Expression of Antisense Long Noncoding RNAs as Potential Regulators in Rainbow Trout with Different Tolerance to Plant-Based Diets

ABSTRACT

Reformulation of aquafeeds in salmonid diets to include more plant proteins is critical for sustainable aquaculture. However, increasing plant proteins can lead to stunted growth and enteritis. Toward an understanding of the regulatory mechanisms behind plant protein utilization, directional RNA sequencing of liver tissues from a rainbow trout strain selected for growth on an all plant-protein diet and a control strain, both fed a plant diet for 12 weeks, were utilized to construct long noncoding RNAs. Antisense long noncoding RNAs were selected for differential expression and functional analyses since they have been shown to have regulatory actions within a genome. A total of 142 unique antisense long noncoding RNAs were differentially expressed between strains, 60 of which could be mapped to a gene. Genes underlying these noncoding RNAs are indicated in lipid metabolism and immunity. Six noncoding transcripts were also found to overlap with differentially expressed protein-coding genes, all of which were co-expressed. Associating variation in regulatory elements between rainbow trout strains with differing tolerance to plant-protein diets will assist in future studies toward increased gains throughout carnivorous aquaculture.

KEYWORDS:

• Alternative feeds
• antisense transcripts
• gene regulation
• lncRNA
• noncoding
• salmonid
• sustainable aquaculture

Acknowledgments

The authors would like to thank Dr. Thomas Welker, Karen Frank, Michael Becerra and Lorrie VanTassel at the Hagerman Fish Culture Experiment Station for their help in fish husbandry and fish sampling. We thank Dr. Rick Barrows, Jason Frost, Carley Stone and Aaron Nistler at the USDA-ARS, Fish Technology Center in Bozeman, Montana for their assistance in diet formulation and diet production. This work was performed by the USDA—Agricultural Research Service. Mention of trade names or commercial products is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the United States Department of Agriculture. The USDA is an equal opportunity provider and employer.

Additional information

Funding

This work was performed by the USDA—Agricultural Research Service under funds appropriated for the Trout-Grains Project (project #2050-21310-005-00-D).