The phosphorus uptake （PU） in above-ground parts of plant, root characteristics and root exudations as well as the quantitative trait loci （QTLs） associated with these characteristics were determined for a F2：3 p...The phosphorus uptake （PU） in above-ground parts of plant, root characteristics and root exudations as well as the quantitative trait loci （QTLs） associated with these characteristics were determined for a F2：3 population derived from the cross of two contrasting maize （Zea mays L.） genotypes, 082 and Yel07. A total of 241 F2：3 families were evaluated in replicated trials under deficient phosphorus conditions in 2007 at two sites （Kaixian County and Southwest University, Chongqing, P. R. China）. The results show pleiotropy and close linkage among QTLs. Four common regions in different environments were in bnlg100- bnlg1268b （bins 1.02） for QTL of H＋, bnlg1268a-umc1290a （bins 1.09） for QTL of AP （acid phospbatase activity）, dupssrl5- P 1MT/a （bins 6.06） for QTLs of PU （phosphorus uptake） and RW （root weight）, and P IM3/d-P1M3/g （bins9.04） for QTLs of PU and AP. These QTLs are non-environment or minor QTLs x environment. By epistatic analysis, three main QTLs and eighteen QTLs x QTLs interactions were detected for the seven measured characteristics. These QTLs may affect trait expression by epistatic interaction with the other loci, and make a substantial contribution to phosphorus utilization efficiency, which should be considered when breeding maize varieties with high P efficiency. Two regions were detected in dupssrl 5- P1MT/a （bins 6.06） for QTL of RW and P1M3/d- P 1M3/g （bins 9.04） for QTL of PU and AP. They were detected in two different environments and by two methods of QTL analysis, which were useful for marker-assisted selection.展开更多
With completion of the Populus genome sequencing project and the availability of many expressed sequence tags （ESTs） databases in forest trees, attention is now rapidly shifting towards the study of individual genet...With completion of the Populus genome sequencing project and the availability of many expressed sequence tags （ESTs） databases in forest trees, attention is now rapidly shifting towards the study of individual genetic variation in natural populations. The most abundant form of genetic variation in many eukaryotic species is represented by single nucleotide polymorphisms （SNPs）, which can account for heritable inter-individual differences in complex phenotypes. Unlike humans, the linkage disequilibrium （LD） rapidly decays within candidate genes in forest trees. Thus, SNPs-based candidate gene association studies are considered to be a most effective approach to dissect the complex quantitative traits in forest trees. The present study demonstrates that LD mapping can be used to identify alleles associated with quantitative traits and suggests that this new approach could be particularly useful for performing breeding programs in forest trees. In this review, we will describe the fundamentals, patterns of SNPs distribution and frequency, summarize recent advances in SNPs discovery and LD and comment on the application of LD in the dissection of complex quantitative traits in forest tress. We also put forward the outlook for future SNPs-based association analysis of quantitative traits in forest trees.展开更多
Objective To study the association of DTNBP1 gene with some symptom factors of schizophrenia.Methods A total of 285 unrelated schizophrenic individuals were recruited from December 2004 to January 2009 for genetic ana...Objective To study the association of DTNBP1 gene with some symptom factors of schizophrenia.Methods A total of 285 unrelated schizophrenic individuals were recruited from December 2004 to January 2009 for genetic analysis,and their symptom factors were assessed based on the Positive and Negative Syndrome Scale(PANSS).The quantitative trait test was performed by the UNPHASED program(version 3.0.12) to investigate the association between scored positive and negative symptoms and the single nucleotide polymorphisms(SNPs) in DTNBP1 gene.Results The quantitative trait test showed allelic association of rs909706 with the excitement symptom of schizophrenia(P<0.05,adjusted by 10 000 permutations),while the genotype C/G of rs2619539 with a negative symptom,lack of spontaneity and flow of conversation(P<0.05,adjusted by 10 000 permutations).Conclusion DTNBP1 variations are possibly associated with some symptoms of schizophrenia,which could partly explain the relationship between the susceptibility gene DTNBP1 and that disease.展开更多
Acacia hybrids offer a great potential for paper industry in Southeast Asia due to their fast growth and ability to grow on abandoned or marginal lands. Breeding Acacia hybrids with desirable traits can be achieved th...Acacia hybrids offer a great potential for paper industry in Southeast Asia due to their fast growth and ability to grow on abandoned or marginal lands. Breeding Acacia hybrids with desirable traits can be achieved through marker assisted selection(MAS) breeding. To develop a MAS program requires development of linkage maps and QTL analysis. Two mapping populations were developed through interspecific hybridization for linkage mapping and QTL analysis. All seeds per pod were cultured initially to improve hybrid yield as quality and density of linkage mapping is affected by the size of the mapping population. Progenies from two mapping populations were field planted for phenotypic and genotypic evaluation at three locations in Malaysia,(1) Forest Research Institute Malaysia field station at Segamat, Johor,(2) Borneo Tree Seeds and Seedlings Supplies Sdn, Bhd.