The evolution of cancer genomic medicine in Japan and the role of the National Cancer Center Japan

The journey to implement cancer genomic medicine(CGM)in oncology practice began in the 1980s,which is considered the dawn of genetic and genomic cancer research.At the time,a variety of activating oncogenic alterations and their functional significance were unveiled in cancer cells,which led to the development of molecular targeted therapies in the 2000s and beyond.Although CGM is still a relatively new discipline and it is difficult to predict to what extent CGM will benefit the diverse pool of cancer patients,the National Cancer Center(NCC)of Japan has already contributed considerably to CGM advancement for the conquest of cancer.Looking back at these past achievements of the NCC,we predict that the future of CGM will involve the following:1)A biobank of paired cancerous and non-cancerous tissues and cells from various cancer types and stages will be developed.The quantity and quality of these samples will be compatible with omics analyses.All biobank samples will be linked to longitudinal clinical information.2)New technologies,such as whole-genome sequencing and artificial intelligence,will be introduced and new bioresources for functional and pharmacologic analyses(e.g.,a patient-derived xenograft library)will be systematically deployed.3)Fast and bidirectional translational research(bench-to-bedside and bedside-to-bench)performed by basic researchers and clinical investigators,preferably working alongside each other at the same institution,will be implemented;4)Close collaborations between academia,industry,regulatory bodies,and funding agencies will be established.5)There will be an investment in the other branch of CGM,personalized preventive medicine,based on the individual's genetic predisposition to cancer.

Construction and validation of somatic mutation-derived long noncoding RNAs signatures of genomic instability to predict prognosis of hepatocellular carcinoma

BACKGROUND Long non-coding RNAs(LncRNAs)have been found to be a potential prognostic factor for cancers,including hepatocellular carcinoma(HCC).Some LncRNAs have been confirmed as potential indicators to quantify genomic instability(GI).Nevertheless,GI-LncRNAs remain largely unexplored.This study established a GI-derived LncRNA signature(GILncSig)that can predict the prognosis of HCC patients.AIM To establish a GILncSig that can predict the prognosis of HCC patients.METHODS Identification of GI-LncRNAs was conducted by combining LncRNA expression and somatic mutation profiles.The GI-LncRNAs were then analyzed for functional enrichment.The GILncSig was established in the training set by Cox regression analysis,and its predictive ability was verified in the testing set and TCGA set.In addition,we explored the effects of the GILncSig and TP53 on prognosis.RESULTS A total of 88 GI-LncRNAs were found,and functional enrichment analysis showed that their functions were mainly involved in small molecule metabolism and GI.The GILncSig was constructed by 5 LncRNAs(miR210HG,AC016735.1,AC116351.1,AC010643.1,LUCAT1).In the training set,the prognosis of high-risk patients was significantly worse than that of low-risk patients,and similar results were verified in the testing set and TCGA set.Multivariate Cox regression analysis and stratified analysis confirmed that the GILncSig could be used as an independent prognostic factor.Receiver operating characteristic curve analysis of the GILncSig showed that the area under the curve(0.773)was higher than the two LncRNA signatures published recently.Furthermore,the GILncSig may have a better predictive performance than TP53 mutation status alone.CONCLUSION We established a GILncSig that can predict the prognosis of HCC patients,which will help to guide prognostic evaluation and treatment decisions.

Timosaponin AⅢ induces drug-metabolizing enzymes by activating constitutive androstane receptor (CAR) via dephosphorylation of the EGFR signaling pathway

