Key genes and metabolites that regulate wool fibre diameter identified by combined transcriptome and metabolome analysis.

BACKGROUND: Fibre diameter is an important economic trait of wool fibre. As the fibre diameter decreases, the economic value of wool increases. Therefore, understanding the mechanism of wool fibre diameter regulation is important in improving the value of wool. RESULTS: In this study, we used non-targeted metabolome and reference transcriptome data to detect differences in metabolites and genes in groups of Alpine Merino sheep with different wool fibre diameter gradients, and integrated metabolome and transcriptome data to identify key genes and metabolites that regulate wool fibre diameter. We found 464 differentially abundant metabolites (DAMs) and 901 differentially expressed genes (DEGs) in four comparisons of groups with different wool fibre diameters. Approximately 25% of the differentially abundant metabolites were lipid and lipid-like molecules. These molecules were predicted to be associated with skin development and keratin filament by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses. Key genes, including COL5A2, COL5A3, CREB3L4, COL1A1, and SFRP4, were identified by gene set enrichment analysis. CONCLUSIONS: Key genes regulating wool fibre diameter were identified, the effects of lipid molecules on wool performance were investigated, and potential synergies between genes and metabolites were postulated, providing a theoretical framework for fine wool sheep breeding.

Construction of a high-density genetic map and QTL localization of body weight and wool production related traits in Alpine Merino sheep based on WGR.

BACKGROUND: The Alpine Merino is a new breed of fine-wool sheep adapted to the cold and arid climate of the plateau in the world. It has been popularized in Northwest China due to its superior adaptability as well as excellent production performance. Those traits related to body weight, wool yield, and wool fiber characteristics, which are economically essential traits in Alpine Merino sheep, are controlled by QTL (Quantitative Trait Loci). Therefore, the identification of QTL and genetic markers for these key economic traits is a critical step in establishing a MAS (Marker-Assisted Selection) breeding program. RESULTS: In this study, we constructed the high-density genetic linkage map of Alpine Merino sheep by sequencing 110 F1 generation individuals using WGR (Whole Genome Resequencing) technology. 14,942 SNPs (Single Nucleotide Polymorphism) were identified and genotyped. The map spanned 2,697.86 cM, with an average genetic marker interval of 1.44 cM. A total of 1,871 high-quality SNP markers were distributed across 27 linkage groups, with an average of 69 markers per LG (Linkage Group). Among them, the smallest genetic distance is 19.62 cM for LG2, while the largest is 237.19 cM for LG19. The average genetic distance between markers in LGs ranged from 0.24 cM (LG2) to 3.57 cM (LG17). The marker density in the LGs ranged from LG14 (39 markers) to LG1 (150 markers). CONCLUSIONS: The first genetic map of Alpine Merino sheep we constructed included 14,942 SNPs, while 46 QTLs associated with body weight, wool yield and wool fiber traits were identified, laying the foundation for genetic studies and molecular marker-assisted breeding. Notably, there were QTL intervals for overlapping traits on LG4 and LG8, providing potential opportunities for multi-trait co-breeding and further theoretical support for selection and breeding of ultra-fine and meaty Alpine Merino sheep.

Selection signatures of wool color in Gangba sheep revealed by genome-wide SNP discovery.

BACKGROUND: Gangba sheep as a famous breed of Tibetan sheep, its wool color is mainly white and black. Gangba wool is economically important as a high-quality raw material for Tibetan blankets and Tibetan serge. However, relatively few studies have been conducted on the wool color of Tibetan sheep. RESULTS: To fill this research gap, this study conducted an in-depth analysis of two populations of Gangba sheep (black and white wool color) using whole genome resequencing to identify genetic variation associated with wool color. Utilizing PCA, Genetic Admixture, and N-J Tree analyses, the present study revealed a consistent genetic relationship and structure between black and white wool colored Gangba sheep populations, which is consistent with their breed history. Analysis of selection signatures using multiple methods (FST, π ratio, Tajima's D), 370 candidate genes were screened in the black wool group (GBB vs GBW); among them, MC1R, MLPH, SPIRE2, RAB17, SMARCA4, IRF4, CAV1, USP7, TP53, MYO6, MITF, MC2R, TET2, NF1, JAK1, GABRR1 genes are mainly associated with melanin synthesis, melanin delivery, and distribution. The enrichment results of the candidate genes identified 35 GO entries and 19 KEGG pathways associated with the formation of the black phenotype. 311 candidate genes were screened in the white wool group (GBW vs GBB); among them, REST, POU2F1, ADCY10, CCNB1, EP300, BRD4, GLI3, and SDHA genes were mainly associated with interfering with the differentiation of neural crest cells into melanocytes, affecting the proliferation of melanocytes, and inhibiting melanin synthesis. 31 GO entries and 22 KEGG pathways were associated with the formation of the white phenotype. CONCLUSIONS: This study provides important information for understanding the genetic mechanism of wool color in Gangba, and provides genetic knowledge for improving and optimizing the wool color of Tibetan sheep. Genetic improvement and selective breeding to produce wool of specific colors can meet the demand for a diversity of wool products in the Tibetan wool textile market.

