Identification of some unknown transcripts from SSH cDNA library of buffalo follicular oocytes

Role of bone morphogenetic protein signaling in bovine early embryonic development and stage specific embryotropic actions of follistatin†

Characterization of the molecular factors regulating early embryonic development and their functional mechanisms is critical for understanding the causes of early pregnancy loss in monotocous species (cattle, human). We previously characterized a stage specific functional role of follistatin, a TGF-beta superfamily binding protein, in promoting early embryonic development in cattle. The mechanism by which follistatin mediates this embryotropic effect is not precisely known as follistatin actions in cattle embryos are independent of its classically known activin inhibition activity. Apart from activin, follistatin is known to bind and modulate the activity of the bone morphogenetic proteins (BMPs), which signal through SMAD1/5 pathway and regulate several aspects of early embryogenesis in other mammalian species. Present study was designed to characterize the activity and functional requirement of BMP signaling during bovine early embryonic development and to investigate if follistatin involves BMP signaling for its stage specific embryotropic actions. Immunostaining and western blot analysis demonstrated that SMAD1/5 signaling is activated after embryonic genome activation in bovine embryos. However, days 1-3 follistatin treatment reduced the abundance of phosphorylated SMAD1/5 in cultured embryos. Inhibition of active SMAD1/5 signaling (8-16 cell to blastocyst) using pharmacological inhibitors and/or lentiviral-mediated inhibitory SMAD6 overexpression showed that SMAD1/5 signaling is required for blastocyst production, first cell lineage determination as well as mRNA and protein regulation of TE (CDX2) cell markers. SMAD1/5 signaling was also found to be essential for embryotropic actions of follistatin during days 4-7 but not days 1-3 of embryo development suggesting a role for follistatin in regulation of SMAD1/5 signaling in bovine embryos.

A novel lincRNA identified in buffalo oocytes with protein binding characteristics could hold the key for oocyte competence

Studying the maternal oocyte-specific genes, in farm animals is a significant step towards delineating the underlying mechanisms that regulate oocyte quality, early embryonic development and survival. With the creation of buffalo oocyte-specific subtracted cDNA library, it has raised new questions which need to be answered. The present study has characterized one of the ESTs selected from the library and highlighted its importance in the oocyte quality. The selected EST was made full length by RLM-RACE and four transcript variants were identified. Bioinformatics analysis indicated the novelty of full-length transcript along with conserved intergenic nature. The largest transcript was identified as long intergenic noncoding RNA based upon coding potential calculator output. The expression analysis at different hours of oocyte maturation showed a significant variation in developmentally competent oocytes to that of incompetent ones. Along with this, the transcript was also found to have protein binding ability which was confirmed by RNA electrophoretic mobility shift assay. The protein used in the experiment was isolated from oocyte and cumulus cells via sonication. A novel lincRNA has been reported here that might have an important role in maturation of oocytes, inferred from its relative gene expression study and protein binding characteristics.

Identification of the JY-1 in sika deer and its effects on granulosa cells cultured in vitro

The oocyte-specific protein JY-1 was reported as an important regulator of both function of ovarian granulosa cells and early embryogenesis in cattle. Here, we found that the transcripts of JY-1 were also present in sika deer granulosa cells (GCs) through in situ hybridization and qRT-PCR. The complete sika deer JY-1 coding sequence was identified, which had three exons separated by two introns. It was detected that JY-1 knockdown caused apoptosis and abnormal cell cycle progression in GCs of sika deer cultured in vitro. Taken together, these data suggest that JY-1 is involved in the regulation of proliferation in sika deer ovarian GCs.

