Heat shock induces apoptosis related gene expression and apoptosis in porcine parthenotes developing in vitro

Whole genome resequencing reveals the adaptability of native chickens to drought, tropical and frigid environments in Xinjiang

Chickens exhibit extensive genetic diversity and are distributed worldwide. Different chicken breeds have evolved to thrive in diverse environmental conditions. However, research on the genetic mechanisms underlying chicken adaptation to extreme environments, such as tropical, frigid and drought-prone regions, remains limited. In this study, we conducted whole-genome sequencing of 240 individuals from six native chicken breeds in Xinjiang, China, as well as 4 publicly available chicken breeds inhabiting regions with varying annual precipitations, temperatures, and altitudes. Our analysis revealed several genetic variants among the examined breeds. Furthermore, we investigated the genetic diversity and population structure of breeds residing in extreme drought and temperature environments by comparing them. Notably, native chicken breeds exhibited different genetic diversity and population structures. Moreover, we identified candidate genes associated with chicken adaptability to the environment, such as CORO2A, CTNNA3, AGMO, GRID2, BBOX1, COL3A1, INSR, SOX5, MAP2 and PLPPR1. Additionally, pathways such as lysosome, cysteine and methionine metabolism, glycosaminoglycan degradation, and Wnt signaling may be play crucial roles in regulating chicken adaptation to drought environments. Overall, these findings contribute to our understanding of the genetic mechanisms governing chicken adaptation to extreme environments, and also offer insights for enhancing the resilience of chicken breeds to different climatic conditions.

Alpha-lipoic acid attenuates heat stress-induced apoptosis via upregulating the heat shock response in porcine parthenotes

Heat stress (HS) is a long-standing hurdle that animals face in the living environment. Alpha-lipoic acid (ALA) is a strong antioxidant synthesized by plants and animals. The present study evaluated the mechanism of ALA action in HS-induced early porcine parthenotes development. Parthenogenetically activated porcine oocytes were divided into three groups: control, high temperature (HT) (42 °C for 10 h), and HT + ALA (with 10 µM ALA). The results show that HT treatment significantly reduced the blastocyst formation rate compared to the control. The addition of ALA partially restored the development and improved the quality of blastocysts. Moreover, supplementation with ALA not only induced lower levels of reactive oxygen species and higher glutathione levels but also markedly reduced the expression of glucose regulatory protein 78. The protein levels of heat shock factor 1 and heat shock protein 40 were higher in the HT + ALA group, which suggests activation of the heat shock response. The addition of ALA reduced the expression of caspase 3 and increased the expression of B-cell lymphoma-extra-large protein. Collectively, this study revealed that ALA supplementation ameliorated HS-induced apoptosis by suppressing oxidative and endoplasmic reticulum stresses via activating the heat shock response, which improved the quality of HS-exposed porcine parthenotes.

Effects of alpha lipoic acid treatment during in vitro maturation on the development of porcine somatic cell nuclear transfer embryos

Oxidative stress influences the embryo production efficiency in vitro. We investigated the effects of alpha lipoic acid (ALA) treatment during the in vitro maturation (IVM) period on the porcine somatic cell nuclear transfer (SCNT) embryo production. After IVM, maturation rates of the 12.5- and 25-μM ALA-treated groups were not significantly different from those of the 0-μM ALA-treated group. Compared to those in the 0-μM ALA-treated group, the reactive oxygen species and glutathione levels were significantly decreased and increased, respectively, in the cytoplasm of matured oocytes in the 12.5-50-μM ALA-treated groups. Apoptosis rate in cumulus cells after IVM was significantly lower in the 12.5-50-μM ALA-treated groups than in the 0-μM ALA-treated group. Blastocyst formation rate was significantly higher in parthenogenetic oocytes treated with 12.5-μM ALA than in the 0-, 25-, and 50-μM ALA-treated groups. Similarly, in SCNT embryos, the 12.5-μM ALA-treated group showed a significantly higher blastocyst formation rate than the 0-μM ALA-treated group. Apoptosis rate in SCNT blastocysts was significantly decreased by 12.5-μM ALA treatment. The results showed that treatment with 12.5-μM ALA during IVM improves porcine SCNT embryo development and partial quality.

