Studies that investigated the genetic basis of source and sink related traits have been widely conducted.However, the vascular system that links source and sink received much less attention. When maize was domesticate...Studies that investigated the genetic basis of source and sink related traits have been widely conducted.However, the vascular system that links source and sink received much less attention. When maize was domesticated from its wild ancestor, teosinte, the external morphology has changed dramatically; however, less is known for the internal anatomy changes. In this study, using a large maize-teosinte experimental population, we performed a high-resolution quantitative trait locus（QTL） mapping for the number of vascular bundle in the uppermost internode of maize stem.The results showed that vascular bundle number is dominated by a large number of small-effect QTLs, in which a total of 16 QTLs that jointly accounts for 52.2% of phenotypic variation were detected, with no single QTL explaining more than 6% of variation. Different from QTLs for typical domestication traits, QTLs for vascular bundle number might not be under directional selection following domestication.Using Near Isogenic Lines（NILs） developed from heterogeneous inbred family（HIF）, we further validated the effect of one QTL qVb9-2 on chromosome 9 and fine mapped the QTL to a 1.8-Mb physical region. This study provides important insights for the genetic architecture of vascular bundle number in maize stem and sets basis for cloning of qVb9-2.展开更多
The Tibetan antelope （Pantholops hodgsonii）, indigenous to China, became an endangered species because of considerable reduction both in number and distribution during the 20th century. Presently, it is listed as an...The Tibetan antelope （Pantholops hodgsonii）, indigenous to China, became an endangered species because of considerable reduction both in number and distribution during the 20th century. Presently, it is listed as an Appendix Ⅰ species by CITES and as Category I by the Key Protected Wildlife List of China. Understanding the genetic diversity and population structure of the Tibetan antelope is significant for the development of effective conservation plans that will ensure the recovery and future persistence of this species. Twenty-five microsatellites were selected to obtain loci with sufficient levels of polymorphism that can provide information for the analysis of population structure. Among the 25 loci that were examined, nine of them showed high levels of genetic diversity. The nine variable loci （MCM38, MNS64, IOBT395, MCMAL TGLA68, BM1329, BMSI341, BM3501, and MB066） were used to examine the genetic diversity of the Tibetan antelope （n = 75） in Hoh Xil National Nature Reserve（HXNNR）, Qinghai, China. The results obtained by estimating the number of population suggested that all the 75 Tibetan antelope samples were from the same population. The mean number of alleles per locus was 9.4 ± 0.5300 （range, 7-12） and the mean effective number of alleles was 6.519± 0.5271 （range, 4.676-9.169）. The observed mean and expected heterozygosity were 0.844 ± 0.0133 （range, 0.791-0.897） and 0.838 ± 0.0132 （range, 0.786-0.891）, respectively. Mean Polymorphism Information Content （PIC） was 0.818 ± 0.0158 （range, 0.753-0.881）. The value of Fixation index （Fis） ranged from -0.269 to -0.097 with the mean of -0.163 ± 0.0197. Mean Shannon＇s information index was 1.990 ± 0.0719 among nine loci （range, 1.660-2.315）. These results provide baseline data for the evaluation of the level of genetic variation in Tibetan antelope, which will be important for the development of conservation strategies in future.展开更多
The common marmoset(Callithrix jacchus)has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies.Epileptic marmosets have been independ...The common marmoset(Callithrix jacchus)has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies.Epileptic marmosets have been independently reported in two Asian primate research centers.Nevertheless,the population genetics within these primate centers and the specific genetic variants associated with epilepsy in marmosets have not yet been elucidated.Here,we characterized the genetic relationships and risk variants for epilepsy in 41 samples from two epileptic marmoset pedigrees using whole-genome sequencing.We identified 14558184 single nucleotide polymorphisms(SNPs)from the 41 samples and found higher chimerism levels in blood samples than in fingernail samples.Genetic analysis showed fourth-degree of relatedness among marmosets at the primate centers.In addition,SNP and copy number variation(CNV)analyses suggested that the WW domain-containing oxidoreductase(WWOX)and Tyrosine-protein phosphatase nonreceptor type 21(PTPN21)genes may be associated with epilepsy in marmosets.Notably,KCTD18-like gene deletion was more common in epileptic marmosets than control marmosets.This study provides valuable population genomic resources for marmosets in two Asian primate centers.Genetic analyses identified a reasonable breeding strategy for genetic diversity maintenance in the two centers,while the case-control study revealed potential risk genes/variants associated with epilepsy in marmosets.展开更多
