Assessing the conservation impact of Chinese indigenous chicken populations between ex-situ and in-situ using genome-wide SNPs

Conservation programs require rigorous evaluation to ensure the preservation of genetic diversity and viability of conservation populations. In this study, we conducted a comparative analysis of two indigenous Chinese chicken breeds, Gushi and Xichuan black-bone, using whole-genome SNPs to understand their genetic diversity, track changes over time and population structure. The breeds were divided into five conservation populations(GS1, 2010, ex-situ;GS2, 2019, ex-situ;GS3, 2019, in-situ;XB1, 2010, in-situ;and XB2, 2019, in-situ) based on conservation methods and generations. The genetic diversity indices of three conservation populations of Gushi chicken showed consistent trends, with the GS3 population under in-situ strategy having the highest diversity and GS2 under ex-situ strategy having the lowest. The degree of inbreeding of GS2 was higher than that of GS1 and GS3. Conserved populations of Xichuan black-bone chicken showed no obvious changes in genetic diversity between XB1 and XB2. In terms of population structure, the GS3 population were stratified relative to GS1 and GS2. According to the conservation priority, GS3 had the highest contribution to the total gene and allelic diversity in GS breed, whereas the contribution of XB1 and XB2 were similar. We also observed that the genetic diversity of GS2 was lower than GS3, which were from the same generation but under different conservation programs(in-situ and ex-situ). While XB1 and XB2 had similar levels of genetic diversity. Overall, our findings suggested that the conservation programs performed in ex-situ could slow down the occurrence of inbreeding events, but could not entirely prevent the loss of genetic diversity when the conserved population size was small, while in-situ conservation populations with large population size could maintain a relative high level of genetic diversity.

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.

Leveraging the potential of big genomic and phenotypic data for genome-wide association mapping in wheat

Genome-wide association mapping studies(GWAS)based on Big Data are a potential approach to improve marker-assisted selection in plant breeding.The number of available phenotypic and genomic data sets in which medium-sized populations of several hundred individuals have been studied is rapidly increasing.Combining these data and using them in GWAS could increase both the power of QTL discovery and the accuracy of estimation of underlying genetic effects,but is hindered by data heterogeneity and lack of interoperability.In this study,we used genomic and phenotypic data sets,focusing on Central European winter wheat populations evaluated for heading date.We explored strategies for integrating these data and subsequently the resulting potential for GWAS.Establishing interoperability between data sets was greatly aided by some overlapping genotypes and a linear relationship between the different phenotyping protocols,resulting in high quality integrated phenotypic data.In this context,genomic prediction proved to be a suitable tool to study relevance of interactions between genotypes and experimental series,which was low in our case.Contrary to expectations,fewer associations between markers and traits were found in the larger combined data than in the individual experimental series.However,the predictive power based on the marker-trait associations of the integrated data set was higher across data sets.Therefore,the results show that the integration of medium-sized to Big Data is an approach to increase the power to detect QTL in GWAS.The results encourage further efforts to standardize and share data in the plant breeding community.

Genome-Wide Association Study of Cooked Rice Textural Attributes and Starch Physicochemical Properties in indica Rice

Rice cooking and eating qualities(CEQ)are mainly determined by cooked rice textural parameters and starch physicochemical properties.However,the genetic bases of grain texture and starch properties in rice have not been fully understood.We conducted a genome-wide association study for apparent amylose content(AAC),starch pasting viscosities,and cooked rice textural parameters using 279 indica rice accessions from the 3000 Rice Genome Project.We identified 26 QTLs in the whole population and detected single nucleotide polymorphisms(SNPs)with the lowest P-value at the Waxy(Wx)locus for all traits except pasting temperature and cohesiveness.Additionally,we detected significant SNPs at the SUBSTANDARD STARCH GRAIN6(SSG6)locus for AAC,setback(SB),hardness,adhesiveness,chewiness(CHEW),gumminess(GUM),and resilience.We subsequently divided the population using a SNP adjacent to the Waxy locus,and identified 23 QTLs and 12 QTLs in two sub-panels,WxT and WxA,respectively.In these sub-panels,SSG6 was also identified to be associated with pasting parameters,including peak viscosity,hot paste viscosity,cold paste viscosity,and consistency viscosity.Furthermore,a candidate gene encoding monosaccharide transporter 5(OsMST5)was identified to be associated with AAC,breakdown,SB,CHEW,and GUM.In total,39 QTLs were co-localized with known genes or previously reported QTLs.These identified genes and QTLs provide valuable information for genetic manipulation to improve rice CEQ.

