Previous study indicated that the thermo-sensitive genic malesterile(TGMS) gene in rice was regulated by temperature.TGMS rice plays an important role in hybrid rice production,because the application of the TGMS syst...Previous study indicated that the thermo-sensitive genic malesterile(TGMS) gene in rice was regulated by temperature.TGMS rice plays an important role in hybrid rice production,because the application of the TGMS system in two-line breeding is laborsaving,timesaving,simple,inexpensive,efficient,and eliminating the limitations of the cytoplasmic male sterility(CMS) system.'AnnongS' is the first discovered and deeply studied TGMS rice lines in China.'AnnongS-1' and 'Y58S',two derivatives of TGMS line AnnongS,were both controlled by a single recessive gene named tms5,which was genetically mapped on chromosome 2.In this study,three populations('AnnongS-1' × 'Nanjing11','Y58S' × 'Q611',and 'Y58S' × 'Guanghui122') were developed and used for the molecular fine mapping of the tms5 gene.By analyzing recombination events in the sterile individuals using a total of 125 probes covering the tms5 region,the tms5 gene was physically mapped to a 19-kb DNA fragment between two markers 4039-1 and 4039-2,which were located on the BAC clone AP004039.After the construction of the physical map between two markers 4039-1 and 4039-2,a member(ONAC023) of the NAC(NAM-ATAF-CUC-related) gene family was identified as the candidate gene of the tms5 gene.展开更多
Gene expression profiling at early stages(0～2 DPA) of fiber development in Gossypium hirsutum identified a number of transcription factors which were down regulated in fiberless mutants relative to wild type controls...Gene expression profiling at early stages(0～2 DPA) of fiber development in Gossypium hirsutum identified a number of transcription factors which were down regulated in fiberless mutants relative to wild type controls and which could play a role in controlling early fiber development.Chief among these was GhMYB25,a Mixta-like MYB gene.Transgenic GhMYB25-silenced cotton展开更多
Background:Meta-analysis of quantitative trait locus(QTL)is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies.The combination of meta-QTL i...Background:Meta-analysis of quantitative trait locus(QTL)is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies.The combination of meta-QTL intervals,significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants.Results:In our study,884 QTLs associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1,as a result,74 meta-QTLs were identified,including 19 meta-QTLs for fiber length;18 meta-QTLs for fiber strength;11 meta-QTLs for fiber uniformity;11 meta-QTLs for fiber elongation;and 15 meta-QTLs for micronaire.Combined with 8589 significant single nucleotide polymorphisms associated with fiber quality traits collected from 15 studies,297 candidate genes were identified in the meta-QTL intervals,20 of which showed high expression levels specifically in the developing fibers.According to the function annotations,some of the 20 key candidate genes are associated with the fiber development.Conclusions:This study provides not only stable QTLs used for marker-assisted selection,but also candidate genes to uncover the molecular mechanisms for cotton fiber development.展开更多
Soybean bacterial spot disease caused by Pseudomonas syringae pv.Glycinea which is a bacterial disease seriously affects soybean yield.Ten soybean germplasms and recombinant inbred lines(RILs)population were used to i...Soybean bacterial spot disease caused by Pseudomonas syringae pv.Glycinea which is a bacterial disease seriously affects soybean yield.Ten soybean germplasms and recombinant inbred lines(RILs)population were used to identify the resistant trait after inoculated with P.sg(P.sgneau001)in this study.High-density genetic mapping was obtained by specific length amplified fragment sequencing(SLAF-seq)of 149 RILs population which was derived from the crossing between Charleston and Dongnong594.The results indicated that 10 germplasm resources had four resistant germplasms included highly resistant cultivar Charleston,four susceptible varieties included Dongnong594 and two moderately resistant cultivars.Five quantitative trait locus(QTLs)were detected in RILs population by the composite interval mapping(CIM)method,and located on Linkage Group(LG)D1b(chromosome two),LG C2(chromosome six)and LG H(chromosome 12),respectively.LOD scores ranged from 2.68 to 4.95 and the phenotypic variation percentage was from 6%to 11%.Six candidate genes were detected,according to the result of gene annotation information.Four of them had relationship with protein kinase activity,protein phosphorylation and leucine rich repeat(LRR)transmembrane protein,which had high expression after inoculated with P.sg by qRT-PCR.展开更多
