Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds

Background The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by,and formed due to,past and current admixture events.Adaptation to diverse environments,including acclimation to harsh climatic conditions,has also left selection footprints in breed genomes.Results Using the Chicken 50K_CobbCons SNP chip,we genotyped four divergently selected breeds:two aboriginal,cold tolerant Ushanka and Orloff Mille Fleur,one egg-type Russian White subjected to artificial selection for cold tolerance,and one meat-type White Cornish.Signals of selective sweeps were determined in the studied breeds using three methods:(1)assessment of runs of homozygosity islands,(2)F_(ST) based population differential analysis,and(3)haplotype differentiation analysis.Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds.In these regions,we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies.Amongst them,SOX5,ME3,ZNF536,WWP1,RIPK2,OSGIN2,DECR1,TPO,PPARGC1A,BDNF,MSTN,and beta-keratin genes can be especially mentioned as candidates for cold adaptation.Epigenetic factors may be involved in regulating some of these important genes(e.g.,TPO and BDNF).Conclusion Based on a genome-wide scan,our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds.These include genes representing the sine qua non for adaptation to harsh environments.Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals,and this warrants further investigation.

Bull spermatozoa selected by thermotaxis exhibit high DNA integrity,specific head morphometry,and improve ICSI outcome

Background Sperm migration by thermotaxis is a guidance mechanism that operates along the oviduct and it has proved to be a valid method for selecting spermatozoa with low DNA fragmentation(SDF)in mice,humans,and stallions.This study aimed to analyse if bull spermatozoa could be selected by thermotaxis and to assess their quality in terms of SDF as well as determine the presence of a specific sperm subpopulation based on sperm morphometry and assess their fertilizing capacity by ICSI.Methods We used frozen-thawed sperm from 6 bulls and sperm selection by thermotaxis was performed with TALP medium supplemented with 25 mmol/L of HEPES and 5 mmol/L of caffeine.In these conditions,sperm selection was achieved,obtaining a net thermotaxis of 3.6%.Subsequently,we analysed the SDF of the migrated and not-migrated spermatozoa using the neutral COMET assay,and we evaluated the size of the sperm head using Hemacolor■ staining with Motic Images Plus 3 software.Additionally,migrated and not-migrated spermatozoa by thermotaxis were used to fertilize bovine in vitro matured(IVM)oocytes by ICSI,a very inefficient procedure in cattle that is only successful when the oocyte is artificially activated.Results The results showed lower SDF(χ^(2),P<0.001,13.3%reduction,n=8)and lower head size parameters(length and width,P<0.01;and perimeter and area,P<0.001;n=4)in those spermatozoa migrated in comparison to those not-migrated.The distribution of sperm subpopulations structure varied between groups,highlighting cluster 2,characterized by spermatozoa with small head size,and high ellipticity and elongated heads,as the most abundant in the thermotaxis migrated group.When performed ICSI(without oocyte artificial activation)with the thermotactic sperm,the blastocyst rate was 32.2%±9.3%in the group microinjected with the thermotactic spermatozoa vs.8.3%±7.8%in the group of not-migrated sperm(χ^(2),P<0.05).Conclusion Our results showed that bull sperm selection by thermotaxis has a much higher DNA integrity,small and elongated head size parameters,and different sperm subpopulation structure than the not-selected spermatozoa.Additionally,we evidenced that thermotactic spermatozoa improve ICSI success rates.

The Power of Patronage Exercised in the Translation of Selected Works of Deng Xiaoping

By referring to Lefevere’s theory of patronage, this paper examines the issue of patronage in the translation of Selected Works of Deng Xiaoping, a remarkable political work of our country. It addresses the questions like"Who are the patrons?","What is the structure of patronage?", and "How does patronage work in the translation?"Through investigating these issues, the paper concludes that if it had not been for the powerful manipulation by patronage, there could not have been the high-quality translation of such voluminous works. The power of patronage made undeniable contribution to the translation of Selected Works of Deng Xiaoping.