Genome-wide association study of seedling nitrogen-use efficiency-associated traits in common wheat(Triticum aestivum L.)

Nitrogen(N)fertilizer application is essential for crop-plant growth and development.Identifying genetic loci associated with N-use efficiency(NUE)could increase wheat yields and reduce environmental pollution caused by overfertilization.We subjected a panel of 389 wheat accessions to N and chlorate(a nitrate analog)treatments to identify quantitative trait loci(QTL)controlling NUE-associated traits at the wheat seedling stage.Genotyping the panel with a 660K single-nucleotide polymorphism(SNP)array,we identified 397 SNPs associated with N-sensitivity index and chlorate inhibition rate.These SNPs were merged into 49 QTL,of which eight were multi-environment stable QTL and 27 were located near previously reported QTL.A set of 135 candidate genes near the 49 QTL included TaBOX(F-box family protein)and TaERF(ethylene-responsive transcription factor).A Tabox mutant was more sensitive to low-N stress than the wild-type plant.We developed two functional markers for Hap 1,the favorable allele of TaBOX.

Genome-Wide Analysis for Yield-Related Agronomic and Biochemical Traits of Chinese and Bangladeshi Grass Pea Genotypes Using SSR Markers

Grass pea(Lathyrus sativus L.)is an imperative food crop cultured in dryland agricultural ecology.It is a vital source of dietary protein to millions of populaces living in low-income countries in South-East Asia and Africa.This study highlights the improvement of genomic properties and their application in marker-trait relationships for 17 yield-related characters in 400 grass pea genotypes from China and Bangladesh.These characters were assessed via 56 polymorphic markers using general linear model(GLM)(P+G+Q)and mixed linear model(MLM)(P+G+Q+K)in the tassel software based on the linkage disequilibrium and population structure analysis.Population structure analysis showed two major groups and one admixed group in the populace.Statistically significant loci pairs of linkage disequilibrium(LD)mean value(D′)was 0.479.A total of 99 and 61 marker-trait associations in GLM and MLM models allied to the 17 traits were accepted at a 5%level of significance.Among these markers,21 markers were associated with more than one trait;12 marker-trait associations passed the Bonferroni correction threshold.Both models found six markers C41936,C39067,C34100,C47146,C47638,and C43047 significantly associated with days to maturity,flower color,plant height,and seed per pod were detected in the Hebei and Liaoyang location(p≤0.01),and the interpretation rate(R^(2)value)11.2%to 43.6%.Conferring to the consequences,the association analysis methodology may operative system for quantitative,qualitative,and biochemical traits related to gene position mapping and support breeders in improving novel approaches for advancing the grass pea quality.

Genome-wide association mapping and genomic prediction of stalk rot in two mid-altitude tropical maize populations

Maize stalk rot reduces grain yield and quality.Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait.Genomic prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted selection.We performed a genome-wide association study(GWAS)and genomic prediction of resistance in testcross hybrids of 677 inbred lines from the Tuxpe?o and non-Tuxpe?o heterotic pools grown in three environments and genotyped with 200,681 single-nucleotide polymorphisms(SNPs).Eighteen SNPs associated with stalk rot shared genomic regions with gene families previously associated with plant biotic and abiotic responses.More favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred lines.Incorporating genotype-by-environment(G×E)interaction increased genomic prediction accuracy.

