Root system architecture plays an essential role in water and nutrient acquisition in plants,and it is significantly involved in plant adaptations to various environmental stresses.In this study,a panel of 242 cotton ...Root system architecture plays an essential role in water and nutrient acquisition in plants,and it is significantly involved in plant adaptations to various environmental stresses.In this study,a panel of 242 cotton accessions was collected to investigate six root morphological traits at the seedling stage,including main root length(MRL),root fresh weight(RFW),total root length(TRL),root surface area(RSA),root volume(RV),and root average diameter(AvgD).The correlation analysis of the six root morphological traits revealed strong positive correlations of TRL with RSA,as well as RV with RSA and AvgD,whereas a significant negative correlation was found between TRL and AvgD.Subsequently,a genome-wide association study(GWAS)was performed using the root phenotypic and genotypic data reported previously for the 242 accessions using 56,010 single nucleotide polymorphisms(SNPs)from the CottonSNP80K array.A total of 41 quantitative trait loci(QTLs)were identified,including nine for MRL,six for RFW,nine for TRL,12 for RSA,12 for RV and two for AvgD.Among them,eight QTLs were repeatedly detected in two or more traits.Integrating these results with a transcriptome analysis,we identified 17 candidate genes with high transcript values of transcripts per million(TPM)≥30 in the roots.Furthermore,we functionally verified the candidate gene GH_D05G2106,which encodes a WPP domain protein 2in root development.A virus-induced gene silencing(VIGS)assay showed that knocking down GH_D05G2106significantly inhibited root development in cotton,indicating its positive role in root system architecture formation.Collectively,these results provide a theoretical basis and candidate genes for future studies on cotton root developmental biology and root-related cotton breeding.展开更多
Avian metapneumovirus(aMPV) is a highly contagious pathogen that causes acute upper respiratory tract diseases in chickens and turkeys, resulting in serious economic losses. Subtype B aMPV has recently become the domi...Avian metapneumovirus(aMPV) is a highly contagious pathogen that causes acute upper respiratory tract diseases in chickens and turkeys, resulting in serious economic losses. Subtype B aMPV has recently become the dominant epidemic strain in China. We developed an attenuated aMPV subtype B strain by serial passaging in Vero cells and evaluated its safety and efficacy as a vaccine candidate. The safety test showed that after the 30th passage, the LN16-A strain was fully attenuated, as clinical signs of infection and histological lesions were absent after inoculation.The LN16-A strain did not revert to a virulent strain after five serial passages in chickens. The genomic sequence of LN16-A differed from that of the parent wild-type LN16(wtLN16) strain and had nine amino acid mutations. In chickens, a single immunization with LN16-A induced robust humoral and cellular immune responses, including the abundant production of neutralizing antibodies, CD4^(+) T lymphocytes, and the Th1(IFN-γ) and Th2(IL-4 and IL-6)cytokines. We also confirmed that LN16-A provided 100% protection against subtype B aMPV and significantly reduced viral shedding and turbinate inflammation. Our findings suggest that the LN16-A strain is a promising live attenuated vaccine candidate that can prevent infection with subtype B aMPV.展开更多
Ethylene plays essential roles in plant growth,development and stress responses.The ethylene signaling pathway and molecular mechanism have been studied extensively in Arabidopsis and rice but limited in peanuts.Here,...Ethylene plays essential roles in plant growth,development and stress responses.The ethylene signaling pathway and molecular mechanism have been studied extensively in Arabidopsis and rice but limited in peanuts.Here,we established a sand-culture method to screen pingyangmycin mutagenized peanut lines based on their specific response to ethylene(“triple response”).An ethylene-insensitive mutant,inhibition of peanut hypocotyl elongation 1(iph1),was identified that showed reduced sensitivity to ethylene in both hypocotyl elongation and root growth.Through bulked segregant analysis sequencing,a major gene related to iph1,named AhIPH1,was preliminarily mapped at the chromosome Arahy.01,and further narrowed to a 450-kb genomic region through substitution mapping strategy.A total of 7014 genes were differentially expressed among the ACC treatment through RNA-seq analysis,of which only the Arahy.5BLU0Q gene in the candidate mapping interval was differentially expressed between WT and mutant iph1.Integrating sequence variations,functional annotation and transcriptome analysis revealed that a predicated gene,Arahy.5BLU0Q,encoding SNF1 protein kinase,may be the candidate gene for AhIPH1.This gene contained two single-nucleotide polymorphisms at promoter region and was more highly expressed in iph1 than WT.Our findings reveal a novel ethylene-responsive gene,which provides a theoretical foundation and new genetic resources for the mechanism of ethylene signaling in peanuts.展开更多
The nutritional composition and overall quality of maize kernels are largely determined by the key chemical com-ponents:protein,oil,and starch.Nevertheless,the genetic basis underlying these nutritional quality traits...The nutritional composition and overall quality of maize kernels are largely determined by the key chemical com-ponents:protein,oil,and starch.Nevertheless,the genetic basis underlying these nutritional quality traits during grainfilling remains poorly understood.In this study,the concentrations of protein,oil,and starch were studied in 204 recombinant inbred lines resulting from a cross between DH1M and T877 at four different stages post-pollination.All the traits exhibited considerable phenotypic variation.During the grain-filling stage,the levels of protein and starch content generally increased,whereas oil content decreased,with significant changes observed between 30 and 40 days after pollination.Quantitative trait locus(QTL)mapping was conducted and a total of 32 QTLs,comprising 14,12,and 6 QTLs for grain protein,oil,and starch content were detected,respectively.Few QTLs were consistently detectable across different time points.By integrating QTL analysis,glo-bal gene expression profiling,and comparative genomics,we identified 157,86,and 54 differentially expressed genes harboring nonsynonymous substitutions between the parental lines for grain protein,oil,and starch con-tent,respectively.Subsequent gene function annotation prioritized 15 candidate genes potentially involved in reg-ulating grain quality traits,including those encoding transcription factors(NAC,MADS-box,bZIP,and MYB),cell wall invertase,cellulose-synthase-like protein,cell division cycle protein,trehalase,auxin-responsive factor,and phloem protein 2-A13.Our study offers significant insights into the genetic architecture of maize kernel nutritional quality and identifies promising QTLs and candidate genes,which are crucial for the genetic enhance-ment of these traits in maize breeding programs.展开更多
Stripe rust, caused by Puccinia striiformis f. sp. tritici(Pst), threatens wheat production worldwide, and resistant varieties tend to become susceptible after a period of cultivation owing to the variation of pathoge...Stripe rust, caused by Puccinia striiformis f. sp. tritici(Pst), threatens wheat production worldwide, and resistant varieties tend to become susceptible after a period of cultivation owing to the variation of pathogen races. In this study, a new resistance gene against Pst race CYR34 was identified and predicted using the descendants of a cross between AS1676, a highly resistant Chinese landrace, and Avocet S, a susceptible cultivar. From a heterozygous plant from a F7recombinant inbred line(RIL) population lacking the Yr18 gene, a near-isogenic line(NIL) population was developed to map the resistance gene. An allstage resistance gene, YrAS1676, was identified on chromosome arm 1AL via bulked-segregant exomecapture sequencing. By analyzing a large NIL population consisting of 6537 plants, the gene was further mapped to the marker interval between KA1A_485.36 and KA1A_490.13, spanning 485.36–490.13 Mb on1AL. A total of 66 annotated genes have been reported in this region. To characterize and predict the candidate gene(s), an RNA-seq was performed using NIL-R and NIL-S seedlings 3 days after CYR34 inoculation. Compared to NIL-S plants, NIL-R plants showed stronger immune reaction and higher expression levels of genes encoding pathogenesis-associated proteins. These differences may help to explain why NIL-R plants were more resistant to Pst race CYR34 than NIL-S plants. By combining fine-mapping and transcriptome sequencing, a calcium-dependent protein kinase gene was finally predicted as the potential candidate gene of YrAS1676. This gene contained a single-nucleotide polymorphism. The candidate gene was more highly expressed in NIL-R than in NIL-S plants. In field experiments with Pst challenge,the YrAS1676 genotype showed mitigation of disease damage and yield loss without adverse effects on tested agronomic traits. These results suggest that YrAS1676 has potential use in wheat stripe rust resistance breeding.展开更多
