Impact of different genomic relationship matrix construction methods on the accuracy of genomic prediction in different species.

Objective: Genomic best linear unbiased prediction (GBLUP) is a key method in genomic prediction, relying on the construction of a genomic relationship matrix (G-matrix). Although various methods for G-matrix construction have been proposed, the performance of these methods across different species has not been thoroughly compared.

Methods: This study systematically evaluated the performance of six genomic relationship matrix (G-matrix) construction methods in improving the prediction accuracy of GBLUP models across four species: pigs, bulls, wheat, and mice.

Atmospheric Switching between Etching and High-Quality Fluorination of Graphene by XeF.

Fluorinated graphene (FG), a two-dimensional graphene derivative, has attracted wide attention due to its extraordinary physical and chemical properties, as well as its underlying applications. The treatment of xenon difluoride (XeF) has proved to be an effective way to achieve FG with different stoichiometric F/C ratios without graphene being etched. Here we compare the fluorination of mechanically exfoliated graphene by a home-built XeF fluorination system and a commercial Orbis XeF etching system.

Plasmon-Enhanced Visible and Near-Infrared Photodetection with Gold Nanorods UCNPs/MoS Hybrid Device.

The near-infrared photodetection of monolayer MoS can be achieved using upconverted nanoparticles (UCNPs). Herein, we demonstrated that gold nanorods (Au NRs) further enhanced the near-infrared photoresponsivity of a hybrid device via the surface plasmon enhancement of the localized field. We synthesized a three-layer device comprising Au NRs, UCNPs (NaYF:Yb, Er), and monolayer MoS, and examined its photoelectric characteristics using laser irradiation with varying power densities at 980 nm, the excitation wavelength of UCNPs.

Photodegradation and van der Waals Passivation of Violet Phosphorus.

Violet phosphorus (VP), a novel two-dimensional (2D) nanomaterial, boasts structural anisotropy, a tunable optical bandgap, and superior thermal stability compared with its allotropes. Its multifunctionality has sparked widespread interest in the community. Yet, the VP's air susceptibility impedes both probing its intrinsic features and device integration, thus making it of urgent significance to unveil the degradation mechanism.

Underwater dynamic polarization imaging without dependence on the background region.

Active-polarization imaging holds significant promise for achieving clear underwater vision. However, only static targets were considered in previous studies, and a background region was required for image restoration. To address these issues, this study proposes an underwater dynamic polarization imaging method based on image pyramid decomposition and reconstruction.

Exact optical path difference and complete performance analysis of a spectral zooming imaging spectrometer.

The optical path difference (OPD) equations of the dual Wollaston prisms (DWP) with an adjustable air gap (AG) are derived by the wave normal tracing method, which is suitable for arbitrary incidence plane and angle. The spatial distribution of the OPD for various AG is presented. The validity of the OPD equation is verified by comparing the calculated interferograms with experimentally observed one.

Near-Infrared Photoelectric Properties of Multilayer BiOSe Nanofilms.

The near-infrared (NIR) photoelectric properties of multilayer BiOSe nanofilms were systematically studied in this paper. Multilayer BiOSe nanofilms demonstrate a sensitive photo response to NIR, including a high photoresponsivity (~ 101 A/W), a quick response time (~ 30 ms), a high external quantum efficiency (~ 20,300%), and a high detection rate (1.9 × 10 Jones).

Bolometric Effect in Bi O Se Photodetectors.

Bi O Se is emerging as a photosensitive functional material for optoelectronics, and its photodetection mechanism is mostly considered to be a photoconductive regime in previous reports. Here, the bolometric effect is discovered in Bi O Se photodetectors. The coexistence of photoconductive effect and bolometric effect is generally observed in multiwavelength photoresponse measurements and then confirmed with microscale local heating experiments.

In-plane anisotropy in twisted bilayer graphene probed by Raman spectroscopy.

Monolayer graphene has high symmetrical crystal structure and exhibits in-plane isotropic physical properties. However, twisted bilayer graphene (tBLG) is expected to differ physically, due to the broken symmetry introduced by the interlayer coupling between adjacent graphene layers. This symmetry breaking is usually accompanied by in-plane anisotropy in their electrical, optical and thermal properties.

Interlayer Difference of Bilayer-Stacked MoS Structure: Probing by Photoluminescence and Raman Spectroscopy.

This work reports the interlayer difference of exciton and phonon performance between the top and bottom layer of a bilayer-stacked two-dimensional materials structure (BSS). Through photoluminescence (PL) and Raman spectroscopy, we find that, compared to that of the bottom layer, the top layer of BSS demonstrates PL redshift, Raman E 2 g 1 mode redshift, and lower PL intensity. Spatial inhomogeneity of PL and Raman are also observed in the BSS.

Assessment of Autozygosity Derived From Runs of Homozygosity in Jinhua Pigs Disclosed by Sequencing Data.

Jinhua pig, a well-known Chinese indigenous breed, has evolved as a pig breed with excellent meat quality, greater disease resistance, and higher prolificacy. The reduction in the number of Jinhua pigs over the past years has raised concerns about inbreeding. Runs of homozygosity (ROH) along the genome have been applied to quantify individual autozygosity to improve the understanding of inbreeding depression and identify genes associated with traits of interest.