Porcine endometrial heat shock proteins are differentially influenced by pregnancy status, heat stress, and altrenogest supplementation during the peri-implantation period

Heat stress (HS) deleteriously affects multiple components of porcine reproduction and is causal to seasonal infertility. Environment-induced hyperthermia causes a HS response (HSR) typically characterized by increased abundance of intracellular heat shock proteins (HSP). Gilts exposed to HS during the peri-implantation period have compromised embryo survival, however if (or how) HS disrupts the porcine endometrium is not understood. Study objectives were to evaluate the endometrial HSP abundance in response to HS during this period and assess the effect of oral progestin (altrenogest; ALT) supplementation. Postpubertal gilts (n = 42) were artificially inseminated during behavioral estrus (n = 28) or were kept cyclic (n = 14), and randomly assigned to thermal neutral (TN; 21 ± 1 °C) or diurnal HS (35 ± 1 °C for 12 h/31.6 ± 1 °C for 12 h) conditions from day 3 to 12 postestrus (dpe). Seven of the inseminated gilts from each thermal treatment group received ALT (15 mg/d) during this period. Using quantitative PCR, transcript abundance of HSP family A (Hsp70) member 1A (HSPA1A, P = 0.001) and member 6 (HSPA6, P < 0.001), and HSP family B (small) member 8 (HSB8, P = 0.001) were increased while HSP family D (Hsp60) member 1 (HSPD1, P = 0.01) was decreased in the endometrium of pregnant gilts compared to the cyclic gilts. Protein abundance of HSPA1A decreased (P = 0.03) in pregnant gilt endometrium due to HS, while HSP family B (small) member 1 (HSPB1) increased (P = 0.01) due to HS. Oral ALT supplementation during HS reduced the transcript abundance of HSP90α family class B member 1 (HSP90AB1, P = 0.04); but HS increased HSP90AB1 (P = 0.001), HSPA1A (P = 0.02), and HSPA6 (P = 0.04) transcript abundance irrespective of ALT. ALT supplementation decreased HSP90α family class A member 1 (HSP90AA1, P = 0.001) protein abundance, irrespective of thermal environment, whereas ALT only decreased HSPA6 (P = 0.02) protein abundance in TN gilts. These results indicate a notable shift of HSP in the porcine endometrium during the peri-implantation period in response to pregnancy status and heat stress.

High Temperature Disrupts Organelle Distribution and Functions Affecting Meiotic Maturation in Porcine Oocytes

Heat stress (HS) has been known to cause reproductive failure in animals, especially in summer. HS severely affects the developmental potential of oocytes and leads to low fertility rates. Previous studies have reported that HS compromises embryo development in bovine oocytes, and reduces ovarian development in mice, thereby impairing reproductive function in animals. However, the effect of high temperature (HT) on the organelles of porcine oocytes is unknown. In this study, we reported that exposure to HT for 24 h (41°C) significantly decreased meiotic maturation in porcine oocytes (p < 0.05). Further experiments on organelles found that HT induced mitochondrial dysfunction, increased abnormal mitochondrial distribution, and decreased mitochondrial membrane potential (MMP). We also found that HT induced abnormal endoplasmic reticulum (ER) distribution and higher expression of glucose regulatory protein 78 (GRP78), suggesting that HT exposure induces ER stress. Our results also indicated that exposure to HT induced abnormal distribution and dysfunction of the Golgi apparatus, which resulted from a decrease in the expression of the vesicle transporter, Ras-related protein Rab-11A (RAB11A). In addition, we found that HT exposure led to lysosomal damage by increasing the expression of lysosome-associated membrane protein 2 (LAMP2) and microtubule-associated protein 1A/1B-light chain 3 (LC3). In summary, our study revealed that HT exposure disrupts organelle dynamics, which further leads to the failure of meiotic maturation in porcine oocytes.

Seasonality and photoperiod influence in vitro production of buffalo embryos

Buffalo is considered short-day breeder in tropical and subtropical part of the world and seasonality and photoperiodism impart major influence on its fertility. However, its impact on in vitro embryo production (IVEP) remains elusive. Therefore, this study investigated the effect of seasonal variations and photoperiodism on morphological and molecular parameters of IVEP in buffalo. For this purpose, we conducted two different experiments on the oocytes obtained by aspirating follicles from abattoir derived ovaries. In Exp. I, retrospective analysis was performed for oocyte recovery, blastocyst and hatching rate, during four consecutive seasonal periods (i.e. January-March, April-June, July-September and October-December). In Exp. II, oocytes from peak breeding and non-breeding seasons were subjected to 24 hr in vitro maturation and evaluated for polar body extrusion to assess maturation rate. Results showed that embryo development was markedly low during second quarter (April-June) and maximum during fourth quarter (October-December) of the year; referred as non-breeding and breeding seasons, respectively. Comparative data analysis demonstrated that poor oocyte quality is major reason for lesser efficiency of embryo production during non-breeding season than peak breeding season as suggested by poor oocyte recovery (2.31 ± 0.10 vs. 3.65 ± 0.27) and maturation rate (33.32 ± 2.1 vs. 63.15 ± 7.31). Subsequently, comparative gene expression analysis of blastocysts during peak breeding season significantly upregulated pluripotency gene (OCT-4) and downregulated heat shock protein 90, as compared to non-breeding season. Therefore, it could be divulged from the present study that seasonal variations and photoperiodism have profound effect on oocyte quality and subsequent embryo development. It is recommended to find suitable additives for in vitro maturation that could mitigate seasonal effects.