Fruit cracking is a phenomenon in which the peel cracks during grape berry development,which seriously affects the yield and quality of the fruit.However,there are few studies on the mining of candidate genes related ...Fruit cracking is a phenomenon in which the peel cracks during grape berry development,which seriously affects the yield and quality of the fruit.However,there are few studies on the mining of candidate genes related to berry cracking.In order to better understand the genetic basis of berry cracking,we used the results of previous quantitative trait locus(QTL)mapping,combined with field surveys of berry-cracking types and the berry-cracking rate,to mine candidate berry-cracking genes.The results showed that three identical QTL loci were detected in two years(2019 and 2020);and three candidate genes were annotated in the QTL interval.In mature berries,the expressions of the candidate genes were more abundant in the cracking-susceptible parent(‘Crimson Seedless’)than in the cracking-resistant parent(‘Muscat Hamburg’).Grape berry cracking is a complex trait controlled by multiple genes,mainly including genes encoding cellulose synthase–like protein H1,glucan endo-1,3-beta-glucosidase 12,and brassinosteroid insensitive 1-associated receptor kinase 1.The high expression of the candidate berry-cracking genes may promote the occurrence of berry cracking.This study helps elucidate the genetic mechanism of grape berry cracking.展开更多
Gummy stem blight(GSB),caused by Didymella bryoniae,is a serious fungal disease that leads to decline in cucumber yield and quality.The molecular mechanism of GSB resistance in cucumber remains unclear.Here,we investi...Gummy stem blight(GSB),caused by Didymella bryoniae,is a serious fungal disease that leads to decline in cucumber yield and quality.The molecular mechanism of GSB resistance in cucumber remains unclear.Here,we investigated the GSB resistance of cucumber core germplasms from four geographic groups at the seedling and adult stages.A total of 9 SNPs related to GSB resistance at the seedling stage and 26 SNPs at the adult stage were identified,of which some are co-localized to previously mapped Quantitative trait loci(QTLs)for GSB resistance(gsb3.2/gsb3.3,gsb5.1,and gsb-s6.2).Based on haplotype analysis and expression levels after inoculation,four candidate genes were identified within the region identified by both Genome-wide association study(GWAS)and previous identified QTL mapping,including Csa3G129470 for gsb3.2/gsb3.3,Csa5G606820 and Csa5G606850 for gsb5.1,and Csa6G079730 for gsb-s6.2.The novel GSB resistant accessions,significant SNPs,and candidate genes facilitate the breeding of GSB resistant cucumber cultivars and provide a novel idea for understanding GSB resistance mechanism in cucumber.展开更多
Stalk strength increases resistance to stalk lodging,which causes maize(Zea mays L.)production losses worldwide.The genetic mechanisms regulating stalk strength remain unclear.In this study,three stalk strength-relate...Stalk strength increases resistance to stalk lodging,which causes maize(Zea mays L.)production losses worldwide.The genetic mechanisms regulating stalk strength remain unclear.In this study,three stalk strength-related traits(rind penetrometer resistance,stalk crushing strength,and stalk bending strength)and four plant architecture traits(plant height,ear height,stem diameter,stem length)were measured in three field trials.Substantial phenotypic variation was detected for these traits.A genome-wide association study(GWAS)was conducted using general and mixed linear models and 372,331 single-nucleotide polymorphisms(SNPs).A total of 94 quantitative trait loci including 241 SNPs were detected.By combining the GWAS data with public gene expression data,56 candidate genes within 50 kb of the significant SNPs were identified,including genes encoding flavonol synthase(GRMZM2G069298,ZmFLS2),nitrate reductase(GRMZM5G878558,ZmNR2),glucose-1-phosphate adenylyltransferase(GRMZM2G027955),and laccase(GRMZM2G447271).Resequencing GRMZM2G069298 and GRMZM5G878558 in all tested lines revealed respectively 47 and 2 variants associated with RPR.Comparison of the RPR of the zmnr2EMS mutant and the wild-type plant under high-and low-nitrogen conditions verified the GRMZM5G878558 function.These findings may be useful for clarifying the genetic basis of stalk strength.The identified candidate genes and variants may be useful for the genetic improvement of maize lodging resistance.展开更多
Many genetic loci for wheat plant height(PH) have been reported, and 26 dwarfing genes have been catalogued. To identify major and stable genetic loci for PH, here we thoroughly summarized these functionally or geneti...Many genetic loci for wheat plant height(PH) have been reported, and 26 dwarfing genes have been catalogued. To identify major and stable genetic loci for PH, here we thoroughly summarized these functionally or genetic verified dwarfing loci from QTL linkage analysis and genome-wide association study published from 2003 to 2022. A total of 332 QTL, 270 GWAS loci and 83 genes for PH were integrated onto chromosomes according to their locations in the IWGSC RefSeq v2.1 and 65 QTL-rich clusters(QRC) were defined. Candidate genes in each QRC were predicted based on IWGSC Annotation v2.1 and the information on functional validation of homologous genes in other species. A total of 38 candidate genes were predicted for 65 QRC including three GA2ox genes in QRC-4B-IV, QRC-5A-VIII and QRC-6A-II(Rht24) as well as GA 20-oxidase 2(TaSD1-3A) in QRC-3A-IV. These outcomes lay concrete foundations for mapbased cloning of wheat dwarfing genes and application in breeding.展开更多
Rice direct seeding has the significant potential to save labor and water,conserve environmental resources,and reduce greenhouse gas emissions tremendously.Therefore,rice direct seeding is becoming the major cultivati...Rice direct seeding has the significant potential to save labor and water,conserve environmental resources,and reduce greenhouse gas emissions tremendously.Therefore,rice direct seeding is becoming the major cultivation technology applied to rice production in many countries.Identifying and utilizing genes controlling mesocotyl elongation is an effective approach to accelerate breeding procedures and meet the requirements for direct-seeded rice(DSR) production.This study used a permanent mapping population with 144 recombinant inbred lines(RILs) and 2 828 bin-markers to detect quantitative trait loci(QTLs) associated with mesocotyl length in 2019 and 2020.The mesocotyl lengths of the rice RILs and their parents,Lijiangxintuanheigu(LTH) and Shennong 265(SN265),were measured in a growth chamber at 30°C in a dark environment.A total of 16 QTLs for mesocotyl length were identified on chromosomes 1(2),2(4),3(2),4,5,6,7,9,11(2),and 12.Seven of these QTLs,including qML1a,qML1b,qML2d,qML3a,qML3b,qML5,and qML11b,were reproducibly detected in both years via the interval mapping method.The major QTL,qML3a,was reidentified in two years via the composite interval mapping method.A total of 10 to 413 annotated genes for each QTL were identified in their smallest genetic intervals of 37.69 kb to 2.78 Mb,respectively.Thirteen predicted genes within a relatively small genetic interval(88.18 kb) of the major mesocotyl elongation QTL,qML3a,were more thoroughly analyzed.Finally,the coding DNA sequence variations among SN265,LTH,and Nipponbare indicated that the LOC_Os03g50550 gene was the strongest candidate gene for the qML3a QTL controlling the mesocotyl elongation.This LOC_Os03g50550 gene encodes a mitogen-activated protein kinase.Relative gene expression analysis using qRT-RCR further revealed that the expression levels of the LOC_Os03g50550 gene in the mesocotyl of LTH were significantly lower than in the mesocotyl of SN265.In conclusion,these results further strengthen our knowledge about rice’s genetic mechanisms of mesocotyl elongation.This investigation’s discoveries will help to accelerate breeding programs for new DSR variety development.展开更多
