Source: UNIV OF MARYLAND submitted to NRP
WHOLE-GENOME ANALYSES/SELECTION TO INCREASE MUSCLE YIELD AND REDUCE FILLET DOWNGRADING IN RAINBOW TROUT
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1024268
Grant No.
2021-67015-33388
Cumulative Award Amt.
$500,000.00
Proposal No.
2020-02679
Multistate No.
(N/A)
Project Start Date
Jan 1, 2021
Project End Date
Dec 31, 2025
Grant Year
2021
Program Code
[A1231]- Animal Health and Production and Animal Products: Improved Nutritional Performance, Growth, and Lactation of Animals
Recipient Organization
UNIV OF MARYLAND
(N/A)
COLLEGE PARK,MD 20742
Performing Department
Animal & Avian Sciences
Non Technical Summary
Worldwide economic development and population growth have increased seafood demand. Continued expansion of the aquaculture industry requires improvements in production efficiency and product quality. Rainbow trout is the most cultivated cold-water fish in the U.S., and muscle fillet is its most valuable product. Therefore, increasing fillet-yield and reducing fillet quality downgrading in rainbow tout can improve aquaculture production efficiency and economic benefits.Classical breeding approaches can improve fillet-yield and quality but are time-consuming because of long generation intervals. A more efficient approach is to use genomic selection, where thousands of genetic markers (Single Nucleotide Polymorphisms) are used to increase the accuracy of the breeding process and reduce generation interval. There is immense interest from the industry to implement genomic selection in their breeding populations, similar to what has been recently achieved in livestock.Our goal is to utilize genomic analyses to identify genetic markers predictable of muscle-yield/quality and, more importantly, to implement genomic selection to achieve a higher genetic gain in these important traits in selectively-bred fish genetic lines at the USDA/ARS and major commercial producers.The impact of applying genomic selection is that it can reduce animal selection time (from 2-3 years to 3 weeks) and increase production efficiency by 30-50 percent.
Animal Health Component
15%
Research Effort Categories
Basic
85%
Applied
15%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
30337111080100%
Knowledge Area
303 - Genetic Improvement of Animals;

Subject Of Investigation
3711 - Trout;

Field Of Science
1080 - Genetics;
Goals / Objectives
We will use an improved SNP-chip enriched with functional genetic variants in genome-wide analyses to identify/confirm QTL affecting fillet yield/quality and assess the feasibility of genomic selection to improve these important traits by comparing its accuracy with traditional family-based selective breeding in a new USDA/ARS selection line that we recently developed for fillet yield and also in genetic lines from the major commercial producers Troutlodge and Pacific Aquaculture.
Project Methods
An improved SNP-chip enriched with functional genetic variants will be developed and used in genome-wide analyses to identify/confirm QTL affecting fillet yield/quality and assess feasibility of genomic selection to improve these important traits by comparing its accuracy with traditional family-based selective breeding. The 50K SNP chip that we built in our previous NIFA-funded project will be supplemented with SNPs associated with new fillet quality traits and genetic variants in new commercial producers. RAD-Seq will be used to supplement the chip with noncoding SNPs.

Progress 01/01/24 to 12/31/24

Outputs
Target Audience:Aquaculture producers, breeders, and the scientific community. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Thisproject provides excellent opportunities to train 1 postdoctoral fellow, 3 graduate students, and more than 8 undergraduate students. How have the results been disseminated to communities of interest?Through scientific publications, conference presentations, and stakeholder communications. What do you plan to do during the next reporting period to accomplish the goals?Will identify/confirm more QTL and epiQTL affecting fillet yield/quality and assess the feasibility of genomic selection to improve these important traits by comparing its accuracy with traditional family-based selective breeding in a new USDA/ARS selection line.

Impacts
What was accomplished under these goals? A new publication from this projecthighlighted the role of enhancers in quantitative trait loci (QTL) associated with fish growth, muscle yield, fillet quality, and bacterial cold water disease. By cross-matching identified QTLs with newly annotated gene regulatory elements, we found thousands of enhancers overlapping with QTL-containing genes across multiple chromosomes. Notably, 124 QTLs were linked to fish/muscle growth, with transcription factor binding motifs (TFBMs) primarily associated with C/EBP and glucocorticoid receptor (GR) families. These findings suggest that C/EBP and GR transcription factors are crucial in regulating muscle growth and quality in fish, offering potential targets for genetic selection in aquaculture.GigaScience, Volume 13, 2024, giae092,https://doi.org/10.1093/gigascience/giae092

Publications

  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2025 Citation: Ali, A., Gao, G., Al-Tobasei, R. et al. Chromosome level genome assembly and annotation of the Swanson rainbow trout homozygous line. Sci Data 12, 345 (2025). https://doi.org/10.1038/s41597-025-04693-7
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Mohamed Salem, Rafet Al-Tobasei, Ali Ali, Liqi An, Ying Wang, Xuechen Bai, Ye Bi, Huaijun Zhou, Functional annotation of regulatory elements in rainbow trout uncovers roles of the epigenome in genetic selection and genome evolution, GigaScience, Volume 13, 2024, giae092, https://doi.org/10.1093/gigascience/giae092
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Salem M. Chromatin State and DNA Methylation Profiling of the Rainbow Trout Genome Reveal Regulatory Elements Involved in Controlling Gene Expression and Gene Evolution and epiQTL Signatures of Domestication. PAG- 31 Plant & Animal Genomes Conference (January 12-17, 2024), San Diego, California. (International). https://doi.org/10.3390/microorganisms11112704
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Salem M. Chromatin State and DNA Methylation Profiling of the Rainbow Trout Genome Reveal Regulatory Elements Involved in Controlling Gene Expression and Gene Evolution and epiQTL Signatures of Domestication. PAG- 31 Plant & Animal Genomes Conference (January 12-17, 2024), San Diego, California.