The current study aimed to assess the effect of timosaponin AⅢ(T-AⅢ)on drug-metabolizing enzymes during anticancer therapy.The in vivo experiments were conducted on nude and ICR mice.Following a 24-day administration of T-AⅢ,the nude mice exhibited an induction of CYP2B10,MDR1,and CYP3A11 expression in the liver tissues.In the ICR mice,the expression levels of CYP2B10 and MDR1 increased after a three-day T-AⅢ administration.The in vitro assessments with HepG2 cells revealed that T-AⅢ induced the expression of CYP2B6,MDR1,and CYP3A4,along with constitutive androstane receptor(CAR)activation.Treatment with CAR siRNA reversed the T-AⅢ-induced increases in CYP2B6 and CYP3A4 expression.Furthermore,other CAR target genes also showed a significant increase in the expression.The up-regulation of murine CAR was observed in the liver tissues of both nude and ICR mice.Subsequent findings demonstrated that T-AⅢ activated CAR by inhibiting ERK1/2 phosphorylation,with this effect being partially reversed by the ERK activator t-BHQ.Inhibition of the ERK1/2 signaling pathway was also observed in vivo.Additionally,T-AⅢ inhibited the phosphorylation of EGFR at Tyr1173 and Tyr845,and suppressed EGF-induced phosphorylation of EGFR,ERK,and CAR.In the nude mice,T-AⅢ also inhibited EGFR phosphorylation.These results collectively indicate that T-AⅢ is a novel CAR activator through inhibition of the EGFR pathway.

Conservation genomic investigation of an endangered conifer,Thuja sutchuenensis,reveals low genetic diversity but also low genetic load

Endangered species generally have small populations with low genetic diversity and a high genetic load.Thuja sutchuenensis is an endangered conifer endemic to southwestern China.It was once considered extinct in the wild,but in 1999 was rediscovered.However,little is known about its genetic load.We collected 67 individuals from five wild,isolated T.sutchuenensis populations,and used 636,151 SNPs to analyze the level of genetic diversity and genetic load in T.sutchuenensis to delineate the conservation units of T.sutchuenensis,based on whole transcriptome sequencing data,as well as target capture sequencing data.We found that populations of T.sutchuenensis could be divided into three groups.These groups had low levels genetic diversity and were moderately genetically differentiated.Our findings also indicate that T.sutchuenensis suffered two severe bottlenecks around the Last Glaciation Period and Last Glacial Maximum.Among Thuja species,T.sutchuenensis presented the lowest genetic load and hence might have purged deleterious mutations efficiently through purifying selection.However,distribution of fitness effects analysis indicated a high extinction risk for T.sutchuenensis.Multiple lines of evidence identified three management units for T.sutchuenensis.Although T.sutchuenensis possesses a low genetic load,low genetic diversity,suboptimal fitness,and anthropogenic pressures all present an extinction risk for this rare conifer.This might also hold true for many endangered plant species in the mountains all over the world.

Digital signal acquisition system for complex nuclear reaction experiments

A digital data-acquisition system based on XIA LLC products was used in a complex nuclear reaction experiment using radioactive ion beams.A flexible trigger system based on a field-programmable gate array(FPGA)parametrization was developed to adapt to different experimental sizes.A user-friendly interface was implemented,which allows converting script language expressions into FPGA internal control parameters.The proposed digital system can be combined with a conventional analog data acquisition system to provide more flexibility.The performance of the combined system was veri-fied using experimental data.

Gut microbiota dysbiosis contributes toα-synuclein-related pathology associated with C/EBPβ/AEP signaling activation in a mouse model of Parkinson’s disease

Parkinson’s disease is a neurodegenerative disease characterized by motor and gastrointestinal dysfunction.Gastrointestinal dysfunction can precede the onset of motor symptoms by several years.Gut microbiota dysbiosis is involved in the pathogenesis of Parkinson’s disease,whether it plays a causal role in motor dysfunction,and the mechanism underlying this potential effect,remain unknown.CCAAT/enhancer binding proteinβ/asparagine endopeptidase(C/EBPβ/AEP)signaling,activated by bacterial endotoxin,can promoteα-synuclein transcription,thereby contributing to Parkinson’s disease pathology.In this study,we aimed to investigate the role of the gut microbiota in C/EBPβ/AEP signaling,α-synuclein-related pathology,and motor symptoms using a rotenone-induced mouse model of Parkinson’s disease combined with antibiotic-induced microbiome depletion and fecal microbiota transplantation.We found that rotenone administration resulted in gut microbiota dysbiosis and perturbation of the intestinal barrier,as well as activation of the C/EBP/AEP pathway,α-synuclein aggregation,and tyrosine hydroxylase-positive neuron loss in the substantia nigra in mice with motor deficits.However,treatment with rotenone did not have any of these adverse effects in mice whose gut microbiota was depleted by pretreatment with antibiotics.Importantly,we found that transplanting gut microbiota derived from mice treated with rotenone induced motor deficits,intestinal inflammation,and endotoxemia.Transplantation of fecal microbiota from healthy control mice alleviated rotenone-induced motor deficits,intestinal inflammation,endotoxemia,and intestinal barrier impairment.These results highlight the vital role that gut microbiota dysbiosis plays in inducing motor deficits,C/EBPβ/AEP signaling activation,andα-synuclein-related pathology in a rotenone-induced mouse model of Parkinson’s disease.Additionally,our findings suggest that supplementing with healthy microbiota may be a safe and effective treatment that could help ameliorate the progression of motor deficits in patients with Parkinson’s disease.