Background Inflammation of the mammary tissue(mastitis)is one of the most detrimental health conditions in dairy ruminants and is considered the most economically important infectious disease of the dairy sector.Impro...Background Inflammation of the mammary tissue(mastitis)is one of the most detrimental health conditions in dairy ruminants and is considered the most economically important infectious disease of the dairy sector.Improving mastitis resistance is becoming an important goal in dairy ruminant breeding programmes.However,mastitis resistance is a complex trait and identification of mastitis-associated alleles in livestock is difficult.Currently,the only applicable approach to identify candidate loci for complex traits in large farm animals is to combine different information that supports the functionality of the identified genomic regions with respect to a complex trait.Methods To identify the most promising candidate loci for mastitis resistance we integrated heterogeneous data from multiple sources and compiled the information into a comprehensive database of mastitis-associated candidate loci.Mastitis-associated candidate genes reported in association,expression,and mouse model studies were collected by searching the relevant literature and databases.The collected data were integrated into a single database,screened for overlaps,and used for gene set enrichment analysis.Results The database contains candidate genes from association and expression studies and relevant transgenic mouse models.The 2448 collected candidate loci are evenly distributed across bovine chromosomes.Data integration and analysis revealed overlaps between different studies and/or with mastitis-associated QTL,revealing promising candidate genes for mastitis resistance.Conclusion Mastitis resistance is a complex trait influenced by numerous alleles.Based on the number of independent studies,we were able to prioritise candidate genes and propose a list of the 22 most promising.To our knowledge this is the most comprehensive database of mastitis associated candidate genes and could be helpful in selecting genes for functional validation studies.展开更多
The development of resistant maize cultivars is the most effective and sustainable approach to combat fungal diseases.Over the last three decades,many quantitative trait loci(QTL)mapping studies reported numerous QTL ...The development of resistant maize cultivars is the most effective and sustainable approach to combat fungal diseases.Over the last three decades,many quantitative trait loci(QTL)mapping studies reported numerous QTL for fungal disease resistance(FDR)in maize.However,different genetic backgrounds of germplasm and differing QTL analysis algorithms limit the use of identified QTL for comparative studies.The meta-QTL(MQTL)analysis is the meta-analysis of multiple QTL experiments,which entails broader allelic coverage and helps in the combined analysis of diverse QTL mapping studies revealing common genomic regions for target traits.In the present study,128(33.59%)out of 381 reported QTL(from 82 studies)for FDR could be projected on the maize genome through MQTL analysis.It revealed 38 MQTL for FDR(12 diseases)on all chromosomes except chromosome 10.Five MQTL namely 1_4,2_4,3_2,3_4,and 5_4 were linked with multiple FDR.Total of 1910 candidate genes were identified for all the MQTL regions,with protein kinase gene families,TFs,pathogenesis-related,and disease-responsive proteins directly or indirectly associated with FDR.The comparison of physical positions of marker-traits association(MTAs)from genome-wide association studies with genes underlying MQTL interval verified the presence of QTL/candidate genes for particular diseases.The linked markers to MQTL and putative candidate genes underlying identified MQTL can be further validated in the germplasm through marker screening and expression studies.The study also attempted to unravel the underlying mechanism for FDR resistance by analyzing the constitutive gene network,which will be a useful resource to understand the molecular mechanism of defense-response of a particular disease and multiple FDR in maize.展开更多
Background:Hundreds of single-nucleotide polymorphism(SNP)sites have been found to be potential genetic markers of type 2 diabetes mellitus(T2DM).However,SNPs related to T2DM in minipigs have been less reported.This s...Background:Hundreds of single-nucleotide polymorphism(SNP)sites have been found to be potential genetic markers of type 2 diabetes mellitus(T2DM).However,SNPs related to T2DM in minipigs have been less reported.This study aimed to screen the T2DM-susceptible candidate SNP loci in Bama minipigs so as to improve the success rate of the minipig T2DM model.Methods:The genomic DNAs of three Bama minipigs with T2DM,six sibling lowsusceptibility minipigs with T2DM,and three normal control minipigs were compared by whole-genome sequencing.The T2DM Bama minipig-specific loci were obtained,and their functions were annotated.Meanwhile,the Biomart software was used to perform homology alignment with T2DM-related loci obtained from the human genome-wide association study to screen candidate SNP markers for T2DM in Bama miniature pigs.Results:Whole-genome resequencing detected 6960 specific loci in the minipigs with T2DM,and 13 loci corresponding to 9 diabetes-related genes were selected.Further,a set of 122 specific loci in 69 orthologous genes of human T2DM candidate genes were obtained in the pigs.Collectively,a batch of T2DM-susceptible candidate SNP markers in Bama minipigs,covering 16 genes and 135 loci,was established.Conclusions:Whole-genome sequencing and comparative genomics analysis of the orthologous genes in pigs that corresponded to the human T2DM-related variant loci successfully screened out T2DM-susceptible candidate markers in Bama miniature pigs.Using these loci to predict the susceptibility of the pigs before constructing an animal model of T2DM may help to establish an ideal animal model.展开更多
Wireless sensor networks(WSNs)are widely used for various practical applications due to their simplicity and versatility.The quality of service in WSNs is greatly influenced by the coverage,which directly affects the ...Wireless sensor networks(WSNs)are widely used for various practical applications due to their simplicity and versatility.The quality of service in WSNs is greatly influenced by the coverage,which directly affects the monitoring capacity of the target region.However,low WSN coverage and uneven distribution of nodes in random deployments pose significant challenges.This study proposes an optimal node planning strategy for net-work coverage based on an adjusted single candidate optimizer(ASCO)to address these issues.The single candidate optimizer(SCO)is a metaheuristic algorithm with stable implementation procedures.However,it has limitations in avoiding local optimum traps in complex node coverage optimization scenarios.The ASCO overcomes these limitations by incorporating reverse learning and multi-direction strategies,resulting in updated equations.The performance of the ASCO algorithm is compared with other algorithms in the literature for optimal WSN node coverage.The results demonstrate that the ASCO algorithm offers efficient performance,rapid convergence,and expanded coverage capabilities.Notably,the ASCO achieves an archival coverage rate of 88%,while other approaches achieve coverage rates below or equal to 85%under the same conditions.展开更多
Previous study indicated that the thermo-sensitive genic malesterile(TGMS) gene in rice was regulated by temperature.TGMS rice plays an important role in hybrid rice production,because the application of the TGMS syst...Previous study indicated that the thermo-sensitive genic malesterile(TGMS) gene in rice was regulated by temperature.TGMS rice plays an important role in hybrid rice production,because the application of the TGMS system in two-line breeding is laborsaving,timesaving,simple,inexpensive,efficient,and eliminating the limitations of the cytoplasmic male sterility(CMS) system.'AnnongS' is the first discovered and deeply studied TGMS rice lines in China.'AnnongS-1' and 'Y58S',two derivatives of TGMS line AnnongS,were both controlled by a single recessive gene named tms5,which was genetically mapped on chromosome 2.In this study,three populations('AnnongS-1' × 'Nanjing11','Y58S' × 'Q611',and 'Y58S' × 'Guanghui122') were developed and used for the molecular fine mapping of the tms5 gene.By analyzing recombination events in the sterile individuals using a total of 125 probes covering the tms5 region,the tms5 gene was physically mapped to a 19-kb DNA fragment between two markers 4039-1 and 4039-2,which were located on the BAC clone AP004039.After the construction of the physical map between two markers 4039-1 and 4039-2,a member(ONAC023) of the NAC(NAM-ATAF-CUC-related) gene family was identified as the candidate gene of the tms5 gene.展开更多
