Pythium stalk rot(PSR)is a destructive disease of maize,severely affecting yield and grain quality.The identification of quantitative trait loci(QTL)or genes for resistance to PSR forms the basis of diseaseresistant h...Pythium stalk rot(PSR)is a destructive disease of maize,severely affecting yield and grain quality.The identification of quantitative trait loci(QTL)or genes for resistance to PSR forms the basis of diseaseresistant hybrids breeding.In this study,a major QTL,Resistance to Pythium stalk rot 1(RPSR1),was identified from a set of recombinant inbred lines derived from MS71 and POP.Using a recombinant progeny testing strategy,RPSR1 was fine-mapped in a 472 kb interval.Through candidate gene expression,gene knock-down and knock-out studies,a leucine-rich repeat receptor-like kinase gene,PEP RECEPTOR 2(ZmPEPR2),was assigned as a PSR resistance gene.These results provide insights into the genetic architecture of resistance to PSR in maize,which should facilitate breeding maize for resistance to stalk rot.展开更多
Soybean mosaic virus(SMV)is a worldwide disease significantly decreasing soybean yield and seed quality.In this study,a genome-wide association study(GWAS)for SMV-SC3 resistance was conducted by using a deep re-sequen...Soybean mosaic virus(SMV)is a worldwide disease significantly decreasing soybean yield and seed quality.In this study,a genome-wide association study(GWAS)for SMV-SC3 resistance was conducted by using a deep re-sequencing dataset of 547 soybean accessions.A total of 11,405 SNPs and 1566 InDels were significantly associated with disease index(DI)at seedling stage and eight yield-and seed quality-related traits to SC3 resistance under eight environments.Among these genetic loci,952 SNPs and 118 InDels were firstly identified to control SC3 resistance,and 52.42% and 42.37% of them were pleiotropic loci across multiple environments.Notably,the 8.47-8.89 Mb genomic region on chromosome 18 was firstly discovvered to associate with DI at seedling stage and four related traits at adult stage across multiple environments.Furthermore,the causal gene Gm18GRSC3 was identified and validated in this stable and pleiotropic locus for resistance to SC3 via positive and negative transgenic strategies.Overexpression of Gm18GRSC3 significantly decreased the accumulation of SC3 in transgenic soybean hairy roots,while silencing of Gm18GRSC3 significantly increased SC3 accumulation in soybean leaves.A functional marker,FM18GSC3,was developed based on the allelic variation of Gm18GRSC3,and the detection efficiency reached to 76% in another 100 soybean accessions.These findings provide valuable genetic loci and a functional gene for the improvement of SMV resistance in soybean.展开更多
Spike length(SL)is an important factor affecting yield in wheat(Triticum aestivum L.).Here,a recombinant inbred line(RIL)population derived from a cross between Shannong 4155(SN4155)and Shimai 12(SM12)was used to map ...Spike length(SL)is an important factor affecting yield in wheat(Triticum aestivum L.).Here,a recombinant inbred line(RIL)population derived from a cross between Shannong 4155(SN4155)and Shimai 12(SM12)was used to map quantitative trait loci(QTL)controlling SL.A QTL,q SL2B,on chromosome 2B was identified in all experiments and explained 9.92%–12.71%of the phenotypic variation.Through transcriptome and gene expression analysis,we identified a gene encoding Elongation Factor 1-alpha(Tae EF1A)as the candidate gene for q SL2B.Genome editing of Tae EF1A demonstrated that Tae EF1A positively regulates SL,spikelet number per spike(SNS),and grain number per spike(GN).Transcriptome analysis showed that Tae EF1A may affect the protein translation process and photosynthesis to regulate spike development.We used haplotype analysis of wheat germplasm to identify seven types of genetic variations in Tae EF1A,with TypeⅠ,TypeⅡ,and TypeⅢbeing the major haplotypes.Screening of 428 cultivars and breeding lines identified 225 and 203 accessions as TypeⅠand TypeⅡhaplotypes,respectively,with TypeⅢnot detected.Comparison of SL,SNS,and GN between the TypeⅠand TypeⅡhaplotypes revealed that the TypeⅠallele can increase SL,SNS,and GN simultaneously,and is thus preferred for use in wheat molecular breeding efforts to increase SL,SNS,and GN.展开更多
Eye depth is an important agronomic trait affecting tubers'appearance,quality,and processing suitability.Hence,cultivating varieties with uniform shapes and shallow eye depth are important goals for potato breedin...Eye depth is an important agronomic trait affecting tubers'appearance,quality,and processing suitability.Hence,cultivating varieties with uniform shapes and shallow eye depth are important goals for potato breeding.In this study,based on the primary mapping of the tuber eyedepth locus using a small primary-segregating population,a large secondary-segregating population with 2100 individuals was used to map the eye-depth locus further.A major quantitative trait locus for eye-depth on chromosome 10 was identified(designated qEyd10.1)using BSAseq and traditional QTL mapping methods.The qEyd10.1 could explain 55.0%of the eye depth phenotypic variation and was further narrowed to a 309.10 kb interval using recombinant analysis.To predict candidate genes,tissue sectioning and RNA-seq of the specific tuber tissues were performed.Genes encoding members of the peroxidase superfamily with likely roles in indole acetic acid regulation were considered the most promising candidates.These results will facilitate marker-assisted selection for the shallow-eye trait in potato breeding and provide a solid basis for eye-depth gene cloning and the analysis of tuber eye-depth regulatory mechanisms.展开更多
Background Cotton is an important cash crop in China and a key component of the global textile market.Verticil-lium wilt is a major factor affecting cotton yield.Single nucleotide polymorphism(SNP)markers and phenotyp...Background Cotton is an important cash crop in China and a key component of the global textile market.Verticil-lium wilt is a major factor affecting cotton yield.Single nucleotide polymorphism(SNP)markers and phenotypic data can be used to identify genetic markers and loci associated with cotton resistance to Verticillium wilt.We used eight upland cotton parent materials in this study to construct a multiparent advanced generation inter-cross(MAGIC)population comprising 320 lines.The Verticillium wilt resistance of the MAGIC population was identified in the green-house in 2019,and the average relative disease index(ARDI)was calculated.A genome-wide association study(GWAS)was performed to discover SNP markers/genes associated with Verticillium wilt resistance.Results ARDI of the MAGIC population showed wide variation,ranging from 16.7 to 79.4 across three replicates.This variation reflected a diverse range of resistance to Verticillium wilt within the population.Analysis of distribution pat-terns across the environments revealed consistent trends,with coefficients of variation between 12.25%and 21.96%.Families with higher ARDI values,indicating stronger resistance,were more common,likely due to genetic diver-sity and environmental factors.Population structure analysis divided the MAGIC population into three subgroups,with Group I showing higher genetic variation and Groups II and III displaying more uniform resistance performance.Principal component analysis(PCA)confirmed these divisions,highlighting the genetic diversity underlying Verticil-lium wilt resistance.Through GWAS,we identified 19 SNPs significantly associated with Verticillium wilt resistance,distributed across three chromosomes.The screening of candidate genes was performed on the transcriptome derived from resistant and susceptible cultivars,combined with gene annotation and tissue expression patterns,and two key candidate genes,Ghir_A01G006660 and Ghir_A02G008980,were found to be potentially associated with Verticillium wilt resistance.This suggests that these two candidate genes may play an important role in responding to Verticillium wilt.Conclusion This study aims to dissect the genetic basis of Verticillium wilt resistance in cotton by using a MAGIC population and GWAS.The study seeks to provide valuable genetic resources for marker-assisted breeding and enhance the understanding of resistance mechanisms to improve cotton resilience against Verticillium wilt.展开更多
