Identification of Reference Genes for Expression Studies in the Whole-Blood from Three Cattle Breeds under Two States of Livestock Weather Safety

Identification and validation of stable reference genes for expression profiling of target genes in diverse ovine tissues

Quantitative PCR (qPCR) is a widely-used technique for quantifying the expression of target genes across various tissues, as well as under different pathological and physiological conditions. One of the challenges associated with this method is the need to identify optimal reference genes (RGs) that maintain consistent expression levels under diverse experimental settings, thereby ensuring accurate biological interpretation. In this study, we conducted a thorough analysis of 18 candidate RGs (ACTB, BACH1, B2M, GAPDH, HMBS, HPRT1, PGK1, PPIA, PPIB, RPLP0, RPL19, RPS9, RPS15, RPS28, SDHA, TBP, UXT, and YWHAZ) across 10 ovine tissues (muscle, skin, kidney, liver, intestine, rumen, lung, testis, heart, and spleen) obtained from five individual sheep. We aimed to identify genes with stable expression across these tissues. A literature-based survey helped us shortlist candidate genes representing various functional classes from multiple livestock species. We employed four algorithms: geNorm, NormFinder, BestKeeper, and Delta Ct (ΔCt), to rank these genes based on their stability. A consistent trend in the rankings was observed across these different algorithms. RefFinder was then used for a comprehensive ranking, integrating the outputs from the various methods. ACTB, PPIB, BACH1, and B2M emerged as the most stable RGs, while RPS9, RPS15, and PGK1 displayed variable expression. We validated our findings through qPCR analysis of four target genes (ACTN2, CRYAB, DLK1, and TRIM54) in the skin samples from two different sheep breeds. Based on these results, we recommend ACTB, PPIB, BACH1, and B2M as reliable internal control genes for qPCR experiments involving diverse ovine tissues.

Comprehensive evaluation and validation of optimal reference genes for normalization of qPCR data in different caprine tissues

BACKGROUND

Quantitative real-time PCR (qPCR) is a highly reliable method for validating gene expression data in molecular studies due to its sensitivity, specificity, and efficiency. To ensure accurate qPCR results, it's essential to normalize the expression data using stable reference genes.

METHODS

This study aimed to identify suitable reference genes for qPCR studies in goats by evaluating 18 candidate reference genes (ACTB, BACH1, B2M, GAPDH, HMBS, HPRT1, PGK1, PPIA, PPIB, RPLP0, RPL19, RPS9, RPS15, RPS28, SDHA, TBP, UXT, and YWHAZ) in 10 different caprine tissues (heart, intestine, kidney, liver, lung, muscle, rumen, skin, spleen, and testis). An integrated tool called RefFinder, which incorporates various algorithms like NormFinder, GeNorm, BestKeeper, and ΔCt, was used to assess the stability of expression among these genes.

RESULTS

After thorough analysis, ACTB, PPIB, and B2M emerged as the most stable reference genes, while RPL19, RPS15, and RPS9 were found to be the least stable. The suitability of the selected internal control genes was further validated through target gene analysis, confirming their efficacy in ensuring accurate gene expression profiling in goats.

CONCLUSION

The study determined that the geometric average of ACTB, PPIB, and B2M creates an appropriate normalization factor for gene expression studies in goat tissues.

Validation of stable reference genes in peripheral blood mononuclear cells for expression studies involving vector-borne haemoparasitic diseases in bovines