BACKGROUND Hepatocellular carcinoma(HCC)is a common malignant gastrointestinal tumor.There are currently few clinical diagnostic and prognostic markers for HCC.LncRNA cancer susceptibility candidate 9(CASC9)is a long-...BACKGROUND Hepatocellular carcinoma(HCC)is a common malignant gastrointestinal tumor.There are currently few clinical diagnostic and prognostic markers for HCC.LncRNA cancer susceptibility candidate 9(CASC9)is a long-chain non-coding RNA discovered in recent years,and previous studies have found that lncRNA CASC9 participates in the occurrence and development of HCC,but its clinical value remains unclear.AIM To determine the expression of lncRNA CASC9 in HCC and its diagnostic and prognostic value.METHODS Data on CASC9 expression in patients with HCC were collected from the Cancer Genome Atlas(TCGA)database to analyze the relationship between CASC9 and patient survival.A total of 80 HCC patients treated in The First Affiliated Hospital of Guangxi Medical University from May 2012 to January 2014 were enrolled in the patient group,and 50 healthy subjects were enrolled in the control group during the same period.CASC9 expression in the two groups was determined using quantitative real-time polymerase chain reaction,and its diagnostic and prognostic value was analyzed based on the CASC9 data and pathological data in these HCC patients.The relationship between CASC9 and patient survival was assessed during the 5-year follow-up period.RESULTS Analysis of data from TCGA database revealed that control samples showed significantly lower CASC9 expression than carcinoma tissue samples(P<0.001);the low CASC9 expression group had a higher survival rate than the high CASC9 expression group(P=0.011),and the patient group showed significantly increased expression of serum CASC9,with the area under the curve(AUC)of 0.933.CASC9 expression was related to tumor size,combined hepatitis,tumor,node,metastasis(TNM)staging,lymph node metastasis,differentiation and alpha fetoprotein,and the high CASC9 expression group showed lower 1-year,3-year and 5-year survival rates than the low CASC9 expression group(all aP<0.05).Multivariate Cox regression analysis revealed that TNM staging,lymph node metastasis,differentiation,alpha fetoprotein and CASC9 were independent factors affecting the prognosis of patients.Stage I+II patients with lymph node metastasis,low differentiation,and alpha fetoprotein>200 ng/mL had a poor 5-year survival rate.CONCLUSION High CASC9 expression is beneficial in the prognosis of HCC patients.CASC9 is expected to be a potential diagnostic and prognostic indicator of HCC.展开更多
Genetic improvement for drought stress tolerance in rice involves the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome. Yield components and related t...Genetic improvement for drought stress tolerance in rice involves the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome. Yield components and related traits under stressed and well-water conditions were assayed in mapping populations derived from crosses of Azucena×IR64 and Azucena×Bala. To find the candidate rice genes underlying Quantitative Trait Loci (QTL) in these populations, we conducted in silico analysis of a candidate region flanked by the genetic markers RM212 and RM319 on chromosome 1, proximal to the semi-dwarf (sd1) locus. A total of 175 annotated genes were identified from this region. These included 48 genes annotated by functional homology to known genes, 23 pseudogenes, 24 ab initio predicted genes supported by an alignment match to an EST (Expressed sequence tag) of unknown function, and 80 hypothetical genes predicted solely by ab initio means. Among these, 16 candidate genes could potentially be involved in drought stress response.展开更多
Early seedling vigor(ESV)is a major breeding target in rice,especially under direct seeding.To identify quantitative trait locus(QTL)affecting ESV,a recombinant inbred line population derived from a cross between 0242...Early seedling vigor(ESV)is a major breeding target in rice,especially under direct seeding.To identify quantitative trait locus(QTL)affecting ESV,a recombinant inbred line population derived from a cross between 02428 and YZX,two cultivars differing in vigor during early seedling growth,was used for QTL analysis.Nine traits associated with ESV were examined using a high-density map.Of 16 additive loci identified,three were detected in two generations and thus considered stable.Four epistatic interactions were detected,one of which was repeated in two generations.Further analysis of the pyramiding effect of the three stable QTL showed that the phenotypic value could be effectively improved with an increasing number of QTL.These results were combined with results from our previous QTL analysis of the germination index.The lines G58 and G182 combined all the favourable alleles of all three stable QTL for ESV and three QTL for germination speed.These two lines showed rapid germination and strong ESV.A total of 37 candidate differentially expressed genes were obtained from the regions of the three stable QTL by analysis of the dynamic transcriptomic expression profile during the seedling growth period of the two parents.The QTL are targets for ESV breeding and the candidate genes await functional validation.This study provides a theoretical basis and a genetic resource for the breeding of directseeded rice.展开更多
Drought is one of the primary abiotic stress factors affecting the yield,growth,and development of soybeans.In extreme cases,drought can reduce yield by more than 50%.The seedling stage is an important determinant of ...Drought is one of the primary abiotic stress factors affecting the yield,growth,and development of soybeans.In extreme cases,drought can reduce yield by more than 50%.The seedling stage is an important determinant of soybean growth:the number and vigor of seedlings will affect growth and yield at harvest.Therefore,it is important to study the drought resistance of soybean seedlings.In this study,a recombinant inbred line(RIL)population comprising 234 F_(6:10)lines(derived from Zhonghuang35×Jindou 21)and a panel of 259 soybean accessions was subjected to drought conditions to identify the effects on phenotypic traits under these conditions.Using a genetic map constructed by single nucleotide polymorphism(SNPs)markers,18 quantitative trait loci(QTL)on 7 soybean chromosomes were identified in two environments.This included 9 QTL clusters identified in the RIL population.Fifty-three QTL were identified in 19 soybean chromosomes by genome-wide association analysis(GWAS)in the panel of accessions,including 69 significant SNPs(-log_(10)(P)≥3.97).A combination of the two populations revealed that two SNPs(-log_(10)(P)≥3.0)fell within two of the QTL(qPH7-4 and qPH7-6)confidence intervals.We not only re-located several previously reported drought-resistance genes in soybean and other crops but also identified several non-synonymous stress-related mutation site differences between the two parents,involving Glyma.07 g093000,Glyma.07 g093200,Glyma.07 g094100 and Glyma.07 g094200.One previously unreported new gene related to drought stress,Glyma.07 g094200,was found by regional association analysis.The significant SNP CHR7-17619(G/T)was within an exon of the Glyma.07 g094200 gene.In the RIL population,the DSP value of the"T"allele of CHR7-17619 was significantly(P<0.05)larger than the"G"allele in different environments.The results of our study lay the groundwork for cloning and molecular marker-assisted selection of droughtresistance genes in soybeans at the seedling stage.展开更多
基金supported by the Jiangsu Natural Science Foundation,China(BK20231468)the Fundamental Research Funds for the Central Universities,China(ZJ24195012)+3 种基金the National Natural Science Foundation in China(31871668)the Jiangsu Key R&D Program,China(BE2022384)the Xinjiang Uygur Autonomous Region Science and Technology Support Program,China(2021E02003)the Jiangsu Collaborative Innovation Center for Modern Crop Production Project,China(No.10)。
文摘Root system architecture plays an essential role in water and nutrient acquisition in plants,and it is significantly involved in plant adaptations to various environmental stresses.In this study,a panel of 242 cotton accessions was collected to investigate six root morphological traits at the seedling stage,including main root length(MRL),root fresh weight(RFW),total root length(TRL),root surface area(RSA),root volume(RV),and root average diameter(AvgD).The correlation analysis of the six root morphological traits revealed strong positive correlations of TRL with RSA,as well as RV with RSA and AvgD,whereas a significant negative correlation was found between TRL and AvgD.Subsequently,a genome-wide association study(GWAS)was performed using the root phenotypic and genotypic data reported previously for the 242 accessions using 56,010 single nucleotide polymorphisms(SNPs)from the CottonSNP80K array.A total of 41 quantitative trait loci(QTLs)were identified,including nine for MRL,six for RFW,nine for TRL,12 for RSA,12 for RV and two for AvgD.Among them,eight QTLs were repeatedly detected in two or more traits.Integrating these results with a transcriptome analysis,we identified 17 candidate genes with high transcript values of transcripts per million(TPM)≥30 in the roots.Furthermore,we functionally verified the candidate gene GH_D05G2106,which encodes a WPP domain protein 2in root development.A virus-induced gene silencing(VIGS)assay showed that knocking down GH_D05G2106significantly inhibited root development in cotton,indicating its positive role in root system architecture formation.Collectively,these results provide a theoretical basis and candidate genes for future studies on cotton root developmental biology and root-related cotton breeding.
