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. 2020 Oct 9;15(10):e0240308.
doi: 10.1371/journal.pone.0240308. eCollection 2020.

Transcriptome analysis of the growth performance of hybrid mandarin fish after food conversion

Wen-Zhi Guan  1   2 , Gao-Feng Qiu  1 , Feng-Liu  2
Affiliations

Transcriptome analysis of the growth performance of hybrid mandarin fish after food conversion

Wen-Zhi Guan et al. PLoS One. .

Abstract

During recent years, China has become a hotspot for the domestication of mandarin fish, and this is of great commercial value. Although the food preference of domesticated mandarin fish has been studied, little is known about genes regulating their growth. We raised hybrid mandarin fish on artificial feed for 3 months, the results showed that the survival rate of hybrid mandarin fish was 60.00%. Their total length and body weight were 18.34 ±0.43 cm and 100.44 ±4.87 g. The absolute length and weight gain rates were 0.14 cm/d and 1.08 g/d, respectively. Finally, RNA sequencing (RNA-Seq) was performed to identify potential genes and pathways activated in response to growth performance. The transcriptome analysis generated 68, 197 transcripts and 45,871 unigenes. Among them, 1025 genes were up-regulated and 593 genes were down-regulated between the fast- and slow-growth fish. Finally, we obtained 32 differentially expressed genes, which were mainly related to fatty acid biosynthesis (e.g. FASN and ACACB), collecting duct acid secretion (e.g. ATP6E and KCC4), cell cycle (e.g. CDC20 and CCNB), and the insulin-like growth factor (IGF) system (IGFBP1). These pathways might be related to the growth of hybrid mandarin fish. In addition, more potential single nucleotide polymorphisms (SNPs) were detected in the fast-growth fish than in the slow-growth fish. The results suggest that the interaction of metabolism and abundant alleles might determine the growth of hybrid mandarin fish after food conversion.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. The growth performance of hybrid mandarin fish.
(A) The survival number of hybrid mandarin fish. (B) The morphology of domesticated hybrid mandarin fish. (C) The change of total length of hybrid mandarin fish. (D) The change of body weight of hybrid mandarin fish. IM, Initial Measurement (0 day). FM, Final Measurement (90days).
Fig 2
Fig 2. Functional annotation of hybrid mandarin fish transcripts based on GO categorization.
Fig 3
Fig 3. DEGs analysis and volcano plot for fast- (F) and slow-growth (S) groups of hybrid mandarin fish.
The x-axis is the value of Log2 (Fold Change), and the y-axis is the value of -Log10 (padjust). The red and blue dots reveal the up- and down-regulated DEGs, the black dots reveal non-significantly genes.
Fig 4
Fig 4. Hierarchical cluster analysis of DEGs involved in the growth superiority.
Red and blue gradients indicate the up- and down- regulation of DEGs, respectively.
Fig 5
Fig 5
A, SNPs distribution in samples. The X-axis represents the type of SNP, and the y-axis represents the number of SNPs in different samples. B, the percentage of different SSR motifs. Different colors represent the number of different SSR types.
Fig 6
Fig 6. Validation of RNA-seq data by qRT-PCR.
(A) The RNA-seq data. (B) The qRT-PCR data. The values are the ratio of gene expression levels in the fast-growth group to those in the slow-growth group by the two methods.
Fig 7
Fig 7. The predicted map of DEGs regulated growth superiority.
Red and purple represent the up- and down-regulation of DEGs, respectively.
See this image and copyright information in PMC

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