Flower-infecting fungi have caused many economically important diseases in crop production.The fungal pathogen Ustilaginoidea virens infects developing rice florets,causing false smut disease,which leads to reduced gr...Flower-infecting fungi have caused many economically important diseases in crop production.The fungal pathogen Ustilaginoidea virens infects developing rice florets,causing false smut disease,which leads to reduced grain yield and quality,as well as contamination with mycotoxins that pose hazards to human health and food security.To ensure rice production,substantial efforts have been made to understand the interaction between rice and U.virens.In this review,we summarize the current understanding of rice resistance mechanisms to U.virens.We discuss the evaluation of false smut resistance,quantitative resistance loci,potential defense strategies of rice panicles,pathogen effector-driven identification of resistance-related genes,and engineering of false smut resistance.We conclude by proposing an integrated defense system that includes disease avoidance,immune response,metabolic adaptation,and the inhibition of susceptibility factors.Furthermore,we outline four critical stages of interaction between rice and U.virens that are essential for understanding and enhancing organ-specific rice resistance to false smut disease.展开更多
Objective Pneumoconiosis,a lung disease caused by irreversible fibrosis,represents a significant public health burden.This study investigates the causal relationships between gut microbiota,gene methylation,gene expre...Objective Pneumoconiosis,a lung disease caused by irreversible fibrosis,represents a significant public health burden.This study investigates the causal relationships between gut microbiota,gene methylation,gene expression,protein levels,and pneumoconiosis using a multi-omics approach and Mendelian randomization(MR).Methods We analyzed gut microbiota data from MiBioGen and Esteban et al.to assess their potential causal effects on pneumoconiosis subtypes(asbestosis,silicosis,and inorganic pneumoconiosis)using conventional and summary-data-based MR(SMR).Gene methylation and expression data from Genotype-Tissue Expression and eQTLGen,along with protein level data from deCODE and UK Biobank Pharma Proteomics Project,were examined in relation to pneumoconiosis data from FinnGen.To validate our findings,we assessed self-measured gut flora from a pneumoconiosis cohort and performed fine mapping,drug prediction,molecular docking,and Phenome-Wide Association Studies to explore relevant phenotypes of key genes.Results Three core gut microorganisms were identified:Romboutsia(OR=0.249)as a protective factor against silicosis,Pasteurellaceae(OR=3.207)and Haemophilus parainfluenzae(OR=2.343)as risk factors for inorganic pneumoconiosis.Additionally,mapping and quantitative trait loci analyses revealed that the genes VIM,STX8,and MIF were significantly associated with pneumoconiosis risk.Conclusions This multi-omics study highlights the associations between gut microbiota and key genes(VIM,STX8,MIF)with pneumoconiosis,offering insights into potential therapeutic targets and personalized treatment strategies.展开更多
Efficient and accurate identification of candidate causal genes within quantitative trait loci(QTL)is a significant challenge in genetic research.Conventional linkage analysis methods often require substantial time an...Efficient and accurate identification of candidate causal genes within quantitative trait loci(QTL)is a significant challenge in genetic research.Conventional linkage analysis methods often require substantial time and resources to identify causal genes.This paper proposes a QTG-LGBM method for prioritizing causal genes in maize based on the Light GBM algorithm.QTG-LGBM dynamically adjusts gene weights and sample proportions during training to mitigate the effects of class imbalance.The method prevents overfitting in datasets with small samples by introducing a regularization term.Experimental results on maize traits,including plant height(PH),flowering time(FT),and tassel branch number(TBN),demonstrated that QTG-LGBM outperforms the commonly used methods QTG-Finder,GBDT,XGBoost,Bernoulli NB,SVM,CNN,and ensemble learning.We validated the generalization of QTG-LGBM using Arabidopsis,rice,Setaria,and sorghum.We also applied QTG-LGBM using reported QTL that affect traits of maize PH,FT and TBN,and FT in Arabidopsis,rice,and sorghum,as well as known causal genes within the QTL.When examining the top 20%of ranked genes,QTG-LGBM demonstrated a significantly higher recall rate of causal genes compared to random selection methods.We identified key gene features affecting phenotypes through feature importance analysis.QTG-LGBM is available at http://www.deepcba.com/QTG-LGBM.展开更多
The present investigation aims at unveiling the main causes of the recorded disparate phylogeographic patterning among the two highly dispersive coastal crab species Carcinus aestuarii and Pachygrapsus marmoratus in t...The present investigation aims at unveiling the main causes of the recorded disparate phylogeographic patterning among the two highly dispersive coastal crab species Carcinus aestuarii and Pachygrapsus marmoratus in the Mediterranean Sea.For this purpose,available mitochondrial and nuclear data for both species were re-analyzed and investigated for genetic polymorphism and differentiation patterns across three defined geographic scales in their distribution ranges,but also across the same locations in the Mediterranean Sea.The temporal frame of genetic diversification was also determined for both species in order to check whether observed differences in phylogeographic patterns among these coastal decapods could be attributed to different evolutionary histories.The obtained results revealed a more variable and diversified gene pool in the green crab C.aestuarii than the one recorded in the marbled crab P.marmoratus.Lack of significant correlation between pairwise genetic dissimilarities observed among C.aestuarii populations and those detected for P.marmoratus was notably discerned across the same defined Mediterranean locations.This finding indicates that the pattern of pairwise genetic differentiation does not vary in the same way in both examined crab species.Significant outputs of population genetic differentiation,retrieved within both species,were shown to be differently associated with the potential effects of various kinds of isolation processes(related to geography,environment and biogeographic boundary).Evolutionary history reconstruction showed older genetic diversification event in C.aestuarii than the one recorded in P.marmoratus.These recorded temporal frames suggest different modes of genetic diversification in both crab species(glacial vicariance for C.aestuarii and interglacial dispersal for P.marmoratus).They may also provide an explanation for the recorded differences in variation of patterns of population genetic diversity and structure,when integrated with species ecological requirements and life-history traits.展开更多