Objective: To investigate the cooperative interaction among five genetic systems (phosphoglucomutase locus 1, adenosine deaminase locus 1, acid phosphatase locus 1, adenylate kinase locus 1, and haptoglobin) concernin...Objective: To investigate the cooperative interaction among five genetic systems (phosphoglucomutase locus 1, adenosine deaminase locus 1, acid phosphatase locus 1, adenylate kinase locus 1, and haptoglobin) concerning their effects on natural fertility in humans. Natural fertility has been evaluated by a model of age related differences between the distributions of types among pregnant women. Methods: A total of 137 nonsmoking consecutive puerperaes from the white population who had delivered their first born baby in the Maternity Department of S. Massimo Hospital of Penne were studied. The phenotypes of the five systems studied were determined by starch gel electrophoresis. Statistical analysis was performed using the statistical package for the social science. Results: There was a highly significant negative correlation between maternal age and the number of genetic factors showing a lower maternal age at the birth of the first child, which suggested a positive cooperative interaction among these factors concerning their effects on fertility. Conclusions:In the relationship of mother-fetus, besides nutritional factors, genetic factors involved in immunological interaction of the embryo with the mother are of paramount importance. Haptoglobin and adenosine deaminase locus 1 polymorphisms are involved in immune reactions and our data indicate that genetic variability within these systems gives a more important contribution to variation of human fertility as compared to acid phosphatase locus 1, phosphoglucomutase locus 1 and adenylate kinase locus 1 that are mainly involved in metabolic functions.展开更多
背景与目的:在DNA水平进行个体同一认定及亲缘鉴定,是目前获得准确结论的最直接的方法,而短串联重复序列(short tandem repeat,STR)复合扩增荧光检测技术是目前应用最广泛的DNA技术。但已有研究表明STR基因座在肿瘤组织中会发生明显高...背景与目的:在DNA水平进行个体同一认定及亲缘鉴定,是目前获得准确结论的最直接的方法,而短串联重复序列(short tandem repeat,STR)复合扩增荧光检测技术是目前应用最广泛的DNA技术。但已有研究表明STR基因座在肿瘤组织中会发生明显高于正常组织或血液的变异。该研究的目的为探索20个常染色体STR基因座及Amel基因座在人肺癌组织中的变异规律,为肺癌组织的个人识别及亲缘鉴定提供依据。方法:收集75例人肺癌组织和相对应的癌旁正常组织,采用组织DNA提取试剂盒提取DNA,MicroreaderTM 21Direct ID System试剂盒进行PCR扩增,采用3130序列分析仪进行毛细管电泳,用Gene Mapper ID V3.2基因分析软件进行基因分型。结果:75例癌组织中有24例发生了STR位点的变异(32%),在21个常用STR基因座上共检出55次变异,其中等位基因增加10次,杂合性等位基因完全丢失10次,部分性丢失35次。D2S441、Penta E基因座未检出变异。结合目前实验结果与肺癌患者的临床资料分析,发现STR位点的变异与肺癌的分型、患者性别无联系(P>0.05),与肺癌的分期及患者年龄正相关,各组间比较差异有统计学意义(P<0.05)。结论:肺癌组织中STR基因座较常发生变异,并且变异更可能在年龄大、恶性程度高的肺癌中发生;该实验检出D2S441、Penta E基因座无变异,在今后的研究中可加大样本量,进一步验证可否将其纳入稳定的STR基因座,为肿瘤组织等特殊检材的鉴定提供依据。展开更多
Ancherythroculter nigrocauda is a fish endemic to the upper areas of the Changjiang(Yangtze)River in China.Quantitative trait locus(QTL)mapping is a powerful tool to identify potential genes affecting traits of econom...Ancherythroculter nigrocauda is a fish endemic to the upper areas of the Changjiang(Yangtze)River in China.Quantitative trait locus(QTL)mapping is a powerful tool to identify potential genes affecting traits of economic importance in domestic animals.In this study,a high-density genetic map was constructed with 5901 single nucleotide polymorphism(SNP)makers by sequencing 92 individual fish from a F1 family using the specific-locus amplified fragment sequencing approach.Initially,48 QTLs for total length,body length,body height,and body weight were identified according to the high density of the genetic map with 24 LGs,a total length of 3839.4 cM,and marker spacing of about 0.82 cM.These QTLs explained 27.1%-49.9%of phenotypic variance.The results of this study suggest that major QTLs are responsible for the growth of A.nigrocauda,and these are potentially useful in comparative genomics research,genome assembly,and marker-assisted breeding programs for this species.展开更多
基金supported by the National Hi-Tech Research and Development Program of China(2012AA10A307)National Natural Science Foundation of China(31322042)+1 种基金the Recruitment Program of Global Expertsthe Fundamental Research Funds for the Central Universities
