Myocardial infarction (MI) may cause heart failure and seriously harm human health. During the genesis of cardiac fibrosis after MI, the proliferation and migration of cardiac fibroblasts contribute to secretion and maintenance of extracellular matrix (ECM) components. Many miRNAs have been highly implicated in the processes of cardiac fibrosis after MI. However, the molecular mechanisms for how miRNAs involve in cardiac fibrosis remain largely unexplored. Based on MI model in miniature pigs, the potential miRNAs involved in MI were identified by using small RNA sequencing. Using human cardiac fibroblasts (HCFs) as a cellular model, EdU, Transwell, and the expression of ECM-related proteins were applied to investigate the cell proliferation, migration and collagen synthesis. In this study, using MI model based on miniature pigs, 84 miRNAs were identified as the differentially expressed miRNAs between MI and control group, and miR-144-3p, one of differentially expressed miRNAs, was identified to be higher expressed in infarct area. The cell proliferation, migration activity, and the mRNA and protein levels of the ECM-related genes were significantly increased by miR-144-3p mimic but significantly decreased by miR-144-3p inhibitor in cardiac fibroblasts. Furthermore, miR-144-3p was observed to repress transcription and translation of PTEN, and interfering with the expression of PTEN up-regulated the mRNAs and proteins levels of α-SMA, Col1A1, and Col3A1, and promoted the proliferation and migration of cardiac fibroblasts, which was in line with that of miR-144-3p mimics, but this observation could be reversed by miR-144-3p inhibitor. Collectively, miR-144-3p promotes cell proliferation, migration, and collagen production by targeting PTEN in cardiac fibroblasts, suggesting that miR-144-3p-mediated-PTEN regulation might be a novel therapeutic target for cardiac fibrosis after MI.

In the pig industry, reproductive traits constantly influence the production efficiency. To identify markers and candidate genes underlying porcine reproductive traits, a genome-wide association study (GWAS) was performed in a Duroc pig population. In total, 1067 pigs were genotyped using single-nucleotide polymorphism (SNP) chips, and four reproductive traits, including litter size at birth (LSB), litter weight at birth (LWB), litter size at weaning (LSW), and litter weight at weaning (LWW), were examined. The results showed that 20 potential SNPs reached the level of suggestive significance and were associated with these traits of interest. Several important candidate genes, including TXN2, KCNA1, ENSSSCG00000003546, ZDHHC18, MAP2K6, BICC1, FAM135B, EPHB2, SEMA4D, ST3GAL1, KCTD3, FAM110A, TMEM132D, TBX3, and FAM110A, were identified and might compose the underlying genetic architecture of porcine reproductive traits. These findings help to understand the genetic basis of porcine reproductive traits and provide important information for molecular breeding in pigs.

Previous studies have implicated the attractive and promising role of miR‐590‐3p to restore the cardiac function following myocardial infarction (MI). However, the molecular mechanisms for how miR‐590‐3p involves in cardiac fibrosis remain largely unexplored. Using human cardiac fibroblasts (HCFs) as the cellular model, luciferase report assay, mutation, EdU assay and transwell migration assay were applied to investigate the biological effects of miR‐590‐3p on the proliferation, differentiation, migration and collagen synthesis of cardiac fibroblasts. We found that miR‐590‐3p significantly suppressed cell proliferation and migration of HCFs. The mRNA and protein expression levels of α‐SMA, Col1A1 and Col3A were significantly decreased by miR‐590‐3p. Moreover, miR‐590‐3p directly targeted at the 3’UTR of ZEB1 to repress the translation of ZEB1. Interfering with the expression of ZEB1 significantly decreased the cell proliferation, migration activity, mRNA and protein expressions of α‐SMA, Col1A1 and Col3A. Furthermore, the expressions of miR‐590‐3p and ZEB1 were identified in infarct area of MI model in pigs. Collectively, miR‐590‐3p suppresses the cell proliferation, differentiation, migration and collagen synthesis of cardiac fibroblasts by targeting ZEB1. These works will provide useful biological information for future studies on potential roles of miR‐590‐3p as the therapeutic target to recover cardiac function following MI.

