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ARS Home » Southeast Area » Auburn, Alabama » Aquatic Animal Health Research » Research » Publications at this Location » Publication #420970
Research Project: Integrated Research to Improve Aquatic Animal Health in Warmwater Aquaculture

Location: Aquatic Animal Health Research

Title: Gene expression profiling of Pacific white shrimp (Litopenaeus vannamei) reared in conditions of varying dissolved oxygen

Author
item Abernathy, Jason
item SAN ANDRES, CRISTHIAN - Auburn University
item Garcia, Julio
item SANKAPPA, NITHIN - Orise Fellow
item ARAUJO, ADELA - Auburn University
item CORBY, TRENTON - Auburn University
item NGUYEN, KHANH - Auburn University
item RHODES, MELANIE - Auburn University
item ROY, LUKE - Auburn University
item DAVIS, ALLEN - Auburn University

Submitted to: NIH Gene Expression Omnibus (GEO) Database
Publication Type: Database / Dataset
Publication Acceptance Date: 11/6/2024
Publication Date: 7/17/2025
Citation: Abernathy, J.W., San Andres, C., Garcia, J.C., Sankappa, N.M., Araujo, A., Corby, T., Nguyen, K., Rhodes, M., Roy, L., Davis, A.D. 2025. Gene expression profiling of Pacific white shrimp (Litopenaeus vannamei) reared in conditions of varying dissolved oxygen. NIH Gene Expression Omnibus (GEO) Database. GSE281217.

Interpretive Summary:

Technical Abstract: World aquaculture production of the Pacific white shrimp (Litopenaeus vannamei) is estimated to account for 80% of the total shrimp produce worldwide. The global demand for shrimp has driven the industry to utilize and rely on semi-intensive and intensive shrimp systems. In the United States, Pacific white shrimp production can take place in semi-intensive earthen ponds, recirculating aquaculture systems (RAS), biofloc technology and green water. In this study, the effects of lowering dissolved oxygen conditions in outdoor green water tanks on global gene expression is examined. Twelve (800 L) round tanks were stocked each with 35 shrimp (1.99 ± 0.06g) and reared in 15 ppt green water system tanks. Four of the tanks were aerated at 0.25 cubic feet per second (cfs; low), four at 0.35 cfs (medium) and four at 0.7 cfs (high). The experiment was terminated 42 days after stocking, when two shrimp per tank were randomly collected, and gill (fourth gill filament from one side) and intestine were extracted and preserved for RNA sequencing. After sequencing to a read-depth of >25M paired-end (2 x 150bp) reads on an Illumina sequencer, each sample underwent analysis for quality control, alignment of reads to the Pacific white shrimp reference genome assembly, counts data extracted, and pairwise differential gene expression analyzed via edgeR, whereby low and medium aeration levels were compared to the control (high). We identified only a single significant (P-adj < 0.05; fold-change ± 2) differentially expressed gene among the comparisons, suggesting that Pacific white shrimp exposed to lowering dissolved oxygen set points does not induce global changes in gene expression at these levels. The raw RNA sequencing data along with processed counts information have been made available to the public at the NCBI Gene Expression Omnibus, accessible under Accession #GSE281217.