Motion measurements of explosive shock waves based on an event camera.

Shock wave measurement is vital in assessing explosive power and designing warheads. To obtain satisfactory observation data of explosive shock waves, it is preferable for optical sensors to possess high-dynamic range and high-time resolution capabilities. In this paper, the event camera is first employed to observe explosive shock waves, leveraging its high dynamic range and low latency. A comprehensive procedure is devised to measure the motion parameters of shock waves accurately. Firstly, the plane lines-based calibration method is proposed to compute the calibration parameters of the event camera, which utilizes the edge-sensitive characteristic of the event camera. Then, the fitted ellipse parameters of the shock wave are estimated based on the concise event data, which are gained by utilizing the characteristics of the event triggering and shock waves' morphology. Finally, the geometric relationship between the ellipse parameters and the radius of the shock wave is derived, and the motion parameters of the shock wave are estimated. To verify the performance of our method, we compare our measurement results in the TNT explosion test with the pressure sensor results and empirical formula prediction. The relative measurement error compared to pressure sensors is the lowest at 0.33% and the highest at 7.58%. The experimental results verify the rationality and effectiveness of our methods.

Widespread reductions in cortical thickness following ketamine abuse.

BACKGROUND: Esketamine is a version of ketamine that has been approved for treatment-resistant depression, but our previous studies showed a link between non-medical use of ketamine and brain structural and functional alterations, including dorsal prefrontal grey matter reduction among chronic ketamine users. In this study, we sought to determine cortical thickness abnormalities following long-term, non-medical use of ketamine. METHODS: We acquired structural brain images for patients with ketamine use disorder and drug-free healthy controls. We used FreeSurfer software to measure cortical thickness for 68 brain regions. We compared cortical thickness between the 2 groups using analysis of covariance with covariates of age, gender, educational level, smoking, drinking, and whole-brain mean cortical thickness. RESULTS: We included images from 95 patients with ketamine use disorder and 169 controls. Compared with healthy controls, patients with ketamine use disorder had widespread decreased cortical thickness, with the most extensive reductions in the frontal (including the dorsolateral prefrontal cortex) and parietal (including the precuneus) lobes. Increased cortical thickness was not observed among ketamine users relative to comparison participants. Estimated total lifetime ketamine consumption was correlated with reductions in the right inferior parietal and the right rostral middle frontal cortical thickness. LIMITATIONS: We conducted a retrospective cross-sectional study, but longitudinal studies are needed to further validate decreased cortical thickness after nonmedical use of ketamine. CONCLUSION: This study provided evidence that, compared with healthy controls, chronic ketamine users have widespread reductions in cortical thickness. Our study underscores the importance of the long-term effects of ketamine on brain structure and serves as a reference for the antidepressant use of ketamine.

Alterations and Significance of Computed Tomography Pulmonary Angiography-Derived Parameters in Older Patients With Acute Pulmonary Embolism.

