Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka F2 chicken population

Chicken growth traits are economically important, but the relevant genetic mechanisms have not yet been elucidated. Herein, we performed a genome-wide association study to identify the variants associated with growth traits. In total, 860 chickens from a Gushi-Anka F₂ resource population were phenotyped for 68 growth and carcass traits, and 768 samples were genotyped based on the genotyping-by-sequencing (GBS) method. Finally, 734 chickens and 321,314 SNPs remained after quality control and removal of the sex chromosomes, and these data were used to carry out a GWAS analysis. A total of 470 significant single-nucleotide polymorphisms (SNPs) for 43 of the 68 traits were detected and mapped on chromosomes (Chr) 1–6, -9, -10, -16, -18, -23, and -27. Of these, the significant SNPs in Chr1, -4, and -27 were found to be associated with more than 10 traits. Multiple traits shared significant SNPs, indicating that the same mutation in the region might have a large effect on multiple growth or carcass traits. Haplotype analysis revealed that SNPs within the candidate region of Chr1 presented a mosaic pattern. The significant SNPs and pathway enrichment analysis revealed that the MLNR, MED4, CAB39L, LDB2, and IGF2BP1 genes could be putative candidate genes for growth and carcass traits. The findings of this study improve our understanding of the genetic mechanisms regulating chicken growth and carcass traits and provide a theoretical basis for chicken breeding programs.Subject terms: Genome-wide association studies, Genetic linkage study, Development, DNA sequencing, Animal breeding     

The CREB/KMT5A complex regulates PTP1B to modulate high glucose-induced endothelial inflammatory factor levels in diabetic nephropathy

Diabetic nephropathy (DN) is the primary microvascular complication of diabetes mellitus and may result in end-stage renal disease. The overproduction of various inflammatory factors is involved in the pathogenesis of DN. Protein tyrosine phosphatase 1B (PTP1B) modulates the expression of a series of cytokines and nuclear factor kappa B (NF-κB) activity. cAMP response element-binding protein (CREB) and lysine methyltransferase 5A (KMT5A) have been reported to participate in the maintenance of a healthy endothelium. In the present study, we hypothesise that CREB associates with KMT5A to modulate PTP1B expression, thus contributing to high glucose-mediated glomerular endothelial inflammation. Our analyses revealed that plasma inflammatory factor levels, glomerular endothelial p65 phosphorylation and PTP1B expression were increased in DN patients and rats. In vitro, high glucose increased endothelial inflammatory factor levels and p65 phosphorylation by augmenting PTP1B expression in human umbilical vein endothelial cells (HUVECs). Moreover, high glucose decreased CREB and KMT5A expression. CREB overexpression and KMT5A overexpression both inhibited high glucose-induced PTP1B expression, p65 phosphorylation and endothelial inflammatory factor levels. si-CREB- and sh-KMT5A-induced p65 phosphorylation and endothelial inflammatory factor levels were reversed by si-PTP1B. Furthermore, CREB was associated with KMT5A. Mechanistic research indicated that CREB and histone H4 lysine 20 methylation (H4K20me1, a downstream target of KMT5A) occupy the PTP1B promoter region. sh-KMT5A augmented PTP1B promoter activity and activated the positive effect of si-CREB on PTP1B promoter activity. Our in vivo study demonstrated that CREB and KMT5A were downregulated in glomerular endothelial cells of DN patients and rats. In conclusion, CREB associates with KMT5A to promote PTP1B expression in vascular endothelial cells, thus contributing to hyperglycemia-induced inflammatory factor levels in DN patients and rats.Subject terms: Diabetes complications, Type 2 diabetes     

Joint analysis of WES and RNA-Seq identify signature genes related to metastasis in prostate cancer

Prostate cancer (PCa) has a certain degree of heritability, and metastasis occurs as cancer progresses. However, its underlying mechanism remains largely unknown. We sequenced four cases of cancer without metastasis, four metastatic cancer, and four benign hyperplasia tissues as controls. A total of 1839 damaging mutations were identified. Pathway analysis, gene clustering, and weighted gene co-expression network analysis were employed to find characteristics associated with metastasis. Chr19 had the most mutation density and 1p36 had the highest mutation frequency across the genome. These mutations occurred in 1630 genes, including the most frequently mutated genes TTN and PLEC, and dozens of metastasis-related genes, such as FOXA1, NCOA1, CD34, and BRCA2. Ras signalling and arachidonic acid metabolism were uniquely enriched in metastatic cancer. Gene programmes 10 and 11 showed the signatures indicating the occurrence of metastasis better. A module (135 genes) was specifically associated with metastasis. Of them, 67.41% reoccurred in program 10, with 26 genes further retained as the signature genes related to PCa metastasis, including AGR3, RAPH1, SOX14, DPEP1, and UBL4A. Our study provides new molecular perspectives on PCa metastasis. The signature genes and pathways could be served as potential therapeutic targets for metastasis or cancer progression.     