基金supported by the National Key Research and Development Program of China (2022YFD1800604)the China Agricultural Research System (CARS-41)the Heilongjiang Touyan Innovation Team Program of China
文摘Avian metapneumovirus(aMPV) is a highly contagious pathogen that causes acute upper respiratory tract diseases in chickens and turkeys, resulting in serious economic losses. Subtype B aMPV has recently become the dominant epidemic strain in China. We developed an attenuated aMPV subtype B strain by serial passaging in Vero cells and evaluated its safety and efficacy as a vaccine candidate. The safety test showed that after the 30th passage, the LN16-A strain was fully attenuated, as clinical signs of infection and histological lesions were absent after inoculation.The LN16-A strain did not revert to a virulent strain after five serial passages in chickens. The genomic sequence of LN16-A differed from that of the parent wild-type LN16(wtLN16) strain and had nine amino acid mutations. In chickens, a single immunization with LN16-A induced robust humoral and cellular immune responses, including the abundant production of neutralizing antibodies, CD4^(+) T lymphocytes, and the Th1(IFN-γ) and Th2(IL-4 and IL-6)cytokines. We also confirmed that LN16-A provided 100% protection against subtype B aMPV and significantly reduced viral shedding and turbinate inflammation. Our findings suggest that the LN16-A strain is a promising live attenuated vaccine candidate that can prevent infection with subtype B aMPV.
基金supported by the National Natural Science Foundation of China(32001578)Qingdao Science&Technology Key Projects(22-1-3-1-zyyd-nsh,23-1-3-8-zyyd-nsh)+1 种基金Salt-Alkali Agriculture Industry System of Shandong Province(SDAIT-29-03)Science&Technology Specific Projects in Agricultural High-tech Industrial Demonstration Area of the Yellow River Delta(2022SZX19)。
文摘Ethylene plays essential roles in plant growth,development and stress responses.The ethylene signaling pathway and molecular mechanism have been studied extensively in Arabidopsis and rice but limited in peanuts.Here,we established a sand-culture method to screen pingyangmycin mutagenized peanut lines based on their specific response to ethylene(“triple response”).An ethylene-insensitive mutant,inhibition of peanut hypocotyl elongation 1(iph1),was identified that showed reduced sensitivity to ethylene in both hypocotyl elongation and root growth.Through bulked segregant analysis sequencing,a major gene related to iph1,named AhIPH1,was preliminarily mapped at the chromosome Arahy.01,and further narrowed to a 450-kb genomic region through substitution mapping strategy.A total of 7014 genes were differentially expressed among the ACC treatment through RNA-seq analysis,of which only the Arahy.5BLU0Q gene in the candidate mapping interval was differentially expressed between WT and mutant iph1.Integrating sequence variations,functional annotation and transcriptome analysis revealed that a predicated gene,Arahy.5BLU0Q,encoding SNF1 protein kinase,may be the candidate gene for AhIPH1.This gene contained two single-nucleotide polymorphisms at promoter region and was more highly expressed in iph1 than WT.Our findings reveal a novel ethylene-responsive gene,which provides a theoretical foundation and new genetic resources for the mechanism of ethylene signaling in peanuts.
基金supported by the Key Research and Development Program of Jiangsu Province(BE2022343)the Seed Industry Revitalization Project of Jiangsu Province(JBGS[2021]009)+2 种基金the National Natural Science Foundation of China(32061143030 and 31972487)Jiangsu Province University Basic Science Research Project(21KJA210002)the Innovative Research Team of Universities in Jiangsu Province,the High-End Talent Project of Yangzhou University,the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD),and Qing Lan Project of Jiangsu Province.
文摘The nutritional composition and overall quality of maize kernels are largely determined by the key chemical com-ponents:protein,oil,and starch.Nevertheless,the genetic basis underlying these nutritional quality traits during grainfilling remains poorly understood.In this study,the concentrations of protein,oil,and starch were studied in 204 recombinant inbred lines resulting from a cross between DH1M and T877 at four different stages post-pollination.All the traits exhibited considerable phenotypic variation.During the grain-filling stage,the levels of protein and starch content generally increased,whereas oil content decreased,with significant changes observed between 30 and 40 days after pollination.Quantitative trait locus(QTL)mapping was conducted and a total of 32 QTLs,comprising 14,12,and 6 QTLs for grain protein,oil,and starch content were detected,respectively.Few QTLs were consistently detectable across different time points.By integrating QTL analysis,glo-bal gene expression profiling,and comparative genomics,we identified 157,86,and 54 differentially expressed genes harboring nonsynonymous substitutions between the parental lines for grain protein,oil,and starch con-tent,respectively.Subsequent gene function annotation prioritized 15 candidate genes potentially involved in reg-ulating grain quality traits,including those encoding transcription factors(NAC,MADS-box,bZIP,and MYB),cell wall invertase,cellulose-synthase-like protein,cell division cycle protein,trehalase,auxin-responsive factor,and phloem protein 2-A13.Our study offers significant insights into the genetic architecture of maize kernel nutritional quality and identifies promising QTLs and candidate genes,which are crucial for the genetic enhance-ment of these traits in maize breeding programs.
基金supported by the Major Program of National Agricultural Science and Technology of China (NK20220607)the National Natural Science Foundation of China (32272059 and31971883)the Science and Technology Department of Sichuan Province (2022ZDZX0014, 2021YFYZ0002, 2021YJ0297, and23NSFTD0045)。
文摘Stripe rust, caused by Puccinia striiformis f. sp. tritici(Pst), threatens wheat production worldwide, and resistant varieties tend to become susceptible after a period of cultivation owing to the variation of pathogen races. In this study, a new resistance gene against Pst race CYR34 was identified and predicted using the descendants of a cross between AS1676, a highly resistant Chinese landrace, and Avocet S, a susceptible cultivar. From a heterozygous plant from a F7recombinant inbred line(RIL) population lacking the Yr18 gene, a near-isogenic line(NIL) population was developed to map the resistance gene. An allstage resistance gene, YrAS1676, was identified on chromosome arm 1AL via bulked-segregant exomecapture sequencing. By analyzing a large NIL population consisting of 6537 plants, the gene was further mapped to the marker interval between KA1A_485.36 and KA1A_490.13, spanning 485.36–490.13 Mb on1AL. A total of 66 annotated genes have been reported in this region. To characterize and predict the candidate gene(s), an RNA-seq was performed using NIL-R and NIL-S seedlings 3 days after CYR34 inoculation. Compared to NIL-S plants, NIL-R plants showed stronger immune reaction and higher expression levels of genes encoding pathogenesis-associated proteins. These differences may help to explain why NIL-R plants were more resistant to Pst race CYR34 than NIL-S plants. By combining fine-mapping and transcriptome sequencing, a calcium-dependent protein kinase gene was finally predicted as the potential candidate gene of YrAS1676. This gene contained a single-nucleotide polymorphism. The candidate gene was more highly expressed in NIL-R than in NIL-S plants. In field experiments with Pst challenge,the YrAS1676 genotype showed mitigation of disease damage and yield loss without adverse effects on tested agronomic traits. These results suggest that YrAS1676 has potential use in wheat stripe rust resistance breeding.
