Reference gene selection for the shell gland of laying hens in response to time-points of eggshell formation and nicarbazin

Identification of suitable reference genes for normalization of quantitative real-time PCR-based gene expression in chicken (Gallus gallus)

The recent availability of genome information greatly facilitates the fundamental research on chicken. In different organs, gene expression patterns can provide clues to understanding the biological functions. For rapid and accurate quantification of gene expression, quantitative real-time PCR (qPCR) has become one of the most widely used methods. However, the success of qPCR data normalization depends on the use of a suitable reference gene and a single reference gene is not universally suitable for all the experiments. Therefore, reference gene validation is a crucial step for different organ tissues of chicken where suitable reference genes for qPCR analysis in varieties of tissues have not been investigated exhaustively so far. In this study, we have selected 30 Gallus gallus candidate reference genes from NCBI, amplified and studied their expression profiles by qPCR in different organ tissues (breast muscle, thigh muscle, heart, liver, spleen, gizzard, and bursa) of chicken. The result showed that, for breast muscle HSP10 and RPL23, thigh muscle RPL14 and RPL13, liver ALB and HSP70, spleen ALB and GAPDH, heart CYCS and TUBA8B, gizzard RPL5 and 18S rRNA, and bursa EEF1A1 and PGK2 are most stable genes respectively. The results also showed that for different organ tissues, individual or a combination of reference genes should be selected for data normalization. In this study, we have identified and validated 30 reference genes in seven different organ tissues to provide accurate transcript normalization and quantification, which can be useful for gene expression studies in other avian species.

Identification of reliable reference genes for expression studies in the magnum of laying hens housed in cage and cage-free systems

Stress factors during poultry production can evoke changes in gene transcription and protein synthesis in the hen oviduct and could affect the internal and external egg quality. Studies of relative gene expression require the identification of the most stable reference genes for the quantitative polymerase chain reaction (qPCR) to investigate the reproductive tissues' response in laying hens kept in different production systems. The objective of this study was to determine the most stable reference genes of the magnum tissues of laying hens housed in two different production systems. Hy-Line Brown hens were reared under the same sanitary conditions until 15 weeks of age. Later on, they were transferred into two different production systems, conventional cage (CC) and cage free (CF), up to 82 weeks of age. At 50 and 60 weeks, a total of six hens from each production system were euthanized, and magnum samples were collected. The qPCR was used to determine the RNA transcription level of five reference genes, ACTB, 18S, GAPDH, MSX2 and HMBS. These genes were evaluated for transcript expression in magnum tissues by NormFinder, BestKeeper, geNorm and RefFinder software. The results indicated that the most stable gene in the CF housing system was HMBS in three of the algorithms and in the CC housing system was the 18S, and the best combination of reference genes was HMBS/GAPDH in CF and 18S/HMBS in CC. In conclusion, HMBS, 18S and GAPDH genes could be used together as reference genes for the normalization of the magnum tissues transcript expression of hens in CF and CC housing systems.

Identification of stable genes in the corpus luteum of lactating Holstein cows in pregnancy and luteolysis: Implications for selection of reverse-transcription quantitative PCR reference genes