文摘Studies that investigated the genetic basis of source and sink related traits have been widely conducted.However, the vascular system that links source and sink received much less attention. When maize was domesticated from its wild ancestor, teosinte, the external morphology has changed dramatically; however, less is known for the internal anatomy changes. In this study, using a large maize-teosinte experimental population, we performed a high-resolution quantitative trait locus（QTL） mapping for the number of vascular bundle in the uppermost internode of maize stem.The results showed that vascular bundle number is dominated by a large number of small-effect QTLs, in which a total of 16 QTLs that jointly accounts for 52.2% of phenotypic variation were detected, with no single QTL explaining more than 6% of variation. Different from QTLs for typical domestication traits, QTLs for vascular bundle number might not be under directional selection following domestication.Using Near Isogenic Lines（NILs） developed from heterogeneous inbred family（HIF）, we further validated the effect of one QTL qVb9-2 on chromosome 9 and fine mapped the QTL to a 1.8-Mb physical region. This study provides important insights for the genetic architecture of vascular bundle number in maize stem and sets basis for cloning of qVb9-2.
基金Conservation Technology for Endangered Wildlife Program, Social Service Project of the Ministry of Science and Technology (No. 2001DIB100058)National Key Project of 10th Five-Year Plan (No. 2001BA510B10).
文摘The Tibetan antelope （Pantholops hodgsonii）, indigenous to China, became an endangered species because of considerable reduction both in number and distribution during the 20th century. Presently, it is listed as an Appendix Ⅰ species by CITES and as Category I by the Key Protected Wildlife List of China. Understanding the genetic diversity and population structure of the Tibetan antelope is significant for the development of effective conservation plans that will ensure the recovery and future persistence of this species. Twenty-five microsatellites were selected to obtain loci with sufficient levels of polymorphism that can provide information for the analysis of population structure. Among the 25 loci that were examined, nine of them showed high levels of genetic diversity. The nine variable loci （MCM38, MNS64, IOBT395, MCMAL TGLA68, BM1329, BMSI341, BM3501, and MB066） were used to examine the genetic diversity of the Tibetan antelope （n = 75） in Hoh Xil National Nature Reserve（HXNNR）, Qinghai, China. The results obtained by estimating the number of population suggested that all the 75 Tibetan antelope samples were from the same population. The mean number of alleles per locus was 9.4 ± 0.5300 （range, 7-12） and the mean effective number of alleles was 6.519± 0.5271 （range, 4.676-9.169）. The observed mean and expected heterozygosity were 0.844 ± 0.0133 （range, 0.791-0.897） and 0.838 ± 0.0132 （range, 0.786-0.891）, respectively. Mean Polymorphism Information Content （PIC） was 0.818 ± 0.0158 （range, 0.753-0.881）. The value of Fixation index （Fis） ranged from -0.269 to -0.097 with the mean of -0.163 ± 0.0197. Mean Shannon＇s information index was 1.990 ± 0.0719 among nine loci （range, 1.660-2.315）. These results provide baseline data for the evaluation of the level of genetic variation in Tibetan antelope, which will be important for the development of conservation strategies in future.
基金supported by the National Natural Science Foundation of China (82001372)National Key Research and Development Program of China (2018YFE0126700)+3 种基金Shanghai Jiao Tong University 2030 Initiative (WH510363001-7)Shanghai Municipal Commission of Science and Technology Program (21dz2210100)Shanghai Education Commission Research and Innovation Program (2019-01-07-00-02-E00037)a National Institutes of Health (NIH)grant (5R01HG002385)to E.E.E。
文摘The common marmoset(Callithrix jacchus)has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies.Epileptic marmosets have been independently reported in two Asian primate research centers.Nevertheless,the population genetics within these primate centers and the specific genetic variants associated with epilepsy in marmosets have not yet been elucidated.Here,we characterized the genetic relationships and risk variants for epilepsy in 41 samples from two epileptic marmoset pedigrees using whole-genome sequencing.We identified 14558184 single nucleotide polymorphisms(SNPs)from the 41 samples and found higher chimerism levels in blood samples than in fingernail samples.Genetic analysis showed fourth-degree of relatedness among marmosets at the primate centers.In addition,SNP and copy number variation(CNV)analyses suggested that the WW domain-containing oxidoreductase(WWOX)and Tyrosine-protein phosphatase nonreceptor type 21(PTPN21)genes may be associated with epilepsy in marmosets.Notably,KCTD18-like gene deletion was more common in epileptic marmosets than control marmosets.This study provides valuable population genomic resources for marmosets in two Asian primate centers.Genetic analyses identified a reasonable breeding strategy for genetic diversity maintenance in the two centers,while the case-control study revealed potential risk genes/variants associated with epilepsy in marmosets.
