Genome-wide unraveling SNP pairwise epistatic effects associated with sheep body weight.

Epistatic effects are an important part of the genetic effect of complex traits in livestock. In this study, we used 218 synthetic ewes from the Xinjiang Academy of Agricultural Reclamation in China to identify interacting paired with genome-wide single nucleotide polymorphisms (SNPs) associated with birth weight, weaning weight, and one-yearling weight. We detected 2 and 66 SNP-SNP interactions of sheep birth weight and weaning weight, respectively. No significant epistatic interaction of one-year-old body weight was detected. The genetic interaction of sheep body weight is dynamic and time-dependent. Most significant interactions of weaning body weight contributed 1% or higher. In the weaning weight trait, 66 significant SNP pairs consisted of 98 single SNPs covering 23 chromosomes, 5 of which were nonsynonymous SNPs (nsSNPs), resulting in single amino acid substitution. We found that genes that interact with transcription factors (TFs) are target genes for the corresponding TFs. Four epitron networks affecting weaning weight, including subnetworks of HIVEP3 and BACH2 transcription factors, constructed using significant SNP pairs, were also analyzed and annotated. These results suggest that transcription factors may play an important role in explaining epistatic effects. It provides a new idea to study the genetic mechanism of weight developing.

Uncovering the candidate genes related to sheep body weight using multi-trait genome-wide association analysis.

In sheep, body weight is an economically important trait. This study sought to map genetic loci related to weaning weight and yearling weight. To this end, a single-trait and multi-trait genome-wide association study (GWAS) was performed using a high-density 600 K single nucleotide polymorphism (SNP) chip. The results showed that 43 and 56 SNPs were significantly associated with weaning weight and yearling weight, respectively. A region associated with both weaning and yearling traits (OARX: 6.74-7.04 Mb) was identified, suggesting that the same genes could play a role in regulating both these traits. This region was found to contain three genes (TBL1X, SHROOM2 and GPR143). The most significant SNP was Affx-281066395, located at 6.94 Mb (p = 1.70 × 10-17), corresponding to the SHROOM2 gene. We also identified 93 novel SNPs elated to sheep weight using multi-trait GWAS analysis. A new genomic region (OAR10: 76.04-77.23 Mb) with 22 significant SNPs were discovered. Combining transcriptomic data from multiple tissues and genomic data in sheep, we found the HINT1, ASB11 and GPR143 genes may involve in sheep body weight. So, multi-omic anlaysis is a valuable strategy identifying candidate genes related to body weight.

Genome-wide association analysis of milk production, somatic cell score, and body conformation traits in Holstein cows.

Milk production and body conformation traits are critical economic traits for dairy cows. To understand the basic genetic structure for those traits, a genome wide association study was performed on milk yield, milk fat yield, milk fat percentage, milk protein yield, milk protein percentage, somatic cell score, body form composite index, daily capacity composite index, feed, and leg conformation traits, based on the Illumina Bovine HD100k BeadChip. A total of 57, 12 and 26 SNPs were found to be related to the milk production, somatic cell score and body conformation traits in the Holstein cattle. Genes with pleiotropic effect were also found in this study. Seven significant SNPs were associated with multi-traits and were located on the PLEC, PLEKHA5, TONSL, PTGER4, and LCORL genes. In addition, some important candidate genes, like GPAT3, CEBPB, AGO2, SLC37A1, and FNDC3B, were found to participate in fat metabolism or mammary gland development. These results can be used as candidate genes for milk production, somatic cell score, and body conformation traits of Holstein cows, and are helpful for further gene function analysis to improve milk production and quality.

KLF4, a Key Regulator of a Transitive Triplet, Acts on the TGF-ß Signaling Pathway and Contributes to High-Altitude Adaptation of Tibetan Pigs.

Tibetan pigs are native mammalian species on the Tibetan Plateau that have evolved distinct physiological traits that allow them to tolerate high-altitude hypoxic environments. However, the genetic mechanism underlying this adaptation remains elusive. Here, based on multitissue transcriptional data from high-altitude Tibetan pigs and low-altitude Rongchang pigs, we performed a weighted correlation network analysis (WGCNA) and identified key modules related to these tissues. Complex network analysis and bioinformatics analysis were integrated to identify key genes and three-node network motifs. We found that among the six tissues (muscle, liver, heart, spleen, kidneys, and lungs), lung tissue may be the key organs for Tibetan pigs to adapt to hypoxic environment. In the lung tissue of Tibetan pigs, we identified KLF4, BCL6B, EGR1, EPAS1, SMAD6, SMAD7, KDR, ATOH8, and CCN1 genes as potential regulators of hypoxia adaption. We found that KLF4 and EGR1 genes might simultaneously regulate the BCL6B gene, forming a KLF4-EGR1-BCL6B complex. This complex, dominated by KLF4, may enhance the hypoxia tolerance of Tibetan pigs by mediating the TGF-ß signaling pathway. The complex may also affect the PI3K-Akt signaling pathway, which plays an important role in angiogenesis caused by hypoxia. Therefore, we postulate that the KLF4-EGR1-BCL6B complex may be beneficial for Tibetan pigs to survive better in the hypoxia environments. Although further molecular experiments and independent large-scale studies are needed to verify our findings, these findings may provide new details of the regulatory architecture of hypoxia-adaptive genes and are valuable for understanding the genetic mechanism of hypoxic adaptation in mammals.

Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family.

The CCAAT/enhancer binding protein (C/EBP) transcription factors (TFs) regulate many important biological processes, such as energy metabolism, inflammation, cell proliferation etc. A genome-wide gene identification revealed the presence of a total of 99 C/EBP genes in pig and 19 eukaryote genomes. Phylogenetic analysis showed that all C/EBP TFs were classified into 6 subgroups named C/EBPα, C/EBPß, C/EBPδ, C/EBPε, C/EBPγ, and C/EBPζ. Gene expression analysis showed that the C/EBPα, C/EBPß, C/EBPδ, C/EBPγ, and C/EBPζ genes were expressed ubiquitously with inconsistent expression patterns in various pig tissues. Moreover, a pig C/EBP regulatory network was constructed, including C/EBP genes, TFs and miRNAs. A total of 27 feed-forward loop (FFL) motifs were detected in the pig C/EBP regulatory network. Based on the RNA-seq data, gene expression patterns related to FFL sub-network were analyzed in 27 adult pig tissues. Certain FFL motifs may be tissue specific. Functional enrichment analysis indicated that C/EBP and its target genes are involved in many important biological pathways. These results provide valuable information that clarifies the evolutionary relationships of the C/EBP family and contributes to the understanding of the biological function of C/EBP genes.

Effects of TAT-SOD at Acupoints on Essential Hypertension by Monitoring Meridians Electrical Potential.

OBJECTIVES: To investigate the effect on essential hypertension of the topical application of TAT-Cu, Zn-superoxide dismutase (TAT-SOD) at left acupoint Zusanli (ST 36), and to observe whether the change of electrical potential difference (EPD) can be related to the change of blood pressure. METHODS: Sixteen patients with essential hypertension and 16 healthy subjects were included in the study. EPD between the left acupoints of Yanglingquan (GB 34) and Qiuxu (GB 40) was firstly screened out for the EPD detection. An intracellular superoxide quenching enzyme, TAT-SOD, was topically applied to the acupoint ST 36 within an area of 1 cm2 once a day, and the influence on EPD was investigated. The dosage applied to TAT-SOD group (n=8) was 0.2 mL of 3000 U/mL TAT-SOD cream prepared by adding purified TAT-SOD to a vehicle cream, while placebo group (n=8) used the vehicle cream instead. The left acupoints of Yanglingquan (GB 34) and Qiuxu (GB 40) were selected for EPD measurement after comparing EPD readings between 5 acupoints on each of all 12 meridians. RESULTS: EPDs between the left acupoints of GB 34 and GB 40 for 16 patients of essential hypertension and 16 healthy subjects were 44.9±6.4 and 5.6±0.9 mV, respectively. Daily application of TAT-SOD for 15 days at ST 36 of essential hypertension patients significantly decreased systolic blood pressure (SBP) and diastolic blood pressure (DBP) of 179.6 and 81.5 mm Hg to 153.1 and 74.1 mm Hg, respectively. Responding to the change in blood pressure, EPD between the left acupoints of GB 34 and GB 40 also declined from 44.4 to 22.8 mV with the same trend. No change was observed with SBP, DBP and EPD between the left acupoints of GB 34 and GB 40 with the daily application of the placebo cream. CONCLUSION: Enzymatic scavenging of the intracellular superoxide at ST 36 proved to be effective in decreasing SBP and DBP. The results reconfirm the involvement of superoxide anions and its transportation along the meridians, and demonstrate that EPD between acupoints may be an indicator to reflect its functioning status. Moreover, preliminary results suggest a close correlation between EPD and blood pressure readings, implying a possibility of using EPD as a sensitive parameter for blood pressure and to monitor the effect of antihypertensive treatment.

Monitoring the Effects of Acupoint Antioxidant Intervention by Measuring Electrical Potential Difference along the Meridian.

Previous studies suggest that superoxide anions are possibly traveling along acupuncture meridians. The electrical potential difference (EPD) between acupoints may be related to the movement. To test the above hypothesis, we conducted a study investigating the effects of acupoint antioxidant interventions on the meridian EPD. Firstly, ST39 (L) and ST44 (L) were screened out for the EPD detection along the stomach meridian, and ST36 (L) was selected for interventions including acumassage with the control cream, as well as the TAT-SOD cream for 30 minutes, or injection with reduced glutathione sodium. The EPD between ST39 and ST44 was recorded for 80 minutes and measured again 48 h later. While the EPD increased during the acumassage, the acumassage with TAT-SOD cream and the glutathione injection generated waves of EPD increased, indicating the migration or removal from the visceral organ of a greater quantity of superoxide. Remarkably lower EPD readings 48 h later with both antioxidant acupoint interventions than the mere acumassage imply a more complete superoxide flushing out due to the restored superoxide pathway at the acupoint after interventions. The results confirm superoxide transportation along the meridians and demonstrate a possibility of acupoint EPD measurement as a tool to monitor changes in the meridians and acupoints.