Liver transplantation as an alternative for the treatment of neuroendocrine liver metastasis: Appraisal of the current evidence

Background:Liver transplantation(LT)for neuroendocrine liver metastases(NELM)is still in debate.Studies comparing LT with liver resection(LR)for NELM are scarce,as patient selection is heterogeneous and experience is limited.The goal of this review was to provide a critical analysis of the evidence on LT versus LR in the treatment of NELM.Data sources:A scoping literature search on LT and LR for NELM was performed with PubMed,including English articles up to March 2023.Results:International guidelines recommend LR for NELM in resectable,well-differentiated tumors in the absence of extrahepatic metastatic disease with superior results of LR compared to systemic or liver-directed therapies.Advanced liver surgery has extended resectability criteria whilst entailing increased perioperative risk and short disease-free survival.In highly selected patients(based on the Milan criteria)with unresectable NELM,oncologic results of LT are promising.Prognostic factors include tumor biology(G1/G2)and burden,waiting time for LT,patient age and extrahepatic spread.Based on low-level evi-dence,LT for low-grade NELM within the Milan criteria resulted in improved disease-free survival and overall survival compared to LR.The benefits of LT were lost in patients beyond the Milan NELM-criteria.Conclusions:With adherence to strict selection criteria especially tumor biology,LT for NELM is becoming a valuable option providing oncologic benefits compared to LR.Recent evidence suggests even stricter selection criteria with regard to tumor biology.

Artificial intelligence-driven radiomics study in cancer:the role of feature engineering and modeling

Modern medicine is reliant on various medical imaging technologies for non-invasively observing patients’anatomy.However,the interpretation of medical images can be highly subjective and dependent on the expertise of clinicians.Moreover,some potentially useful quantitative information in medical images,especially that which is not visible to the naked eye,is often ignored during clinical practice.In contrast,radiomics performs high-throughput feature extraction from medical images,which enables quantitative analysis of medical images and prediction of various clinical endpoints.Studies have reported that radiomics exhibits promising performance in diagnosis and predicting treatment responses and prognosis,demonstrating its potential to be a non-invasive auxiliary tool for personalized medicine.However,radiomics remains in a developmental phase as numerous technical challenges have yet to be solved,especially in feature engineering and statistical modeling.In this review,we introduce the current utility of radiomics by summarizing research on its application in the diagnosis,prognosis,and prediction of treatment responses in patients with cancer.We focus on machine learning approaches,for feature extraction and selection during feature engineering and for imbalanced datasets and multi-modality fusion during statistical modeling.Furthermore,we introduce the stability,reproducibility,and interpretability of features,and the generalizability and interpretability of models.Finally,we offer possible solutions to current challenges in radiomics research.

Selective internal radiation therapy segmentectomy:A new minimally invasive curative option for primary liver malignancies?

Transarterial radioembolization or selective internal radiation therapy(SIRT)has emerged as a minimally invasive approach for the treatment of tumors.This percutaneous technique involves the local,intra-arterial delivery of radioactive microspheres directly into the tumor.Historically employed as a palliative measure for liver malignancies,SIRT has gained traction over the past decade as a potential curative option,mirroring the increasing role of radiation segmentectomy.The latest update of the BCLC hepatocellular carcinoma guidelines recognizes SIRT as an effective treatment modality comparable to other local ablative methods,particularly well-suited for patients where surgical resection or ablation is not feasible.Radiation segmentectomy is a more selective approach,aiming to deliver high-dose radiation to one to three specific hepatic segments,while minimizing damage to surrounding healthy tissue.Future research efforts in radiation segmentectomy should prioritize optimizing radiation dosimetry and refining the technique for super-selective administration of radiospheres within the designated hepatic segments.