Selection signature reveals genes associated with susceptibility loci affecting respiratory disease due to pleiotropic and hitchhiking effect in Chinese indigenous pigs.

Background: Porcine respiratory disease is one of the most important health problems which causes significant economic losses.

Objective: To understand the genetic basis for susceptibility to swine enzootic pneumonia (EP) in pigs, we detected 102,809 SNPs in a total of 249 individuals based on genome-wide sequencing data.

Methods: Genome comparison of three susceptibility to swine EP pig breeds (Jinhua, Erhualian and Meishan) with two western lines that are considered more resistant (Duroc and Landrace) using XP-EHH and FST statistical approaches identified 691 positively selected genes.

Exploring the Structure of Haplotype Blocks and Genetic Diversity in Chinese Indigenous Pig Populations for Conservation Purpose.

Chinese indigenous pigs in the Taihu Lake region are well known for their high fecundity and other excellent characteristics. To better understand the characteristics of these breeds in this area as well as to provide the government and breeders the molecular basis for formulating a reasonable conservation policy, we explored the structure of haplotype blocks and genetic diversity of the 7 populations which is relevant for the management and conservation of these important genetic resources using next-generation sequencing data. In this study, a total of 131 300 single-nucleotide polymorphisms with minor allele frequencies ⩾0.

Identifying Genetic Differences Between Dongxiang Blue-Shelled and White Leghorn Chickens Using Sequencing Data.

The Dongxiang Blue-shelled chicken is one of the most valuable Chinese indigenous poultry breeds. However, compared to the Italian native White Leghorn, although this Chinese breed possesses numerous favorable characteristics, it also exhibits lower growth performance and fertility. Here, we utilized genotyping sequencing data obtained via genome reduction on a sequencing platform to detect 100,114 single nucleotide polymorphisms and perform further biological analysis and functional annotation.

An Efficient Genotyping Method in Chicken Based on Genome Reducing and Sequencing.

Single nucleotide polymorphisms (SNPs) are essential for identifying the genetic mechanisms of complex traits. In the present study, we applied genotyping by genome reducing and sequencing (GGRS) method to construct a 252-plex sequencing library for SNP discovery and genotyping in chicken. The library was successfully sequenced on an Illumina HiSeq 2500 sequencer with a paired-end pattern; approximately 400 million raw reads were generated, and an average of approximately 1.

A genome-wide scan for selection signatures in Yorkshire and Landrace pigs based on sequencing data.

Pigs have experienced dramatic selection due to domestication, which has led to many different phenotypes when compared to their wild counterparts, especially in the last several decades. Currently, genome-wide scans in both cattle and humans showing positive selection footprints have been investigated. However, few studies have focused on porcine selection footprints, particularly on a genome-wide scale.

Transgenic mice expressing yeast CUP1 exhibit increased copper utilization from feeds.

Copper is required for structural and catalytic properties of a variety of enzymes participating in many vital biological processes for growth and development. Feeds provide most of the copper as an essential micronutrient consumed by animals, but inorganic copper could not be utilized effectively. In the present study, we aimed to develop transgenic mouse models to test if copper utilization will be increased by providing the animals with an exogenous gene for generation of copper chelatin in saliva.

A new genotype imputation method with tolerance to high missing rate and rare variants.

We report a novel algorithm, iBLUP, to impute missing genotypes by simultaneously and comprehensively using identity by descent and linkage disequilibrium information. The simulation studies showed that the algorithm exhibited drastically tolerance to high missing rate, especially for rare variants than other common imputation methods, e.g.

Genotyping by genome reducing and sequencing for outbred animals.

Next-generation sequencing (NGS) approaches are widely used in genome-wide genetic marker discovery and genotyping. However, current NGS approaches are not easy to apply to general outbred populations (human and some major farm animals) for SNP identification because of the high level of heterogeneity and phase ambiguity in the haplotype. Here, we reported a new method for SNP genotyping, called genotyping by genome reducing and sequencing (GGRS) to genotype outbred species.

The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway.

The insulin/insulin growth factor-1(IGF1)/FOXO (IIF) signal transduction pathway plays a core role in the endocrine system. Although the components of this pathway have been well characterized, the evolutionary pattern remains poorly understood. Here, we perform a comprehensive analysis to study whether the differences of signaling transduction elements exist as well as to determine whether the genes are subject to equivalent evolutionary forces and how natural selection shapes the evolution pattern of proteins in an interacting system.

WRKY gene family evolution in Arabidopsis thaliana.

The Arabidopsis thaliana WRKY proteins are characterized by a sequence of 60 amino acids including WRKY domain. It is well established that these proteins are involved in the regulation of various physiological programs unique to plants including pathogen defense, senescence and response to environmental stresses, which attracts attention of the scientific community as to how this family might have evolved. We tried to satisfy this curiosity and analyze reasons for duplications of these gene sequences leading to their diversified gene actions.