Transcriptome analysis provides new insights into the growth superiority of a novel backcross variety, Megalobrama amblycephala ♀ × (M. amblycephala ♀ × Culter alburnus ♂) ♂

Zheng, Guo‐Dong; Wu, Chen; Liu, Juan; Chen, Jie; Zou, Shu‐Ming

doi:10.1016/j.aquaculture.2019.734317

Cited by 17 publications

(13 citation statements)

References 45 publications

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“…In recent years, transcriptional analysis has been conducted in various aquatic species to compare the allelic expression variations between the parents and hybrids, such as brook charr (Bougas et al, 2010(Bougas et al, , 2013, putterfish (Gao et al, 2013), grouper (Sun et al, 2016a,b), crucian (Ren et al, 2016), and bream (Zheng et al, 2019). However, the transcriptional analysis of molluscan heterosis was only reported in the oysters (Hedgecock et al, 2007;Yang et al, 2018) and the sea cucumber (Wang et al, 2018a).…”

Section: Discussionmentioning

confidence: 99%

“…The 30 growth-related genes were mostly ELD-T, or ELOD expressed in DY (Figure 8). The dominant or overdominant expression of growth-related genes was identified in almost all the comparative transcriptional analyzes between hybrids and parents (Di et al, 2013(Di et al, , 2015Sun et al, 2016a;Zhang et al, 2017;Wang et al, 2018a;Zheng et al, 2019). Functions of the ELD and ELOD genes differed within different species, showing the different heterosis generation mechanisms.…”

Section: Discussionmentioning

confidence: 99%

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Integrated Analysis of mRNA and miRNA Changes in Two Haliotis diversicolor Genotypes and Their Hybrid

et al. 2021

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Heterosis is a widely distributed phenomenon in mollusks. It is vital in aquaculture by bringing beneficial traits into hybrids. People have utilized the heterosis theory in aquaculture for years. However, the molecular basis of heterosis remains elusive. Evident growth and survival heterosis were shown in the hybrid (“Dongyou-1”) of two Haliotis diversicolor geographic genotypes (Japan and Taiwan). To explore the molecular basis underlying the hybrid abalone’s heterosis, we conducted comparative mRNA and miRNA transcriptional analysis in the hybrid and parental genotypes. Differentially expression analysis identified 5,562 differentially expressed genes (DEGs) and 102 differentially expressed miRNAs (DEMs) between the three genotypes. 1,789 DEGs and 71 DEMs were found to be non-additively expressed in the hybrid. Meanwhile, both the expression level dominance pattern (ELD) and expression level overdominance pattern (ELOD) were found in the DEGs and DEMs, showing the existence of dominance and overdominance models in the hybrid’s transcriptome and post-transcriptional regulation. Functional analysis showed the non-additively expressed genes, ELD genes, and ELOD genes were significantly enriched in growth, immunity, and stress response related pathways, while some of the pathways were regulated by the mRNA-miRNA interactions. The expression levels of FGF, C1Q, HC, CAT, SEGPX, and MGST were significantly up-regulated in the hybrid compared to the middle parent value. In conclusion, we identified the existence of non-additivity, dominance, and overdominance models in the transcriptome and miRNAome of the H. diversicolor hybrid; these models facilitate the advantageous parental alleles’ integration into the hybrid, contributing to the hybrid’s growth and survival heterosis.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Integrated Analysis of mRNA and miRNA Changes in Two Haliotis diversicolor Genotypes and Their Hybrid

et al. 2021

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“…In order to obtain complete and effective annotation of functional genetic information, different annotation databases were used to analyze the RNA-seq data (Lu et al, 2008;Zheng and Wang, 2008;Ma et al, 2020). Different annotation databases revealed clear differences between the enrichment and annotation information, and GO is the most widely and commonly used among them (Bauer et al, 2008;Eden et al, 2009;Zheng et al, 2019).…”

Section: Functional Annotation and Enrichment Analysismentioning

confidence: 99%

Insights Into the Albinism Mechanism for Two Distinct Color Morphs of Northern Snakehead, Channa argus Through Histological and Transcriptome Analyses

et al. 2020

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The great northern snakehead (Channa argus) is one of the most important economic and conservational fish in China. In this study, the melanocytes in the skin of two distinct color morphs C. argus were investigated and compared through employment of the microscopic analysis, hematoxylin and eosin (H&E) and Masson Fontana staining. Our results demonstrated the uneven distribution of melanocytes with extremely low density and most of them were in the state of aging or death. Meanwhile, there was no obvious pigment layer and melanocytes distribution pattern found in the albino-type (AT), while the melanocytes were evenly distributed with abundance in the bicolor-type (BT). The transcriptome analysis through Illumina HiSeq sequencing showed that a total of 34.93 Gb Clean Data was obtained, and Q30 base percentage reached 92.66%. The BT and AT northern snakeheads transcriptome data included a total of 56,039,701 and 60,410,063 clean reads (n = 3), respectively. In gene expression analyses, the sample correlation coefficients (r) were ranged between 0.92 and 1.00; the contribution of PC1 and PC2 were 50.25 and 13.73% by using PCA cluster analysis, the total number of DEGs were 1024 (559 up-regulated and 465 down-regulated), and the number of annotated DEGs was 767 (COG 172, KEGG 262, GO 288, SwissProt 548, Pfam 579 and NR 765). Additionally, 46,363 ± 873 and 44,947 ± 392 single nucleotide polymorphisms (SNPs) were compiled via genetic structure analysis, respectively. Ten key pigment-related genes were screened using qRT-PCR. And all of them revealed extremely higher expression levels in the skin of BT than those of AT.This is the first study to analyze the mechanism of albino characteristics of Channa via histology and transcriptomics, and also provide the oretical and practical support for the protection and development of germplasm resources for C. argus.

