Differential expression of Gnrh2, Gthβ, and Gthr genes in sterile triploids and fertile tetraploids

Comparative transcriptomic analysis of reproductive characteristics of reciprocal hybrid lineages derived from hybridization between Megalobrama amblycephala and Culter alburnus

BACKGROUND

Distant hybridization is an important breeding technique for creating new strains with superior traits by integrating two different genomes. Successful hybridization of Megalobrama amblycephala (Blunt snout bream, BSB, 2n = 48) and Culter alburnus (Topmouth culter, TC, 2n = 48) was achieved to establish hybrid lineages (BT and TB), which provide valuable materials for exploring the mechanisms of distant hybridization fertility. In this study, the gonadal tissue transcriptomes of BSB, TC, BT-F1, and TB-F1 were sequenced using Illumina high-throughput sequencing technology to analyze the reproductive characteristics of BT and TB.

RESULTS

Differential gene expression analysis showed that the differentially expressed genes in BT vs BSB and BT vs TC were mainly enriched in signaling pathways not directly associated with meiosis. While, the differentially expressed genes of TB vs BSB and TB vs TC were mainly enriched in pathways related to meiosis, and most of them were down-regulated, indicating that meiosis is suppressed in TB. Under-dominance (UD) genes were enriched in pathways related to meiosis and DNA repair in TB. Over-dominance (OD) genes were enriched in MAPK signaling pathway, expression level dominance-BSB (ELD-B) genes were enriched in pathways related to steroid hormone synthesis and expression level dominance-TC (ELD-T) genes were not significantly enriched in any pathway in both BT and TB.

CONCLUSIONS

These results suggest that meiotic progression may not be affected in BT, whereas it is clearly inhibited in TB. Offspring of M. amblycephala maternal parent may have better genomic compatibility and fertility. Our study provides important information on the molecular mechanisms of breaking reproductive isolation in distantly hybridized fertile lineages.

Elevated expression of inhibin α gene in sterile allotriploid crucian carp

Inhibin and Activin, belong to the transforming growth factor β superfamily (TGF-β), which associate with the regulation of the reproductive process by the modulation of the hypothalamic-pituitary-gonad (HPG) axis. In this study, we reported the molecular cloning and tissue expression of inhibin α in allotriploid crucian carp and its parent- diploid red crucian carp. The full-length cDNA of inhibin α were respectively 1632 bp and 1642 bp in allotriploids and diploids, which both consisted of a 1044 bp open reading frame (ORF) encoding 347 amino acids. Real-time quantitative PCR (RT-qPCR) showed that allotriploids and diploids had significant expression of inhibin α in testis and ovary, and the expression of inhibin α in the gonads of allotriploids was higher than that of diploids. The immunohistochemistry indicated that the ovarian development of allotriploids was abnormal, and the expression of Inhibin α in the ovary of allotriploids was higher than that of diploids. Results of co-immunoprecitation (co-IP) demonstrated that the Inhibin α and Activin β_A, Inhibin α and Activin β_B can form dimers. These findings suggested that the elevated expression of inhibin α and the competitive binding of Inhibin α subunit with Activin β subunits in allotriploids may be releted to the sterility of allotriploids. Furthermore, these results will facilitate the investigation of reproduction characteristics in allotriploids and provide theoretical basis for the study of polyploid breeding in the future.

Comparative analyses of hypothalamus transcriptomes reveal fertility-, growth-, and immune-related genes and signal pathways in different ploidy cyprinid fish

Triploid crucian carp (TCC) is obtained by hybridization of female diploid red crucian carp (Carassius auratus red var., RCC) and male allotetraploid hybrids. In this study, high-throughput sequencing was used to conduct the transcriptome analysis of the female hypothalamus of diploid RCC, diploid common carp (Cyprinus carpio L., CC) and TCC. The key functional expression genes of the hypothalamus were obtained through functional gene annotation and differential gene expression screening. A total of 71.56 G data and 47,572 genes were obtained through sequencing and genome mapping, respectively. The Fuzzy Analysis Clustering assigned the differentially expressed genes (DEGs) into eight groups, two of which, overdominance expression (6005, 12.62%) and underdominance expression (3849, 8.09%) in TCC were further studied. KEGG enrichment analysis showed that the DEGs in overdominance were mainly enriched in four pathways. The expression of several fertility-related genes was lower levels in TCC, whereas the expression of several growth-related genes and immune-related genes was higher levels in TCC. Besides, 15 DEGs were verified by quantitative real-time PCR (qPCR). The present study can provide a reference for breeding sterility, fast-growth, and disease-resistant varieties by distant hybridization.