Genome-wide expression analysis of the heat stress response in dermal fibroblasts of Tharparkar (zebu) and Karan-Fries (zebu × taurine) cattle

The present study sought to evaluate mRNA expression profiles in the cultured dermal fibroblasts of Tharparkar (zebu) and Karan-Fries (zebu, Tharparkar × taurine, Holstein Friesian) cattle in response to heat stress. Bioinformatics' analysis identified temperature-regulated biological processes and pathways. Biological processes overrepresented among the earliest genes induced by temperature stress include regulation of stress responses, protein repair, metabolism, protein transport, cell division, and apoptosis. The present microarray platform contains 51,338 synthesized oligonucleotide probes corresponding to at least 36,713 unigenes. A total of 11,183 and 8126 transcripts were differentially expressed with a fold change of ≥ 2 in Tharparkar and Karan-Fries cattle, respectively. Randomly selected real-time validation showed 83.33% correlation with microarray data. Functional annotation and pathway study of the differentially expressed transcripts or genes (DEGs) reveal that upregulated genes significantly (P < 0.05) affect protein processing and NOD-like receptor pathways (NLRs), while downregulated genes were significantly (P < 0.05) found to be associated with cell cycle, metabolism, and protein transport. Gene expression changes include activation of heat shock factors (HSFs), increased expression of heat shock proteins (HSPs), and apoptosis, while decreasing protein synthesis and another metabolism. These findings provide insights into the underlying mechanism of the physiology of heat stress in Tharparkar and Karan-Fries cattle. Understanding the biology and mechanisms of heat stress is critical to developing approaches to ameliorate current production issues for improving animal performance and agriculture economics in tropical climatic conditions. In conclusion, the present study indicates that heat stress differentially affects the expression of the significant number of genes associated with stress response, metabolism, apoptosis, and protein transport in dermal fibroblasts of Tharparkar and Karan-Fries cattle.

Optimal doses of EGF and GDNF act as biological response modifiers to improve porcine oocyte maturation and quality

It is well documented that both epidermal growth factor (EGF) and glial cell line-derived neurotrophic factor (GDNF) are critical for porcine oocyte maturation, however, little information is known about their mechanism of action in vitro. To gain insight into the mechanisms of action of the optimum doses of EGF and GDNF on porcine oocyte maturation, porcine cumulus–oocyte complexes (COCs) were matured in defined porcine oocyte medium supplemented with EGF, GDNF or a combination of both at varying concentrations (0–100 ng/ml) for 44 h. Nuclear and cytoplasmic maturation were determined in terms of nuclear stage after DNA staining with Hoechst and cortical granule distribution after lectin labeling, respectively. Mature oocytes were subsequently collected for gene expression analysis or subjected to in vitro fertilization and cultured for 7 days. The results showed that EGF and/or GDNF, when administered in a certain dose (50 ng/μl) to the maturation medium, not only effectively improved the synchronization of nuclear and cytoplasmic maturation processes within the oocyte, but enhanced expression of their corresponding receptors in mature oocytes (P < 0.05). Moreover, supplementation with an optimal combination of EGF + GDNF resulted in elevation of TFAM transcripts as well as a decrease of caspase-3 transcripts compared with the other studied groups (P < 0.05). Collectively, our results indicate that treatment of porcine oocytes with specific-dose combinations of EGF and GDNF stimulates oocyte quality and competence by transcriptional modulation of genes involved in oocyte survival and competence.