Genome-Wide Discovery and Expression Profiling of the SWEET Sugar Transporter Gene Family in Woodland Strawberry (Fragaria vesca) under Developmental and Stress Conditions: Structural and Evolutionary Analysis

The SWEET(sugar will eventually be exported transporter)family proteins are a recently identified class of sugar transporters that are essential for various physiological processes.Although the functions of the SWEET proteins have been identified in a number of species,to date,there have been no reports of the functions of the SWEET genes in woodland strawberries(Fragaria vesca).In this study,we identified 15 genes that were highly homolo-gous to the A.thaliana AtSWEET genes and designated them as FvSWEET1–FvSWEET15.We then conducted a structural and evolutionary analysis of these 15 FvSWEET genes.The phylogenetic analysis enabled us to categor-ize the predicted 15 SWEET proteins into four distinct groups.We observed slight variations in the exon‒intron structures of these genes,while the motifs and domain structures remained highly conserved.Additionally,the developmental and biological stress expression profiles of the 15 FvSWEET genes were extracted and analyzed.Finally,WGCNA coexpression network analysis was run to search for possible interacting genes of FvSWEET genes.The results showed that the FvSWEET10 genes interacted with 20 other genes,playing roles in response to bacterial and fungal infections.The outcomes of this study provide insights into the further study of FvSWEET genes and may also aid in the functional characterization of the FvSWEET genes in woodland strawberries.

Genome-wide and candidate gene association studies identify BnPAP17 as conferring the utilization of organic phosphorus in oilseed rape

Phosphorus(P)is essential for living plants,and P deficiency is one of the key factors limiting the yield in rapeseed production worldwide.As the most important organ for plants,root morphology traits(RMTs)play a key role in P absorption.To investigate the genetic variability of RMT under low P availability,we dissected the genetic structure of RMTs by genome-wide association studies(GWAS),linkage mapping and candidate gene association studies(CGAS).A total of 52 suggestive loci were associated with RMTs under P stress conditions in 405 oilseed rape accessions.The purple acid phosphatase gene BnPAP17 was found to control the lateral root number(LRN)and root dry weight(RDW)under low P stress.The expression of BnPAP17 was increased in shoot tissue in P-efficient cultivars compared to root tissue and P-inefficient cultivars in response to low P stress.Moreover,the haplotype of BnPAP17^(Hap3)was detected for the selective breeding of P efficiency in oilseed rape.Over-expression of the BnPAP17^(Hap3)could promote the shoot and root growth with enhanced tolerance to low P stress and organic phosphorus(Po)utilization in oilseed rape.Collectively,these findings increase our understanding of the mechanisms underlying BnPAP17-mediated low P stress tolerance in oilseed rape.

Genome-Wide Exploration of the Grape GLR Gene Family and Differential Responses of VvGLR3.1 and VvGLR3.2 to Low Temperature and Salt Stress

Grapes,one of the oldest tree species globally,are rich in vitamins.However,environmental conditions such as low temperature and soil salinization significantly affect grape yield and quality.The glutamate receptor(GLR)family,comprising highly conserved ligand-gated ion channels,regulates plant growth and development in response to stress.In this study,11 members of the VvGLR gene family in grapes were identified using whole-genome sequence analysis.Bioinformatic methods were employed to analyze the basic physical and chemical properties,phylogenetic trees,conserved domains,motifs,expression patterns,and evolutionary relationships.Phylogenetic and collinear analyses revealed that the VvGLRs were divided into three subgroups,showing the high conservation of the grape GLR family.These members exhibited 2 glutamate receptor binding regions(GABAb and GluR)and 3-4 transmembrane regions(M1,M2,M3,and M4).Real-time quantitative PCR analysis demonstrated the sensitivity of all VvGLRs to low temperature and salt stress.Subsequent localization studies in Nicotiana tabacum verified that VvGLR3.1 and VvGLR3.2 proteins were located on the cell membrane and cell nucleus.Additionally,yeast transformation experiments confirmed the functionality of VvGLR3.1 and VvGLR3.2 in response to low temperature and salt stress.Thesefindings highlight the significant role of the GLR family,a highly conserved group of ion channels,in enhancing grape stress resistance.This study offers new insights into the grape GLR gene family,providing fundamental knowledge for further functional analysis and breeding of stress-resistant grapevines.