(BTS) field trial site at Bintulu, Sarawak, and(3) Asiaprima RCF field trial site at Lancang, Pahang. During field planting, mislabeling was reported at Segamat, Johor, and a similar problem was suspected for Bintulu, Sarawak. Early screening with two isozymes effectively selected hybrid progenies, and these hybrids were subsequently further confirmed by using species-specific SNPs. During field planting, clonal mislabeling was reported and later confirmed by using a small set of STMS markers. A large set of SNPs were also used to screen all ramets in both populations. A total of 65.36% mislabeled ramets were encountered in the wood density population and 60.34% in the fibre length mapping population. No interpopulation pollen contamination was detected because all ramets found their match within the same population in question.However, mislabeling was detected among ramets of the same population. Mislabeled individuals were identified and grouped as they originated from 93 pods for wood density and 53 pods for fibre length mapping populations.On average 2 meiotically unique seeds per pod(179 seeds/93 pods) for wood density and 3 meiotically unique seeds per pod(174 seeds/53 pods) for fibre length mapping population were found. A single step statistical method was used to evaluate the most informative set of SNPs that could subsequently be used for routine checks for mislabeling in multi-location field trials and for labelling superior clones to protect breeder’s rights. A preliminary set of SNPs with a high degree of informativeness was selected for the mislabeling analysis in conjunction with an assignment test. Two subsets were successfully identified,i.e., 51 SNPs for wood density and 64 SNPs for fibre length mapping populations to identify all mislabeled ramets which had been previously identified. Mislabeling seems to be a common problem due to the complexity involved in the production of mapping populations. Therefore, checking for mislabeling is imperative for breeding activities and for analyses such as linkage mapping in which a correlation between genotypic and phenotypic data is determined.展开更多
Field trials with a set of 108 doubled haploid lines(DHs) derived from a cross between the Chinese winter wheat cvs.CA9613 and H1488 were run at Beijing(China).Phenotypic data were recorded for major agronomic yield t...Field trials with a set of 108 doubled haploid lines(DHs) derived from a cross between the Chinese winter wheat cvs.CA9613 and H1488 were run at Beijing(China).Phenotypic data were recorded for major agronomic yield traits,i.e.grain weight per ear,grain number per ear and thousand grain weight(Tgw) in two field trials at Beijing.Based on the phenotypic data and a genetic map comprising 168 SSR markers,an analysis of quantitative trait loci(QTL) was carried out for yield and yield parameters using the composite interval mapping(CIM) approach.A total of 14 QTL were detected for these traits across two environments.Four of these QTL located on chromosomes 1A and 2B,respectively,exhibited pleiotropic effects.Loci showing pleiotropic effects will be very useful for understanding the homeologous relationships of QTL and designing an appropriate marker-assisted selection programme by multi-trait selection in order to accumulate("pyramide") favorable alleles at different loci.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
基金Funded by Chongqing Key Scientific and Technological Project (No. CSTC2007AB1045)Chinese Key Scientific and Technological Project (No. 2006BAD13B03)
文摘The phosphorus uptake （PU） in above-ground parts of plant, root characteristics and root exudations as well as the quantitative trait loci （QTLs） associated with these characteristics were determined for a F2：3 population derived from the cross of two contrasting maize （Zea mays L.） genotypes, 082 and Yel07. A total of 241 F2：3 families were evaluated in replicated trials under deficient phosphorus conditions in 2007 at two sites （Kaixian County and Southwest University, Chongqing, P. R. China）. The results show pleiotropy and close linkage among QTLs. Four common regions in different environments were in bnlg100- bnlg1268b （bins 1.02） for QTL of H＋, bnlg1268a-umc1290a （bins 1.09） for QTL of AP （acid phospbatase activity）, dupssrl5- P 1MT/a （bins 6.06） for QTLs of PU （phosphorus uptake） and RW （root weight）, and P IM3/d-P1M3/g （bins9.04） for QTLs of PU and AP. These QTLs are non-environment or minor QTLs x environment. By epistatic analysis, three main QTLs and eighteen QTLs x QTLs interactions were detected for the seven measured characteristics. These QTLs may affect trait expression by epistatic interaction with the other loci, and make a substantial contribution to phosphorus utilization efficiency, which should be considered when breeding maize varieties with high P efficiency. Two regions were detected in dupssrl 5- P1MT/a （bins 6.06） for QTL of RW and P1M3/d- P 1M3/g （bins 9.04） for QTL of PU and AP. They were detected in two different environments and by two methods of QTL analysis, which were useful for marker-assisted selection.
文摘With completion of the Populus genome sequencing project and the availability of many expressed sequence tags （ESTs） databases in forest trees, attention is now rapidly shifting towards the study of individual genetic variation in natural populations. The most abundant form of genetic variation in many eukaryotic species is represented by single nucleotide polymorphisms （SNPs）, which can account for heritable inter-individual differences in complex phenotypes. Unlike humans, the linkage disequilibrium （LD） rapidly decays within candidate genes in forest trees. Thus, SNPs-based candidate gene association studies are considered to be a most effective approach to dissect the complex quantitative traits in forest trees. The present study demonstrates that LD mapping can be used to identify alleles associated with quantitative traits and suggests that this new approach could be particularly useful for performing breeding programs in forest trees. In this review, we will describe the fundamentals, patterns of SNPs distribution and frequency, summarize recent advances in SNPs discovery and LD and comment on the application of LD in the dissection of complex quantitative traits in forest tress. We also put forward the outlook for future SNPs-based association analysis of quantitative traits in forest trees.