In lactating dairy cattle, the corpus luteum (CL) is a dynamic endocrine tissue vital for pregnancy maintenance, fertility, and cyclicity. Understanding processes underlying luteal physiology is therefore necessary to increase reproductive efficiency in cattle. A common technique for investigating luteal physiology is reverse-transcription quantitative PCR (RT-qPCR), a valuable tool for quantifying gene expression. However, reference-gene-based RT-qPCR quantification methods require utilization of stably expressed genes to accurately assess mRNA expression. Historically, selection of reference genes in cattle has relied on subjective selection of a small pool of reference genes, many of which may have significant expression variation among different tissues or physiologic states. This is particularly concerning in dynamic tissues such as the CL, with its capacity for rapid physiologic changes during luteolysis, and likely in the less characterized period of CL maintenance during pregnancy. Thus, there is a clear need to identify reference genes well suited for the bovine CL over a wide range of physiological states. Whole-transcriptome RNA sequencing stands as an effective method to identify new reference genes by enabling the assessment of the expression profile of the entire pool of mRNA transcripts. We report the identification of 13 novel putative reference genes using RNA sequencing in the bovine CL throughout early pregnancy and luteolysis: RPL4, UQCRFS1, COX4I1, RPS4X, SSR3, CST3, ZNF266, CDC42, CD63, HIF1A, YWHAE, EIF3E, and PPIB. Independent RT-qPCR analyses were conducted confirming expression stability in another set of CL tissues from pregnancy and regression, with analyses performed for 3 groups of samples: (1) all samples, (2) samples from pregnancy alone, and (3) samples throughout the process of CL regression. Seven genes were found to be more stable in all states than 2 traditional reference genes (ACTB and GAPDH): RPS4X, COX4I1, PPIB, SSR3, RPL4, YWHAE, and CDC42. When CL tissues from pregnant animals alone were analyzed, CST3, HIF1A, and CD63 were also identified as more stable than ACTB and GAPDH. Identification of these new reference genes will aid in accurate normalization of RT-qPCR results, contributing to proper interpretation of gene expression relevant to luteal physiology. Furthermore, our analysis sheds light on the effects of luteolysis and pregnancy on the stability of gene expression in the bovine CL.

Identification of reliable reference genes for quantitative real-time PCR in ovary and uterus of laying hens under heat stress

The main stage in real-time quantitative PCR is a quantification of gene transcriptomes, in which suitable use of reliable reference genes is critical to normalize accurately. To determine the most stable reference genes in laying hens under heat stress, from a panel of nine typical candidate reference genes, the mRNA transcript of ACTB, HMBS, HPRT1, RPL13, RPL32, 18SrRNA, TBP, TFRC, and YWHAZ was evaluated in the ovary and uterus of both control and heat-stress groups of laying hens. Forty 23-week-old White Leghorn laying hens were housed in two rooms. The control (n = 20) and heat-stress (n = 20) groups were maintained at 21-23 °C and 36-38 °C for 8 weeks respectively. Analysis of this set of genes was done with BestKeeper, geNorm, and NormFinder software programs to find the most stable ones. Candidate reference genes ranked in the uterus of heat-stress and control groups of hens included YWHAZ, HPRT1, HMBS, RPL13, TFRC, ACTB, TBP, RPL32, and 18SrRNA; those in the ovary were YWHAZ, HPRT1, TFRC, HMBS, RPL13, TBP, RPL32, ACTB, and 18SrRNA. The overall results indicated that the most stable genes are YWHAZ, HPRT1, HMBS, RPL13, TFRC, TBP, ACTB, RPL32, and 18SrRNA respectively. In addition, the combination of YWHAZ, HPRT1, and HMBS is suggested as the most stable reference group of genes for more accurate quantitative data normalization in the ovarian and uterine tissues of laying hens under control and heat stress conditions. Lay summary Heat stress influences the expression of many genes in the reproductive tissues of birds. Accurate evaluation of these changes via real-time quantitative PCR depends on the determination of reliable reference genes. In this study, nine candidate housekeeping genes were evaluated, and the most stable were YWHAZ, HPRT1, HMBS, RPL13, TFRC, TBP, ACTB, RPL32, and 18SrRNA.

Reference gene selection for gene expression study in shell gland and spleen of laying hens challenged with infectious bronchitis virus

Ten reference genes were investigated for normalisation of candidate target gene expression data in the shell gland and spleen of laying hens challenged with two strains of infectious bronchitis virus (IBV). Data were analysed with geNorm, NormFinder and BestKeeper, and a comprehensive ranking (geomean) was calculated. In the combined data set of IBV challenged shell gland samples, the comprehensive ranking showed TATA-box binding protein (TBP) and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta (YWHAZ) as the two most stable, and succinate dehydrogenase complex flavoprotein subunit A (SDHA) and albumin (ALB) as the two least stable reference genes. In the spleen, and in the combined data set of the shell gland and spleen, the two most stable and the two least stable reference genes were TBP and YWHAZ, and ribosomal protein L4 (RPL4) and ALB, respectively. Different ranking has been due to different algorithms. Validation studies showed that the use of the two most stable reference genes produced accurate and more robust gene expression data. The two most and least stable reference genes obtained in the study, were further used for candidate target gene expression data normalisation of the shell gland and spleen under an IBV infection model.