Generation of a human haploid neural stem cell line for genome-wide genetic screening

BACKGROUND Haploid embryonic stem cells(haESCs)have been established in many species.Differentiated haploid cell line types in mammals are lacking due to spontaneous diploidization during differentiation that compromises lineage-specific screens.AIM To derive human haploid neural stem cells(haNSCs)to carry out lineage-specific screens.METHODS Human haNSCs were differentiated from human extended haESCs with the help of Y27632(ROCK signaling pathway inhibitor)and a series of cytokines to reduce diploidization.Neuronal differentiation of haNSCs was performed to examine their neural differentiation potency.Global gene expression analysis was conducted to compare haNSCs with diploid NSCs and haESCs.Fluorescence activated cell sorting was performed to assess the diploidization rate of extended haESCs and haNSCs.Genetic manipulation and screening were utilized to evaluate the significance of human haNSCs as genetic screening tools.RESULTS Human haESCs in extended pluripotent culture medium showed more compact and smaller colonies,a higher efficiency in neural differentiation,a higher cell survival ratio and higher stability in haploidy maintenance.These characteristics effectively facilitated the derivation of human haNSCs.These human haNSCs can be generated by differentiation and maintain haploidy and multipotency to neurons and glia in the long term in vitro.After PiggyBac transfection,there were multiple insertion sites in the human haNSCs’genome,and the insertion sites were evenly spread across all chromosomes.In addition,after the cells were treated with manganese,we were able to generate a list of manganese-induced toxicity genes,demonstrating their utility as genetic screening tools.CONCLUSION This is the first report of a generated human haploid somatic cell line with a complete genome,proliferative ability and neural differentiation potential that provides cell resources for recessive inheritance and drug targeted screening.

Genome-wide characterization of graft-transmissible mRNA-coding P450 genes of cucumber(Cucumis sativus L.)

P450(cytochrome P450)is a supergene family,which is involved in various metabolic pathways in plants.Based on previous study,we found some of cucumber P450 mRNAs were systemic mobile in cucumber/pumpkin grafts.However,the reason that why P450 mRNAs were endorsed as signaling,and what specific motif(s)did they harbored is not clear yet.Here,we first identified 221 CsaP450 genes in cucumber genomewide level.Combining with graft-transmissiblemRNAs datasets in cucumber,we elucidated 15mobile-CsaP450-coding genes,of which 5 and 10 belonged to A-type and non-A type respectively.Compared with Arabidopsis and pumpkin(Cucubit moschata)graft-induced-transmissible P450 mRNAs,a phylogenetic treewas constructed and divided into eight clans by usingmultiple-sequence alignment.Gene ontology(GO)enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG)annotations indicated that the expression patterns of the mobile-mRNA-coding CsaP450 genes in different tissues of cucumber was specifically enriched in oxidoreductase activity and secondary metabolic pathways.The structures and motifs of these 15 mobile-mRNA-coding CsaP450 genes and their types of regulatory elements told that the proportion of CU-rich motifs was higher than nonmobile-mRNA-coding CsaP450 genes.The integrated analysis of mobility direction and mRNA abundance of 15 mobilemRNA-coding CsaP450 genes allowed to conclude that there was rarely relationship between them.The study provided a new insight into the relationship between the motifs and functional characterization of mobile-mRNA-coding P450 genes of cucumber in genome-wide levels.