Melatonin improves synapse development by PI3K/Akt signaling in a mouse model of autism spectrum disorder

Autism spectrum disorders are a group of neurodevelopmental disorders involving more than 1100 genes,including Ctnnd2 as a candidate gene.Ctnnd2knockout mice,serving as an animal model of autis m,have been demonstrated to exhibit decreased density of dendritic spines.The role of melatonin,as a neuro hormone capable of effectively alleviating social interaction deficits and regulating the development of dendritic spines,in Ctnnd2 deletion-induced nerve injury remains unclea r.In the present study,we discove red that the deletion of exon 2 of the Ctnnd2 gene was linked to social interaction deficits,spine loss,impaired inhibitory neurons,and suppressed phosphatidylinositol-3-kinase(PI3K)/protein kinase B(Akt) signal pathway in the prefrontal cortex.Our findings demonstrated that the long-term oral administration of melatonin for 28 days effectively alleviated the aforementioned abnormalities in Ctnnd2 gene-knockout mice.Furthermore,the administration of melatonin in the prefro ntal cortex was found to improve synaptic function and activate the PI3K/Akt signal pathway in this region.The pharmacological blockade of the PI3K/Akt signal pathway with a PI3K/Akt inhibitor,wo rtmannin,and melatonin receptor antagonists,luzindole and 4-phenyl-2-propionamidotetralin,prevented the melatonin-induced enhancement of GABAergic synaptic function.These findings suggest that melatonin treatment can ameliorate GABAe rgic synaptic function by activating the PI3K/Akt signal pathway,which may contribute to the improvement of dendritic spine abnormalities in autism spectrum disorders.

Na^(+)/K^(+)-ATPase:ion pump,signal transducer,or cytoprotective protein,and novel biological functions

Na^(+)/K^(+)-ATPase is a transmembrane protein that has important roles in the maintenance of electrochemical gradients across cell membranes by transporting three Na^(+)out of and two K^(+)into cells.Additionally,Na^(+)/K^(+)-ATPase participates in Ca^(2+)-signaling transduction and neurotransmitter release by coordinating the ion concentration gradient across the cell membrane.Na^(+)/K^(+)-ATPase works synergistically with multiple ion channels in the cell membrane to form a dynamic network of ion homeostatic regulation and affects cellular communication by regulating chemical signals and the ion balance among different types of cells.Therefo re,it is not surprising that Na^(+)/K^(+)-ATPase dysfunction has emerged as a risk factor for a variety of neurological diseases.However,published studies have so far only elucidated the important roles of Na^(+)/K^(+)-ATPase dysfunction in disease development,and we are lacking detailed mechanisms to clarify how Na^(+)/K^(+)-ATPase affects cell function.Our recent studies revealed that membrane loss of Na^(+)/K^(+)-ATPase is a key mechanism in many neurological disorders,particularly stroke and Parkinson's disease.Stabilization of plasma membrane Na^(+)/K^(+)-ATPase with an antibody is a novel strategy to treat these diseases.For this reason,Na^(+)/K^(+)-ATPase acts not only as a simple ion pump but also as a sensor/regulator or cytoprotective protein,participating in signal transduction such as neuronal autophagy and apoptosis,and glial cell migration.Thus,the present review attempts to summarize the novel biological functions of Na^(+)/K^(+)-ATPase and Na^(+)/K^(+)-ATPase-related pathogenesis.The potential for novel strategies to treat Na^(+)/K^(+)-ATPase-related brain diseases will also be discussed.