Progress 01/01/23 to 12/31/23

Outputs
Target Audience:Aquaculture producers, breeders, and scientific community Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project provides opportunities to train 1 postdoctoral fellow, 3 graduate students, and more than 10 undergraduate students. How have the results been disseminated to communities of interest?Through scientific publications, conference presentations, and stakeholder communications. What do you plan to do during the next reporting period to accomplish the goals?Complete genomics DNA sequencing and identification of SNP markers. Run eQTL and GWASanalysis.

Impacts
What was accomplished under these goals? Measurements of fillet growth and quality traits were completed. RNA sequencing was completed, and SNP identification and annotation are ongoing. Genomic DNA sequencing and SNP identification are still ongoing.

Publications

  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Ahmed O R, Ali A, Leeds T, Salem, M (2023). RNA-Seq Analysis Of The Pyloric Caecum, Liver, And Muscle Reveals Molecular Mechanisms Regulating Fillet Color In Rainbow Trout. BMC Genomics 24, 579
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Ahmed O R, Leeds T, Salem, M (2023). Fecal Microbiome Analysis Distinguishes Bacterial Taxa Biomarkers Associated with Red Fillet Color in Rainbow Trout. Microorganisms 11 (11), 2704.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Salem M. Genomics And Metagenomics Prediction Of Muscle Growth And Fillet Quality Traits In Rainbow Trout. Aquaculture America (Feb. 23-28, 2023), New Orleans, LA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Ahmed OR, Salem M. Gene Expression Signature and Genetic Polymorphism Associated with Fillet Color in Rainbow Trout. PAG- 30, Plant & Animal Genomes Conference; (January 13-18, 2023), San Diego, California.


Progress 01/01/22 to 12/31/22

Outputs
Target Audience:Aquaculture producers, breeders, andscientific community. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project helped train a postdoc, 3 graduate students, and several undergraduate students in understanding and utilizingmolecular biology techniques to improve animal breeding. How have the results been disseminated to communities of interest?In addition to publications and conference presentations, we communicated the results to companies involved in rainbow trout breeding and production. What do you plan to do during the next reporting period to accomplish the goals?Validate the newly identified SNP markers, use the markers to rebuild a new SNP chip, and utilize it in genome-wide association studies to identify QTL affecting fillet growth and quality traits in rainbow trout. In addition, we will use the chip to assess applying genomics selections in one USDA/ARS experimental and one commercialbreeding programs.

Impacts
What was accomplished under these goals? We identified new functional SNPs associated with fish fillet pink and white color, fillet quality attributes including firm fillet, downgraded fillet (fillet gaping), and Omega-3 content. The SNPs will enrich the SNP chip to identify QTL, genes, and gene variants, causing variation in fillet yield and quality.

Publications

  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Ahmed RO, Ali A, Al-Tobasei R, Leeds T, Kenney B, Salem M: Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout. Genes (Basel) 2022, 13(8).
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Salem M, Al-Tobasei R, Ali A, Kenney B: Integrated Analyses of DNA Methylation and Gene Expression of Rainbow Trout Muscle under Variable Ploidy and Muscle Atrophy Conditions. Genes (Basel) 2022, 13(7):1151. doi: 10.3390/genes13071151 Genes 13 (7), 1151
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Salem M. Genomic Selection for Muscle Growth and Fillet Quality Traits in Rainbow Trout, Aquaculture Canada, and World Aquaculture Society, North America conference, August 15-18, 2022, St. Johns, Newfoundland, Canada.


Progress 01/01/21 to 12/31/21

Outputs
Target Audience:Aquaculture, fish, and animal science scientific community. Changes/Problems:We are making progress despite the pandemic and the supply chain disruption issues. What opportunities for training and professional development has the project provided?The project helped in training 1 postdoc, 2 graduate, and 3 undergraduate students. How have the results been disseminated to communities of interest?1 publication: Genomic predictions for fillet yield and firmness in rainbow trout using reduced-density SNP panels. R Al-Tobasei, A Ali, ALS Garcia, D Lourenco, T Leeds, M Salem, BMC genomics 22 (1), 1-11 What do you plan to do during the next reporting period to accomplish the goals?Genotype the fish sampled using RNA-Seq and DNA-Seq and develop an improved functional SNP-chip.

Impacts
What was accomplished under these goals? 100 fish families from F3 genetic line selected for improved fillet yield were phenotyped for fillet yield, color, andfillet gaping/firmness. Fish showing variation infillet gaping/firmness were also sampled from Pacific Aquaculture.

Publications

  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Genomic predictions for fillet yield and firmness in rainbow trout using reduced-density SNP panels R Al-Tobasei, A Ali, ALS Garcia, D Lourenco, T Leeds, M Salem BMC genomics 22 (1), 1-11