Background:Dysregulation of enhancer transcription occurs in multiple cancers.Enhancer RNAs(eRNAs)are transcribed products from enhancers that play critical roles in transcriptional control.Characterizing the genetic ...Background:Dysregulation of enhancer transcription occurs in multiple cancers.Enhancer RNAs(eRNAs)are transcribed products from enhancers that play critical roles in transcriptional control.Characterizing the genetic basis of eRNA expression may elucidate the molecular mechanisms underlying cancers.Methods:Initially,a comprehensive analysis of eRNA quantitative trait loci(eRNAQTLs)was performed in The Cancer Genome Atlas(TCGA),and functional features were characterized using multi-omics data.To establish the first eRNAQTL profiles for colorectal cancer(CRC)in China,epigenomic data were used to define active enhancers,which were subsequently integrated with transcription and genotyping data from 154 paired CRC samples.Finally,largescale case-control studies(34,585 cases and 69,544 controls)were conducted along with multipronged experiments to investigate the potential mechanisms by which candidate eRNAQTLs affect CRC risk.Results:A total of 300,112 eRNAQTLs were identified across 30 different cancer types,which exert their influence on eRNA transcription by modulating chromatin status,binding affinity to transcription factors and RNA-binding proteins.These eRNAQTLs were found to be significantly enriched in cancer risk loci,explaining a substantial proportion of cancer heritability.Additionally,tumor-specific eRNAQTLs exhibited high responsiveness to the development of cancer.Moreover,the target genes of these eRNAs were associated with dysregulated signaling pathways and immune cell infiltration in cancer,highlighting their potential as therapeutic targets.Furthermore,multiple ethnic population studies have confirmed that an eRNAQTL rs3094296-T variant decreases the risk of CRC in populations from China(OR=0.91,95%CI 0.88–0.95,P=2.92×10^(-7))and Europe(OR=0.92,95%CI 0.88–0.95,P=4.61×10^(-6)).Mechanistically,rs3094296 had an allele-specific effect on the transcription of the eRNA ENSR00000155786,which functioned as a transcriptional activator promoting the expression of its target gene SENP7.These two genes synergistically suppressed tumor cell proliferation.Our curated list of variants,genes,and drugs has been made available in CancereRNAQTL(http://canernaqtl.whu.edu.cn/#/)to serve as an informative resource for advancing this field.Conclusion:Our findings underscore the significance of eRNAQTLs in transcriptional regulation and disease heritability,pinpointing the potential of eRNA-based therapeutic strategies in cancers.展开更多
A genetic linkage map with 89 SSR marker loci was constructed based on a maize (Zea mays L.) population consisting of 184 F-2 individuals from the cross, Huangzao 4 X Ye 107. The 184 F-3 families were evaluated in the...A genetic linkage map with 89 SSR marker loci was constructed based on a maize (Zea mays L.) population consisting of 184 F-2 individuals from the cross, Huangzao 4 X Ye 107. The 184 F-3 families were evaluated in the field under well-watered and drought-stressed regimes in Shanxi Province of China. The objectives of the study were to identify genetic segments responsible for the expression of anthesis-silking interval (ASI), ear setting and grain yield, and to examine if the quantitative trait loci (QTLs) for ASI or yield components can be used in marker-assisted selection (MAS) to improve grain yield under drought conditions. Results showed that under well-watered and drought-stressed regimes, three and two QTLs involved in the expression of ASI were detected on chromosomes 1, 2 and 3, and 2 and 5, respectively. Under well-watered regime, two QTLs for ear setting were detected on chromosomes 3 and 6, explaining about 19.9% of the phenotypic variance, and displayed additive and partial dominant effects, respectively. Under drought-stressed condition, four QTLs for ear setting were detected on chromosomes 3, 7 and 10, which were responsible for interpreting 60.4% of the phenotypic variance, and showed dominant or partial dominant effects. Under well-watered condition, four QTLs controlling grain yield were identified on chromosomes 3, 6 and 7, while five QTLs were identified under drought stress on chromosomes 1, 2, 4 and 8. The gene action was of additive or partial dominant effects, and each QTL could explain 7.3% to 22.0% of the phenotypic variance, respectively. Under drought conditions, ASI and ear setting percentage were highly correlated with grain yield, which can be used as secondary traits for grain yield selection. Based on linked markers detected and gene action analyzed, an MAS strategy for yield improvement under drought condition could be established, which consists of QTLs contributing to decreased ASI and to increased ear setting and grain yield, respectively.展开更多
To understand the genetic background of root growth of rice ( Oryza sativa L.) seedlings under different water supply conditions, quantitative trait loci (QTLs) and epistatic effect on seminal root length, maximum adv...To understand the genetic background of root growth of rice ( Oryza sativa L.) seedlings under different water supply conditions, quantitative trait loci (QTLs) and epistatic effect on seminal root length, maximum adventitious root length, adventitious root number, total root dry weight and ratio of root to shoot were detected using molecular map including 103 restriction fragment length polymorphism (RFLP) markers and 104 amplified fragment length polymorphism (AFLP) markers mapped on a recombinant inbred line (RIL) population with 150 lines derived from a cross between an lowland rice IR1552 and an upland rice Azucena in both solution culture (lowland condition) and paper culture (upland condition). Six QTLs and twenty-two pairs of epistatic loci for the four parameters were detected. Three QTLs detected for maximum adventitious root length in solution culture (MARLS), total root dry weight in both solution culture and paper culture (TRDWS and TRDWP) accounted for about 20%, 23% and 13% of the total variations, respectively. Only epistatic loci were found for maximum adventitious root length and adventitious root number in paper culture (MARLP and ARNP), and for ratio of root to shoot in both paper and solution culture (R/SP and R/SS), which accounted for about 12%-61% of the total variations in the parameters, respectively. No identical QTL or epistatic loci were found for the parameters in both solution and paper culture. The results indicate that there is a different genetic system responsible to root growth of rice seedlings under lowland and upland conditions and epistasis might be the major genetic basis for MARLP, ARNP, R/SP and R/SS.展开更多