Hypoglycemic mechanism of Tegillarca granosa polysaccharides on type 2 diabetic mice by altering gut microbiota and regulating the PI3K-akt signaling pathwaye

Type 2 diabetes mellitus(T2DM)is a complex metabolic disease threatening human health.We investigated the effects of Tegillarca granosa polysaccharide(TGP)and determined its potential mechanisms in a mouse model of T2DM established through a high-fat diet and streptozotocin.TGP(5.1×10^(3) Da)was composed of mannose,glucosamine,rhamnose,glucuronic acid,galactosamine,glucose,galactose,xylose,and fucose.It could significantly alleviate weight loss,reduce fasting blood glucose levels,reverse dyslipidemia,reduce liver damage from oxidative stress,and improve insulin sensitivity.RT-PCR and Western blotting indicated that TGP could activate the phosphatidylinositol-3-kinase/protein kinase B signaling pathway to regulate disorders in glucolipid metabolism and improve insulin resistance.TGP increased the abundance of Allobaculum,Akkermansia,and Bifidobacterium,restored the microbiota abundance in the intestinal tracts of mice with T2DM,and promoted short-chain fatty acid production.This study provides new insights into the antidiabetic effects of TGP and highlights its potential as a natural hypoglycemic nutraceutical.

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.

Detection method of forward-scatter signal based on Rényi entropy

The application scope of the forward scatter radar(FSR)based on the Global Navigation Satellite System(GNSS)can be expanded by improving the detection capability.Firstly,the forward-scatter signal model when the target crosses the baseline is constructed.Then,the detection method of the for-ward-scatter signal based on the Rényi entropy of time-fre-quency distribution is proposed and the detection performance with different time-frequency distributions is compared.Simula-tion results show that the method based on the smooth pseudo Wigner-Ville distribution(SPWVD)can achieve the best perfor-mance.Next,combined with the geometry of FSR,the influence on detection performance of the relative distance between the target and the baseline is analyzed.Finally,the proposed method is validated by the anechoic chamber measurements and the results show that the detection ability has a 10 dB improvement compared with the common constant false alarm rate(CFAR)detection.

Genomic Profile of SARS-COV-2 Associated with COVID-19 Outbreaks in N’Djamena, Chad

Background: SARS-CoV-2 has circulated worldwide with dramatic consequences. In Chad, we have no data reported of variants. The aim of this study was to identify the SARS-CoV-2 variants that circulated during the epidemic from 2020 to 2021. Methods: This is a cross-sectional, descriptive study carried out between 2020 and 2021. Samples from patients with suspected COVID-19 were tested in five laboratories in N’Djamena. One hundred quality samples of the positives were sequenced in Kinshasa using Oxford nanopore technologies minion and the Protocol Midnight SARS-CoV2. Data were processed using Excel version 16 software. Results: Of the 100 samples sequenced, 77 (77%) produced sequences, 23 (23%) did not. The genomic profiles were wild-type Wuhan and minor mutations (19A, 19B (A), 20A (B.1, B.2), 20B (AV.1), 20D (B.1.1.1 /C.36), 20C), variant of concern Alpha (20I), variant of concern Delta (21A/J), variant of interest Eta (21D), variant of concern Omicron (21K) and unclassified variant under surveillance (B.1.640). Of these variants, the maximums were detected in patients aged 26 - 35 with 30.26% and 25.26% in 36 - 45. However, 24.67% were in travelers and 75.32% in residents, 35.06% in those vaccinated against COVID-19 and 62.33% in non-vaccinates. The estimated case-fatality rate was 2.44% (107/4374). Conclusion: This work has provided preliminary data on COVID-19 and SARS-CoV-2 variants circulating during the 2020-2021 epidemics in Chad.