Identification of genes influencing formation of the Type III Brush Hair in Yangtze River Delta white goats by differential display of mRNA

Yangtze River Delta white goat is an exclusive indigenous Chinese goat breeds that can produce Brush Hair specialized in making valuable writing brush. The high-grade (Type III) Brush Hair is conical coarse hair but with a tip, which only grows in the cervical carina and back regions of Yangtze River Delta white goats. Screening of genes influencing the formation of Type III Brush Hair was conducted using differential display of mRNA technique in skin including the hair follicles of different goat groups and the differential bands were identified using reverse Northern dot blot, and the positive bands were subsequently cloned and sequenced. The results showed that 20 differentially displayed bands were obtained, seven of which were identified positive as expressed in skin. Three of these seven cDNAs were homologous to certain sequences from GenBank and the other four were respectively homologous to CKLF-like MARVEL transmembrane domain containing 3 (CMTM3), S100 calcium binding protein A4 (S100A4), protein kinase inhibitor gamma (PKIG) and fibulin 1-D. The study would provide a new view to elucidate their roles in hair growth and hair follicle cycle and increase our understanding of the formation of Type III Brush Hair.     

Transformative Network Modeling of Multi-omics Data Reveals Detailed Circuits,Key Regulators,and Potential Therapeutics for Alzheimer’s Disease

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Field management of Sclerotinia stem rot of soybean using biological control agents

Biological control agents (BCAs) were evaluated for their efficacy on reducing the number of sclerotia of Sclerotinia sclerotiorum (Lib.) de Bary in the soil and on Sclerotinia stem rot in soybean production systems in Michigan. BCAs included Coniothyrium minitans CON/M/91–08 (Product name: Contans®WG), Streptomyces lydicus WYEC 108 (Actinovate®AG), Trichoderma harzianum T-22 (PlantShield®HC), and Bacillus subtilis QST 713 (Serenade®MAX). At two field locations, soil artificially infested with S. sclerotiorum sclerotia, was treated by incorporating the above BCAs in the topsoil before planting and boscalid was applied as a foliar fungicide at growth stage R1 as a positive control. C. minitans was the most effective BCA and reduced the disease severity index (DSI) by 68.5% and the number of sclerotia of S. sclerotiorum in the soil by 95.3%. S. lydicus and T. harzianum reduced DSI by 43.1% and 38.5% and sclerotia in soil by 90.6% and 70.8%, respectively. B. subtilis only had a marginal effect on S. sclerotiorum. Populations of Bacillus, Streptomyces, Trichoderma spp., and C. minitans collected from soil samples and at 3, 28, 71, and 169 days after BCA application indicated that the population of Streptomyces, Trichoderma spp., and C. minitans did not change significantly throughout the season, which may be the reason for their effectiveness.     

Functional enrichment of mannanase-treated spent brewer yeast

In this study, the effect of Bacillus amyloliquefaciens-produced β-mannanase on the nutrient diffusion (release) and antioxidant activity of spent brewer yeast (SBY) was investigated. Three pretreatments were performed: (1) autolysis at 50°C for 24?h; (2) autolysis at 50°C for 24?h, with the addition of β-mannanase during the autolysis; (3) autolysis at 50°C for 24?h, and the β-mannanase was added for another 12?h treatment. The pretreatments with the addition of β-mannanase caused significant cell wall degradation, markedly increased the yield of SBY extracts. More importantly, this study found that polysaccharides were degraded to be oligosaccharides with a considerable reduction in molecular weights. Meanwhile, pretreatment with the enzyme also exhibited a higher antioxidant activity in SBY extract compared to autolysis itself. The current study indicated that pretreatment (3) had a better effect than pretreatment (2) in terms of improving in antioxidant activity in SBY extract. These improved characteristics of SBY extracts isolated through enzymatic treatment appear to show promising features for their prospective use as natural functional agents.