Objectives: Auditory neuropathy (AN) is a sensorineural hearing disorder characterized by absent or abnormal auditory brainstem responses (ABRs) and normal cochlear outer hair cell function as measured by otoacoustic ...Objectives: Auditory neuropathy (AN) is a sensorineural hearing disorder characterized by absent or abnormal auditory brainstem responses (ABRs) and normal cochlear outer hair cell function as measured by otoacoustic emissions (OAEs). Many risk factors are thought to be involved in its etiology and pathophysiology. Three Chinese pedigrees with familial AN are presented herein to demonstrate involvement of genetic factors in AN etiology. Methods: Probands of the above - mentioned pedigrees, who had been diagnosed with AN, were evaluated and followed up in the Department of Otolaryngology Head and Neck Surgery, China PLA General Hospital. Their family members were studied and the pedigree diagrams were established. History of illness, physical examination,pure tone audiometry, acoustic reflex, ABRs and transient evoked and distortion- product otoacoustic emissions (TEOAEs and DPOAEs) were obtained from members of these families. DPOAE changes under the influence of contralateral sound stimuli were observed by presenting a set of continuous white noise to the non - recording ear to exam the function of auditory efferent system. Some subjects received vestibular caloric test, computed tomography (CT)scan of the temporal bone and electrocardiography (ECG) to exclude other possible neuropathy disorders. Results: In most affected subjects, hearing loss of various degrees and speech discrimination difficulties started at 10 to16 years of age. Their audiological evaluation showed absence of acoustic reflex and ABRs. As expected in AN, these subjects exhibited near normal cochlear outer hair cell function as shown in TEOAE & DPOAE recordings. Pure- tone audiometry revealed hearing loss ranging from mild to severe in these patients. Autosomal recessive inheritance patterns were observed in the three families. In Pedigree Ⅰ and Ⅱ, two affected brothers were found respectively, while in pedigree Ⅲ, 2 sisters were affected. All the patients were otherwise normal without evidence of peripheral neuropathy at the time of this writing. Conclusions: In this study, patients with feature of non- syndromic hereditary auditory neuropathy were identified in three Chinese families.Pedigree analysis indicates autosomal recessive inheritances in the pedigrees. The observed inheritance and clinical audiologic findings are different from those previously described for non-syndromic low-frequency sensorineural hearing loss. This information should facilitate future molecular candidate genes screening for understanding the mechanism of AN.展开更多
Background:The lateral root is one of the most important organs that constitute the root architecture system in plants.It can directly affect the contact area between plants and soil and plays an important role in pla...Background:The lateral root is one of the most important organs that constitute the root architecture system in plants.It can directly affect the contact area between plants and soil and plays an important role in plant structural support and nutrient absorption.Optimizing root architecture systems can greatly increase crop yields.This study was designed to identify the molecular markers and candidate genes associated with lateral root development in cotton and to evaluate correlations with yield and disease traits.Result:The number of lateral roots for 14-day old seedlings was recorded for 215 Gossypium arboreum accessions.A correlation analysis showed that the number of lateral roots positively correlates with the sympodial branch node and seed index traits,but negatively correlates with lint percentage.A Genome-wide association study(GWAS)identified 18 significant SNPs with 19 candidate genes associated with the lateral root number.Expression analysis identified three genes(FLA 12,WRKY29,and RBOHA)associated with lateral root development.Conclusion:GWAS an alysis identified key SNPs and candidate gen esfor lateral root number,a nd gen es of FLA 12,WRKY29,and RBOHA may play a pivotal role in lateral root development in Asian cotton.展开更多