Normalization of gene expression data using appropriate reference genes is critical to diminish any technical bias in an experiment involving quantitative real-time PCR (qPCR). To the best of our knowledge, this is the first report offering a systematic assessment of 14 potential reference genes (RPLP0, ACTB, RPS28, YWHAZ, SDHA, PPIA, RPS9, RPS15, UXT, GAPDH, B2M, BACH1, HMBS, and PPIB) for the identification of the most stable normalizers for qPCR of target genes in peripheral blood mononuclear cells (PBMCs) of bovines for vector-borne haemoparasitic diseases such as anaplasmosis, babesiosis, theileriosis, and trypanosomiasis. A total of 38 blood samples were collected from healthy as well as diseased cattle and buffaloes representing different haemoparasitic diseases. RNA isolated from the PBMCs was subjected to qPCR for the 14 prospective internal control genes. The comprehensive ranking of the genes was accomplished by the RefFinder tool that integrates the results of three algorithms (geNorm, NormFinder, and BestKeeper) and the comparative C_T method. RPS15, B2M, and GAPDH were ranked to be the most stable genes, whereas, PPIA and HMBS emerged to be the least suitable genes. Validation of the selected reference genes by the qPCR analysis of two immunity genes, ISG15 and GPX7 was congruent with the observations of this study. We recommend that a panel of three reference genes including RPS15, B2M, and GAPDH could prove useful in delineating the transcriptional landscape of PBMCs for vector-borne haemoparasitic diseases in bovines.

Expression profiling of heat shock protein genes in whole blood of Romosinuano cattle breed

Background and Aim: Heat shock proteins are highly conserved proteins that work as molecular chaperones expressed in response to thermal stress. This study aimed to determine the expression profile of genes related to the heat stress response in whole blood obtained from the Romosinuano creole breed. Materials and Methods: Real-time polymerase chain reaction was performed to analyze the transcript of hsp90, hsp70, hsp60, and hsf1 in the whole blood of Romosinuano under different temperature-humidity indices (THIs). Results: The expression levels of the hsp70 and hsf1 genes at the high-THI level were higher (p = 0.0011 and p = 0.0003, respectively) than those at the low-THI level. In addition, no differences in the expression levels of the hsp60 and hsP90 genes were detected between the two THIs. Conclusion: The overexpression of hsf1 and hsp70 genes play an important role in protecting cells from damage induced by heat stress. Keywords: climate change, external environment, heat shock proteins, heat stress, mRNA, temperature-humidity index.

Expression profiling of heat shock protein genes in whole blood of Romosinuano cattle breed

Background and Aim

Heat shock proteins are highly conserved proteins that work as molecular chaperones expressed in response to thermal stress. This study aimed to determine the expression profile of genes related to the heat stress response in whole blood obtained from the Romosinuano creole breed.

Materials and Methods

Real-time polymerase chain reaction was performed to analyze the transcript of hsp90, hsp70, hsp60, and hsf1 in the whole blood of Romosinuano under different temperature-humidity indices (THIs).

Results

The expression levels of the hsp70 and hsf1 genes at the high-THI level were higher (p = 0.0011 and p = 0.0003, respectively) than those at the low-THI level. In addition, no differences in the expression levels of the hsp60 and hsP90 genes were detected between the two THIs.

Conclusion

The overexpression of hsf1 and hsp70 genes play an important role in protecting cells from damage induced by heat stress.

Gene Expression of Aquaporins (AQPs) in Cumulus Oocytes Complex and Embryo of Cattle

Aquaporins (AQPs) are proteins with various functions related to proper cell function and early development in mammals. The aim of this study was to evaluate the presence of AQPs and determine their mRNA levels in the cumulus oocyte complex (COC) of four bovine breeds and in blastocysts of five bovine crosses. Grade I, II and III COCs were collected by ovum pick up from non-lactating heifers of the Brahaman, Holstein, Gir and Romosinuano breeds. Embryos were produced in vitro up to the blastocyst stage of the bovine ♀Gir × ♂Holstein, ♀Holstein × ♂Gir, ♀Brahman × ♂Holstein, ♀Holstein × ♂Brahman, and ♀Romosinuano × ♂Holstein crosses. mRNA expression of AQP1-AQP12b was estimated in COC and embryos by real-time-PCR. The presence of the twelve AQPs in the COCs and bovine embryos was established. Additionally, significant differences were determined in the expression of AQP6 and AQP12b in COCs, as well as in transcripts levels of AQP4, AQP8 and AQP9 from bovine embryos. Gene expression of AQPs in COCs and bovine embryos is consistent with the previously described biological functions. This is the first report of AQPs in COC of Gir, Brahman, Holstein and Romosinuano and embryos of five crossbreeds between Bos indicus and B. taurus.