Genome-wide identification of apple auxin receptor family genes and functional characterization of MdAFB1

The auxin receptor(TIR1/AFBs)family encodes the F-box protein subunit,which is involved in the formation of the E3 ubiquitin ligase SCFTIR1/AFBs complex,a key component of the auxin signaling pathway.However,there are few studies on the auxin receptor family in apple(Malus×domestica).In this study,eight MdAFBs were identified,and phylogenetic analysis showed that they were classified into four groups and distributed on eight chromosomes.Herein,a comprehensive analysis of the MdAFB gene family was conducted to identify cis-acting elements,gene structures,protein structures,aligned sequences,conserved motifs,conserved amino acids,and the protein–protein interaction network.The results of yeast two-hybrid assays showed that MdAFB1 interacted with three auxin repressor proteins.The results of qRT-PCR showed that MdAFB1 responded to osmotic and salt stress.The overexpression of MdAFB1 increased osmotic and salt resistance in apple calli,and the ectopic expression of MdAFB1 enhanced osmotic and salt tolerance in Arabidopsis.This study provided a basis for the identification of auxin receptor genes in apple and their functions in mediating osmotic and salt stress.

Stage at diagnosis of colorectal cancer through diagnostic route:Who should be screened?

BACKGROUND Colorectal cancer(CRC)is a global health concern,with advanced-stage diagnoses contributing to poor prognoses.The efficacy of CRC screening has been well-established;nevertheless,a significant proportion of patients remain unscreened,with>70%of cases diagnosed outside screening.Although identifying specific subgroups for whom CRC screening should be particularly recommended is crucial owing to limited resources,the association between the diagnostic routes and identification of these subgroups has been less appreciated.In the Japanese cancer registry,the diagnostic routes for groups discovered outside of screening are primarily categorized into those with comorbidities found during hospital visits and those with CRC-related symptoms.AIM To clarify the stage at CRC diagnosis based on diagnostic routes.METHODS We conducted a retrospective observational study using a cancer registry of patients with CRC between January 2016 and December 2019 at two hospitals.The diagnostic routes were primarily classified into three groups:Cancer screening,follow-up,and symptomatic.The early-stage was defined as Stages 0 or I.Multivariate and univariate logistic regressions were exploited to determine the odds of early-stage diagnosis in the symptomatic and cancer screening groups,referencing the follow-up group.The adjusted covariates were age,sex,and tumor location.RESULTS Of the 2083 patients,715(34.4%),1064(51.1%),and 304(14.6%)belonged to the follow-up,symptomatic,and cancer screening groups,respectively.Among the 2083 patients,CRCs diagnosed at an early stage were 57.3%(410 of 715),23.9%(254 of 1064),and 59.5%(181 of 304)in the follow-up,symptomatic,and cancer screening groups,respectively.The symptomatic group exhibited a lower likelihood of early-stage diagnosis than the follow-up group[P<0.001,adjusted odds ratio(aOR),0.23;95%confidence interval(95%CI):0.19-0.29].The likelihood of diagnosis at an early stage was similar between the follow-up and cancer screening groups(P=0.493,aOR for early-stage diagnosis in the cancer screening group vs follow-up group=1.11;95%CI=0.82-1.49).CONCLUSION CRCs detected during hospital visits for comorbidities were diagnosed earlier,similar to cancer screening.CRC screening should be recommended,particularly for patients without periodical hospital visits for comorbidities.

Colorectal cancer screening:A review of current knowledge and progress in research

Colorectal cancer(CRC)is one of the most prevalent malignancies worldwide,being the third most commonly diagnosed malignancy and the second leading cause of cancer-related deaths globally.Despite the progress in screening,early diagnosis,and treatment,approximately 20%-25%of CRC patients still present with metastatic disease at the time of their initial diagnosis.Furthermore,the burden of disease is still expected to increase,especially in individuals younger than 50 years old,among whom early-onset CRC incidence has been increasing.Screening and early detection are pivotal to improve CRC-related outcomes.It is well established that CRC screening not only reduces incidence,but also decreases deaths from CRC.Diverse screening strategies have proven effective in decreasing both CRC incidence and mortality,though variations in efficacy have been reported across the literature.However,uncertainties persist regarding the optimal screening method,age intervals and periodicity.Moreover,adherence to CRC screening remains globally low.In recent years,emerging technologies,notably artificial intelligence,and non-invasive biomarkers,have been developed to overcome these barriers.However,controversy exists over the actual impact of some of the new discoveries on CRC-related outcomes and how to effectively integrate them into daily practice.In this review,we aim to cover the current evidence surrounding CRC screening.We will further critically assess novel approaches under investigation,in an effort to differentiate promising inno-vations from mere novelties.