OBJECTIVE: This study aimed to investigate changes of computed tomography pulmonary angiography (CTPA)-derived parameters in older adults with acute pulmonary embolism (APE). METHODS: According to the pulmonary artery obstruction index (PAOI), patients with APE were divided into the A1 (PAOI ≥30%, n = 57) and A2 (PAOI <30%, n = 40) groups. Participants without APE were placed in group B (n = 170). The left atrial (LA) and left ventricular (LV) parameters among the three groups were compared, and the parameter changes in the 44 patients with APE were analyzed before and after treatment. The correlation between APE severity and the parameters was analyzed using correlation analysis. RESULTS: The left-to-right diameters (LR) of LA, and LR × anteroposterior diameters (AP) of LA and LV: A1 < A2 < B; LR of LV: A1 < A2, B; AP of LA and LV: A1, A2 < B. After treatment, LR and LR × AP of the LA and LV were significantly increased in the group A1 and LR of the LV and LR × AP of the LA and LV were elevated in the group A2. Acute pulmonary embolism severity was closely associated with LR × AP ( r = -0.557) and LR ( r = -0.477) of LA. CONCLUSIONS: With an increase in the degree of obstruction, older adults had a smaller LA and LV. Furthermore, the LR and LR × AP values of the LA were significantly decreased. These results contribute to in-time risk stratification.

DIA-Based Proteomic Analysis Reveals MYOZ2 as a Key Protein Affecting Muscle Growth and Development in Hybrid Sheep.

Hybridization of livestock can be used to improve varieties, and different hybrid combinations produce unique breeding effects. In this study, male Southdown and Suffolk sheep were selected to hybridize with female Hu sheep to explore the effects of male parentage on muscle growth and the development of offspring. Using data-independent acquisition technology, we identified 119, 187, and 26 differentially abundant proteins (DAPs) between Hu × Hu (HH) versus Southdown × Hu (NH), HH versus Suffolk × Hu (SH), and NH versus SH crosses. Two DAPs, MYOZ2 and MYOM3, were common to the three hybrid groups and were mainly enriched in muscle growth and development-related pathways. At the myoblast proliferation stage, MYOZ2 expression decreased cell viability and inhibited proliferation. At the myoblast differentiation stage, MYOZ2 expression promoted myoblast fusion and enhanced the level of cell fusion. These findings provide new insights into the key proteins and metabolic pathways involved in the effect of male parentage on muscle growth and the development of hybrid offspring in sheep.

High-quality and high-diversity conditionally generative ghost imaging based on denoising diffusion probabilistic model.

Deep-learning (DL) methods have gained significant attention in ghost imaging (GI) as promising approaches to attain high-quality reconstructions with limited sampling rates. However, existing DL-based GI methods primarily emphasize pixel-level loss and one-to-one mapping from bucket signals or low-quality GI images to high-quality images, tending to overlook the diversity in image reconstruction. Interpreting image reconstruction from the perspective of conditional probability, we propose the utilization of the denoising diffusion probabilistic model (DDPM) framework to address this challenge. Our designed method, known as DDPMGI, can not only achieve better quality but also generate reconstruction results with high diversity. At a sampling rate of 10%, our method achieves an average PSNR of 21.19 dB and an SSIM of 0.64, surpassing the performance of other comparison methods. The results of physical experiments further validate the effectiveness of our approach in real-world scenarios. Furthermore, we explore the potential application of our method in color GI reconstruction, where the average PSNR and SSIM reach 20.055 dB and 0.723, respectively. These results highlight the significant advancements and potential of our method in achieving high-quality image reconstructions in GI, including color image reconstruction.

Treatment of Post-Stroke Dysphagia with Repetitive Transcranial Magnetic Stimulation Based on the Bimodal Balance Recovery Model: A Pilot Study.

BACKGROUND: Brain plasticity and functional reorganization are the main mechanisms of stroke rehabilitation and the theoretical basis for transcranial magnetic therapy. Bimodal balance recovery model suggests that the structural integrity of neural pathways affects the functional reorganization mode of brain recovery after stroke. The principal neural pathway that innervates swallowing is the corticobulbar tract (CBT). The goal is to investigate the impact of corticobulbar tract integrity on swallowing function recovery in post-stroke dysphagia (PSD) patients treated with repetitive transcranial magnetic stimulation (rTMS). METHODS: Thirty-five patients with high CBT integrity (relative fractional anisotropy (rFA) >0.5) and 32 patients with low CBT integrity (rFA ≤0.5) were respectively assigned to three subgroups through a random number table: 5 Hz frequency rTMS group, 1 Hz frequency rTMS group, and Sham rTMS group. The Standardized Swallowing Assessment (SSA), Penetration Aspiration Scale (PAS), and Dysphagia Outcome Severity Scale (DOSS) were analyzed before and after therapy. RESULTS: Significant improvements in SSA (p < 0.05), PAS (p < 0.05), and DOSS scores (p < 0.05) were seen in the high frequency (HF) and low frequency (LF) groups compared with the Sham group for patients with high CBT integrity. Increased SSA (p < 0.05), PAS (p < 0.05), and DOSS scores (p < 0.05) demonstrated that the HF group achieved greater remediation than the LF and Sham groups for patients with low CBT integrity. CONCLUSIONS: Both 5 Hz and 1 Hz rTMS over the contralateral hemisphere are effective for the treatment of swallowing disorders for patients with high CBT integrity after stroke; 5 Hz rTMS over the contralateral hemisphere is more effective than 1 Hz and sham stimulation for patients with low CBT integrity.