基金financial support from the Highlevel Scientific Reuter Foundation of Qingdao Agricultural University(Grant Nos.665/1118011,665/1119002)China Agriculture Research System of MOF and MARA(Grant No.CARS-29-yc-1)Crop Resources Protection Program of Ministry of Agriculture and Rural Affairs of China(Grant No.2130135-34).
文摘Fruit cracking is a phenomenon in which the peel cracks during grape berry development,which seriously affects the yield and quality of the fruit.However,there are few studies on the mining of candidate genes related to berry cracking.In order to better understand the genetic basis of berry cracking,we used the results of previous quantitative trait locus(QTL)mapping,combined with field surveys of berry-cracking types and the berry-cracking rate,to mine candidate berry-cracking genes.The results showed that three identical QTL loci were detected in two years(2019 and 2020);and three candidate genes were annotated in the QTL interval.In mature berries,the expressions of the candidate genes were more abundant in the cracking-susceptible parent(‘Crimson Seedless’)than in the cracking-resistant parent(‘Muscat Hamburg’).Grape berry cracking is a complex trait controlled by multiple genes,mainly including genes encoding cellulose synthase–like protein H1,glucan endo-1,3-beta-glucosidase 12,and brassinosteroid insensitive 1-associated receptor kinase 1.The high expression of the candidate berry-cracking genes may promote the occurrence of berry cracking.This study helps elucidate the genetic mechanism of grape berry cracking.
基金supported by the Earmarked Fund for Modern Agro-industry Technology Research System(Grant No.CARS-23)the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(Grant No.CAASASTIP-IVFCAAS)the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops,Ministry of Agriculture and Rural Affairs,P.R.China.
文摘Gummy stem blight(GSB),caused by Didymella bryoniae,is a serious fungal disease that leads to decline in cucumber yield and quality.The molecular mechanism of GSB resistance in cucumber remains unclear.Here,we investigated the GSB resistance of cucumber core germplasms from four geographic groups at the seedling and adult stages.A total of 9 SNPs related to GSB resistance at the seedling stage and 26 SNPs at the adult stage were identified,of which some are co-localized to previously mapped Quantitative trait loci(QTLs)for GSB resistance(gsb3.2/gsb3.3,gsb5.1,and gsb-s6.2).Based on haplotype analysis and expression levels after inoculation,four candidate genes were identified within the region identified by both Genome-wide association study(GWAS)and previous identified QTL mapping,including Csa3G129470 for gsb3.2/gsb3.3,Csa5G606820 and Csa5G606850 for gsb5.1,and Csa6G079730 for gsb-s6.2.The novel GSB resistant accessions,significant SNPs,and candidate genes facilitate the breeding of GSB resistant cucumber cultivars and provide a novel idea for understanding GSB resistance mechanism in cucumber.
基金supported by the National Natural Science Foundation of China(31972487,31902101,32172009 and 32061143030)the Innovative Research Team of Universities in Jiangsu Province,the Science and Technology Development Plan Project of Henan Province(212102110152)+1 种基金the High-end Talent Project of Yangzhou Universitythe Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)。
文摘Stalk strength increases resistance to stalk lodging,which causes maize(Zea mays L.)production losses worldwide.The genetic mechanisms regulating stalk strength remain unclear.In this study,three stalk strength-related traits(rind penetrometer resistance,stalk crushing strength,and stalk bending strength)and four plant architecture traits(plant height,ear height,stem diameter,stem length)were measured in three field trials.Substantial phenotypic variation was detected for these traits.A genome-wide association study(GWAS)was conducted using general and mixed linear models and 372,331 single-nucleotide polymorphisms(SNPs).A total of 94 quantitative trait loci including 241 SNPs were detected.By combining the GWAS data with public gene expression data,56 candidate genes within 50 kb of the significant SNPs were identified,including genes encoding flavonol synthase(GRMZM2G069298,ZmFLS2),nitrate reductase(GRMZM5G878558,ZmNR2),glucose-1-phosphate adenylyltransferase(GRMZM2G027955),and laccase(GRMZM2G447271).Resequencing GRMZM2G069298 and GRMZM5G878558 in all tested lines revealed respectively 47 and 2 variants associated with RPR.Comparison of the RPR of the zmnr2EMS mutant and the wild-type plant under high-and low-nitrogen conditions verified the GRMZM5G878558 function.These findings may be useful for clarifying the genetic basis of stalk strength.The identified candidate genes and variants may be useful for the genetic improvement of maize lodging resistance.
基金funded by the National Natural Science Foundation of China (32101733)Shandong Provincial Natural Science Foundation (ZR202103020229)+1 种基金the High-Level Talents Project of Qingdao Agricultural University (663/1122023)National Natural Science Foundation of China Regional Innovation and Development Joint Fund Project (U22A20457)。
文摘Many genetic loci for wheat plant height(PH) have been reported, and 26 dwarfing genes have been catalogued. To identify major and stable genetic loci for PH, here we thoroughly summarized these functionally or genetic verified dwarfing loci from QTL linkage analysis and genome-wide association study published from 2003 to 2022. A total of 332 QTL, 270 GWAS loci and 83 genes for PH were integrated onto chromosomes according to their locations in the IWGSC RefSeq v2.1 and 65 QTL-rich clusters(QRC) were defined. Candidate genes in each QRC were predicted based on IWGSC Annotation v2.1 and the information on functional validation of homologous genes in other species. A total of 38 candidate genes were predicted for 65 QRC including three GA2ox genes in QRC-4B-IV, QRC-5A-VIII and QRC-6A-II(Rht24) as well as GA 20-oxidase 2(TaSD1-3A) in QRC-3A-IV. These outcomes lay concrete foundations for mapbased cloning of wheat dwarfing genes and application in breeding.