Genomic study and Medical Subject Headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers

Zebu animals () are known to take longer to reach puberty compared with taurine animals (), limiting the supply of animals for harvest or breeding and impacting profitability. Genomic information can be a helpful tool to better understand complex traits and improve genetic gains. In this study, we performed a genomewide association study (GWAS) to identify genetic variants associated with reproductive traits in Nelore beef cattle. Heifer pregnancy (HP) was recorded for 1,267 genotyped animals distributed in 12 contemporary groups (CG) with an average pregnancy rate of 0.35 (±0.01). Disregarding one of these CG, the number of antral follicles (NF) was also collected for 937 of these animals, with an average of 11.53 (±4.43). The animals were organized in CG: 12 and 11 for HP and NF, respectively. Genes in linkage disequilibrium (LD) with the associated variants can be considered in a functional enrichment analysis to identify biological mechanisms involved in fertility. Medical Subject Headings (MeSH) were detected using the MESHR package, allowing the extraction of broad meanings from the gene lists provided by the GWAS. The estimated heritability for HP was 0.28 ± 0.07 and for NF was 0.49 ± 0.09, with the genomic correlation being -0.21 ± 0.29. The average LD between adjacent markers was 0.23 ± 0.01, and GWAS identified genomic windows that accounted for >1% of total genetic variance on chromosomes 5, 14, and 18 for HP and on chromosomes 2, 8, 11, 14, 15, 16, and 22 for NF. The MeSH enrichment analyses revealed significant ( < 0.05) terms associated with HP-"Munc18 Proteins," "Fucose," and "Hemoglobins"-and with NF-"Cathepsin B," "Receptors, Neuropeptide," and "Palmitic Acid." This is the first study in Nelore cattle introducing the concept of MeSH analysis. The genomic analyses contributed to a better understanding of the genetic control of the reproductive traits HP and NF and provide new selection strategies to improve beef production.

Gene expression profiles of fin regeneration in loach (Paramisgurnus dabryanu)

Teleost fins can regenerate accurate position-matched structure and function after amputation. However, we still lack systematic transcriptional profiling and methodologies to understand the molecular basis of fin regeneration. After histological analysis, we established a suppression subtraction hybridization library containing 418 distinct sequences expressed differentially during the process of blastema formation and differentiation in caudal fin regeneration. Genome ontology and comparative analysis of differential distribution of our data and the reference zebrafish genome showed notable subcategories, including multi-organism processes, response to stimuli, extracellular matrix, antioxidant activity, and cell junction function. KEGG pathway analysis allowed the effective identification of relevant genes in those pathways involved in tissue morphogenesis and regeneration, including tight junction, cell adhesion molecules, mTOR and Jak-STAT signaling pathway. From relevant function subcategories and signaling pathways, 78 clones were examined for further Southern-blot hybridization. Then, 17 genes were chosen and characterized using semi-quantitative PCR. Then 4 candidate genes were identified, including F11r, Mmp9, Agr2 and one without a match to any database. After real-time quantitative PCR, the results showed obvious expression changes in different periods of caudal fin regeneration. We can assume that the 4 candidates, likely valuable genes associated with fin regeneration, deserve additional attention. Thus, our study demonstrated how to investigate the transcript profiles with an emphasis on bioinformatics intervention and how to identify potential genes related to fin regeneration processes. The results also provide a foundation or knowledge for further research into genes and molecular mechanisms of fin regeneration.

Identification of differentially-expressed genes in early developmental ovary of Yellow River carp (Cyprinus carpio var) using Suppression Subtractive Hybridization

Ovary development appears to be under polygenic control, and is influenced by multiple genetic factors that may vary from organism to organism. To gain a better insight into the molecular mechanisms of carp ovary development, Suppression Subtractive Hybridization (SSH) DNA libraries in two species of Yellow River carp were analyzed. Primordial gonads and stage II ovaries were used as testers, and adult ovaries as drivers. One hundred and fifty differentially-expressed candidate genes were examined by Southern blot microarray hybridization. We identified 41 differentially-expressed genes in the PG (Primordial gonad) library and 37 in the stage II ovary library. Gene Ontology Biological Pathway analysis showed the genes were involved in signal transduction, proteolysis process, cell differentiation, TGF-β signal and other biological responses. Twenty-two candidate genes were selected and further characterized using qRT-PCR. Pvalb, epd, and MYH were found specifically expressed in PG, while bmp2b, desmin and fp1 were specifically expressed in stage II ovary. Our results indicate that these genes could be used as biomarkers of the early development of carp ovary. This finding will provide a basis for further understanding of the complex gonad developmental molecular mechanisms in Yellow River carp.