Anti-jamming channel access in 5G ultra-dense networks: a game-theoretic learning approach

This paper investigates the Quality of Experience(QoE)oriented channel access anti-jamming problem in 5th Generation Mobile Communication(5G)ultra-dense networks.Firstly,considering that the 5G base station adopts beamforming technology,an anti-jamming model under Space Division Multiple Access(SDMA)conditions is proposed.Secondly,the confrontational relationship between users and the jammer is formulated as a Stackelberg game.Besides,to achieve global optimization,we design a local cooperation mechanism for users and formulate the cooperation and competition among users as a local altruistic game.By proving that the local altruistic game is an Exact Potential Game(EPG),we further prove the existence of pure strategy Nash Equilibrium(NE)among users and Stackelberg Equilibrium(SE)between users and jammer.Thirdly,to obtain the equilibrium solutions of the proposed games,we propose an anti-jamming channel selection algorithm and improve its convergence speed through heterogeneous learning parameters.The simulation results validate the convergence and effectiveness of the proposed algorithm.Compared with the throughput optimization scheme,our proposed scheme obtain a greater network satisfaction rate.Finally,we also analyze user fairness changes during the algorithm convergence process and get some interesting conclusions.

Cooperative Anti-Jamming and Interference Mitigation for UAV Networks: A Local Altruistic Game Approach

To improve the anti-jamming and interference mitigation ability of the UAV-aided communication systems, this paper investigates the channel selection optimization problem in face of both internal mutual interference and external malicious jamming. A cooperative anti-jamming and interference mitigation method based on local altruistic is proposed to optimize UAVs’ channel selection. Specifically, a Stackelberg game is modeled to formulate the confrontation relationship between UAVs and the jammer. A local altruistic game is modeled with each UAV considering the utilities of both itself and other UAVs. A distributed cooperative anti-jamming and interference mitigation algorithm is proposed to obtain the Stackelberg equilibrium. Finally, the convergence of the proposed algorithm and the impact of the transmission power on the system loss value are analyzed, and the anti-jamming performance of the proposed algorithm can be improved by around 64% compared with the existing algorithms.

Epistasis-aware genome-wide association studies provide insights into the efficient breeding of high-yield and high-quality rice

Marker-assisted selection(MAS)and genomic selection(GS)breeding have greatly improved the efficiency of rice breeding.Due to the influences of epistasis and gene pleiotropy,ensuring the actual breeding effect of MAS and GS is still a difficult challenge to overcome.In this study,113 indica rice varieties(V)and their 565 testcross hybrids(TC)were used as the materials to investigate the genetic basis of 12 quality traits and nine agronomic traits.The original traits and general combining ability of the parents,as well as the original traits and midparent heterosis of TC,were subjected to genome-wide association analysis.In total,381 primary significantly associated loci(SAL)and 1,759 secondary SALs that had epistatic interactions with these primary SALs were detected.Among these loci,322 candidate genes located within or nearby the SALs were screened,204 of which were cloned genes.A total of 39 MAS molecular modules that are beneficial for trait improvement were identified by pyramiding the superior haplotypes of candidate genes and desirable epistatic alleles of the secondary SALs.All the SALs were used to construct genetic networks,in which 91 pleiotropic loci were investigated.Additionally,we estimated the accuracy of genomic prediction in the parent V and TC by incorporating either no SALs,primary SALs,secondary SALs or epistatic effect SALs as covariates.Although the prediction accuracies of the four models were generally not significantly different in the TC dataset,the incorporation of primary SALs,secondary SALs,and epistatic effect SALs significantly improved the prediction accuracies of 5(26%),3(16%),and 11(58%)traits in the V dataset,respectively.These results suggested that SALs and epistatic effect SALs identified based on an additive genotype can provide considerable predictive power for the parental lines.They also provide insights into the genetic basis of complex traits and valuable information for molecular breeding in rice.