Developmental competence and expression profile of genes in buffalo (Bubalus bubalis) oocytes and embryos collected under different environmental stress

The study examined the effects of different environmental stress on developmental competence and the relative abundance (RA) of various gene transcripts in oocytes and embryos of buffalo. Oocytes collected during cold period (CP) and hot period (HP) were matured, fertilized and cultured in vitro to blastocyst hatching stage. The mRNA expression patterns of genes implicated in developmental competence (OCT-4, IGF-2R and GDF-9), heat shock (HSP-70.1), oxidative stress (MnSOD), metabolism (GLUT-1), pro-apoptosis (BAX) and anti-apoptosis (BCL-2) were evaluated in immature and matured oocytes as well as in pre-implantation stage embryos. Oocytes reaching MII stage, cleavage rates, blastocyst yield and hatching rates increased (P < 0.05) during the CP. In MII oocytes and 2-cell embryos, the RA of OCT-4, IGF-2R, GDF-9, MnSOD and GLUT-1 decreased (P < 0.05) during the HP. In 4-cell embryos, the RA of OCT-4, IGF-2R and BCL-2 decreased (P < 0.05) in the HP, whereas GDF-9 increased (P < 0.05). In 8-to 16-cell embryos, the RA of OCT-4 and BCL-2 decreased (P < 0. 05) in the HP, whereas HSP-70.1 and BAX expression increased (P < 0.05). In morula and blastocyst, the RA of OCT-4, IGF-2R and MnSOD decreased (P < 0.05) during the HP, whereas HSP-70.1 was increased (P < 0.05). In conclusion, deleterious seasonal effects induced at the GV-stage carry-over to subsequent embryonic developmental stages and compromise oocyte developmental competence and quality of developed blastocysts.

Trade-off between thermal tolerance and insecticide resistance in Plutella xylostella

Fitness costs associated with resistance to insecticides have been well documented, usually at normal temperature conditions, in many insect species. In this study, using chlorpyrifos-resistant homozygote (RR) and chlorpyrifos-susceptible homozygote (SS) of resistance ace1 allele of Plutella xylostella (DBM), we confirmed firstly that high temperature experience in pupal stage influenced phenotype of wing venation in insecticide-resistant and insecticide-susceptible Plutella xylostella, and SS DBM showed significantly higher thermal tolerance and lower damages of wing veins under heat stress than RR DBM. As compared to SS DBM, RR DBM displayed significantly lower AChE sensitivity to chlorpyrifos, higher basal GSTs activity and P450 production at 25°C, but higher inhibitions on the enzyme activities and P450 production as well as reduced resistance to chlorpyrifos under heat stress. Furthermore, RR DBM displayed significantly higher basal expressions of hsp69s, hsp72s, hsp20,hsp90,Apaf-1, and caspase-7 at 25°C, but lower induced expressions of hsps and higher induced expressions of Apaf-1,caspase-9, and caspase-7 under heat stress. These results suggest that fitness costs of chlorpyrifos resistance in DBM may partly attribute to excess consumption of energy caused by over production of detoxification enzymes and hsps when the proteins are less demanded at conducive environments but reduced expressions when they are highly demanded by the insects to combat environmental stresses, or to excess expressions of apoptotic genes under heat stress, which results in higher apoptosis. The evolutionary and ecological implications of these findings at global warming are discussed.

Developmental competence and expression pattern of bubaline (Bubalus bubalis) oocytes subjected to elevated temperatures during meiotic maturation in vitro

OBJECTIVE

To determine the direct effect of physiologically relevant high temperatures (40.5 and 41.5 °C) for two time periods (12 and 24 h) on bubaline oocytes during in vitro maturation.

METHOD

The control group oocytes were cultured at 38.5 °C for 24 h. The treatment 1 (T1) and 3 (T3) group oocytes were cultured at 40.5 and 41.5 °C respectively, for the first 12 h and at 38.5 °C for rest of the 12 h. However, treatment 2 (T2) and 4 (T4) group oocytes were cultured at 40.5 and 41.5 °C for complete 24 h.

RESULTS

Development of oocytes to blastocyst was severely compromised (p < 0.001) when matured at 40.5 and 41.5 °C for both exposure periods (12 h and 24 h). It was found that the cleavage rates, blastocyst yield and mean cell number decreased remarkably (p < 0.001) in the treatment groups compared to control. The relative mRNA expression of heat shock protein (Hsp 70.1, 70.2, 70.8, 60, 10 and HSF1), pro-apoptotic (caspases-3, -7, -8, Bid and Bax) and oxidative stress (iNOS) related genes was significantly higher (p < 0.05) in all the treatment groups compared to control. However, mRNA abundance of anti-apoptotic (Bcl-2, Mcl-1, Bcl-xl), glucose transport (Glut1, Glut3 and IGF1R), developmental competence (ZAR1 and BMP15) and oxidative stress (MnSOD) related genes was significantly decreased (p < 0.05) in the treatment groups compared to control.

