Transcriptome Analysis Revealed the Embryo-Induced Gene Expression Patterns in the Endometrium from Meishan and Yorkshire Pigs

Huang, Jingshu; Liu, Ruize; Su, Long; Xiao, Qian; Yu, Mei

doi:10.3390/ijms160922692

Cited by 16 publications

(17 citation statements)

References 65 publications

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“…However, the other two genes GLP1R and LRP1B had no expression in these two tissues from the above data. The APOB gene had very low expression in porcine endometrium during early (gestational day 15) and mid-gestation (gestational days 26 and 50) [ 60 , 62 ]. Based on the Yorkshire endometrium RNA-seq deep sequencing results (Size = 10Gb, unpublished data from our group), the AACS gene was highly expressed in the endometrium during early embryo implantation (RPKM > 250) and the expression of APOB gene was sharply increased at gestational day 15 (RPKM = 16.72) compared with day 12 (RPKM = 1.60).…”

Section: Resultsmentioning

confidence: 99%

Genetic determinants of pig birth weight variability

Wang

Deng

et al. 2016

BMC Genet

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BackgroundPiglet birth weight variability, a trait also known as the within-litter homogeneity of birth weight, reflects the sow’s prolificacy, because it is positively genetically correlated with preweaning mortality but negatively correlated with the mean growth of piglets during sucking. In addition, the maternal additive genetic variance and heritability has been found exist for this trait, thus, reduction in the variability of piglet birth weight to improve the sow prolificacy is possible by selective breeding.ResultsWe performed a genome wide association study (GWAS) in 82 sows with extreme standard deviation of birth weights within the first parity to identify significant SNPs, and finally 266 genome-wide significant SNPs (p < 0.01) were identified. These SNPs were mainly enriched on chromosome 7, 1, 13, 14, 15 and 18. We further scanned genes of the top 50 SNPs with the lowest p values and found some genes involved in plasma glucose homeostasis (GLP1R) and lipid metabolism as well as maternal-fetal lipid transport (AACS, APOB, OSBPL10 and LRP1B) which may contribute to the birth weight variability trait.ConclusionsBirth weight variability trait has a low heritability. It is not easy to get significant signal by GWAS using small sample size. Herein, we identified some candidate chromosome regions especially chromosome 7 and suggested five genes which may provide some information for the further study.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0309-6) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Genetic determinants of pig birth weight variability

Wang

Deng

et al. 2016

BMC Genet

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“…In the past several breed-specific DEGs in porcine endometrium during early pregnancy were also reported [6,46]. For instance, the comparison of endometrium at 12D of early pregnancy between Meishan and Yorkshire [6] allowed to find 17,076 microarray probe-sets in at least two Affymetrix arrays and a total of 14,951 and 14,558 DEG-transcript-probes were identified in Meishan and Yorkshire endometrium respectively.…”

Section: Identification Of Deg Transcripts In Porcine Endometrium Durmentioning

confidence: 99%

“…In our study, we have found 43,603 probe-sets "present" in at least all three pooled arrays and a total of 6049 (3665 upregulated and 2384 downregulated) (Table S5), 374 (184 upregulated and 190 downregulated) (Table S7) and 6034 (2166 upregulated and 3868 downregulated) (Table S9), during 9D vs. 12D, 9D vs. 16D and 12D vs. 16D of early pregnancy in PLW gilts. In another study on breed-specific gene expression comparison of the endometrium [46], during early gestation [15D] vs. mid-gestation period [26D and 50D], revealed a total of 689 and 1649 annotated genes to be differentially expressed in Meishan and Yorkshire endometrium. This study allowed further annotation of DEGs and 73 of them were unique to Meishan endometrium, 536 were unique to Yorkshire endometrium and 228 DEGs were common in Meishan and Yorkshire endometrium.…”

Section: Identification Of Deg Transcripts In Porcine Endometrium Durmentioning

confidence: 99%

Identification of Differentially Expressed Gene Transcripts in Porcine Endometrium during Early Stages of Pregnancy