基金supported by grants from the Natural Science Foundation of Heilongjiang Province, China (LH2020C098)the Fundamental Research Funds for the Research Institutes of Heilongjiang Province, China (CZKYF2020A001)+1 种基金the National Key Research and Development Program of China (2016YFD0300104)the Heilongjiang Province Agricultural Science and Technology Innovation Project, China (2020JCQN001, 2019JJPY007, 2020FJZX049, 2021QKPY009, 2021CQJC003)。
文摘Rice direct seeding has the significant potential to save labor and water,conserve environmental resources,and reduce greenhouse gas emissions tremendously.Therefore,rice direct seeding is becoming the major cultivation technology applied to rice production in many countries.Identifying and utilizing genes controlling mesocotyl elongation is an effective approach to accelerate breeding procedures and meet the requirements for direct-seeded rice(DSR) production.This study used a permanent mapping population with 144 recombinant inbred lines(RILs) and 2 828 bin-markers to detect quantitative trait loci(QTLs) associated with mesocotyl length in 2019 and 2020.The mesocotyl lengths of the rice RILs and their parents,Lijiangxintuanheigu(LTH) and Shennong 265(SN265),were measured in a growth chamber at 30°C in a dark environment.A total of 16 QTLs for mesocotyl length were identified on chromosomes 1(2),2(4),3(2),4,5,6,7,9,11(2),and 12.Seven of these QTLs,including qML1a,qML1b,qML2d,qML3a,qML3b,qML5,and qML11b,were reproducibly detected in both years via the interval mapping method.The major QTL,qML3a,was reidentified in two years via the composite interval mapping method.A total of 10 to 413 annotated genes for each QTL were identified in their smallest genetic intervals of 37.69 kb to 2.78 Mb,respectively.Thirteen predicted genes within a relatively small genetic interval(88.18 kb) of the major mesocotyl elongation QTL,qML3a,were more thoroughly analyzed.Finally,the coding DNA sequence variations among SN265,LTH,and Nipponbare indicated that the LOC_Os03g50550 gene was the strongest candidate gene for the qML3a QTL controlling the mesocotyl elongation.This LOC_Os03g50550 gene encodes a mitogen-activated protein kinase.Relative gene expression analysis using qRT-RCR further revealed that the expression levels of the LOC_Os03g50550 gene in the mesocotyl of LTH were significantly lower than in the mesocotyl of SN265.In conclusion,these results further strengthen our knowledge about rice’s genetic mechanisms of mesocotyl elongation.This investigation’s discoveries will help to accelerate breeding programs for new DSR variety development.
基金Slovenian Research Agency for funding through the progra mme grant no.P40220postgradua te"young researchers"funding to ZB。
文摘Background Inflammation of the mammary tissue(mastitis)is one of the most detrimental health conditions in dairy ruminants and is considered the most economically important infectious disease of the dairy sector.Improving mastitis resistance is becoming an important goal in dairy ruminant breeding programmes.However,mastitis resistance is a complex trait and identification of mastitis-associated alleles in livestock is difficult.Currently,the only applicable approach to identify candidate loci for complex traits in large farm animals is to combine different information that supports the functionality of the identified genomic regions with respect to a complex trait.Methods To identify the most promising candidate loci for mastitis resistance we integrated heterogeneous data from multiple sources and compiled the information into a comprehensive database of mastitis-associated candidate loci.Mastitis-associated candidate genes reported in association,expression,and mouse model studies were collected by searching the relevant literature and databases.The collected data were integrated into a single database,screened for overlaps,and used for gene set enrichment analysis.Results The database contains candidate genes from association and expression studies and relevant transgenic mouse models.The 2448 collected candidate loci are evenly distributed across bovine chromosomes.Data integration and analysis revealed overlaps between different studies and/or with mastitis-associated QTL,revealing promising candidate genes for mastitis resistance.Conclusion Mastitis resistance is a complex trait influenced by numerous alleles.Based on the number of independent studies,we were able to prioritise candidate genes and propose a list of the 22 most promising.To our knowledge this is the most comprehensive database of mastitis associated candidate genes and could be helpful in selecting genes for functional validation studies.
基金supported by Indian Council of Agricultural Research(ICAR),New Delhi for assistance.
文摘The development of resistant maize cultivars is the most effective and sustainable approach to combat fungal diseases.Over the last three decades,many quantitative trait loci(QTL)mapping studies reported numerous QTL for fungal disease resistance(FDR)in maize.However,different genetic backgrounds of germplasm and differing QTL analysis algorithms limit the use of identified QTL for comparative studies.The meta-QTL(MQTL)analysis is the meta-analysis of multiple QTL experiments,which entails broader allelic coverage and helps in the combined analysis of diverse QTL mapping studies revealing common genomic regions for target traits.In the present study,128(33.59%)out of 381 reported QTL(from 82 studies)for FDR could be projected on the maize genome through MQTL analysis.It revealed 38 MQTL for FDR(12 diseases)on all chromosomes except chromosome 10.Five MQTL namely 1_4,2_4,3_2,3_4,and 5_4 were linked with multiple FDR.Total of 1910 candidate genes were identified for all the MQTL regions,with protein kinase gene families,TFs,pathogenesis-related,and disease-responsive proteins directly or indirectly associated with FDR.The comparison of physical positions of marker-traits association(MTAs)from genome-wide association studies with genes underlying MQTL interval verified the presence of QTL/candidate genes for particular diseases.The linked markers to MQTL and putative candidate genes underlying identified MQTL can be further validated in the germplasm through marker screening and expression studies.The study also attempted to unravel the underlying mechanism for FDR resistance by analyzing the constitutive gene network,which will be a useful resource to understand the molecular mechanism of defense-response of a particular disease and multiple FDR in maize.
基金National Natural Science Foundation of China,Grant/Award Number:3147205731802021.Specialized Research Fund for Laboratory Animal Science of PLA,Grant/Award Number:SYDW[2020]01SYDW[2020]02.
文摘Background:Hundreds of single-nucleotide polymorphism(SNP)sites have been found to be potential genetic markers of type 2 diabetes mellitus(T2DM).However,SNPs related to T2DM in minipigs have been less reported.This study aimed to screen the T2DM-susceptible candidate SNP loci in Bama minipigs so as to improve the success rate of the minipig T2DM model.Methods:The genomic DNAs of three Bama minipigs with T2DM,six sibling lowsusceptibility minipigs with T2DM,and three normal control minipigs were compared by whole-genome sequencing.The T2DM Bama minipig-specific loci were obtained,and their functions were annotated.Meanwhile,the Biomart software was used to perform homology alignment with T2DM-related loci obtained from the human genome-wide association study to screen candidate SNP markers for T2DM in Bama miniature pigs.Results:Whole-genome resequencing detected 6960 specific loci in the minipigs with T2DM,and 13 loci corresponding to 9 diabetes-related genes were selected.Further,a set of 122 specific loci in 69 orthologous genes of human T2DM candidate genes were obtained in the pigs.Collectively,a batch of T2DM-susceptible candidate SNP markers in Bama minipigs,covering 16 genes and 135 loci,was established.Conclusions:Whole-genome sequencing and comparative genomics analysis of the orthologous genes in pigs that corresponded to the human T2DM-related variant loci successfully screened out T2DM-susceptible candidate markers in Bama miniature pigs.Using these loci to predict the susceptibility of the pigs before constructing an animal model of T2DM may help to establish an ideal animal model.
基金supported by the VNUHCM-University of Information Technology’s Scientific Research Support Fund.
文摘Wireless sensor networks(WSNs)are widely used for various practical applications due to their simplicity and versatility.The quality of service in WSNs is greatly influenced by the coverage,which directly affects the monitoring capacity of the target region.However,low WSN coverage and uneven distribution of nodes in random deployments pose significant challenges.This study proposes an optimal node planning strategy for net-work coverage based on an adjusted single candidate optimizer(ASCO)to address these issues.The single candidate optimizer(SCO)is a metaheuristic algorithm with stable implementation procedures.However,it has limitations in avoiding local optimum traps in complex node coverage optimization scenarios.The ASCO overcomes these limitations by incorporating reverse learning and multi-direction strategies,resulting in updated equations.The performance of the ASCO algorithm is compared with other algorithms in the literature for optimal WSN node coverage.The results demonstrate that the ASCO algorithm offers efficient performance,rapid convergence,and expanded coverage capabilities.Notably,the ASCO achieves an archival coverage rate of 88%,while other approaches achieve coverage rates below or equal to 85%under the same conditions.