Molecular Mechanism of m6A Methylation Modification Genes METTL3 and FTO in Regulating Heat Stress in Sheep.

Heat stress is an important environmental factor affecting livestock production worldwide. Primary hepatocytes and preadipocytes derived from Hu sheep were used to establish a heat stress model. Quantitative reverse transcriptase-PCR (qRT-PCR) analysis showed that heat induction significantly increased the expression levels of heat stress protein (HSP) genes and the N6-methyladenosine (m6A) methylation modification genes: methyltransferase-like protein 3 (METTL3), methyltransferase-like protein 14 (METTL14), and fat mass and obesity associated protein (FTO). Heat stress simultaneously promoted cell apoptosis. Transcriptome sequencing identified 3980 upregulated genes and 2420 downregulated genes related to heat stress. A pathway enrichment analysis of these genes revealed significant enrichment in fatty acid biosynthesis, degradation, and the PI3K-Akt and peroxisome proliferator-activated receptor (PPAR) signaling pathways. Overexpression of METTL3 in primary hepatocytes led to significant downregulation of HSP60, HSP70, and HSP110, and significantly increased mRNA m6A methylation; FTO interference generated the opposite results. Primary adipocytes showed similar results. Transcriptome analysis of cells under METTL3 (or FTO) inference and overexpression revealed differentially expressed genes enriched in the mitogen-activated protein kinase (MAPK) signaling pathways, as well as the PI3K-Akt and Ras signaling pathways. We speculate that METTL3 may increase the level of m6A methylation to inhibit fat deposition and/or inhibit the expression of HSP genes to enhance the body's resistance to heat stress, while the FTO gene generated the opposite molecular mechanism. This study provides a scientific basis and theoretical support for sheep feeding and management practices during heat stress.

Proteome Analysis of Alpine Merino Sheep Skin Reveals New Insights into the Mechanisms Involved in Regulating Wool Fiber Diameter.

Wool fiber is a textile material that is highly valued based on its diameter, which is crucial in determining its economic value. To analyze the molecular mechanisms regulating wool fiber diameter, we used a Data-independent acquisition-based quantitative proteomics approach to analyze the skin proteome of Alpine Merino sheep with four fiber diameter ranges. From three contrasts of defined groups, we identified 275, 229, and 190 differentially expressed proteins (DEPs). Further analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed that pathways associated with cyclic adenosine monophosphate and peroxisome proliferator-activated receptor signaling are relevant to wool fiber diameter. Using the K-means method, we investigated the DEP expression patterns across wool diameter ranges. Using weighted gene co-expression network analysis, we identified seven key proteins (CIDEA, CRYM, MLX, TPST2, GPD1, GOPC, and CAMK2G) that may be involved in regulating wool fiber diameter. Our findings provide a theoretical foundation for identifying DEPs and pathways associated with wool fiber diameter in Alpine Merino sheep to enable a better understanding of the molecular mechanisms underlying the genetic regulation of wool fiber quality.

The Piks allele of the NLR immune receptor Pik breaks the recognition of AvrPik effectors of rice blast fungus.