DNA methylation and long noncoding RNAs (lncRNAs) exhibit an indispensable role in follicular development. However, the specific mechanisms regarding lncRNAs mediated by DNA methylation in follicular development remain unclearly. In this study, we found that inhibiting the expression of DNMT1 promoted granulosa cells (GCs) apoptosis to inhibit follicular development. A novel follicular development-associated lncRNA named inhibitory factor of follicular development (IFFD) was mediated by DNMT1 and showed to arrest follicular development by inhibiting GCs proliferation and estrogen (E2) secretion but promoting GCs apoptosis. Mechanistically, the deactivated Cas9-TET1 demonstrated that the hypomethylation in −1261/−1254 region of IFFD promoted the transcription of IFFD by recruiting SP1. IFFD induced the expression of GLI family zinc finger 1 through competitive binding miR-370, thereby up-regulating the expression of CASP3 to promote GCs apoptosis, as well as downregulating the expressions of PCNA and CYP19A1 to inhibit GCs proliferation and E2 secretion. Collectively, DNMT1-mediated IFFD might be a novel target for the regulation of follicular development.

South China indigenous pigs are famous for their superior meat quality and crude feed tolerance. Saba and Baoshan pigs without saddleback were located in the high-altitude area of Yunnan Province, while Tunchang and Ding’an pigs with saddleback were located in the low-altitude area of Hainan Province. Although these pigs are different in appearance, the underlying genetic differences have not been investigated. In this study, based on the single-nucleotide polymorphism (SNP) genotypes of 124 samples, both the cross-population extended haplotype homozygosity (XP-EHH) and the fixation index (F_ST) statistic were used to identify potential signatures of selection in these pig breeds. We found nine potential signatures of selection detected simultaneously by two methods, annotated 22 genes in Hainan pigs, when Baoshan pigs were used as the reference group. In addition, eleven potential signatures of selection detected simultaneously by two methods, annotated 24 genes in Hainan pigs compared with Saba pigs. These candidate genes were most enriched in GO: 0048015~phosphatidylinositol-mediated signaling and ssc00604: Glycosphingolipid biosynthesis—ganglio series. These selection signatures were likely to overlap with quantitative trait loci associated with meat quality traits. Furthermore, one potential selection signature, which was associated with different coat color, was detected in Hainan pigs. These results contribute to a better understanding of the underlying genetic architecture of South China indigenous pigs.

In recent years, with the development of high-throughput sequencing technology and the commercial availability of genotyping bead chips, more attention is being directed towards the utilization of abundant genetic markers in animal and plant breeding programs, human disease risk prediction and personal medicine. Several useful approaches to accomplish genomic prediction have been developed and used widely, but still have room for improvement to gain more accuracy. In this study, an improved Bayesian approach, termed BayesBπ, which differs from the original BayesB in priors assigning, is proposed. An effective method for calculating the locus-specific π by converting p-values from association between SNPs and traits’ phenotypes is given and systemically validated using a German Holstein dairy cattle population. Furthermore, the new method is applied to a loblolly pine (Pinus taeda) dataset. Compared with the original BayesB, BayesBπ can improve the accuracy of genomic prediction up to 7.62 % for milk fat percentage, a trait which shows a large effect of quantitative trait loci (QTL). For milk yield, which is controlled by small to moderate effect genes, the accuracy of genomic prediction can be improved up to 4.94 %. For somatic cell score, of which no large effect QTL has been reported, GBLUP performs better than Bayesian methods. BayesBπ outperforms BayesCπ in 10 out of 12 scenarios in the dairy cattle population, especially in small to moderate population sizes where accuracy of BayesCπ are dramatically low. Results of the loblolly pine dataset show that BayesBπ outperforms BayesB in 14 out of 17 traits and BayesCπ in 8 out of 17 traits, respectively. For traits controlled by large effect genes, BayesBπ can improve the accuracy of genomic prediction and unbiasedness of BayesB in moderate size populations. Knowledge of traits’ genetic architectures can be integrated into practices of genomic prediction by assigning locus-specific priors to markers, which will help Bayesian approaches perform better in variable selection and marker effects shrinkage.