2D DOA Estimation of Coherent Signals with a Separated Linear Acoustic Vector-Sensor Array

In this paper, a two-dimensional(2D) DOA estimation algorithm of coherent signals with a separated linear acoustic vector-sensor(AVS) array consisting of two sparse AVS arrays is proposed. Firstly,the partitioned spatial smoothing(PSS) technique is used to construct a block covariance matrix, so as to decorrelate the coherency of signals. Then a signal subspace can be obtained by singular value decomposition(SVD) of the covariance matrix. Using the signal subspace, two extended signal subspaces are constructed to compensate aperture loss caused by PSS.The elevation angles can be estimated by estimation of signal parameter via rotational invariance techniques(ESPRIT) algorithm. At last, the estimated elevation angles can be used to estimate automatically paired azimuth angles. Compared with some other ESPRIT algorithms, the proposed algorithm shows higher estimation accuracy, which can be proved through the simulation results.

A feedback control method for phase signal demodulation in fber-optic hydrophones

In the realm of acoustic signal detection,the identification of weak signals,particularly in the presence of negative signal-to-noise ratios,poses a significant challenge.This challenge is further heightened when signals are acquired through fiber-optic hydrophones,as these signals often lack physical significance and resist clear systematic modeling.Conventional processing methods,e.g.,low-pass filter(LPF),require a thorough understanding of the effective signal bandwidth for noise reduction,and may introduce undesirable time lags.This paper introduces an innovative feedback control method with dual Kalman filters for the demodulation of phase signals with noises in fiber-optic hydrophones.A mathematical model of the closed-loop system is established to guide the design of the feedback control,aiming to achieve a balance with the input phase signal.The dual Kalman filters are instrumental in mitigating the effects of signal noise,observation noise,and control execution noise,thereby enabling precise estimation for the input phase signals.The effectiveness of this feedback control method is demonstrated through examples,showcasing the restoration of low-noise signals,negative signal-to-noise ratio signals,and multi-frequency signals.This research contributes to the technical advancement of high-performance devices,including fiber-optic hydrophones and phase-locked amplifiers.

Exploring the Unknown: The Application and Prospects of Artificial Intelligence in Genomics and Bioinformatics

This review comprehensively explores the core application of artificial intelligence (AI) in the fields of genomics and bioinformatics, and deeply analyzes how it leads the innovative progress of science. In the cutting-edge fields of genomics and bioinformatics, the application of AI is propelling a deeper understanding of complex genetic mechanisms and the development of innovative therapeutic approaches. The precision of AI in genomic sequence analysis, coupled with breakthroughs in precise gene editing, such as AI-designed gene editors, significantly enhances our comprehension of gene functions and disease associations . Moreover, AI’s capabilities in disease prediction, assessing individual disease risks through genomic data analysis, provide robust support for personalized medicine. AI applications extend beyond gene identification, gene expression pattern prediction, and genomic structural variant analysis, encompassing key areas such as epigenetics, multi-omics data integration, genetic disease diagnosis, evolutionary genomics, and non-coding RNA function prediction. Despite challenges including data privacy, algorithm transparency, and bioethical issues, the future of AI is expected to continue revolutionizing genomics and bioinformatics, ushering in a new era of personalized medicine and precision treatments.

Emotion Measurement Using Biometric Signal

In recent years, research on the estimation of human emotions has been active, and its application is expected in various fields. Biological reactions, such as electroencephalography (EEG) and root mean square successive difference (RMSSD), are indicators that are less influenced by individual arbitrariness. The present study used EEG and RMSSD signals to assess the emotions aroused by emotion-stimulating images in order to investigate whether various emotions are associated with characteristic biometric signal fluctuations. The participants underwent EEG and RMSSD while viewing emotionally stimulating images and answering the questionnaires. The emotions aroused by emotionally stimulating images were assessed by measuring the EEG signals and RMSSD values to determine whether different emotions are associated with characteristic biometric signal variations. Real-time emotion analysis software was used to identify the evoked emotions by describing them in the Circumplex Model of Affect based on the EEG signals and RMSSD values. Emotions other than happiness did not follow the Circumplex Model of Affect in this study. However, ventral attentional activity may have increased the RMSSD value for disgust as the β/θ value increased in right-sided brain waves. Therefore, the right-sided brain wave results are necessary when measuring disgust. Happiness can be assessed easily using the Circumplex Model of Affect for positive scene analysis. Improving the current analysis methods may facilitate the investigation of face-to-face communication in the future using biometric signals.