Transcriptomic evidence of luteinizing hormone-releasing hormone agonist (LHRH-A) regulation on lipid metabolism in grass carp (Ctenopharyngodon idella)

In this study, RNA sequencing was used to identify the hepatic gene expression profile in grass carp associated with luteinizing hormone-releasing hormone agonist (LHRH-A) treatment. A total of 93,912,172 reads were generated by HiSeq 4000 sequencing platform. After filtering, 83,450,860 clean reads were mapped to the reference genome. By calculating the FPKM of genes, 1475 differentially expressed genes were identified. PPAR signaling pathway was enriched with upregulated genes in LHRH-A injection group showing the regulation of the lipid metabolism by LHRH-A. The expression of eight key genes in PPAR signaling pathway was confirmed by qPCR and the results suggested that ACSL4A, ACSL4B, ANGPTL4, LPL, RXRBA and SLC27A1B were significantly stimulated by LHRH-A injection. This investigation provides the evidence that LHRH-A could play a role in lipid metabolism.

Differential expression of activin βA and βB genes in female allotriploid and diploid red crucian carp Carassius auratus red var

activin β_A and β_B from diploid and allotriploid crucian carp were cloned.The differential expression of activin β_A and β_B genes in female allotriploid and diploid red crucian carp Carassius auratus red var. were studied and found to be expressed in all the tested tissues; particularly, the expression of activin β_A and β_B was elevated in the ovaries of allotriploids and differential expression in pituitaries during the non-breeding season and the breeding season period. The immunohistochemistry indicated that the abnormal triploid ovaries were dominated by small oogonium-like cells with dense signals and that the elevated expression of activin β_A and β_B in the ovaries of allotriploids may be related to allotriploid sterility.

Differential expression of HPG-axis genes in autotetraploids derived from red crucian carp Carassius auratus red var., ♀ × blunt snout bream Megalobrama amblycephala, ♂

Autotetraploid fish (4n = 200, abbreviated as 4nRR), which reach sexual maturity at 1 year of age, were derived from the whole genome duplication of red crucian carp Carassius auratus red var. (RCC; 2n = 100) and possess four sets of chromosomes from RCC. The histological features of the gonads showed that the RCC and 4nRR both possessed normal gonadal structure and could arrive at maturation. To understand the expression characteristics of genes related to reproductive development in the autotetraploid fish, we analysed the nucleotide sequence and expression characteristics of the gnrh2, gthb and gthr genes, which are the pivotal genes of the hypothalamic-pituitary-gonadal (HPG) axis. We found that the gnrh2, gthb and gthr genes in 4nRR share remarkable homology with RCC, but there were obvious differences in expression levels between 4nRR and RCC. These results demonstrate that autotetraploidization can lead to gene expression changes. This study provides insights into the molecular mechanism underlying the reproductive development of autotetraploid fish and is expected to be of great significance for subsequent research on polyploidization.

Determination of dosage compensation and comparison of gene expression in a triploid hybrid fish

Background

Polyploidy and hybridization are both recognized as major forces in evolution. Most of our current knowledge about differences in gene regulation in polyploid hybrids comes from plant studies. The gene expression of diverged genomes and regulatory interactions are still unclear in lower vertebrates.

Results

We generated 229 million cleaned reads (42.23 Gbp) from triploid of maternal grass carp (Ctenopharyngodon idellus, Cyprininae, 2n = 48) × paternal blunt snout bream (Megalobrama amblycephala, Cultrinae, 2n = 48) and their diploid parents using next-generation sequencing. In total, 157,878 contigs were assembled and 15,444 genes were annotated. We examined gene expression level changes among the parents and their triploid offspring. The mechanisms of dosage compensation that reduced triploid expression levels to the diploid state were determined in triploid fish. In this situation, novel gene expression and gene silencing were observed. Then, we established a model to determine the extent and direction of expression level dominance (ELD) and homoeolog expression bias (HEB) based on the relative expression level among the parents and their triploid offspring.

Conclusions

Our results showed that the genome-wide ELD was biased toward maternal genome in triploid. Extensive alterations in homoeolog expression suggested a combination of regulatory and epigenetic interactions through the transcriptome network. Additionally, the expression patterns of growth genes provided insights into the relationship between the characteristics of growth and underlying mechanisms in triploids. Regulation patterns of triploid state suggest that various expression levels from the initial genomic merger have important roles in adaptation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3424-5) contains supplementary material, which is available to authorized users.