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“…Studies in transcriptomics, proteomics, metabolism, and epigenomics have provided new insights into parental genomic interactions, leading to regulatory and network changes and heterosis [1,8,9]. Recently, the differentially expressed genes (DEGs) and pathways related to heterosis have been identified through the transcriptome profiles analysis in aquatic species, such as hybrid grouper (Epinephelus fuscogutatus ♀× E. lanceolatus ♂) [10,11], hybrid pufferfish (Takifugu obscurus ♀× T. rubripes ♂) [12], hybrid tambacu (Colossoma macropomum ♀× Piaractus mesopotamicus ♂) [13], hybrid tilapia (Oreochromis niloticus ♀× O. aureus ♂) [14,15], hybrid carp (Hypophthalmichthys nobilis ♀× H. molitrix ♂) [16], hybrid seabream (Acanthopagrus schlegelii ♂× Pagrus major ♀) [17], hybrid cypriniformes [Megalobrama amblycephala ♀× (M. amblycephala ♀× Culter alburnus ♂) ♂] [18], hybrid Chinese soft-shelled turtle (Pelodiscus sinensis Japanese strain ♀× P.sinensis Qingxi black turtle ♂) [19], sea cucumber (Chinese Apostichopus japonicus ♀× Russian A. japonicus ♂) [20], and hybrid abalone (Haliotis gigantea ♀× H. discus hannai ♂) [21]. These works could help us to further understand the molecular mechanism of the heterosis in various aquatic species.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Profiling Revealed Basis for Growth Heterosis in Hybrid Tilapia (Oreochromis niloticus ♀ × O. aureus ♂)

Zhu

Zou

et al. 2022

Fishes

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Hybrid tilapia were produced from hybridization of Nile tilapia (Oreochromis niloticus) and blue tilapia (O. aureus). Comparative transcriptome analysis was carried out on the liver of hybrid tilapia and their parents by RNA sequencing. A total of 2319 differentially expressed genes (DEGs) were identified. Trend co-expression analysis showed that non-additive gene expression accounted for 67.1% of all DEGs. Gene Ontology and KEGG enrichment analyses classified the respective DEGs. Gene functional enrichment analysis indicated that most up-regulated genes, such as FASN, ACSL1, ACSL3, ACSL6, ACACA, ELOVL6, G6PD, ENO1, GATM, and ME3, were involved in metabolism, including fatty acid biosynthesis, unsaturated fatty acid biosynthesis, glycolysis, pentose phosphate pathway, amino acid metabolism, pyruvate metabolism, and the tricarboxylic acid cycle. The expression levels of a gene related to ribosomal biosynthesis in eukaryotes, GSH-Px, and those associated with heat shock proteins (HSPs), such as HSPA5 and HSP70, were significantly down-regulated compared with the parent tilapia lineages. The results revealed that the metabolic pathway in hybrid tilapia was up-regulated, with significantly improved fatty acid metabolism and carbon metabolism, whereas ribosome biosynthesis in eukaryotes and basal defense response were significantly down-regulated. These findings provide new insights into our understanding of growth heterosis in hybrid tilapia.

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Transcriptome analysis provides new insights into the growth superiority of a novel backcross variety, Megalobrama amblycephala ♀ × (M. amblycephala ♀ × Culter alburnus ♂) ♂

Cited by 17 publications

References 45 publications

Integrated Analysis of mRNA and miRNA Changes in Two Haliotis diversicolor Genotypes and Their Hybrid

Integrated Analysis of mRNA and miRNA Changes in Two Haliotis diversicolor Genotypes and Their Hybrid

Insights Into the Albinism Mechanism for Two Distinct Color Morphs of Northern Snakehead, Channa argus Through Histological and Transcriptome Analyses

Transcriptome Profiling Revealed Basis for Growth Heterosis in Hybrid Tilapia (Oreochromis niloticus ♀ × O. aureus ♂)

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Transcriptome analysis provides new insights into the growth superiority of a novel backcross variety, Megalobrama amblycephala ♀ × (M. amblycephala ♀ × Culter alburnus ♂) ♂

Cited by 17 publications

References 45 publications

Integrated Analysis of mRNA and miRNA Changes in Two Haliotis diversicolor Genotypes and Their Hybrid

Integrated Analysis of mRNA and miRNA Changes in Two Haliotis diversicolor Genotypes and Their Hybrid

Insights Into the Albinism Mechanism for Two Distinct Color Morphs of Northern Snakehead, Channa argus Through Histological and Transcriptome Analyses

Transcriptome Profiling Revealed Basis for Growth Heterosis in Hybrid Tilapia (Oreochromis niloticus ♀ × O. aureus ♂)

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Transcriptome analysis provides new insights into the growth superiority of a novel backcross variety, Megalobrama amblycephala ♀ × (M. amblycephala ♀ × Culter alburnus ♂) ♂