基金Supported by National High Technology Research and Development Program of China (863 Program) (2006AA02A407)National Basic Research Program (973 Program) (2010CB529603)Beijing Natural Science Foundation (7102109)
文摘Objective To study the association of DTNBP1 gene with some symptom factors of schizophrenia.Methods A total of 285 unrelated schizophrenic individuals were recruited from December 2004 to January 2009 for genetic analysis,and their symptom factors were assessed based on the Positive and Negative Syndrome Scale(PANSS).The quantitative trait test was performed by the UNPHASED program(version 3.0.12) to investigate the association between scored positive and negative symptoms and the single nucleotide polymorphisms(SNPs) in DTNBP1 gene.Results The quantitative trait test showed allelic association of rs909706 with the excitement symptom of schizophrenia(P<0.05,adjusted by 10 000 permutations),while the genotype C/G of rs2619539 with a negative symptom,lack of spontaneity and flow of conversation(P<0.05,adjusted by 10 000 permutations).Conclusion DTNBP1 variations are possibly associated with some symptoms of schizophrenia,which could partly explain the relationship between the susceptibility gene DTNBP1 and that disease.
基金provided by the Ministry of Science,Technology and Innovation Malaysia(IRPA 01-02-02-0015PR0003/03-02,02-01-02-SF0403)Universiti Kebangsaan Malaysia(UKM-AP-BPB-13-2009,GUP-2013-039)
文摘Acacia hybrids offer a great potential for paper industry in Southeast Asia due to their fast growth and ability to grow on abandoned or marginal lands. Breeding Acacia hybrids with desirable traits can be achieved through marker assisted selection(MAS) breeding. To develop a MAS program requires development of linkage maps and QTL analysis. Two mapping populations were developed through interspecific hybridization for linkage mapping and QTL analysis. All seeds per pod were cultured initially to improve hybrid yield as quality and density of linkage mapping is affected by the size of the mapping population. Progenies from two mapping populations were field planted for phenotypic and genotypic evaluation at three locations in Malaysia,(1) Forest Research Institute Malaysia field station at Segamat, Johor,(2) Borneo Tree Seeds and Seedlings Supplies Sdn, Bhd.(BTS) field trial site at Bintulu, Sarawak, and(3) Asiaprima RCF field trial site at Lancang, Pahang. During field planting, mislabeling was reported at Segamat, Johor, and a similar problem was suspected for Bintulu, Sarawak. Early screening with two isozymes effectively selected hybrid progenies, and these hybrids were subsequently further confirmed by using species-specific SNPs. During field planting, clonal mislabeling was reported and later confirmed by using a small set of STMS markers. A large set of SNPs were also used to screen all ramets in both populations. A total of 65.36% mislabeled ramets were encountered in the wood density population and 60.34% in the fibre length mapping population. No interpopulation pollen contamination was detected because all ramets found their match within the same population in question.However, mislabeling was detected among ramets of the same population. Mislabeled individuals were identified and grouped as they originated from 93 pods for wood density and 53 pods for fibre length mapping populations.On average 2 meiotically unique seeds per pod(179 seeds/93 pods) for wood density and 3 meiotically unique seeds per pod(174 seeds/53 pods) for fibre length mapping population were found. A single step statistical method was used to evaluate the most informative set of SNPs that could subsequently be used for routine checks for mislabeling in multi-location field trials and for labelling superior clones to protect breeder’s rights. A preliminary set of SNPs with a high degree of informativeness was selected for the mislabeling analysis in conjunction with an assignment test. Two subsets were successfully identified,i.e., 51 SNPs for wood density and 64 SNPs for fibre length mapping populations to identify all mislabeled ramets which had been previously identified. Mislabeling seems to be a common problem due to the complexity involved in the production of mapping populations. Therefore, checking for mislabeling is imperative for breeding activities and for analyses such as linkage mapping in which a correlation between genotypic and phenotypic data is determined.
文摘Field trials with a set of 108 doubled haploid lines(DHs) derived from a cross between the Chinese winter wheat cvs.CA9613 and H1488 were run at Beijing(China).Phenotypic data were recorded for major agronomic yield traits,i.e.grain weight per ear,grain number per ear and thousand grain weight(Tgw) in two field trials at Beijing.Based on the phenotypic data and a genetic map comprising 168 SSR markers,an analysis of quantitative trait loci(QTL) was carried out for yield and yield parameters using the composite interval mapping(CIM) approach.A total of 14 QTL were detected for these traits across two environments.Four of these QTL located on chromosomes 1A and 2B,respectively,exhibited pleiotropic effects.Loci showing pleiotropic effects will be very useful for understanding the homeologous relationships of QTL and designing an appropriate marker-assisted selection programme by multi-trait selection in order to accumulate("pyramide") favorable alleles at different loci.
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.