Quantitative trait loci(QTL)were detected for 8 internal organ traits,3 carcass length traits,and teat number trait in 214 pigs in a resource population that included 180 F2 individuals.A total of 39 microsatellite ma...Quantitative trait loci(QTL)were detected for 8 internal organ traits,3 carcass length traits,and teat number trait in 214 pigs in a resource population that included 180 F2 individuals.A total of 39 microsatellite markers were examined on SSC4,SSC6,SSC7,SSC8,and SSC13.The genetic traits included heart weight(HW),lung weight(LW),liver and gallbladder weight(LGW),spleen weight(SPW),stomach weight(STW),small intestine weight(S1W),large intestine weight(LIW),kidney weight(KW),carcass length to the first cervical vertebra(CL1),carcass length to the first thoracic vertebra(CL2),rib numbers(RNS),and teat numbers(TNS).Results indicated that,3 highly significant QTL(P≤0.01 at chromosome-wise level)for HW(at 30 cM on SSC6),RNS(at 115 cM on SSC7),TNS(at 110 cM on SSC7),and 6 significant QTL(P≤0.05 at chromosome-wise level)for LW(at 119 cM on SSC13),LGW(at 94 cM on SSC6),SPW(at 106 cM on SSC8),SIW(0 cM on SSC4),LIW(170 cM on SSC 4),and TNS(at 95 cM on SSC6)were detected.The phenotypic variances for which these QTL were accounted ranged from 0.04%to 14.06%.Most of these QTL had not been previously reported.展开更多
Grain weight, one of the major factors determining rice yield, is a typical quantitative trait control ed by multiple genes. With Guangluai 4 as recipient and Nipponbare as donor, a population of 119 chromosome single...Grain weight, one of the major factors determining rice yield, is a typical quantitative trait control ed by multiple genes. With Guangluai 4 as recipient and Nipponbare as donor, a population of 119 chromosome single segment substitution lines had been developed. Correlation analysis between grain weight and grain shape by SPSS revealed that 1 000-grain weight shared extremely significant posi-tive correlation with grain length and length-width ratio, but no significant correlation with grain width and thickness. The QTL analysis of grain weight was carried out using one-way analysis of variance and Dunnett＇s test. Nineteen stable QTLs re-sponsible for grain weight were identified over two years. Al 19 QTLs were identi-fied on al chromosomes except for chromosome 10 and 12 at a significance level of P≤0.001. Among them, 10 QTLs had a positive effect and were derived from the Nipponbare al ele, the additive effect of these QTLs ranged from 0.49 to 2.74 g, and the contributions of the additive effects ranged from 2.00% to 11.05%. Another 9 QTLs had a negative effect and were al derived from Guangluai 4 al ele, the ad-ditive effect of these QTLs ranged from 0.60 to 2.35 g, and the contributions of the additive effects ranged from 2.40% to 9.84%. The results provide a basis for the fine mapping and gene cloning of novel locus associated with rice grain weight.展开更多
This paper studies the offspring＇s genotype frequency of the selfing population on multiple alleles with limited loci.A recursive algorithm is given for it.It is discovered that the genotype frequency of homozygous g...This paper studies the offspring＇s genotype frequency of the selfing population on multiple alleles with limited loci.A recursive algorithm is given for it.It is discovered that the genotype frequency of homozygous gene of limited loci increases by generations.Relative increment reduces by generations and the genotype frequency tends to a definite value finally.The genotype frequency of limited loci with hybrid gene tends to 0 finally.But it is possibility that the genotype frequency increases in previous generations then reduces later.It is found that the number of the hybrid gene are more,the speeds tending to 0 are quicker.展开更多
The Chinese Bamboo Partridge(Bambusicola thoracica) is a gamebird endemic to China.Ten polymorphic microsatellite(simple sequence repeat) markers were obtained through cross-species amplification for this partridge fr...The Chinese Bamboo Partridge(Bambusicola thoracica) is a gamebird endemic to China.Ten polymorphic microsatellite(simple sequence repeat) markers were obtained through cross-species amplification for this partridge from its relative species Gallus gallus.The number of alleles per locus varied from 4 to 13.The observed heterozygosity ranged from 0.1220 to 1.0000 and the expected heterozygosity from 0.1183 to 0.8898.Four microsatellite loci showed significant differences from the Hardy-Weinberg equilibrium.These polymorphic loci provide a valuable tool for the investigation of the phylogeography and conservation genetics of this partridge.展开更多
To investigate the levels of polymorphisms and Mendelian segregation ratio in clone “TB01” (P. tomentosa×P. bolleana) ×clone “LM50” (P. tomentosa) BC 1 population at the entire genome level, ampl...To investigate the levels of polymorphisms and Mendelian segregation ratio in clone “TB01” (P. tomentosa×P. bolleana) ×clone “LM50” (P. tomentosa) BC 1 population at the entire genome level, amplified fragment length polymorphisms (AFLPs) analysis was conducted for both parents and 120 progenies. Forty one pairs of selective primers were used to detect 2?707 bands, of which 712 (26.4%) were polymorphic. Chi\|square tests were performed to examine if the observed genotypic frequencies of AFLP loci deviated from expected 1∶1 Mendelian segregation ratio ( P <0.01) in BC 1 population. Among the 712 loci 571 (80.2%) fit to Mendelian 1∶1 segregation ratio, corresponding to DNA polymorphisms heterozygous in one parent and a null in the other. The result shows that the AFLP markers are very suitable for fingerprinting and genetic mapping in the Chinese white poplar (Populus tomentosa Carr.).展开更多
In this study, a population of chromosome segment substitution lines （CSSLs） derived from the cross between 9311 （indica） and Nipponbare （japonica） was employed to map the quantitative trait loci （QTLs） for sa...In this study, a population of chromosome segment substitution lines （CSSLs） derived from the cross between 9311 （indica） and Nipponbare （japonica） was employed to map the quantitative trait loci （QTLs） for salt tolerance under the salt stress simulated with 0.5% NaCI, using survival rate as the index. The data were analyzed by QTL IciMapping v3.1, and the results showed that one QTL （QSsr3） related to salt tolerance was located in the vicinity of the marker RM1350 on chromosome 3, into a genetic interval of 113.2-132.8 cM, with a contribution rate of 17.75%. The additive effect was 10.9, indicating that the QTL derived from the parent Nipponbare improved the salt tolerance of rice at seedling stage. This study will provide a theoretical basis for the selection of salt tolerant rice germplasm.展开更多
基金supported by National Natural Science Foundation of China(32302371 to Junbin Chen)the National Key Research and Development Program,Ministry of Science and Technology of China(2022YFD1201802 to Wangsheng Zhu)Research Program from State Key Laboratory of Maize Biobreeding(SKLMB2424 to Wangsheng Zhu).