Homoeologue expression insights into the basis of growth heterosis at the intersection of ploidy and hybridity in Cyprinidae

Hybridization and polyploidization are considered important driving forces that form new epigenetic regulations. To study the changing patterns of expression accompanying hybridization and polyploidization, we used RNA-seq and qRT-PCR to investigate global expression and homoeologue expression in diploid and tetraploid hybrids of Carassius auratus red var. (♀) (R) and Cyprinus carpio (♂) (C). By comparing the relative expression levels between the hybrids and their parents, we defined the expression level dominance (ELD) and homoeologue expression bias (HEB) in liver tissue. The results showed that polyploidization contributed to the conversion of homoeologue ELD. In addition, hybridization had more effect on the change in HEB than polyploidization, while polyploidization had more effect on the change of global gene expression than hybridization. Meanwhile, similar expression patterns were found in growth-related genes. The results suggested that hybridization and polyploidization result in differential degrees of maternal HEB in three tissues (liver, muscle and ovary) tested. The results of this study will increase our understanding of the underlying regulation mechanism of rapid growth in diploid hybrids and allotetraploids. The differential degrees of global expression and homoeologue expression contribute to growth heterosis in newly formed hybrids, ensuring the on-going success of allotetraploid speciation.

MicroRNA profiles reveal female allotetraploid hybrid fertility

BACKGROUND

The bisexual fertile tetraploid fish is important in biological evolution. Tetraploid fish fertility is the key factor for stable inheritance. Therefore, elucidating tetraploid fish fertility at the molecular level is essential. MicroRNAs regulate gene expression and are involved in many aspects of gonad development.

METHODS

Total RNA was isolated using TRIzol, followed by constructing small RNA libraries. And then, the qualified libraries were sequenced with the HiSeq 2500 SE50 system. The obtained clean reads were analyzed to identify conserved and novel miRNAs, and evaluate the expression, and also predict the target genes. The differential expressions of miRNAs were confirmed by RT-PCR.

RESULTS

In this study, allotetraploid hybrid fish (4nAT) and diploid red crucian carp (RCC) ovaries were used to compare miRNA profiles. The results indicated that most of the highly expressed miRNAs were closely correlated with ovary maturation, and displayed no significant differences in expression. Moreover, 34 up-regulated and nine down-regulated miRNAs were found in 4nAT. The differentially expressed miRNAs were primarily involved in metabolism, defense mechanisms, and cytoskeleton production.

CONCLUSIONS

This is the first study to provide new epigenetic evidences for tetraploid fish fertility and phenotypic changes as a result of increased ploidy.

Elevated expression of Piwi and piRNAs in ovaries of triploid crucian carp

Increasing piRNAs provide RNA-interference pathways to regulate transposons and gene expression in germline cells. We demonstrate that Piwi transcripts are exclusively expressed in adult testes and ovaries in teleosts, with triploids showing the highest Piwi expression in the ovaries. Studies in vivo and in vitro showed that hCG and E2 treatment suppressed Piwi expression. We further cloned 200 small RNAs in the three kinds of fish. Seven piRNAs were obtained from all the three different ploidy fishes. During ovulation, five piRNAs showed significantly higher expression in the ovaries of sterile triploids than fertile diploids and tetraploids. Furthermore, E2 suppressed the expression of the six piRNAs at different levels in vivo and in vitro. The present study bridges the gap between the HPG axis and Piwi-piRNA pathway by suggesting that a dysfunctional HPG axis abrogated the piRNA suppression in triploid fish.

Involvement of GnRH, PACAP and PRP in the reproduction of blue gourami females (Trichogaster trichopterus)

In vertebrates, gonadotropin-releasing hormone (GnRH) and pituitary adenylate cyclase-activating polypeptide (PACAP) are key hormones regulating growth and reproduction in the brain-pituitary axis. The regulating hormonal interactions are of great interest, therefore, the aim of this study is to provide novel insights into the involvement of brain GnRH and PACAP in oogensis and spermatogenesis in a fish model, the blue gourami (Trichogaster trichopterus). cDNA cloning of two GnRH forms combined with phylogenetic analysis revealed that three paralogous GnRH forms exist in blue gourami and evolve as a result of genome duplication. GnRH1 mRNA levels are related to final oocyte maturation (FOM), and this peptide stimulated β follicle-stimulating hormone (βFSH) and growth hormone (GH) gene expression; GnRH2 stimulated β gonadotropins (GtH) gene expression and GnRH analog combined with PACAP-38 synergistically upregulate GH and βFSH gene expression. The data presented, together with previous studies in our lab, enable suggesting mechanisms explaining the physiological relevance of these peptides in the regulation of gametogenesis and steroidogenesis in blue gourami females. These findings support the biological importance of the GnRH and PACAP hormones family, enabling them to stimulate differential biological functions in the regulation of growth and reproduction.