Thermal Stability and Degeneration Behavior of Solar Selective Absorber Based on WTi-Al_(2)O_(3)Cermet

A WTi-Al_(2)O_(3)cermet-based solar selective absorber was prepared to investigate the atomic diffusion induced spectral selectivity degeneration.The as-deposited coating exhibits superior absorptance(0.934)and low thermal emittance(0.098),as well as excellent thermal stability with a selectivity of 0.900/0.07 even after annealing at 923 K for 400 h in Ar ambient.However,the multilayer coating failed after being subjected to annealing at 923 K for 400 h in an air environment,as indicated by a decrease in solar absorptance to 0.912 and an increase in thermal emittance to 0.634.The microstructure characterizations reveal that the annealed coating exhibits a columnar morphology along the vertical direction of the substrate.The presence of abundant grain boundaries in the multilayer coating promotes the outward diffusion of Cr and Mn atoms in the stainless-steel substrate.The Mn atoms,in particular,possess the capability to migrate towards the surface of the coating and undergo an oxidation reaction with oxygen,facilitating the formation of a thick Mn_(2)O_(3)layer.The roughness of the coating surface was significantly increased in this case,adversely affecting solar absorptance due to amplified sunlight reflection.In addition,the rocketing of thermal emittance is attributed to the destabilization of W infrared reflective layer during the annealing.These findings highlight the importance of considering the outward diffusion of Mn and Cr elements in the stainless-steel substrate when optimizing solar selective absorbers.

Bird species present in urban parks are more colorful than urban avoiders:A test in the Argentinian Pampas

Bird plumage color has been assessed as a possible trait driving the presence of bird species in urban areas.Although some species can see the ultraviolet(UV) spectrum,the mentioned studies did not take into account UV reflectance when characterizing bird plumage.This study aimed to use a recent database of the colorfulness in passerines that incorporated the UV spectrum to compare bird colorfulness and other traits between urban parks and rural areas in Central-East Argentina.Birds in urban parks were surveyed in 51 parks in 6 cities during breeding and non-breeding seasons.A list of Passeriformes species from parks was created,and a list of urban avoider species was created from the bibliography.Species traits were body mass,clutch size,migratory status,nesting site,diet and habitat breadth,and plumage colorfulness.A total of 85 species were detected in the regional pool,of which 30 species were detected in urban parks.Bird species present in urban parks were more colorful than bird species only present in rural areas.In addition,bird presence in urban parks was positively related to their regional frequency and diet breadth.Moreover,urban presence was related to nesting on trees and buildings,whereas species not present in urban parks nested on the ground.The results obtained showed that bird color is significantly associated with presence of bird species in urban parks.

Transcatheter aortic valve implantation versus surgery:4-year survival according to life expectancy

Background In the last years,transcatheter aortic valve implantation(TAVI)indication has expanded to younger and lower risk patients.Consequently,interest in mid and long-term follow up and in the role of life expectancy,as a key factor for selecting the most tailored treatment,has grown.The aim of this retrospective study is to compare the 4-year survival of patients who underwent aortic valve replacement(AVR)vs.TAVI at our department.Methods From September 2017 to December 2020,673 consecutive patients with severe aortic valve stenosis were enrolled for AVR(n=283)or TAVI(n=390).Inclusion criteria was isolated severe aortic stenosis,while exclusion criteria were redo surgery,valve-in-valve procedure and the need for concomitant surgical procedures.Based on the Lee index,patients were divided into four groups according to their 4-year life expectancy.Four-year survival was assessed and reported using the Kaplan-Meier method.A multivariate regression analysis of risk factors for 4-year mortality was performed.Results Four years survival is always superior in the AVR patients(89.8%vs.75.6%,P<0.001).Surgery is associated with a higher incidence of acute kidney injury(23%vs.5.1%,P<0.001),while TAVI is related to a higher incidence of new onset left bundle branch block(0 vs.23.8%,P<0.001),pace-maker implantation(2.5%vs.11.8%,P=0,02)and mild-to-moderate paravalvular leak(0.3%vs.5.4%,P<0.001).The independent risk factors for 4-years mortality are post-procedural AKI,poor mobility and transcatheter procedure.Conclusion In our analysis,4 years survival is always superior in the AVR patients.Life expectancy is a key factor for selecting the most appropriate approach for each patient.A longer follow up is mandatory before extending TAVI indication to patients with a long-life expectancy.