Esophageal cancer screening,early detection and treatment:Current insights and future directions

Esophageal cancer ranks among the most prevalent malignant tumors globally,primarily due to its highly aggressive nature and poor survival rates.According to the 2020 global cancer statistics,there were approximately 604000 new cases of esophageal cancer,resulting in 544000 deaths.The 5-year survival rate hovers around a mere 15%-25%.Notably,distinct variations exist in the risk factors associated with the two primary histological types,influencing their worldwide incidence and distribution.Squamous cell carcinoma displays a high incidence in specific regions,such as certain areas in China,where it meets the cost-effect-iveness criteria for widespread endoscopy-based early diagnosis within the local population.Conversely,adenocarcinoma(EAC)represents the most common histological subtype of esophageal cancer in Europe and the United States.The role of early diagnosis in cases of EAC originating from Barrett's esophagus(BE)remains a subject of controversy.The effectiveness of early detection for EAC,particularly those arising from BE,continues to be a debated topic.The variations in how early-stage esophageal carcinoma is treated in different regions are largely due to the differing rates of early-stage cancer diagnoses.In areas with higher incidences,such as China and Japan,early diagnosis is more common,which has led to the advancement of endoscopic methods as definitive treatments.These techniques have demonstrated remarkable efficacy with minimal complications while preserving esophageal functionality.Early screening,prompt diagnosis,and timely treatment are key strategies that can significantly lower both the occurrence and death rates associated with esophageal cancer.

A mixed-coordination electron trapping-enabled high-precision touch-sensitive screen for wearable devices

Touch-sensitive screens are crucial components of wearable devices.Materials such as reduced graphene oxide(rGO),carbon nanotubes(CNTs),and graphene offer promising solutions for flexible touch-sensitive screens.However,when stacked with flexible substrates to form multilayered capacitive touching sensors,these materials often suffer from substrate delamination in response to deformation;this is due to the materials having different Young’s modulus values.Delamination results in failure to offer accurate touch screen recognition.In this work,we demonstrate an induced charge-based mutual capacitive touching sensor capable of high-precision touch sensing.This is enabled by electron trapping and polarization effects related to mixed-coordinated bonding between copper nanoparticles and vertically grown graphene nanosheets.Here,we used an electron cyclotron resonance system to directly fabricate graphene-metal nanofilms(GMNFs)using carbon and copper,which are firmly adhered to flexible substrates.After being subjected to 3000 bending actions,we observed almost no change in touch sensitivity.The screen interaction system,which has a signal-to-noise ratio of 41.16 dB and resolution of 650 dpi,was tested using a handwritten Chinese character recognition trial and achieved an accuracy of 94.82%.Taken together,these results show the promise of touch-sensitive screens that use directly fabricated GMNFs for wearable devices.

Development and validation of a prediction model for early screening of people at high risk for colorectal cancer