文摘Objective: To investigate the cooperative interaction among five genetic systems (phosphoglucomutase locus 1, adenosine deaminase locus 1, acid phosphatase locus 1, adenylate kinase locus 1, and haptoglobin) concerning their effects on natural fertility in humans. Natural fertility has been evaluated by a model of age related differences between the distributions of types among pregnant women. Methods: A total of 137 nonsmoking consecutive puerperaes from the white population who had delivered their first born baby in the Maternity Department of S. Massimo Hospital of Penne were studied. The phenotypes of the five systems studied were determined by starch gel electrophoresis. Statistical analysis was performed using the statistical package for the social science. Results: There was a highly significant negative correlation between maternal age and the number of genetic factors showing a lower maternal age at the birth of the first child, which suggested a positive cooperative interaction among these factors concerning their effects on fertility. Conclusions:In the relationship of mother-fetus, besides nutritional factors, genetic factors involved in immunological interaction of the embryo with the mother are of paramount importance. Haptoglobin and adenosine deaminase locus 1 polymorphisms are involved in immune reactions and our data indicate that genetic variability within these systems gives a more important contribution to variation of human fertility as compared to acid phosphatase locus 1, phosphoglucomutase locus 1 and adenylate kinase locus 1 that are mainly involved in metabolic functions.
文摘背景与目的:在DNA水平进行个体同一认定及亲缘鉴定,是目前获得准确结论的最直接的方法,而短串联重复序列(short tandem repeat,STR)复合扩增荧光检测技术是目前应用最广泛的DNA技术。但已有研究表明STR基因座在肿瘤组织中会发生明显高于正常组织或血液的变异。该研究的目的为探索20个常染色体STR基因座及Amel基因座在人肺癌组织中的变异规律,为肺癌组织的个人识别及亲缘鉴定提供依据。方法:收集75例人肺癌组织和相对应的癌旁正常组织,采用组织DNA提取试剂盒提取DNA,MicroreaderTM 21Direct ID System试剂盒进行PCR扩增,采用3130序列分析仪进行毛细管电泳,用Gene Mapper ID V3.2基因分析软件进行基因分型。结果:75例癌组织中有24例发生了STR位点的变异(32%),在21个常用STR基因座上共检出55次变异,其中等位基因增加10次,杂合性等位基因完全丢失10次,部分性丢失35次。D2S441、Penta E基因座未检出变异。结合目前实验结果与肺癌患者的临床资料分析,发现STR位点的变异与肺癌的分型、患者性别无联系(P>0.05),与肺癌的分期及患者年龄正相关,各组间比较差异有统计学意义(P<0.05)。结论:肺癌组织中STR基因座较常发生变异,并且变异更可能在年龄大、恶性程度高的肺癌中发生;该实验检出D2S441、Penta E基因座无变异,在今后的研究中可加大样本量,进一步验证可否将其纳入稳定的STR基因座,为肿瘤组织等特殊检材的鉴定提供依据。
基金Supported by the Technical Innovation Project of Hubei Province(No.2018ABA105)the Enterprise Technology Innovation Project of Wuhan(No.39 of 2019 WuKe)。
文摘Ancherythroculter nigrocauda is a fish endemic to the upper areas of the Changjiang(Yangtze)River in China.Quantitative trait locus(QTL)mapping is a powerful tool to identify potential genes affecting traits of economic importance in domestic animals.In this study,a high-density genetic map was constructed with 5901 single nucleotide polymorphism(SNP)makers by sequencing 92 individual fish from a F1 family using the specific-locus amplified fragment sequencing approach.Initially,48 QTLs for total length,body length,body height,and body weight were identified according to the high density of the genetic map with 24 LGs,a total length of 3839.4 cM,and marker spacing of about 0.82 cM.These QTLs explained 27.1%-49.9%of phenotypic variance.The results of this study suggest that major QTLs are responsible for the growth of A.nigrocauda,and these are potentially useful in comparative genomics research,genome assembly,and marker-assisted breeding programs for this species.
