Mapping short tandem repeats for liver gene expression traits helps prioritize potential causal variants for complex traits in pigs

Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study investigates the effects of STRs on gene expression in liver tissues based on the whole-genome sequences and RNA-Seq data of a discovery cohort of 260 F6 individuals and a validation population of 296 F7 individuals from a heterogeneous population generated from crosses among eight pig breeds.Results:We identified 5203 and 5868 significantly expression STRs(eSTRs,FDR<1%)in the F6 and F7 populations,respectively,most of which could be reciprocally validated(π1=0.92).The eSTRs explained 27.5%of the cisheritability of gene expression traits on average.We further identified 235 and 298 fine-mapped STRs through the Bayesian fine-mapping approach in the F6 and F7 pigs,respectively,which were significantly enriched in intron,ATAC peak,compartment A and H3K4me3 regions.We identified 20 fine-mapped STRs located in 100 kb windows upstream and downstream of published complex trait-associated SNPs,which colocalized with epigenetic markers such as H3K27ac and ATAC peaks.These included eSTR of the CLPB,PGLS,PSMD6 and DHDH genes,which are linked with genome-wide association study(GWAS)SNPs for blood-related traits,leg conformation,growth-related traits,and meat quality traits,respectively.Conclusions:This study provides insights into the effects of STRs on gene expression traits.The identified eSTRs are valuable resources for prioritizing causal STRs for complex traits in pigs.

Most root-derived carbon inputs do not contribute to long-term global soil carbon storage

Plant root-derived carbon(C)inputs(I_(root))are the primary source of C in mineral bulk soil.However,a fraction of I_(root)may lose quickly(I_(loss),e.g.,via rhizosphere microbial respiration,leaching and fauna feeding)without contributing to long-term bulk soil C storage,yet this loss has never been quantified,particularly on a global scale.In this study we integrated three observational global data sets including soil radiocarbon content,allocation of photo synthetically assimilated C,and root biomass distribution in 2,034 soil profiles to quantify I_(root)and its contribution to the bulk soil C pool.We show that global average I_(root)in the 0-200 cm soil profile is 3.5 Mg ha^(-1)yr^(-1),~80%of which(i.e.,I_(loss))is lost rather than co ntributing to long-term bulk soil C storage.I_(root)decreases exponentially with soil depth,and the top 20 cm soil contains>60%of total I_(root).Actual C input contributing to long-term bulk soil storage(i.e.,I_(root)-I_(loss))shows a similar depth distribution to I_(root).We also map I_(loss)and its depth distribution across the globe.Our results demonstrate the global significance of direct C losses which limit the contribution of I_(root)to bulk soil C storage;and provide spatially explicit data to facilitate reliable soil C predictions via separating direct C losses from total root-derived C inputs.

Chaiqinchengqi decoction regulates necrosis-apoptosis via regulating the release of mitochondrial cytochrome c and caspase-3 in rats with acute necrotizing pancreatitis

OBJECTIVE: To explore the effect and the mechanism of Chaiqinchengqi decoction(CQCQD) on the apoptosis-necrosis switch of pancreatic acinar cells in acute necrotizing pancreatitis(ANP) in rats.METHODS: Sixty Sprague-Dawley rats were randomized into the control group, the ANP group and the CQCQD group. The acute pancreatitis(AP)model was induced by intraperitoneal injections of4 g/kg 8% L-Arginine(PH 7.0) twice with a 1 h interval. Rats in the CQCQD group were intragastrically administered CQCQD(20 mL/kg every 2 h, 3 times,then 20 mL/kg every 6 h, 3 times). Rats were killed at the 6 and 24 h after the induction of AP.The pancreatic tissues were collected for pathology and to isolate pancreatic acinar cells and mitochondria.RESULTS: CQCQD significantly ameliorated the severity of ANP by reducing the pancreatic histopathology score, indicated by lactate dehydrogenase levels at the 6 and 24 h. The CQCQD group promoted the apoptosis of pancreatic acinar cells by raising the apoptosis index compared with the ANP group and the control group. Mitochondrial cytochrome c at the 6 and 24 h in the ANP group were lower than that in the control group or the CQCQD group(0.67±0.13 vs 1.54±0.03 vs 0.81±0.09; 0.71±0.08 vs 1.55±0.09 vs 0.89±0.16, P<0.01). The cytochrome c levels in the cytoplasm at the 6 and 2 h in the CQCQD group were higher than in the control group(1.36±0.15 vs 0.67±0.04, 1.46±0.08 vs 0.59±0.09, P<0.01), or the ANP group(0.96±0.13, P>0.05;0.97±0.09, P<0.05). CQCQD increased caspase-3 activity over the ANP group at the 6 h.CONCLUSION: CQCQD can induce apoptosis and relieve the necrosis of pancreatic acinar cells via promoting the release of mitochondrial cytochrome c and increasing pancreatic caspase-3 activity in ANP rats.

The complete mitochondrial genome of Odontolabis fallaciosa(Coleoptera: Lucanidae) with its phylogenetic implications

In this study, the complete mitochondrial genome of Odontolabis fallaciosa was sequenced for the first time using the next generation sequencing method. Like most reported mitogenomes of scarab beetles, it was a double-stranded circular molecule, consisting of 13 protein-coding genes（PCGs）, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. The mitogenome of O. fallaciosa was 19,614 bp in length. The base nucleotide composition in the mitogenome of O. fallaciosa was： A（40.0%）, T（30.5%）, C（18.5%） and G（11.0%）, with the total AT content of 70.5%. The phylogenetic analysis of twelve species of stag beetles and other three scarab beetles showed that O. fallaciosa and Aegus angustus share a common ancestor. The mitogenomic data could provide a reliable reference for the future study on conservation, phylogeny and even evolution of these species.