CONCLUSION

The present study clearly establishes that physiologically relevant elevated temperatures during in vitro meiotic maturation reduce developmental competence of bubaline oocytes.

Paternal breed effects on expression of IGF-II, BAK1 and BCL2-L1 in bovine preimplantation embryos

The effects of the paternal breed on early embryo and later pre- and postnatal development are well documented. Several recent studies have suggested that such paternal effects may be mediated by the paternally induced epigenetic modifications during early embryogenesis. The objective of this study was to investigate the effects of the paternal breed on the early embryonic development and relative expression of the maternally imprinted gene, IGF-II, and the apoptosis-related genes BAK1 and BCL2-L1 in in vitro produced (IVP) bovine embryos derived from two unrelated paternal breeds (Holstein and Brown Swiss). The degree of correlation of IGF-II expression pattern with embryo developmental competence and apoptosis-related genes was also investigated. The relative abundance of IGF-II, BCL2-L1 and BAK1 transcripts in day 8 embryos was measured by quantitative reverse-transcription polymerase chain reaction using the comparative Cp method. Our data revealed that the paternal breed did not influence cleavage rate, blastocyst rate and relative abundance of IGF-II, BAK1 and BCL2-L1 in day 8 blastocysts (P > 0.05). Nevertheless, IGF-II expression levels were highly correlated with embryonic developmental competence (r = 0.66, P < 0.1), relative expression of BCL2-L1 (r = 0.72, P < 0.05) and ratio of BCL2-L1/BAK1 (r = 0.78, P < 0.05). In conclusion, our data show that IGF-II, BCL2-L1 and BAK1 expression is not related to the chosen combination of paternal breed, but that IGF-II expression is correlated with embryonic viability and apoptosis-related gene expression.

Effect of 7,8-dihydroxyflavone as an antioxidant on in vitro maturation of oocytes and development of parthenogenetic embryos in pigs

One of the factors that impairs in vitro produced porcine embryos is the oxidative stress that is mainly caused by the imbalance between reactive oxygen species (ROS) generation and antioxidants activity, especially that of glutathione (GSH). Here, we examined the effect of 7,8-dihydroxyflavone (7,8-DHF), a kind of flavonoid antioxidant, on porcine oocyte maturation and its developmental competence. Porcine oocytes were cultured in media supplemented with 0, 1, 5 and 10 μM 7,8-DHF during both in vitro maturation (IVM) and in vitro culture (IVC) after parthenogenetic activation. Maturation of oocytes was evaluated based on first polar body (PB) extrusion and intracellular GSH level, and developmental competence was assessed through observing cleavage and blastocyst formation. In each step, the levels of intracellular GSH and ROS were assessed by fluorescence intensity, and the apoptosis-related gene expression was examined using semiquantitative RT-PCR. The group treated with 1 μM 7,8-DHF during IVM and IVC showed increased cytoplasmic maturation and reached the blastocysts stage (36.1%) at a higher rate than the other groups (24.7, 16.0 and 10.3% for 0, 5 and 10 μM, P<0.05). In that group, the intracellular GSH level was significantly increased while ROS generation was significantly decreased after IVM and IVC (P<0.05). Moreover, it showed high expression of an anti-apoptotic gene (BCL2L1) and low expression of a pro-apoptotic gene (BAK1) (P<0.05). In conclusion, treatment with 1 μM 7,8-DHF during IVM and IVC showed an anti-apoptotic effect by increasing intracellular GSH synthesis and scavenging ROS and therefore improved the developmental competence of porcine embryos.

Effect of physiologically relevant heat shock on development, apoptosis and expression of some genes in buffalo (Bubalus bubalis) embryos produced in vitro