PCR-HRM for Genomic Surveillance of SARS-CoV-2: A Variant Detection Tool in Côte d’Ivoire, West Africa

The rise of new viruses, like SARS-CoV-2 causing the COVID-19 outbreak, along with the return of antibiotic resistance in harmful bacteria, demands a swift and efficient reaction to safeguard the health and welfare of the global population. It is crucial to have effective measures for prevention, intervention, and monitoring in place to address these evolving and recurring risks, ensuring public health and international security. In countries with limited resources, utilizing recombinant mutation plasmid technology in conjunction with PCR-HRM could help differentiate the existence of novel variants. cDNA synthesis was carried out on 8 nasopharyngeal samples following viral RNA extraction. The P1 segment of the SARS-CoV-2 Spike S protein was amplified via conventional PCR. Subsequently, PCR products were ligated with the pGEM-T Easy vector to generate eight recombinant SARS-CoV-2 plasmids. Clones containing mutations were sequenced using Sanger sequencing and analyzed through PCR-HRM. The P1 segment of the S gene from SARS-CoV-2 was successfully amplified, resulting in 8 recombinant plasmids generated from the 231 bp fragment. PCR-HRM analysis of these recombinant plasmids differentiated three variations within the SARS-CoV-2 plasmid population, each displaying distinct melting temperatures. Sanger sequencing identified mutations A112C, G113T, A114G, G214T, and G216C on the P1 segment, validating the PCR-HRM findings of the variations. These mutations led to the detection of L452R or L452M and F486V protein mutations within the protein sequence of the Omicron variant of SARS-CoV-2. In summary, PCR-HRM is a vital and affordable tool for distinguishing SARS-CoV-2 variants utilizing recombinant plasmids as controls.

Special Section on High-Dimensional Signal Processing

Massive amounts of data are acquired in modern and future information technology industries such as communication,radar,and remote sensing.The presence of large dimensionality and size in these data offers new opportunities to enhance the performance of signal processing in such applications and even motivate new ones.However,the curse of dimensionality is always a challenge when processing such high-dimensional signals.In practical tasks,high-dimensional signals need to be acquired,processed,and analyzed with high accuracy,robustness,and computational efficiency.This special section aims to address these challenges,where articles attempt to develop new theories and methods that are best suited to the high dimensional nature of the signals involved,and explore modern and emerging applications in this area.

Large‑scale transcriptomic and genomic analyses reveal a novel functional gene SERPINB6 for chicken carcass traits

Background Carcass traits are crucial indicators of meat production efficiency.However,the molecular regulatory mechanisms associated with these traits remain unclear.Results In this study,we conducted comprehensive transcriptomic and genomic analyses on 399 Tiannong partridge chickens to identify key genes and variants associated with carcass traits and to elucidate the underlying regulatory mechanisms.Based on association analyses with the elastic net(EN)model,we identified 12 candidate genes(AMY1A,AP3B2,CEBPG,EEF2,EIF4EBP1,FGFR1,FOXD3,GOLM1,LOC107052698,PABPC1,SERPINB6 and TBC1D16)for 4 carcass-related traits,namely live weight,dressed weight,eviscerated weight,and breast muscle weight.SERPINB6 was identified as the only overlapping gene by 3 analyses,EN model analysis,weighted gene co-expression network analysis and differential expression analysis.Cell-level experiments confirmed that SERPINB6 promotes the proliferation of chicken DF1 cells and primary myoblasts.Further expression genome-wide association study and association analysis indicated that rs317934171 is the critical site that enhances SERPINB6 expression.Furthermore,a dual-luciferase reporter assay proved that gga-miR-1615 targets the 3′UTR of SERPINB6.Conclusions Collectively,our findings reveal that SERPINB6 serves as a novel gene for chicken carcass traits by promoting fibroblast and myoblast proliferation.Additionally,the downstream variant rs317934171 regulates SERPINB6 expression.These results identify a new target gene and molecular marker for the molecular mechanisms of chicken carcass traits.

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.