Pareto Optimization as the Basic for Selecting Robotic Mechanic Assembly Technologies

The task of selecting robotic mechanic assembly technologies (RMAT) is considered as a multi-criteria optimization task, which in this formulation is solved on the set of previously obtained solutions regarding the selection of RMAT. The purpose of the paper is to increase the efficiency of technological preparation of robotic mechanical assembly production of machine and instrument engineering due to a new approach to the selection of RMAT using Pareto optimization and the peculiarities of the selection task formulation. The novelty consists in the further development of a science-based approach to solving multi-criteria selection task, based on the first proposed formalisms of the specified process, which reflect the peculiarities of the selection task formulation, its meaningful essence and the content of the Pareto optimization method. The practical value of the research lies in the proposed engineering-acceptable approach to solving applied multi-criteria selection tasks on the example of RMAT selection, which is invariant to the statement of the selection task, the dimension of the task, and its meaningful essence. The methods of discrete optimization, fuzzy multi-criteria selection of alternatives, and the Pareto optimization method were used for the research. The main results of this work consist of the development of formalisms and the demonstration of the efficiency of the proposed approach for the applied task of RMAT selection. The peculiarity of the developed approach is the combination of Pareto optimization, performed on a discrete set of local criteria. Directions for further research are presented.

Effect of an Airbag-selective Portal Vein Blood Arrester on the Liver after Hepatectomy:A New Technique for Selective Clamping of the Portal Vein

Objective:A novel technique was explored using an airbag-selective portal vein blood arrester that circumvents the need for an intraoperative assessment of anatomical variations in patients with complex intrahepatic space-occupying lesions.Methods:Rabbits undergoing hepatectomy were randomly assigned to 4 groups:intermittent portal triad clamping(PTC),intermittent portal vein clamping(PVC),intermittent portal vein blocker with an airbag-selective portal vein blood arrester(APC),and without portal blood occlusion(control).Hepatic ischemia and reperfusion injury were assessed by measuring the 7-day survival rate,blood loss,liver function,hepatic pathology,hepatic inflammatory cytokine infiltration,hepatic malondialdehyde levels,and proliferating cell nuclear antigen levels.Results:Liver damage was substantially reduced in the APC and PVC groups.The APC animals exhibited transaminase levels similar to or less oxidative stress damage and inflammatory hepatocellular injury compared to those exhibited by the PVC animals.Bleeding was significantly higher in the control group than in the other groups.The APC group had less bleeding than the PVC group because of the avoidance of portal vein skeletonization during hepatectomy.Thus,more operative time was saved in the APC group than in the PVC group.Moreover,the total 7-day survival rate in the APC group was higher than that in the PTC group.Conclusion:Airbag-selective portal vein blood arresters may help protect against hepatic ischemia and reperfusion injury in rabbits undergoing partial hepatectomy.This technique may also help prevent liver damage in patients requiring hepatectomy.

Using multi-omics analysis to explore diagnostic tool and optimize drug therapy selection for patients with glioma based on cross-talk gene signature