For investigating the effects of physiologically relevant heat shock, buffalo oocytes/embryos were cultured at 38.5°C (control) or were exposed to 39.5°C (Group II) or 40.5°C (Group III) for 2 h once every day throughout in vitro maturation (IVM), fertilization (IVF) and culture (IVC). Percentage of oocytes that developed to 8-cell, 16-cell or blastocyst stage was lower (p < 0.05) and the number of apoptotic nuclei was higher (p < 0.05) for Group III > Group II > controls. At both 8-16-cell and blastocyst stages, relative mRNA abundance of stress-related genes HSP 70.1 and HSP 70.2 and pro-apoptotic genes CASPASE-3, BID and BAX was higher (p < 0.05) in Groups III and II than that in controls with the exception of stress-related gene HSF1. Expression level of anti-apoptotic genes BCL-XL and MCL-1 was also higher (p < 0.05) in Groups III and II than that in controls at both 8-16-cell and blastocyst stages. Among the genes related to embryonic development, at 8-16-cell stage, the expression level of GDF9 was higher (p < 0.05) in Group III than that in controls, whereas that of GLUT1, ZAR1 and BMP15 was not significantly different among the three groups. At the blastocyst stage, relative mRNA abundance of GLUT1 and GDF9 was higher (p < 0.05) in Group II than that in controls, whereas that of ZAR-1 and BMP15 was not affected. The results of this study demonstrate that exposure of buffalo oocytes and embryos to elevated temperatures for duration of time that is physiologically relevant severely compromises their developmental competence, increases apoptosis and affects stress-, apoptosis- and development-related genes.

Heat stress on reproductive function and fertility in mammals

In most mammalian species including cattle, heat stress has deleterious effects on nutritional, physiological and reproductive functions. Exposure of animals to a hot environment causes an increase in body temperature in mammals, including domestic animals. High ambient temperature also causes a decrease in the length and intensity of estrus by disturbing ovarian function as well as decreasing pregnancy rate after artificial insemination. Therefore, it is important to understand the effects of heat stress on reproductive function in order to improve the production of domestic animals. Heat stress decreases appetite, weight gain, and milk yield in dairy cattle. It also adversely affects the reproductive performance of both sexes. In males, it reduces spermatogenic activity, while in females it adversely impacts oogenesis, oocyte maturation, fertilization development and implantation rate. Detection and evaluation of the deteriorating effects of heat stress on reproductive organs and cells can help to design measures to prevent them and improve reproductive functions. In this review, we discuss the impacts of heat stress on reproductive functions.

Enhanced developmental potential of heat-shocked porcine parthenogenetic embryos is related to accelerated mitogen-activated protein kinase dephosphorylation

Recently, we demonstrated that a 9-h heat shock of 42°C can have marked stimulatory effects on porcine parthenogenetic embryo development if applied immediately after oocyte activation. Developmental discrepancies between heat-shocked (HS) and non-HS embryos were manifest as early as 3 h after activation, suggesting involvement of maturation promoting factor (MPF) and/or mitogen-activated protein kinase (MAPK). Analysis of cdc2 kinase activity showed that MPF inactivation occurred at similar rates in HS and control embryos upon oocyte activation. However, MAPK dephosphorylation was accelerated in HS embryos compared with controls. Okadaic acid, a protein phosphatase inhibitor, maintained MAPK activity at high levels in both non-HS and HS embryos and sensitised HS embryos to the effects of elevated temperatures. No increase in heat shock proteins was observed in pronuclear-stage HS embryos. These data suggest that the acceleration of development observed in HS porcine parthenogenetic embryos is associated with a precocious inactivation of the MAPK signalling cascade. The faster cleavage divisions observed in HS embryos may be linked physiologically to their enhanced developmental potential in vitro.

Advances in swine transcriptomics

The past five years have seen a tremendous rise in porcine transcriptomic data. Available porcine Expressed Sequence Tags (ESTs) have expanded greatly, with over 623,000 ESTs deposited in Genbank. ESTs have been used to expand the pig-human comparative maps, but such data has also been used in many ways to understand pig gene expression. Several methods have been used to identify genes differentially expressed (DE) in specific tissues or cell types under different treatments. These include open screening methods such as suppression subtractive hybridization, differential display, serial analysis of gene expression, and EST sequence frequency, as well as closed methods that measure expression of a defined set of sequences such as hybridization to membrane arrays and microarrays. The use of microarrays to begin large-scale transcriptome analysis has been recently reported, using either specialized or broad-coverage arrays. This review covers published results using the above techniques in the pig, as well as unpublished data provided by the research community, and reports on unpublished Affymetrix data from our group. Published and unpublished bioinformatics efforts are discussed, including recent work by our group to integrate two broad-coverage microarray platforms. We conclude by predicting experiments that will become possible with new anticipated tools and data, including the porcine genome sequence. We emphasize that the need for bioinformatics infrastructure to efficiently store and analyze the expanding amounts of gene expression data is critical, and that this deficit has emerged as a limiting factor for acceleration of genomic understanding in the pig.