a medium‐density single nucleotide polymorphism (SNP) array. Here, the impact of lower‐density SNP panels on the accuracy of genomic predictions was investigated in a commercial rainbow trout breeding population. Using progeny performance data, the accuracy of genomic bre ...
- DOI:
- 10.1111/jbg.12335
- CHORUS:
- 10.1111/jbg.12335
- Chorus Open Access:
- 10.1111/jbg.12335
- https://doi.org/10.1111/jbg.12335
- Author:
- Guangtu Gao, et al. ; Roger L. Vallejo; Yniv Palti; Sixin Liu; Jason P. Evenhuis; Caird E. Rexroad III; Gregory D. Wiens; Show all 7 Authors
- Source:
- Marine biotechnology 2014 v.16 no.3 pp. 349-360
- ISSN:
- 1436-2228
- Subject:
- Flavobacterium psychrophilum; Oncorhynchus mykiss; chromosome mapping; crossing; disease resistance; fish; genetic markers; genetic variation; genome; linkage (genetics); loci; marker-assisted selection; microsatellite repeats; phenotypic variation; quantitative trait loci; sires
- Abstract:
- ... Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. We previously detected genetic variation in survival following challenge with Flavobacterium psychrophilum (Fp), the causative agent of BCWD in rainbow trout (Oncorhynchus mykiss). A family-based selection program to improve resistance was initiated in 2005 at the USDA National Center for Cool and Cold Wa ...
- Handle:
- 10113/58723
- DOI:
- 10.1007/s10126-013-9553-9
- https://doi.org/10.1007/s10126-013-9553-9
- Author:
- Guangtu Gao, et al. ; Yniv Palti; Michael R. Miller; Roger L. Vallejo; Paul A Wheeler; Edwige Quillet; Jianbo Yao; Gary H. Thorgaard; Mohamed Salem; Caird E. Rexroad III; Show all 10 Authors
- Source:
- Molecular Ecology Resources 2014 v.14 no.3 pp. 588-596
- ISSN:
- 1755-098X
- Subject:
- DNA; Oncorhynchus mykiss; data collection; doubled haploids; gene frequency; genome; genotype; haploidy; sequence analysis; single nucleotide polymorphism
- Abstract:
- ... Salmonid genomes are considered to be in a pseudo-tetraploid state as a result of an evolutionarily recent genome duplication event. This situation complicates single nucleotide polymorphism (SNP) discovery in rainbow trout as many putative SNPs are actually paralogous sequence variants (PSVs) and not simple allelic variants. To minimize false discovery of PSVs we used a panel of 19 homozygous dou ...
- Handle:
- 10113/59070
- DOI:
- 10.1111/1755-0998.12204
- PubMed:
- 24251403
- https://doi.org/10.1111/1755-0998.12204
- Author:
- Guangtu Gao, et al. ; Yniv Palti; Carine Genet; Yuqin Hu; Frank M. You; Mekki Boussaha; Caird E. Rexroad III; Ming-Cheng Luo; Show all 8 Authors
- Source:
- Marine Biotechnology 2012 v.14 no. pp. 343-357
- ISSN:
- 1436-2228
- Subject:
- DNA fingerprinting; DNA libraries; Danio rerio; Gasterosteidae; Oncorhynchus mykiss; bacterial artificial chromosomes; chromosome mapping; clones; databases; fish; genome; libraries; linkage groups; microsatellite repeats; proteins; reading; sequence homology
- Abstract:
- ... DNA fingerprints and end sequences from bacterial artificial chromosomes (BACs) from two new libraries were generated to improve the first generation integrated physical and genetic map of the rainbow trout (Oncorhynchus mykiss) genome. The current version of the physical map is composed of 167,989 clones of which 158,670 are assembled into contigs and 9,319 are singletons. The number of contigs w ...
- Handle:
- 10113/55696
- DOI:
- 10.1007/s10126-011-9418-z
- https://doi.org/10.1007/s10126-011-9418-z
- Author:
- Guangtu Gao, et al. ; Yniv Patli; Carine Genet; Ming-Cheng Luo; Aurelie Charlet; Yuqin Hu; Cecilia Castano-Sanchez; Kamila Tabet-Canale; Francine Krieg; Jianbo Yao; Roger L. Vallejo; Caird E. Rexroad III; Show all 12 Authors
- Source:
- BMC genomics 2011 v.12 no. pp. 1-9
- ISSN:
- 1471-2164
- Subject:
- Oncorhynchus mykiss; bacterial artificial chromosomes; chromosome mapping; freshwater fish; genes; genetic improvement; genetic markers; genomics; linkage groups; marker-assisted selection; quantitative trait loci; screening; single nucleotide polymorphism
- Abstract:
- ... Rainbow trout (Oncorhynchus mykiss) are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. Coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production efficiency traits justifies the continued development of genomics research resources. Many quantitative trait loci (QTL ...
- Handle:
- 10113/56828
- DOI:
- 10.1186/1471-2164-12-180
- PubMed:
- 21473775
- PubMed Central:
- PMC3079668
- https://doi.org/10.1186/1471-2164-12-180