Investigation of chicken housekeeping genes using next-generation sequencing data

Accurate normalization of the gene expression assays, using housekeeping genes (HKGs), is critically necessary. To do so, selection of a proper set of HKGs for a specific experiment is of great importance. Despite many studies, there is no consensus about the suitable set of HKGs for implementing in the quantitative real-time PCR analyses of chicken tissues. A limited number of HKGs have been widely used. However, wide utilization of a little number of HKGs for all tissues is challenging. The emergence of high-throughput gene expression RNA-seq data has enabled the simultaneous comparison of the stability of multiple HKGs. Therefore, employing the average coefficient of variations of at least three datasets per tissue, we sorted all reliably expressed genes (REGs; with FPKM ≥ 1 in at least one sample) and introduced the top 10 most suitable and stable reference genes for each of the 16 chicken tissues. We evaluated the consistency of the results of five tissues using the same methodology on other datasets. Furthermore, we assessed 96 previously widely used HKGs (WU-HKGs) in order to challenge the accuracy of the previous studies. The New Tuxedo software suite was used for the main analyses. The results revealed novel, different sets of reference genes for each of the tissues with 17 common genes among the top 10 genes lists of 16 tissues. The results did disprove the suitability of WU-HKGs such as Actb, Ldha, Scd, B2m, and Hprt1 for any of the tissues examined. On the contrary, a total of 6, 13, 14, 23, and 32 validated housekeeping genes (V-HKGs) were discovered as the most stable and suitable reference genes for muscle, spleen, liver, heart, and kidney tissues, respectively. Although we identified a few new HKGs usable for multiple tissues, the selection of suitable HKGs is required to be tissue specific. The newly introduced reference genes from the present study, despite lacking experimental validation, will be able to contribute to the more accurate normalization for future expression analysis of chicken genes.

Effect of acute heat shock on stress gene expression and DNA methylation in zebu (Bos indicus) and crossbred (Bos indicus × Bos taurus) dairy cattle

Environmental temperature is one of the major factors to affect health and productivity of dairy cattle. Gene expression networks within the cells and tissues coordinate stress response, metabolism, and milk production in dairy cattle. Epigenetic DNA methylations were found to mediate the effect of environment by regulating gene expression patterns. In the present study, we compared three Indian native zebu cattle, Bos indicus (Sahiwal, Tharparkar, and Hariana) and one crossbred Bos indicus × Bos taurus (Vrindavani) for stress gene expression and differences in the DNA methylation patterns. The results indicated acute heat shock to cultured PBMC affected their proliferation, stress gene expression, and DNA methylation. Interestingly, expressions of HSP70, HSP90, and STIP1 were found more pronounced in zebu cattle than the crossbred cattle. However, no significant changes were observed in global DNA methylation due to acute heat shock, even though variations were observed in the expression patterns of DNA methyltransferases (DNMT1, DNMT3a) and demethylases (TET1, TET2, and TET3) genes. The treatment 5-AzaC (5-azacitidine) that inhibit DNA methylation in proliferating PBMC caused significant increase in heat shock-induced HSP70 and STIP1 expression indicating that hypomethylation facilitated stress gene expression. Further targeted analysis DNA methylation in the promoter regions revealed no significant differences for HSP70, HSP90, and STIP1. However, there was a significant hypomethylation for BDNF in both zebu and crossbred cattle. Similarly, NR3C1 promoter region showed hypomethylation alone in crossbred cattle. Overall, the results indicated that tropically adapted zebu cattle had comparatively higher expression of stress genes than the crossbred cattle. Furthermore, DNA methylation may play a role in regulating expression of certain genes involved in stress response pathways.