Identifying SNPs associated with birth weight and days to 100 kg traits in Yorkshire pigs based on genotyping-by-sequencing

Birth weight(BW)and days to 100 kg(D100)are important economic traits that are both affected by polygenes.However,the genetic architecture of these quantitative traits is still elusive.Genotyping-by-sequencing(GBS)data containing a large number of single nucleotide polymorphisms(SNPs)have become a powerful tool in genomic analysis.To better understand their complex genetic structure,a total of 600 Yorkshire pigs were sequenced using GBS technology.After quality control,279787 SNPs were generated for subsequent genome-wide association study(GWAS).A total of 30 genome-wide SNPs(P<1.79 E–07)were identified for D100.Furthermore,a total of 22 and 2 suggestive SNPs(P<3.57 E–06)were detected for D100 and BW,respectively.Of these,one locus located on SSC12(position:46226512 bp)were evaluated to affect both BW and D100 in Yorkshire pigs,indicating the pleiotropism in different traits.Considering the function of candidate genes,two genes,NSRP1 and DOCK7,were suggested as the most promising candidate genes involved in growth traits.Thus,use of GBS is able to identify novel variants and potential candidate genes for BW and D100,and provide an opportunity for improving pig growth traits using genomic selection in pigs.

Genome-wide scan for selection signatures based on whole-genome re-sequencing in Landrace and Yorkshire pigs

We performed a genome-wide scan to detect selection signatures that showed evidence of positive selection in the domestication process by re-sequencing the whole genomes of Landrace and Yorkshire pigs.Fifteen annotated elements with 13 associated genes were identified using the Z-transformed FST(Z(FST))method,and 208 annotated elements with 140 associated genes were identified using the Z-transformed heterozygosity(ZHp)method.The functional analysis and the results of previous studies showed that most of the candidate genes were associated with basic metabolism,disease resistance,cellular processes,and biochemical signals,and several were related to body morphology and organs.They included PPP3CA,which plays an essential role in the transduction of intracellular Ca2+-mediated signals,and WWTR1,which plays a pivotal role in organ size control and tumor suppression.These results suggest that genes associated with body morphology were subject to selection pressure during domestication,whereas genes involved in basic metabolism and disease resistance were subject to selection during artificial breeding.Our findings provide new insights into the potential genetic variation of phenotypic diversity in different pig breeds and will help to better understand the selection effects of modern breeding in Landrace and Yorkshire pigs.

Epigenome-wide DNA methylation analysis reveals differentially methylation patterns in skeletal muscle between Chinese Chenghua and Qingyu pigs

Chenghua(CH)pig and Qingyu(QY)pig are typical Chinese native fatty breeds.CH pig is mainly distributed in Chengdu Plain,while QY pig is widely distributed throughout the mountain areas around the Sichuan Basin.There are significant differences in their phenotypic traits,including body image,growth performance,and meat quality.This study compared several meat quality traits of CH and QY pigs and conducted a genome-wide DNA methylation analysis using reduced representation bisulfite sequencing(RRBS).It was observed that the pH at 45 min(pH_(45min),P=5.22e-13),lightness at 45 min(L^(*)_(45min),P=4.85e-5),and lightness at 24 h(L^(*)_(24h),P=3.57e-5)of CH pigs were higher than those of QY pigs.We detected 10699 differentially methylated cytosines(DMCs)and 2760 differentially methylated genes(DMGs)associated with these DMCs.Functional analysis showed that these DMGs were mainly enriched in the AMPK signaling pathway,Type II diabetes mellitus,Insulin signaling pathway,mTOR signaling pathway,and Insulin resistance.Furthermore,15 DMGs were associated with fat metabolism(ACACA,CAB39,CRADD,CRTC2,FASN,and GCK),muscle development(HK2,IKBKB,MTOR,PIK3CD,PPARGC1A,and RPTOR),or meat quality traits(PCK1,PRKAG2,and SLC2A4).The findings may help to understand further the epigenetic regulation mechanisms of meat quality traits in pigs and provide new basic data for the study of local pigs.

Early use of mTOR inhibitors-based immunosuppression in heart transplantation recipients: a systematic review and meta-analysis of randomized controlled trials

The aim of our study is to assess the efficacy and safety of early use of m TOR inhibitors-based immunosuppression compared with standard immunosuppression in heart transplantation recipients. We reviewed eight randomized controlled trials identified from Medline/Pub Med, Embase, web of science, Transplant Library and Cochrane Library to evaluate the effects of m TOR inhibitors therapy on outcomes of biopsy-proven acute rejection,acute rejection associated with hemodynamic compromise, death, cytomegalovirus infection, post-transplant malignancy, cardiac allograft vasculopathy, maximal intimal thickness and renal function. Meta-analysis including 2066recipients showed a significantly lower incidence of biopsy-proven acute rejection, cytomegalovirus infection, cardiac allograft vasculopathy and decreased maximal intimal thickness change. In conclusion, our meta-analysis suggested that early use of m TOR inhibitors-based immunosuppression were more effective and safer compared with standard immunosuppression in heart transplant recipients, especially in reducing acute rejection, cytomegalovirus infection, cardiacallograft vasculopathy and preserving renal function when combined with reduced calcineurin inhibitors.