Pierzchała

Ogłuszka

et al. 2020

Life

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During the early stages of pregnancy, the uterine endometrium undergoes dramatic morphologic and functional changes accompanied with dynamic variation in gene expression. Pregnancy-stage specific differentially expressed gene (DEG)-transcript-probes were investigated and identified by comparing endometrium transcriptome at 9th day (9D), 12th day (12D) and 16th day (16D) of early pregnancy in Polish large-white (PLW) gilts. Endometrium comparisons between 9D-vs-12D, 9D-vs-16D and 12D-vs-16D of early pregnancy identified 6049, 374 and 6034 highly significant DEG-transcript-probes (p < 0.001; >2 FC). GO term enrichment analysis identified commonly shared upregulated endometrial DEG-transcript-probes (p < 0.001; >2 FC), that were regulating the gene functions of anatomic structure development and transport (TG), DNA-binding and methyltransferase activity (ZBTB2), ion-binding and kinase activity (CKM), cell proliferation and apoptosis activity (IL1B). Downregulated DEG-transcript-probes (p < 0.001; >2 FC) were involved in regulating the gene functions of phosphatase activity (PTPN11), TC616413 gene-transcript and Sus-scrofa LOC100525539. Moreover, blastn comparison of microarray-probes sequences against sus-scrofa11 assembly identified commonly shared upregulated endometrial DEG-transcript-probes (E < 0.06; >2 FC), that were regulating the gene functions of reproduction and growth (SELENOP), cytoskeleton organization and kinase activity (CDC42BPA), phosphatase activity (MINPP1), enzyme-binding and cell-population proliferation (VAV3), cancer-susceptibility candidate gene (CASC4), cytoskeletal protein-binding (COBLL1), ion-binding, enzyme regulator activity (ACAP2) Downregulated endometrial DEG-transcript-probes (E < 0.06; >2FC) were involved in regulating the gene functions of signal-transduction (TMEM33), catabolic and metabolic processes (KLHL15). Microarray validation experiment on selected candidate genes showed complementarity to significant endometrial DEG-transcript-probes responsible for the regulation of immune response (IL1B, S100A11), lipid metabolism (FABP3, PPARG), cell-adhesion (ITGAV), angiogenesis (IL1B), intercellular transmission (NMB), cell-adhesion (OPN) and response to stimuli (RBP4) was confirmed by RT-PCR. This study provides a clue that identified pregnancy-stage specific microarray transcript probes could be considered as candidate genes for recognition and establishment of early pregnancy in the pig.

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“…Previous studies show that Meishan pigs have less embryo loss than other commercial breeds, not only during early gestation but also mid-late gestation [4,5,19]. The studies conducted using microarrays and RNA-seq to identify and characterize the genes and miRNAs expressed in the uterine endometrium during early gestation [20][21][22][23] are an important step toward understanding the complex processes that govern the establishment and maintenance of pregnancy. However, little is known about genes and miRNAs expressed in the uterine endometrium during mid-late gestation.…”

Section: Introductionmentioning

confidence: 99%

Integrated Analysis of miRNA-mRNA Network Reveals Different Regulatory Patterns in the Endometrium of Meishan and Duroc Sows during Mid-Late Gestation

Yang

Wang

et al. 2020

Animals

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Embryo loss is a major factor affecting profitability in the pig industry. Embryonic mortality occurs during peri-implantation and mid-late gestation in pigs. Previous investigations have shown that the embryo loss rate in Meishan pigs is significantly lower than in commercial breeds. Most studies have focused on embryonic mortality during early gestation, but little is known about losses during mid-late gestation. In this study, we performed a transcriptome analysis of endometrial tissue in mid-late gestation sows (gestation days 49 and 72) sampled from two breeds (Meishan (MS) and Duroc (DU)) that have different embryo loss rates. We identified 411, 1113, 697, and 327 differentially expressed genes, and 14, 36, 57, and 43 differentially expressed miRNAs in four comparisons (DU49 vs. DU72, DU49 vs. MS49, DU72 vs. MS72, and MS49 vs. MS72), respectively. Subsequently; seven differentially expressed mRNAs and miRNAs were validated using qPCR. Functional analysis suggested the differentially expressed genes and miRNAs target genes mainly involved in regulation of hormone levels, blood vessel development, developmental process involved in reproduction, embryonic placenta development, and the immune system. A network analysis of potential miRNA-gene interactions revealed that differentially expressed miRNAs in Meishan pigs are involved in the response to estradiol and oxygen levels, and affect angiogenesis and blood vessel development. The binding site on ssc-miR-503 for epidermal growth factor (EGF) and the binding site on ssc-miR-671-5p for estrogen receptor α (ESR1) were identified using a dual luciferase assay. The results of this study will enable further exploration of miRNA-mRNA interactions important in pig pregnancy and will help to uncover molecular mechanisms affecting embryonic mortality in pigs during mid-late gestation.

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Transcriptome Analysis Revealed the Embryo-Induced Gene Expression Patterns in the Endometrium from Meishan and Yorkshire Pigs

Cited by 16 publications

References 65 publications

Genetic determinants of pig birth weight variability

Genetic determinants of pig birth weight variability

Identification of Differentially Expressed Gene Transcripts in Porcine Endometrium during Early Stages of Pregnancy

Integrated Analysis of miRNA-mRNA Network Reveals Different Regulatory Patterns in the Endometrium of Meishan and Duroc Sows during Mid-Late Gestation

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