文摘Pythium stalk rot(PSR)is a destructive disease of maize,severely affecting yield and grain quality.The identification of quantitative trait loci(QTL)or genes for resistance to PSR forms the basis of diseaseresistant hybrids breeding.In this study,a major QTL,Resistance to Pythium stalk rot 1(RPSR1),was identified from a set of recombinant inbred lines derived from MS71 and POP.Using a recombinant progeny testing strategy,RPSR1 was fine-mapped in a 472 kb interval.Through candidate gene expression,gene knock-down and knock-out studies,a leucine-rich repeat receptor-like kinase gene,PEP RECEPTOR 2(ZmPEPR2),was assigned as a PSR resistance gene.These results provide insights into the genetic architecture of resistance to PSR in maize,which should facilitate breeding maize for resistance to stalk rot.
基金supported by the Project of Hebei Province Science and Technology Support Program(17927670H)the Science and Technology Innovation Team of Soybean Modern Seed Industry in Hebei(21326313D)。
文摘Soybean mosaic virus(SMV)is a worldwide disease significantly decreasing soybean yield and seed quality.In this study,a genome-wide association study(GWAS)for SMV-SC3 resistance was conducted by using a deep re-sequencing dataset of 547 soybean accessions.A total of 11,405 SNPs and 1566 InDels were significantly associated with disease index(DI)at seedling stage and eight yield-and seed quality-related traits to SC3 resistance under eight environments.Among these genetic loci,952 SNPs and 118 InDels were firstly identified to control SC3 resistance,and 52.42% and 42.37% of them were pleiotropic loci across multiple environments.Notably,the 8.47-8.89 Mb genomic region on chromosome 18 was firstly discovvered to associate with DI at seedling stage and four related traits at adult stage across multiple environments.Furthermore,the causal gene Gm18GRSC3 was identified and validated in this stable and pleiotropic locus for resistance to SC3 via positive and negative transgenic strategies.Overexpression of Gm18GRSC3 significantly decreased the accumulation of SC3 in transgenic soybean hairy roots,while silencing of Gm18GRSC3 significantly increased SC3 accumulation in soybean leaves.A functional marker,FM18GSC3,was developed based on the allelic variation of Gm18GRSC3,and the detection efficiency reached to 76% in another 100 soybean accessions.These findings provide valuable genetic loci and a functional gene for the improvement of SMV resistance in soybean.
基金supported by the Key R&D Program of Shandong province(2022LZGC001,2024CXPT072)the National Natural Science Foundation of China(32201863)the Tai’shan Scholars Program。
文摘Spike length(SL)is an important factor affecting yield in wheat(Triticum aestivum L.).Here,a recombinant inbred line(RIL)population derived from a cross between Shannong 4155(SN4155)and Shimai 12(SM12)was used to map quantitative trait loci(QTL)controlling SL.A QTL,q SL2B,on chromosome 2B was identified in all experiments and explained 9.92%–12.71%of the phenotypic variation.Through transcriptome and gene expression analysis,we identified a gene encoding Elongation Factor 1-alpha(Tae EF1A)as the candidate gene for q SL2B.Genome editing of Tae EF1A demonstrated that Tae EF1A positively regulates SL,spikelet number per spike(SNS),and grain number per spike(GN).Transcriptome analysis showed that Tae EF1A may affect the protein translation process and photosynthesis to regulate spike development.We used haplotype analysis of wheat germplasm to identify seven types of genetic variations in Tae EF1A,with TypeⅠ,TypeⅡ,and TypeⅢbeing the major haplotypes.Screening of 428 cultivars and breeding lines identified 225 and 203 accessions as TypeⅠand TypeⅡhaplotypes,respectively,with TypeⅢnot detected.Comparison of SL,SNS,and GN between the TypeⅠand TypeⅡhaplotypes revealed that the TypeⅠallele can increase SL,SNS,and GN simultaneously,and is thus preferred for use in wheat molecular breeding efforts to increase SL,SNS,and GN.
基金funded by the National Natural Science Foundation of China(Grant No.31801421)the Chinese Academy of Agricultural Sciences Innovation Project(Grant No.CAAS-ASTIPIVFCAAS).
文摘Eye depth is an important agronomic trait affecting tubers'appearance,quality,and processing suitability.Hence,cultivating varieties with uniform shapes and shallow eye depth are important goals for potato breeding.In this study,based on the primary mapping of the tuber eyedepth locus using a small primary-segregating population,a large secondary-segregating population with 2100 individuals was used to map the eye-depth locus further.A major quantitative trait locus for eye-depth on chromosome 10 was identified(designated qEyd10.1)using BSAseq and traditional QTL mapping methods.The qEyd10.1 could explain 55.0%of the eye depth phenotypic variation and was further narrowed to a 309.10 kb interval using recombinant analysis.To predict candidate genes,tissue sectioning and RNA-seq of the specific tuber tissues were performed.Genes encoding members of the peroxidase superfamily with likely roles in indole acetic acid regulation were considered the most promising candidates.These results will facilitate marker-assisted selection for the shallow-eye trait in potato breeding and provide a solid basis for eye-depth gene cloning and the analysis of tuber eye-depth regulatory mechanisms.
基金supported by funding from the fund for National Key Research and Development Program of China(2023YFD2301203-05)National Natural Science Foundation of China(32260510)+3 种基金Special Financial Project for Seed Industry Development in the Autonomous Region(BNZJ2024-10,BNZJ2024-30)Key Project for Science and Technology Development of Shihezi city,Xinjiang Production and Construction Crops(2022NY01)Shihezi University high-level talent research project(RCZK202337)Science and Technol-ogy Planning of Shuanghe city,Xinjiang Production and Construction Crops(2021NY02).