Background: Micronaire is a comprehensive index reflecting the fineness and maturity of cotton fiber.Micronaire is one of the important internal quality indicators of the cotton fiber and is closely related to the val...Background: Micronaire is a comprehensive index reflecting the fineness and maturity of cotton fiber.Micronaire is one of the important internal quality indicators of the cotton fiber and is closely related to the value of the cotton fiber.Understanding the genetic basis of micronaire is required for the genetic improvement of the trait.However,the genetic architecture of micronaire at the genomic level is unclear.The present genome-wide association study(GWAS)aimed to identify the genetic mechanism of the micronaire trait in 83 representa:tive upland cotton lines grown in multiple environments.Results GWAS of micronaire used 83 upland cotton accessions assayed by a Cotton 63 K Illumina Infinium single nucleotide polymorphism(SNP)array.A total of 11 quantitative trait loci(QTLs)for micronaire were detected on 10 chromosomes.These 11 QTLs included 27 identified genes with specific expression patterns.A novel QTL,qFM-A12–1,included 12 significant SNPs,and GhFLA9 was identified as a candidate gene based on haplotype block analysis and on strong and direct linkage disequilibrium between the significantly related SNPs and gene.GhFLA9 was expressed at a high level during secondary wall thickening at 20∼25 days post-anthesis.The expression level of GhFLA9 was significantly higher in the low micronaire line(Msco-12)than that in the high micronaire line(Chuangyou-9).Conclusions: This study provides a genetic reference for genetic improvement of cotton fiber micronaire and a foundation for verification of the functions of GhFLA9.展开更多
文摘Previous study indicated that the thermo-sensitive genic malesterile(TGMS) gene in rice was regulated by temperature.TGMS rice plays an important role in hybrid rice production,because the application of the TGMS system in two-line breeding is laborsaving,timesaving,simple,inexpensive,efficient,and eliminating the limitations of the cytoplasmic male sterility(CMS) system.'AnnongS' is the first discovered and deeply studied TGMS rice lines in China.'AnnongS-1' and 'Y58S',two derivatives of TGMS line AnnongS,were both controlled by a single recessive gene named tms5,which was genetically mapped on chromosome 2.In this study,three populations('AnnongS-1' × 'Nanjing11','Y58S' × 'Q611',and 'Y58S' × 'Guanghui122') were developed and used for the molecular fine mapping of the tms5 gene.By analyzing recombination events in the sterile individuals using a total of 125 probes covering the tms5 region,the tms5 gene was physically mapped to a 19-kb DNA fragment between two markers 4039-1 and 4039-2,which were located on the BAC clone AP004039.After the construction of the physical map between two markers 4039-1 and 4039-2,a member(ONAC023) of the NAC(NAM-ATAF-CUC-related) gene family was identified as the candidate gene of the tms5 gene.
文摘Gene expression profiling at early stages(0～2 DPA) of fiber development in Gossypium hirsutum identified a number of transcription factors which were down regulated in fiberless mutants relative to wild type controls and which could play a role in controlling early fiber development.Chief among these was GhMYB25,a Mixta-like MYB gene.Transgenic GhMYB25-silenced cotton
基金This work was supported by the National Natural Science Foundation of China(31760402)Public Welfare Research Projects in the Autonomous Region(KY2019002)Special Programs for New Varieties Cultivation of Shihezi University(YZZX201701).
文摘Background:Meta-analysis of quantitative trait locus(QTL)is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies.The combination of meta-QTL intervals,significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants.Results:In our study,884 QTLs associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1,as a result,74 meta-QTLs were identified,including 19 meta-QTLs for fiber length;18 meta-QTLs for fiber strength;11 meta-QTLs for fiber uniformity;11 meta-QTLs for fiber elongation;and 15 meta-QTLs for micronaire.Combined with 8589 significant single nucleotide polymorphisms associated with fiber quality traits collected from 15 studies,297 candidate genes were identified in the meta-QTL intervals,20 of which showed high expression levels specifically in the developing fibers.According to the function annotations,some of the 20 key candidate genes are associated with the fiber development.Conclusions:This study provides not only stable QTLs used for marker-assisted selection,but also candidate genes to uncover the molecular mechanisms for cotton fiber development.