Arms race co-evolution of plant-pathogen interactions evolved sophisticated recognition mechanisms between host immune receptors and pathogen effectors. Different allelic haplotypes of an immune receptor in the host mount distinct recognition against sequence or non-sequence related effectors in pathogens. We report the molecular characterization of the Piks allele of the rice immune receptor Pik against rice blast pathogen, which requires two head-to-head arrayed nucleotide-binding sites and leucine-rich repeat proteins. Like other Pik alleles, both Piks-1 and Piks-2 are necessary and sufficient for mediating resistance. However, unlike other Pik alleles, Piks does not recognize any known AvrPik variants of Magnaporthe oryzae. Sequence analysis of the genome of an avirulent isolate V86010 further revealed that its cognate avirulence (Avr) gene most likely has no significant sequence similarity to known AvrPik variants. Piks-1 and Pikm-1 have only two amino acid differences within the integrated heavy metal-associated (HMA) domain. Pikm-HMA interacts with AvrPik-A, -D, and -E in vitro and in vivo, whereas Piks-HMA does not bind any AvrPik variants. Characterization of two amino acid residues differing Piks-1 from Pikm-1 reveal that Piks-E229Q derived from the exchange of Glu229 to Gln229 in Piks-1 gains recognition specificity against AvrPik-D but not AvrPik-A or -E, indicating that Piks-E229Q partially restores the Pikm spectrum. By contrast, Piks-A261V derived from the exchange of Ala261 to Val261 in Piks-1 retains Piks recognition specificity. We conclude that Glu229 in Piks-1 is critical for Piks breaking the canonical Pik/AvrPik recognition pattern. Intriguingly, binding activity and ectopic cell death induction is maintained between Piks-A261V and AvrPik-D, implying that positive outcomes from ectopic assays might be insufficient to deduce its immune activity against the relevant effectors in rice and rice blast interaction.

[The value of chromosomal microarray analysis and fluorescence in situ hybridization for the prenatal diagnosis of chromosomal mosaicisms].

OBJECTIVE: To assess the value of chromosomal microarray analysis (CMA) and fluorescence in situ hybridization (FISH) for the prenatal diagnosis of chromosomal mosaicisms. METHODS: A total of 775 pregnant women who had visited the Prenatal Diagnosis Center of Yancheng Maternal and Child Health Care Hospital from January 2018 to December 2020 were selected as study subjects. Chromosome karyotyping analysis and CMA were carried out for all women, and FISH was used to validate the suspected mosaicism cases. RESULTS: Among the 775 amniotic fluid samples, karyotyping has identified 13 mosaicism cases, which yielded a detection rate of 1.55%. Respectively, there were 4, 3, 4 and 2 cases for sex chromosome number mosaicisms, abnormal sex chromosome structure mosaicisms, abnormal autosomal number mosaicisms and abnormal autosomal structure mosaicisms. CMA has only detected only 6 of the 13 cases. Among 3 cases verified by FISH, 2 cases were consistent with the karyotyping and CMA results, and clearly showed low proportion mosaicism, and 1 case was consistent with the result of karyotyping but with a normal result by CMA. Eight pregnant women had chosen to terminate the pregnancy (5 with sex chromosome mosaicisms and 3 with autosomal mosaicisms). CONCLUSION: For fetuses suspected for chromosomal mosaicisms, CMA, FISH and G-banding karyotyping should be combined to determine the type and proportion of mosaicisms more precisely in order to provide more information for genetic counseling.

The Transcriptional Cell Atlas of Testis Development in Sheep at Pre-Sexual Maturity.

Sheep testes undergo a dramatic rate of development with structural changes during pre-sexual maturity, including the proliferation and maturation of somatic niche cells and the initiation of spermatogenesis. To explore this complex process, 12,843 testicular cells from three males at pre-sexual maturity (three-month-old) were sequenced using the 10× Genomics ChromiumTM single-cell RNA-seq (scRNA-seq) technology. Nine testicular somatic cell types (Sertoli cells, myoid cells, monocytes, macrophages, Leydig cells, dendritic cells, endothelial cells, smooth muscle cells, and leukocytes) and an unknown cell cluster were observed. In particular, five male germ cell types (including two types of undifferentiated spermatogonia (Apale and Adark), primary spermatocytes, secondary spermatocytes, and sperm cells) were identified. Interestingly, Apale and Adark were found to be two distinct states of undifferentiated spermatogonia. Further analysis identified specific marker genes, including UCHL1, DDX4, SOHLH1, KITLG, and PCNA, in the germ cells at different states of differentiation. The study revealed significant changes in germline stem cells at pre-sexual maturation, paving the way to explore the candidate factors and pathways for the regulation of germ and somatic cells, and to provide us with opportunities for the establishment of livestock stem cell breeding programs.