文摘Background Cotton is an important cash crop in China and a key component of the global textile market.Verticil-lium wilt is a major factor affecting cotton yield.Single nucleotide polymorphism(SNP)markers and phenotypic data can be used to identify genetic markers and loci associated with cotton resistance to Verticillium wilt.We used eight upland cotton parent materials in this study to construct a multiparent advanced generation inter-cross(MAGIC)population comprising 320 lines.The Verticillium wilt resistance of the MAGIC population was identified in the green-house in 2019,and the average relative disease index(ARDI)was calculated.A genome-wide association study(GWAS)was performed to discover SNP markers/genes associated with Verticillium wilt resistance.Results ARDI of the MAGIC population showed wide variation,ranging from 16.7 to 79.4 across three replicates.This variation reflected a diverse range of resistance to Verticillium wilt within the population.Analysis of distribution pat-terns across the environments revealed consistent trends,with coefficients of variation between 12.25%and 21.96%.Families with higher ARDI values,indicating stronger resistance,were more common,likely due to genetic diver-sity and environmental factors.Population structure analysis divided the MAGIC population into three subgroups,with Group I showing higher genetic variation and Groups II and III displaying more uniform resistance performance.Principal component analysis(PCA)confirmed these divisions,highlighting the genetic diversity underlying Verticil-lium wilt resistance.Through GWAS,we identified 19 SNPs significantly associated with Verticillium wilt resistance,distributed across three chromosomes.The screening of candidate genes was performed on the transcriptome derived from resistant and susceptible cultivars,combined with gene annotation and tissue expression patterns,and two key candidate genes,Ghir_A01G006660 and Ghir_A02G008980,were found to be potentially associated with Verticillium wilt resistance.This suggests that these two candidate genes may play an important role in responding to Verticillium wilt.Conclusion This study aims to dissect the genetic basis of Verticillium wilt resistance in cotton by using a MAGIC population and GWAS.The study seeks to provide valuable genetic resources for marker-assisted breeding and enhance the understanding of resistance mechanisms to improve cotton resilience against Verticillium wilt.
基金supported by grants from the Sichuan Natural Science Foundation(2024NSFSC0335 and SCCXTD-2024-SD-4 to D.-Q.L.)the National Natural Science Foundation of China(32372490 and 32072503 to J.F.)。
文摘Flower-infecting fungi have caused many economically important diseases in crop production.The fungal pathogen Ustilaginoidea virens infects developing rice florets,causing false smut disease,which leads to reduced grain yield and quality,as well as contamination with mycotoxins that pose hazards to human health and food security.To ensure rice production,substantial efforts have been made to understand the interaction between rice and U.virens.In this review,we summarize the current understanding of rice resistance mechanisms to U.virens.We discuss the evaluation of false smut resistance,quantitative resistance loci,potential defense strategies of rice panicles,pathogen effector-driven identification of resistance-related genes,and engineering of false smut resistance.We conclude by proposing an integrated defense system that includes disease avoidance,immune response,metabolic adaptation,and the inhibition of susceptibility factors.Furthermore,we outline four critical stages of interaction between rice and U.virens that are essential for understanding and enhancing organ-specific rice resistance to false smut disease.
基金the Central Guidance for Regional Science and Technology Development Projects(YDZJSX2024B010)Research project of Shanxi Provincial Health Commission(2024067)。
文摘Objective Pneumoconiosis,a lung disease caused by irreversible fibrosis,represents a significant public health burden.This study investigates the causal relationships between gut microbiota,gene methylation,gene expression,protein levels,and pneumoconiosis using a multi-omics approach and Mendelian randomization(MR).Methods We analyzed gut microbiota data from MiBioGen and Esteban et al.to assess their potential causal effects on pneumoconiosis subtypes(asbestosis,silicosis,and inorganic pneumoconiosis)using conventional and summary-data-based MR(SMR).Gene methylation and expression data from Genotype-Tissue Expression and eQTLGen,along with protein level data from deCODE and UK Biobank Pharma Proteomics Project,were examined in relation to pneumoconiosis data from FinnGen.To validate our findings,we assessed self-measured gut flora from a pneumoconiosis cohort and performed fine mapping,drug prediction,molecular docking,and Phenome-Wide Association Studies to explore relevant phenotypes of key genes.Results Three core gut microorganisms were identified:Romboutsia(OR=0.249)as a protective factor against silicosis,Pasteurellaceae(OR=3.207)and Haemophilus parainfluenzae(OR=2.343)as risk factors for inorganic pneumoconiosis.Additionally,mapping and quantitative trait loci analyses revealed that the genes VIM,STX8,and MIF were significantly associated with pneumoconiosis risk.Conclusions This multi-omics study highlights the associations between gut microbiota and key genes(VIM,STX8,MIF)with pneumoconiosis,offering insights into potential therapeutic targets and personalized treatment strategies.
基金supported by the Biological Breeding-Major Projects(2023ZD04067)Hubei Provincial Natural Science Foundation of China(2023AFB832)+1 种基金Guizhou Provincial Basic Research Program(Natural Science)(MS[2025]096)Major Project of Hubei Hongshan Laboratory(2022HSZD031)。
文摘Efficient and accurate identification of candidate causal genes within quantitative trait loci(QTL)is a significant challenge in genetic research.Conventional linkage analysis methods often require substantial time and resources to identify causal genes.This paper proposes a QTG-LGBM method for prioritizing causal genes in maize based on the Light GBM algorithm.QTG-LGBM dynamically adjusts gene weights and sample proportions during training to mitigate the effects of class imbalance.The method prevents overfitting in datasets with small samples by introducing a regularization term.Experimental results on maize traits,including plant height(PH),flowering time(FT),and tassel branch number(TBN),demonstrated that QTG-LGBM outperforms the commonly used methods QTG-Finder,GBDT,XGBoost,Bernoulli NB,SVM,CNN,and ensemble learning.We validated the generalization of QTG-LGBM using Arabidopsis,rice,Setaria,and sorghum.We also applied QTG-LGBM using reported QTL that affect traits of maize PH,FT and TBN,and FT in Arabidopsis,rice,and sorghum,as well as known causal genes within the QTL.When examining the top 20%of ranked genes,QTG-LGBM demonstrated a significantly higher recall rate of causal genes compared to random selection methods.We identified key gene features affecting phenotypes through feature importance analysis.QTG-LGBM is available at http://www.deepcba.com/QTG-LGBM.
文摘The present investigation aims at unveiling the main causes of the recorded disparate phylogeographic patterning among the two highly dispersive coastal crab species Carcinus aestuarii and Pachygrapsus marmoratus in the Mediterranean Sea.For this purpose,available mitochondrial and nuclear data for both species were re-analyzed and investigated for genetic polymorphism and differentiation patterns across three defined geographic scales in their distribution ranges,but also across the same locations in the Mediterranean Sea.The temporal frame of genetic diversification was also determined for both species in order to check whether observed differences in phylogeographic patterns among these coastal decapods could be attributed to different evolutionary histories.The obtained results revealed a more variable and diversified gene pool in the green crab C.aestuarii than the one recorded in the marbled crab P.marmoratus.Lack of significant correlation between pairwise genetic dissimilarities observed among C.aestuarii populations and those detected for P.marmoratus was notably discerned across the same defined Mediterranean locations.This finding indicates that the pattern of pairwise genetic differentiation does not vary in the same way in both examined crab species.Significant outputs of population genetic differentiation,retrieved within both species,were shown to be differently associated with the potential effects of various kinds of isolation processes(related to geography,environment and biogeographic boundary).Evolutionary history reconstruction showed older genetic diversification event in C.aestuarii than the one recorded in P.marmoratus.These recorded temporal frames suggest different modes of genetic diversification in both crab species(glacial vicariance for C.aestuarii and interglacial dispersal for P.marmoratus).They may also provide an explanation for the recorded differences in variation of patterns of population genetic diversity and structure,when integrated with species ecological requirements and life-history traits.