Gene expression profile changes induced by acute toxicity of [C16 mim]Cl in loach (Paramisgurnus dabryanus)

Ionic liquids (ILs) are widely used as reaction media in various commercial applications. Many reports have indicated that most ILs are poorly decomposed by microorganisms and are toxic to aquatic organisms. In this study, differential gene expression profiling was conducted using a suppression subtraction hybridization cDNA library from hepatic tissue of the loach (Paramisgurnus dabryanus) after exposure to 1-hexadecyl-3-methylimidazolium chloride ([C₁₆ mim]Cl), a representative IL. Two hundred and fifty-nine differentially expressed candidate genes, whose expression was altered by >2.0-fold by the [C₁₆ mim]Cl treatment, were identified, including 127 upregulated genes and 132 downregulated genes. A gene ontology analysis of the known genes isolated in this study showed that [C₁₆ mim]Cl-responsive genes were involved in cell cycle, stimulus response, defense response, DNA damage response, oxidative stress responses, and other biological responses. To identify candidate genes that may be involved in [C₁₆ mim]Cl-induced toxicity, 259 clones were examined by Southern blot macroarray hybridization, and 20 genes were further characterized using quantitative real-time polymerase chain reaction. Finally, six candidate genes were selected, including three DNA damage response genes, two toxic substance metabolic genes, and one stress protein gene. Our results indicate that these changes in gene expression are associated with [C₁₆ mim]Cl-induced toxicity, and that these six candidate genes can be promising biomarkers for detecting [C₁₆ mim]Cl-induced toxicity. Therefore, this study demonstrates the use of a powerful assay to identify genes potentially involved in [C₁₆ mim]Cl toxicity, and it provides a foundation for the further study of related genes and the molecular mechanism of [C₁₆ mim]Cl toxicity. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 404-416, 2017.

Polymorphism of JY-1 gene is not associated with reproductive traits in goats

Reproductive traits show either low to moderate heritability and are measured late in life. Thus molecular markers are required to improve the pace of genetic gain in these traits of economic value. Recent publications report the association of polymorphism in JY-1 gene with cattle reproductive traits. In this study, the only known single nucleotide polymorphism (C15329T) of caprine JY-1 gene was explored for its association with reproductive traits; age at first heat, age at first service and age at first kidding. Black Bengal (n = 70), a sexually precocious and prolific goat breed of India was genotyped for the SNP by designing PCR-RFLP. Effect of year of birth and genotype was found to be non-significant at 1% for all three traits. However, the effect of season of birth was highly significant (p ≤ 0.01) on age at first kidding. Polymorphism in 3'UTR of the JY-1 gene is not associated with the reproductive traits of goats. In future, studies involving large number of animals from different goat breeds as well as investigation of other regions of this gene would be exciting to perform.

Characterization of the exonic regions of the JY-1 gene in zebu cattle and buffaloes

Protein JY-1 is an oocyte-specific protein that plays an important regulatory role in the granulosa cell layer and during the early embryo development stages. It is the first specific protein of maternal origin discovered in a single-ovulating species. In this study, the exon regions of the JY-1 gene were characterized by sequencing in 20 unrelated cattle (Bos taurus indicus) and 20 unrelated buffaloes (Bubalus bubalis). Eighteen polymorphisms were detected in cattle and 10 polymorphisms in buffaloes. Some of the polymorphisms were identified in codifying regions and caused amino acid changes. The insertion of a thymine was detected in the codifying region of exon 3 of the buffalo sequence when compared to the cattle one. This insertion causes a change in the codons frameshift from this point onwards, modifying the 19 terminal amino acids of the buffalo protein and creating a premature stop codon. This finding may explain reproductive differences between cattle and buffaloes in terms of follicle recruitment, embryo development and incidence of twin pregnancies.