Engineering the Morphology and Microenvironment of a Graphene-Supported Co-N-C Single-Atom Electrocatalyst for Enhanced Hydrogen Evolution.

Graphene-supported single-atom catalysts (SACs) are promising alternatives to precious metals for catalyzing the technologically important hydrogen evolution reaction (HER), but their performances are limited by the low intrinsic activity and insufficient mass transport. Herein, a highly HER-active graphene-supported Co-N-C SAC is reported with unique design features in the morphology of the substrate and the microenvironment of the single metal sites: i) the crumpled and scrolled morphology of the graphene substrate circumvents the issues encountered by stacked nanoplatelets, resulting in improved exposure of the electrode/electrolyte interfaces (≈10 times enhancement); ii) the in-plane holes in graphene preferentially orientate the Co atoms at the edge sites with low-coordinated Co-N3 configuration that exhibits enhanced intrinsic activity (≈2.6 times enhancement compared to the conventional Co-N4 moiety), as evidenced by detailed experiments and density functional theory calculations. As a result, this catalyst exhibits significantly improved HER activity with an overpotential (η) of merely 82 mV at 10 mA cm-2 , a small Tafel slope of 59.0 mV dec-1 and a turnover frequency of 0.81 s-1 at η = 100 mV, ranking it among the best Co-N-C SACs.

Higher glutamatergic activity in the medial prefrontal cortex in chronic ketamine users.

BACKGROUND: The medial prefrontal cortex (mPFC) plays an important role in depression and addiction. Previous studies have shown alterations in glutamatergic activity in the mPFC following the administration of ketamine in patients with depression and healthy controls. However, it remains unclear whether chronic, nonmedical use of ketamine affects metabolites in the mPFC. METHODS: Using proton magnetic resonance spectroscopy, we measured metabolites (glutamate and glutamine [Glx]; phosphocreatine and creatine [PCr+Cr]; myo-inositol; N-acetyl-aspartate; and glycerophosphocholine and phosphocholine [GPC+PC]) in the mPFC of chronic ketamine users (n = 20) and healthy controls (n = 43). Among ketamine users, 60% consumed ketamine once per day or more, 10% consumed it every 2 days and 30% consumed it every 3 or more days. Using analysis of covariance, we evaluated between-group differences in the ratios of Glx:PCr+Cr, myo-inositol:PCr+Cr, N-acetyl-aspartate:PCr+Cr and GPC+PC:PCr+Cr. RESULTS: Chronic ketamine users showed significantly higher Glx:PCr+Cr ratios than healthy controls (median 1.05 v. 0.95, p = 0.008). We found no significant differences in myoinositol:PCr+Cr, N-acetyl-aspartate:PCr+Cr or GPC+PC:PCr+Cr ratios between the 2 groups. We found a positive relationship between N-acetyl-aspartate:PCr+Cr and Glx:PCr+Cr ratios in the healthy control group (R = 0.345, p = 0.023), but the ketamine use group failed to show such an association (ρ = 0.197, p = 0.40). LIMITATIONS: The cross-sectional design of this study did not permit causal inferences related to higher Glx:PCr+Cr ratios and chronic ketamine use. CONCLUSION: This study provides the first evidence that chronic ketamine users have higher glutamatergic activity in the mPFC than healthy controls; this finding may provide new insights relevant to the treatment of depression with ketamine.

m6A mRNA methylation analysis provides novel insights into heat stress responses in the liver tissue of sheep.

N6-methyladenosine (m6A) mRNA methylation varies in response to stress. However, no map of m6A mRNA methylation has been obtained for sheep, nor is it known what effect this has on regulating heat stress in sheep. Here, we obtained m6A methylation maps of sheep liver tissues with and without heat stress by MeRIP-seq. In total, 8306 m6A peaks associated with 2697 genes were detected in the heat stress group, and 12,958 m6A peaks associated with 5494 genes were detected in the control group. Peaks were mainly enriched in coding regions and near stop codons with classical RRACH motifs. Methylation levels of heat stress and control sheep were higher near stop codons, although methylation was significantly lower in heat stress sheep. GO and KEGG revealed that differential m6A-containing genes were significantly enriched in the stress response and fat metabolism. Our results showed that m6A mRNA methylation modifications regulate heat stress in sheep.

A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing.