基金supported by the National Science Fund for Excellent Young Scholars(NSFC-82322058)the Program of National Natural Science Foundation of China(NSFC-82103929,NSFC-82273713)+10 种基金the Young Elite Scientists Sponsorship Program by CAST(2022QNRC001)the National Science Fund for Distinguished Young Scholars of Hubei Province of China(2023AFA046)the Fundamental Research Funds for the Central Universities(WHU:2042022kf1205)Fundamental Research Funds for the Central Universities(WHU:2042022kf1031)for Ying Zhuthe Fundamental Research Funds for the Central Universities(2042022rc0026,2042023kf1005)for Xiao-Ping Miaothe Knowledge Innovation Program of Wuhan(whkxjsj011,2023020201010073)for Jian-Bo Tianthe Science and Technology Innovation Seed Fund of Zhongnan Hospital of Wuhan University(znpy2019060)for Yong-Chang Weithe Distinguished Young Scholars of China(NSFC-81925032)the Key Program of National Natural Science Foundation of China(NSFC-82130098)the Youth Program of National Natural Science Foundation of China(NSFC-82003547)the Program of Health Commission of Hubei Province(WJ2023M045)。
文摘Background:Dysregulation of enhancer transcription occurs in multiple cancers.Enhancer RNAs(eRNAs)are transcribed products from enhancers that play critical roles in transcriptional control.Characterizing the genetic basis of eRNA expression may elucidate the molecular mechanisms underlying cancers.Methods:Initially,a comprehensive analysis of eRNA quantitative trait loci(eRNAQTLs)was performed in The Cancer Genome Atlas(TCGA),and functional features were characterized using multi-omics data.To establish the first eRNAQTL profiles for colorectal cancer(CRC)in China,epigenomic data were used to define active enhancers,which were subsequently integrated with transcription and genotyping data from 154 paired CRC samples.Finally,largescale case-control studies(34,585 cases and 69,544 controls)were conducted along with multipronged experiments to investigate the potential mechanisms by which candidate eRNAQTLs affect CRC risk.Results:A total of 300,112 eRNAQTLs were identified across 30 different cancer types,which exert their influence on eRNA transcription by modulating chromatin status,binding affinity to transcription factors and RNA-binding proteins.These eRNAQTLs were found to be significantly enriched in cancer risk loci,explaining a substantial proportion of cancer heritability.Additionally,tumor-specific eRNAQTLs exhibited high responsiveness to the development of cancer.Moreover,the target genes of these eRNAs were associated with dysregulated signaling pathways and immune cell infiltration in cancer,highlighting their potential as therapeutic targets.Furthermore,multiple ethnic population studies have confirmed that an eRNAQTL rs3094296-T variant decreases the risk of CRC in populations from China(OR=0.91,95%CI 0.88–0.95,P=2.92×10^(-7))and Europe(OR=0.92,95%CI 0.88–0.95,P=4.61×10^(-6)).Mechanistically,rs3094296 had an allele-specific effect on the transcription of the eRNA ENSR00000155786,which functioned as a transcriptional activator promoting the expression of its target gene SENP7.These two genes synergistically suppressed tumor cell proliferation.Our curated list of variants,genes,and drugs has been made available in CancereRNAQTL(http://canernaqtl.whu.edu.cn/#/)to serve as an informative resource for advancing this field.Conclusion:Our findings underscore the significance of eRNAQTLs in transcriptional regulation and disease heritability,pinpointing the potential of eRNA-based therapeutic strategies in cancers.
文摘A genetic linkage map with 89 SSR marker loci was constructed based on a maize (Zea mays L.) population consisting of 184 F-2 individuals from the cross, Huangzao 4 X Ye 107. The 184 F-3 families were evaluated in the field under well-watered and drought-stressed regimes in Shanxi Province of China. The objectives of the study were to identify genetic segments responsible for the expression of anthesis-silking interval (ASI), ear setting and grain yield, and to examine if the quantitative trait loci (QTLs) for ASI or yield components can be used in marker-assisted selection (MAS) to improve grain yield under drought conditions. Results showed that under well-watered and drought-stressed regimes, three and two QTLs involved in the expression of ASI were detected on chromosomes 1, 2 and 3, and 2 and 5, respectively. Under well-watered regime, two QTLs for ear setting were detected on chromosomes 3 and 6, explaining about 19.9% of the phenotypic variance, and displayed additive and partial dominant effects, respectively. Under drought-stressed condition, four QTLs for ear setting were detected on chromosomes 3, 7 and 10, which were responsible for interpreting 60.4% of the phenotypic variance, and showed dominant or partial dominant effects. Under well-watered condition, four QTLs controlling grain yield were identified on chromosomes 3, 6 and 7, while five QTLs were identified under drought stress on chromosomes 1, 2, 4 and 8. The gene action was of additive or partial dominant effects, and each QTL could explain 7.3% to 22.0% of the phenotypic variance, respectively. Under drought conditions, ASI and ear setting percentage were highly correlated with grain yield, which can be used as secondary traits for grain yield selection. Based on linked markers detected and gene action analyzed, an MAS strategy for yield improvement under drought condition could be established, which consists of QTLs contributing to decreased ASI and to increased ear setting and grain yield, respectively.
文摘To understand the genetic background of root growth of rice ( Oryza sativa L.) seedlings under different water supply conditions, quantitative trait loci (QTLs) and epistatic effect on seminal root length, maximum adventitious root length, adventitious root number, total root dry weight and ratio of root to shoot were detected using molecular map including 103 restriction fragment length polymorphism (RFLP) markers and 104 amplified fragment length polymorphism (AFLP) markers mapped on a recombinant inbred line (RIL) population with 150 lines derived from a cross between an lowland rice IR1552 and an upland rice Azucena in both solution culture (lowland condition) and paper culture (upland condition). Six QTLs and twenty-two pairs of epistatic loci for the four parameters were detected. Three QTLs detected for maximum adventitious root length in solution culture (MARLS), total root dry weight in both solution culture and paper culture (TRDWS and TRDWP) accounted for about 20%, 23% and 13% of the total variations, respectively. Only epistatic loci were found for maximum adventitious root length and adventitious root number in paper culture (MARLP and ARNP), and for ratio of root to shoot in both paper and solution culture (R/SP and R/SS), which accounted for about 12%-61% of the total variations in the parameters, respectively. No identical QTL or epistatic loci were found for the parameters in both solution and paper culture. The results indicate that there is a different genetic system responsible to root growth of rice seedlings under lowland and upland conditions and epistasis might be the major genetic basis for MARLP, ARNP, R/SP and R/SS.