Background:The heterogeneity of prognosis and treatment benefits among patients with gliomas is due to tumor microenvironment characteristics.However,biomarkers that reflect microenvironmental characteristics and predict the prognosis of gliomas are limited.Therefore,we aimed to develop a model that can effectively predict prognosis,differentiate microenvironment signatures,and optimize drug selection for patients with glioma.Materials and Methods:The CIBERSORT algorithm,bulk sequencing analysis,and single-cell RNA(scRNA)analysis were employed to identify significant cross-talk genes between M2 macrophages and cancer cells in glioma tissues.A predictive model was constructed based on cross-talk gene expression,and its effect on prognosis,recurrence prediction,and microenvironment characteristics was validated in multiple cohorts.The effect of the predictive model on drug selection was evaluated using the OncoPredict algorithm and relevant cellular biology experiments.Results:A high abundance of M2 macrophages in glioma tissues indicates poor prognosis,and cross-talk between macrophages and cancer cells plays a crucial role in shaping the tumor microenvironment.Eight genes involved in the cross-talk between macrophages and cancer cells were identified.Among them,periostin(POSTN),chitinase 3 like 1(CHI3L1),serum amyloid A1(SAA1),and matrix metallopeptidase 9(MMP9)were selected to construct a predictive model.The developed model demonstrated significant efficacy in distinguishing patient prognosis,recurrent cases,and characteristics of high inflammation,hypoxia,and immunosuppression.Furthermore,this model can serve as a valuable tool for guiding the use of trametinib.Conclusions:In summary,this study provides a comprehensive understanding of the interplay between M2 macrophages and cancer cells in glioma;utilizes a cross-talk gene signature to develop a predictive model that can predict the differentiation of patient prognosis,recurrence instances,and microenvironment characteristics;and aids in optimizing the application of trametinib in glioma patients.

Unlocking the potential of ultra-thin two-dimensional antimony materials:Selective growth and carbon coating for efficient potassium-ion storage

Antimony-based anodes have attracted wide attention in potassium-ion batteries due to their high theoretical specific capacities(∼660 mA h g^(-1))and suitable voltage platforms.However,severe capacity fading caused by huge volume change and limited ion transportation hinders their practical applications.Recently,strategies for controlling the morphologies of Sb-based materials to improve the electrochemical performances have been proposed.Among these,the two-dimensional Sb(2D-Sb)materials present excellent properties due to shorted ion immigration paths and enhanced ion diffusion.Nevertheless,the synthetic methods are usually tedious,and even the mechanism of these strategies remains elusive,especially how to obtain large-scale 2D-Sb materials.Herein,a novel strategy to synthesize 2D-Sb material using a straightforward solvothermal method without the requirement of a complex nanostructure design is provided.This method leverages the selective adsorption of aldehyde groups in furfural to induce crystal growth,while concurrently reducing and coating a nitrogen-doped carbon layer.Compared to the reported methods,it is simpler,more efficient,and conducive to the production of composite nanosheets with uniform thickness(3–4 nm).The 2D-Sb@NC nanosheet anode delivers an extremely high capacity of 504.5 mA h g^(-1) at current densities of 100 mA g^(-1) and remains stable for more than 200 cycles.Through characterizations and molecular dynamic simulations,how potassium storage kinetics between 2D Sb-based materials and bulk Sb-based materials are explored,and detailed explanations are provided.These findings offer novel insights into the development of durable 2D alloy-based anodes for next-generation potassium-ion batteries.

Theoretical investigations of population trapping phenomena in atomic four-color,three-step photoionization scheme

The four-color three-step selective photoionization process of atom is very important in laser isotope separation technology.The population trapping phenomena and their influences are studied theoretically in monochromatic and non-monochromatic laser fields based on the density matrix theory in this work.Time evolutions of the photoionization properties of the four-color,three-step process are given.The population trapping effects occur intensely in monochromatic excitation,while it gradually turns weak as the laser bandwidth increases.The effects of bandwidth,Rabi frequency,time delay,and frequency detuning on the population trapping effect are investigated in monochromatic and non-monochromatic laser fields.The effects of laser process parameters and atomic parameters on the effective selective photoionization are also discussed.The ionization probability and selectivity factors,as evaluation indexes,are difficult to improve synchronously by adjusting systematic parameters.Besides,the existence of metastable state may play a negative role when its population is low enough.

Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maize

Genetic transformation has been an effective technology for improving the agronomic traits of maize.However,it is highly reliant on the use of embryonic callus(EC)and shows a serious genotype dependence.In this study,we performed genomic sequencing for 80 core maize germplasms and constructed a high-density genomic variation map using our newly developed pipeline(MQ2Gpipe).Based on the induction rate of EC(REC),these inbred lines were categorized into three subpopulations.The low-REC germplasms displayed more abundant genetic diversity than the high-REC germplasms.By integrating a genome-wide selective signature screen and region-based association analysis,we revealed 95.23 Mb of selective regions and 43 REC-associated variants.These variants had phenotypic variance explained values ranging between 21.46 and 49.46%.In total,103 candidate genes were identified within the linkage disequilibrium regions of these REC-associated loci.These genes mainly participate in regulation of the cell cycle,regulation of cytokinesis,and other functions,among which MYB15 and EMB2745 were located within the previously reported QTL for EC induction.Numerous leaf area-associated variants with large effects were closely linked to several REC-related loci,implying a potential synergistic selection of REC and leaf size during modern maize breeding.

Evaluating the performance of genomic selection on purebred population by incorporating crossbred data in pigs

Genomic selection(GS)has been widely used in livestock,which greatly accelerated the genetic progress of complex traits.The population size was one of the significant factors affecting the prediction accuracy,while it was limited by the purebred population.Compared to directly combining two uncorrelated purebred populations to extend the reference population size,it might be more meaningful to incorporate the correlated crossbreds into reference population for genomic prediction.In this study,we simulated purebred offspring(PAS and PBS)and crossbred offspring(CAB)base on real genotype data of two base purebred populations(PA and PB),to evaluate the performance of genomic selection on purebred while incorporating crossbred information.The results showed that selecting key crossbred individuals via maximizing the expected genetic relationship(REL)was better than the other methods(individuals closet or farthest to the purebred population,CP/FP)in term of the prediction accuracy.Furthermore,the prediction accuracy of reference populations combining PA and CAB was significantly better only based on PA,which was similar to combine PA and PAS.Moreover,the rank correlation between the multiple of the increased relationship(MIR)and reliability improvement was 0.60-0.70.But for individuals with low correlation(Cor(Pi,PA or B),the reliability improvement was significantly lower than other individuals.Our findings suggested that incorporating crossbred into purebred population could improve the performance of genetic prediction compared with using the purebred population only.The genetic relationship between purebred and crossbred population is a key factor determining the increased reliability while incorporating crossbred population in the genomic prediction on pure bred individuals.

Chromosome-level genome and population genomics of the intermediate horseshoe bat(Rhinolophus affinis)reveal the molecular basis of virus tolerance in Rhinolophus and echolocation call frequency variation

Horseshoe bats(genus Rhinolophus,family Rhinolophidae)represent an important group within chiropteran phylogeny due to their distinctive traits,including constant high-frequency echolocation,rapid karyotype evolution,and unique immune system.Advances in evolutionary biology,supported by high-quality reference genomes and comprehensive whole-genome data,have significantly enhanced our understanding of species origins,speciation mechanisms,adaptive evolutionary processes,and phenotypic diversity.However,genomic research and understanding of the evolutionary patterns of Rhinolophus are severely constrained by limited data,with only a single published genome of R.ferrumequinum currently available.In this study,we constructed a high-quality chromosome-level reference genome for the intermediate horseshoe bat(R.affinis).Comparative genomic analyses revealed potential genetic characteristics associated with virus tolerance in Rhinolophidae.Notably,we observed expansions in several immune-related gene families and identified various genes functionally associated with the SARS-CoV-2 signaling pathway,DNA repair,and apoptosis,which displayed signs of rapid evolution.In addition,we observed an expansion of the major histocompatibility complex class II(MHC-II)region and a higher copy number of the HLA-DQB2 gene in horseshoe bats compared to other chiropteran species.Based on whole-genome resequencing and population genomic analyses,we identified multiple candidate loci(e.g.,GLI3)associated with variations in echolocation call frequency across R.affinis subspecies.This research not only expands our understanding of the genetic characteristics of the Rhinolophus genus but also establishes a valuable foundation for future research.