BACKGROUND: Copy number variation (CNV) is an important source of genetic variation that has a significant influence on phenotypic diversity, economically important traits and the evolution of livestock species. In this study, the genome-wide CNV distribution characteristics of 32 fine-wool sheep from three breeds were analyzed using resequencing. RESULTS: A total of 1,747,604 CNVs were detected in this study, and 7228 CNV regions (CNVR) were obtained after merging overlapping CNVs; these regions accounted for 2.17% of the sheep reference genome. The average length of the CNVRs was 4307.17 bp. "Deletion" events took place more frequently than "duplication" or "both" events. The CNVRs obtained overlapped with previously reported sheep CNVRs to variable extents (4.39-55.46%). Functional enrichment analysis showed that the CNVR-harboring genes were mainly involved in sensory perception systems, nutrient metabolism processes, and growth and development processes. Furthermore, 1855 of the CNVRs were associated with 166 quantitative trait loci (QTL), including milk QTLs, carcass QTLs, and health-related QTLs, among others. In addition, the 32 fine-wool sheep were divided into horned and polled groups to analyze for the selective sweep of CNVRs, and it was found that the relaxin family peptide receptor 2 (RXFP2) gene was strongly influenced by selection. CONCLUSIONS: In summary, we constructed a genomic CNV map for Chinese indigenous fine-wool sheep using resequencing, thereby providing a valuable genetic variation resource for sheep genome research, which will contribute to the study of complex traits in sheep.

Genome-wide association studies detects candidate genes for wool traits by re-sequencing in Chinese fine-wool sheep.

BACKGROUND: The quality and yield of wool determine the economic value of the fine-wool sheep. Therefore, discovering markers or genes relevant to wool traits is the cornerstone for the breeding of fine-wool sheep. In this study, we used the Illumina HiSeq X Ten platform to re-sequence 460 sheep belonging to four different fine-wool sheep breeds, namely, Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Aohan fine-wool sheep (AHS) and Qinghai fine-wool sheep (QHS). Eight wool traits, including fiber diameter (FD), fiber diameter coefficient of variance (FDCV), fiber diameter standard deviation (FDSD), staple length (SL), greasy fleece weight (GFW), clean wool rate (CWR), staple strength (SS) and staple elongation (SE) were examined. A genome-wide association study (GWAS) was performed to detect the candidate genes for the eight wool traits. RESULTS: A total of 8.222 Tb of raw data was generated, with an average of approximately 8.59X sequencing depth. After quality control, 12,561,225 SNPs were available for analysis. And a total of 57 genome-wide significant SNPs and 30 candidate genes were detected for the desired wool traits. Among them, 7 SNPs and 6 genes are related to wool fineness indicators (FD, FDCV and FDSD), 10 SNPs and 7 genes are related to staple length, 13 SNPs and 7 genes are related to wool production indicators (GFW and CWR), 27 SNPs and 10 genes associated with staple elongation. Among these candidate genes, UBE2E3 and RHPN2 associated with fiber diameter, were found to play an important role in keratinocyte differentiation and cell proliferation. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results, revealed that multitude significant pathways are related to keratin and cell proliferation and differentiation, such as positive regulation of canonical Wnt signaling pathway (GO:0090263). CONCLUSION: This is the first GWAS on the wool traits by using re-sequencing data in Chinese fine-wool sheep. The newly detected significant SNPs in this study can be used in genome-selective breeding for the fine-wool sheep. And the new candidate genes would provide a good theoretical basis for the fine-wool sheep breeding.

Observing two-photon subwavelength interference of broadband chaotic light in a polarization-selective Michelson interferometer.

We demonstrated a method to achieve the two-photon subwavelength effect of true broadband chaotic light in polarization-selective Michelson interferometer based on two-photon absorption detection. To our knowledge, it is the first time that this effect has been observed with broadband chaotic light. In theory, the two-photon polarization coherence matrix and probability amplitudes matrix are combined to develop polarized two-photon interference terms, which explains the experimental results well. To make better use of this interferometer to produce the subwavelength effect, we also make a series of error analyses to find out the relationship between the visibility and the degree of polarization error. Our experimental and theoretical results contribute to the understanding of the two-photon subwavelength interference, which shed light on the development of the two-photon interference theory of vector light field based on quantum mechanics. The characteristic of the two-photon subwavelength effect have significant applications in temporal ghost imaging, such as it helps to improve the resolution of temporal objects.