基金supported by the State Key Basic Research and Development Plan of China(No.2006CB102102)the National Natural Science Foundation of China(No.30500358).
文摘Quantitative trait loci(QTL)were detected for 8 internal organ traits,3 carcass length traits,and teat number trait in 214 pigs in a resource population that included 180 F2 individuals.A total of 39 microsatellite markers were examined on SSC4,SSC6,SSC7,SSC8,and SSC13.The genetic traits included heart weight(HW),lung weight(LW),liver and gallbladder weight(LGW),spleen weight(SPW),stomach weight(STW),small intestine weight(S1W),large intestine weight(LIW),kidney weight(KW),carcass length to the first cervical vertebra(CL1),carcass length to the first thoracic vertebra(CL2),rib numbers(RNS),and teat numbers(TNS).Results indicated that,3 highly significant QTL(P≤0.01 at chromosome-wise level)for HW(at 30 cM on SSC6),RNS(at 115 cM on SSC7),TNS(at 110 cM on SSC7),and 6 significant QTL(P≤0.05 at chromosome-wise level)for LW(at 119 cM on SSC13),LGW(at 94 cM on SSC6),SPW(at 106 cM on SSC8),SIW(0 cM on SSC4),LIW(170 cM on SSC 4),and TNS(at 95 cM on SSC6)were detected.The phenotypic variances for which these QTL were accounted ranged from 0.04%to 14.06%.Most of these QTL had not been previously reported.
基金Supported by National Natural Science Foundation of China(31101131)National Key Technology Research and Development Program(2011BAD16B03)+1 种基金Agricultural Science Independent Innovation Foundation of Jiangsu Province[CX(12)1003]Key Technology Research and Development Program of Jiangsu Province(BE2012309)~~
文摘Grain weight, one of the major factors determining rice yield, is a typical quantitative trait control ed by multiple genes. With Guangluai 4 as recipient and Nipponbare as donor, a population of 119 chromosome single segment substitution lines had been developed. Correlation analysis between grain weight and grain shape by SPSS revealed that 1 000-grain weight shared extremely significant posi-tive correlation with grain length and length-width ratio, but no significant correlation with grain width and thickness. The QTL analysis of grain weight was carried out using one-way analysis of variance and Dunnett＇s test. Nineteen stable QTLs re-sponsible for grain weight were identified over two years. Al 19 QTLs were identi-fied on al chromosomes except for chromosome 10 and 12 at a significance level of P≤0.001. Among them, 10 QTLs had a positive effect and were derived from the Nipponbare al ele, the additive effect of these QTLs ranged from 0.49 to 2.74 g, and the contributions of the additive effects ranged from 2.00% to 11.05%. Another 9 QTLs had a negative effect and were al derived from Guangluai 4 al ele, the ad-ditive effect of these QTLs ranged from 0.60 to 2.35 g, and the contributions of the additive effects ranged from 2.40% to 9.84%. The results provide a basis for the fine mapping and gene cloning of novel locus associated with rice grain weight.
基金Supported by Research Project from Education Department of Guangxi(200807MS065)Mathematical Modeling in Population Genetics from Talents Scheme of Universities in Guangxi~~
文摘This paper studies the offspring＇s genotype frequency of the selfing population on multiple alleles with limited loci.A recursive algorithm is given for it.It is discovered that the genotype frequency of homozygous gene of limited loci increases by generations.Relative increment reduces by generations and the genotype frequency tends to a definite value finally.The genotype frequency of limited loci with hybrid gene tends to 0 finally.But it is possibility that the genotype frequency increases in previous generations then reduces later.It is found that the number of the hybrid gene are more,the speeds tending to 0 are quicker.
基金supported by the National Natural Science Foundation of China (Grant No. 30760036,30960051)Young Scientists (Jinggang Star) Training Scheme of Jiangxi ProvinceNatural Science Foundation of Jiangxi Province (2009GZN0075)
文摘The Chinese Bamboo Partridge(Bambusicola thoracica) is a gamebird endemic to China.Ten polymorphic microsatellite(simple sequence repeat) markers were obtained through cross-species amplification for this partridge from its relative species Gallus gallus.The number of alleles per locus varied from 4 to 13.The observed heterozygosity ranged from 0.1220 to 1.0000 and the expected heterozygosity from 0.1183 to 0.8898.Four microsatellite loci showed significant differences from the Hardy-Weinberg equilibrium.These polymorphic loci provide a valuable tool for the investigation of the phylogeography and conservation genetics of this partridge.
文摘To investigate the levels of polymorphisms and Mendelian segregation ratio in clone “TB01” (P. tomentosa×P. bolleana) ×clone “LM50” (P. tomentosa) BC 1 population at the entire genome level, amplified fragment length polymorphisms (AFLPs) analysis was conducted for both parents and 120 progenies. Forty one pairs of selective primers were used to detect 2?707 bands, of which 712 (26.4%) were polymorphic. Chi\|square tests were performed to examine if the observed genotypic frequencies of AFLP loci deviated from expected 1∶1 Mendelian segregation ratio ( P <0.01) in BC 1 population. Among the 712 loci 571 (80.2%) fit to Mendelian 1∶1 segregation ratio, corresponding to DNA polymorphisms heterozygous in one parent and a null in the other. The result shows that the AFLP markers are very suitable for fingerprinting and genetic mapping in the Chinese white poplar (Populus tomentosa Carr.).
文摘In this study, a population of chromosome segment substitution lines （CSSLs） derived from the cross between 9311 （indica） and Nipponbare （japonica） was employed to map the quantitative trait loci （QTLs） for salt tolerance under the salt stress simulated with 0.5% NaCI, using survival rate as the index. The data were analyzed by QTL IciMapping v3.1, and the results showed that one QTL （QSsr3） related to salt tolerance was located in the vicinity of the marker RM1350 on chromosome 3, into a genetic interval of 113.2-132.8 cM, with a contribution rate of 17.75%. The additive effect was 10.9, indicating that the QTL derived from the parent Nipponbare improved the salt tolerance of rice at seedling stage. This study will provide a theoretical basis for the selection of salt tolerant rice germplasm.