文摘Previous study indicated that the thermo-sensitive genic malesterile(TGMS) gene in rice was regulated by temperature.TGMS rice plays an important role in hybrid rice production,because the application of the TGMS system in two-line breeding is laborsaving,timesaving,simple,inexpensive,efficient,and eliminating the limitations of the cytoplasmic male sterility(CMS) system.'AnnongS' is the first discovered and deeply studied TGMS rice lines in China.'AnnongS-1' and 'Y58S',two derivatives of TGMS line AnnongS,were both controlled by a single recessive gene named tms5,which was genetically mapped on chromosome 2.In this study,three populations('AnnongS-1' × 'Nanjing11','Y58S' × 'Q611',and 'Y58S' × 'Guanghui122') were developed and used for the molecular fine mapping of the tms5 gene.By analyzing recombination events in the sterile individuals using a total of 125 probes covering the tms5 region,the tms5 gene was physically mapped to a 19-kb DNA fragment between two markers 4039-1 and 4039-2,which were located on the BAC clone AP004039.After the construction of the physical map between two markers 4039-1 and 4039-2,a member(ONAC023) of the NAC(NAM-ATAF-CUC-related) gene family was identified as the candidate gene of the tms5 gene.
文摘BACKGROUND Hepatocellular carcinoma(HCC)is a common malignant gastrointestinal tumor.There are currently few clinical diagnostic and prognostic markers for HCC.LncRNA cancer susceptibility candidate 9(CASC9)is a long-chain non-coding RNA discovered in recent years,and previous studies have found that lncRNA CASC9 participates in the occurrence and development of HCC,but its clinical value remains unclear.AIM To determine the expression of lncRNA CASC9 in HCC and its diagnostic and prognostic value.METHODS Data on CASC9 expression in patients with HCC were collected from the Cancer Genome Atlas(TCGA)database to analyze the relationship between CASC9 and patient survival.A total of 80 HCC patients treated in The First Affiliated Hospital of Guangxi Medical University from May 2012 to January 2014 were enrolled in the patient group,and 50 healthy subjects were enrolled in the control group during the same period.CASC9 expression in the two groups was determined using quantitative real-time polymerase chain reaction,and its diagnostic and prognostic value was analyzed based on the CASC9 data and pathological data in these HCC patients.The relationship between CASC9 and patient survival was assessed during the 5-year follow-up period.RESULTS Analysis of data from TCGA database revealed that control samples showed significantly lower CASC9 expression than carcinoma tissue samples(P<0.001);the low CASC9 expression group had a higher survival rate than the high CASC9 expression group(P=0.011),and the patient group showed significantly increased expression of serum CASC9,with the area under the curve(AUC)of 0.933.CASC9 expression was related to tumor size,combined hepatitis,tumor,node,metastasis(TNM)staging,lymph node metastasis,differentiation and alpha fetoprotein,and the high CASC9 expression group showed lower 1-year,3-year and 5-year survival rates than the low CASC9 expression group(all aP<0.05).Multivariate Cox regression analysis revealed that TNM staging,lymph node metastasis,differentiation,alpha fetoprotein and CASC9 were independent factors affecting the prognosis of patients.Stage I+II patients with lymph node metastasis,low differentiation,and alpha fetoprotein>200 ng/mL had a poor 5-year survival rate.CONCLUSION High CASC9 expression is beneficial in the prognosis of HCC patients.CASC9 is expected to be a potential diagnostic and prognostic indicator of HCC.
基金Project supported partly by the Rockefeller Foundation thesis dis-sertation training grant and the National Hi-Tech Research and De-velopment Program (863) of China
文摘Genetic improvement for drought stress tolerance in rice involves the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome. Yield components and related traits under stressed and well-water conditions were assayed in mapping populations derived from crosses of Azucena×IR64 and Azucena×Bala. To find the candidate rice genes underlying Quantitative Trait Loci (QTL) in these populations, we conducted in silico analysis of a candidate region flanked by the genetic markers RM212 and RM319 on chromosome 1, proximal to the semi-dwarf (sd1) locus. A total of 175 annotated genes were identified from this region. These included 48 genes annotated by functional homology to known genes, 23 pseudogenes, 24 ab initio predicted genes supported by an alignment match to an EST (Expressed sequence tag) of unknown function, and 80 hypothetical genes predicted solely by ab initio means. Among these, 16 candidate genes could potentially be involved in drought stress response.
基金This research was supported by the Breeding New Varieties of Rice Suitable for Light and Simple Cultivation and Mechanized Production Project(2017YFD0100104)the Research and Development Plan for Key Areas in Guangdong Province(2018B020206002)+1 种基金the China Agriculture Research System(CARS-01-17)Special thanks are due to the South China Agricultural University Doctoral Innovative Talents(Domestic Training)Cultivation Program(CX2019N044)。
文摘Early seedling vigor(ESV)is a major breeding target in rice,especially under direct seeding.To identify quantitative trait locus(QTL)affecting ESV,a recombinant inbred line population derived from a cross between 02428 and YZX,two cultivars differing in vigor during early seedling growth,was used for QTL analysis.Nine traits associated with ESV were examined using a high-density map.Of 16 additive loci identified,three were detected in two generations and thus considered stable.Four epistatic interactions were detected,one of which was repeated in two generations.Further analysis of the pyramiding effect of the three stable QTL showed that the phenotypic value could be effectively improved with an increasing number of QTL.These results were combined with results from our previous QTL analysis of the germination index.The lines G58 and G182 combined all the favourable alleles of all three stable QTL for ESV and three QTL for germination speed.These two lines showed rapid germination and strong ESV.A total of 37 candidate differentially expressed genes were obtained from the regions of the three stable QTL by analysis of the dynamic transcriptomic expression profile during the seedling growth period of the two parents.The QTL are targets for ESV breeding and the candidate genes await functional validation.This study provides a theoretical basis and a genetic resource for the breeding of directseeded rice.
基金National Key Research and Development Program of China(2016YFD0100201)Scientific Research Conditions Construction and Achievement Transformation Project of Gansu Academy of Agricultural Sciences(Modern Biological Breeding)(2019GAAS07)+1 种基金Science and Technology Major Project of Gansu Province(18ZD2NA008)Crop Germplasm Resources Protection(2017NWB036-5)。
文摘Drought is one of the primary abiotic stress factors affecting the yield,growth,and development of soybeans.In extreme cases,drought can reduce yield by more than 50%.The seedling stage is an important determinant of soybean growth:the number and vigor of seedlings will affect growth and yield at harvest.Therefore,it is important to study the drought resistance of soybean seedlings.In this study,a recombinant inbred line(RIL)population comprising 234 F_(6:10)lines(derived from Zhonghuang35×Jindou 21)and a panel of 259 soybean accessions was subjected to drought conditions to identify the effects on phenotypic traits under these conditions.Using a genetic map constructed by single nucleotide polymorphism(SNPs)markers,18 quantitative trait loci(QTL)on 7 soybean chromosomes were identified in two environments.This included 9 QTL clusters identified in the RIL population.Fifty-three QTL were identified in 19 soybean chromosomes by genome-wide association analysis(GWAS)in the panel of accessions,including 69 significant SNPs(-log_(10)(P)≥3.97).A combination of the two populations revealed that two SNPs(-log_(10)(P)≥3.0)fell within two of the QTL(qPH7-4 and qPH7-6)confidence intervals.We not only re-located several previously reported drought-resistance genes in soybean and other crops but also identified several non-synonymous stress-related mutation site differences between the two parents,involving Glyma.07 g093000,Glyma.07 g093200,Glyma.07 g094100 and Glyma.07 g094200.One previously unreported new gene related to drought stress,Glyma.07 g094200,was found by regional association analysis.The significant SNP CHR7-17619(G/T)was within an exon of the Glyma.07 g094200 gene.In the RIL population,the DSP value of the"T"allele of CHR7-17619 was significantly(P<0.05)larger than the"G"allele in different environments.The results of our study lay the groundwork for cloning and molecular marker-assisted selection of droughtresistance genes in soybeans at the seedling stage.