BACKGROUND Colorectal cancer(CRC)is a serious threat worldwide.Although early screening is suggested to be the most effective method to prevent and control CRC,the current situation of early screening for CRC is still not optimistic.In China,the incidence of CRC in the Yangtze River Delta region is increasing dramatically,but few studies have been conducted.Therefore,it is necessary to develop a simple and efficient early screening model for CRC.AIM To develop and validate an early-screening nomogram model to identify individuals at high risk of CRC.METHODS Data of 64448 participants obtained from Ningbo Hospital,China between 2014 and 2017 were retrospectively analyzed.The cohort comprised 64448 individuals,of which,530 were excluded due to missing or incorrect data.Of 63918,7607(11.9%)individuals were considered to be high risk for CRC,and 56311(88.1%)were not.The participants were randomly allocated to a training set(44743)or validation set(19175).The discriminatory ability,predictive accuracy,and clinical utility of the model were evaluated by constructing and analyzing receiver operating characteristic(ROC)curves and calibration curves and by decision curve analysis.Finally,the model was validated internally using a bootstrap resampling technique.RESULTS Seven variables,including demographic,lifestyle,and family history information,were examined.Multifactorial logistic regression analysis revealed that age[odds ratio(OR):1.03,95%confidence interval(CI):1.02-1.03,P<0.001],body mass index(BMI)(OR:1.07,95%CI:1.06-1.08,P<0.001),waist circumference(WC)(OR:1.03,95%CI:1.02-1.03 P<0.001),lifestyle(OR:0.45,95%CI:0.42-0.48,P<0.001),and family history(OR:4.28,95%CI:4.04-4.54,P<0.001)were the most significant predictors of high-risk CRC.Healthy lifestyle was a protective factor,whereas family history was the most significant risk factor.The area under the curve was 0.734(95%CI:0.723-0.745)for the final validation set ROC curve and 0.735(95%CI:0.728-0.742)for the training set ROC curve.The calibration curve demonstrated a high correlation between the CRC high-risk population predicted by the nomogram model and the actual CRC high-risk population.CONCLUSION The early-screening nomogram model for CRC prediction in high-risk populations developed in this study based on age,BMI,WC,lifestyle,and family history exhibited high accuracy.

Non-participation of asymptomatic candidates in screening protocols reduces early diagnosis and worsens prognosis of colorectal cancer

The Agatsuma et al’s study shows that despite the evidence of the benefits of an early colorectal cancer(CRC)diagnosis,through screening in asymptomatic subjects,up to 50%of candidates reject this option and many of those affected are diagnosed later,in advanced stages.The efficacy of screening programs has been well-established for several years,which reduces the risk of CRC morbidity and mortality,without taking into account the test used for screening,or other tools.Nevertheless,a significant proportion of patients remain unscreened,so understanding the factors involved,as well as the barriers of the population to adherence is the first step to possibly modify the participation rate.These barriers could include a full range of social and political aspects,especially the type of financial provision of each health service.In Japan,health services are universal,and this advantageous situation makes it easier for citizens to access to these services,contributing to the detection of various diseases,including CRC.Interestingly,the symptomatic CRC group had a lower early-stage diagnosis rate than the patients detected during follow-up for other comorbidities,and symptomatic and cancer screening groups showed similar early-stage diagnosis.

Genetic Diversity,Population Structure,and Genome-Wide Association Study of Seven Agronomic Traits in 273 Diverse Upload Cotton Accessions

Upland cotton(Gossypium hirsutum)is the most important plant producing natural fibers for the textile industry.In this study,we first investigated the phenotypic variation of seven agronomic traits of 273 diverse cotton accessions in the years 2017 and 2018,which were from 18 geographical regions.We found large variations among the traits in different geographical regions and only half of the traits in either years 2017 or 2018 followed a normal distribution.We then genotyped the collection with 81,612 high quality SNPs.Phylogenetic tree and population structure revealed a diverse genetic structure of the core collection,and geographical diversification was an important factor,but account for part of the variances of genetic diversification.We then performed genome-wide association study for the seven traits in the years 2017 and 2018,and the average values of each trait in the two years,respectively.We identified a total of 19 significant marker-trait associations and found that Pollen Ole e 1 allergen/extension could be the candidate gene associated with the fall-off cotton bolls from the last three branches.In addition,large variations were observed for the heritability of traits in the years 2017 and 2018.These results provide new potential candidate genes for further functional validation,which could be useful for genetic improvement and breeding of new cotton cultivars with better agronomic performances.