基金Supported by the National Key R&D Program of China(2016YFD0100201)Science Foundation for Distinguished Young Scholars of Heilongjiang Province(JC2016004)Harbin Science Technology Project(2015RQXXJ018)。
文摘Soybean bacterial spot disease caused by Pseudomonas syringae pv.Glycinea which is a bacterial disease seriously affects soybean yield.Ten soybean germplasms and recombinant inbred lines(RILs)population were used to identify the resistant trait after inoculated with P.sg(P.sgneau001)in this study.High-density genetic mapping was obtained by specific length amplified fragment sequencing(SLAF-seq)of 149 RILs population which was derived from the crossing between Charleston and Dongnong594.The results indicated that 10 germplasm resources had four resistant germplasms included highly resistant cultivar Charleston,four susceptible varieties included Dongnong594 and two moderately resistant cultivars.Five quantitative trait locus(QTLs)were detected in RILs population by the composite interval mapping(CIM)method,and located on Linkage Group(LG)D1b(chromosome two),LG C2(chromosome six)and LG H(chromosome 12),respectively.LOD scores ranged from 2.68 to 4.95 and the phenotypic variation percentage was from 6%to 11%.Six candidate genes were detected,according to the result of gene annotation information.Four of them had relationship with protein kinase activity,protein phosphorylation and leucine rich repeat(LRR)transmembrane protein,which had high expression after inoculated with P.sg by qRT-PCR.
基金a grant from the National High Tech Development Project(2001AA221092)and by Beijing Natural Science Foundation(No.7011004)and Beijing Science and Technology Innovation Project(No.H010210160119)grants
文摘Objectives: Auditory neuropathy (AN) is a sensorineural hearing disorder characterized by absent or abnormal auditory brainstem responses (ABRs) and normal cochlear outer hair cell function as measured by otoacoustic emissions (OAEs). Many risk factors are thought to be involved in its etiology and pathophysiology. Three Chinese pedigrees with familial AN are presented herein to demonstrate involvement of genetic factors in AN etiology. Methods: Probands of the above - mentioned pedigrees, who had been diagnosed with AN, were evaluated and followed up in the Department of Otolaryngology Head and Neck Surgery, China PLA General Hospital. Their family members were studied and the pedigree diagrams were established. History of illness, physical examination,pure tone audiometry, acoustic reflex, ABRs and transient evoked and distortion- product otoacoustic emissions (TEOAEs and DPOAEs) were obtained from members of these families. DPOAE changes under the influence of contralateral sound stimuli were observed by presenting a set of continuous white noise to the non - recording ear to exam the function of auditory efferent system. Some subjects received vestibular caloric test, computed tomography (CT)scan of the temporal bone and electrocardiography (ECG) to exclude other possible neuropathy disorders. Results: In most affected subjects, hearing loss of various degrees and speech discrimination difficulties started at 10 to16 years of age. Their audiological evaluation showed absence of acoustic reflex and ABRs. As expected in AN, these subjects exhibited near normal cochlear outer hair cell function as shown in TEOAE & DPOAE recordings. Pure- tone audiometry revealed hearing loss ranging from mild to severe in these patients. Autosomal recessive inheritance patterns were observed in the three families. In Pedigree Ⅰ and Ⅱ, two affected brothers were found respectively, while in pedigree Ⅲ, 2 sisters were affected. All the patients were otherwise normal without evidence of peripheral neuropathy at the time of this writing. Conclusions: In this study, patients with feature of non- syndromic hereditary auditory neuropathy were identified in three Chinese families.Pedigree analysis indicates autosomal recessive inheritances in the pedigrees. The observed inheritance and clinical audiologic findings are different from those previously described for non-syndromic low-frequency sensorineural hearing loss. This information should facilitate future molecular candidate genes screening for understanding the mechanism of AN.
基金supported by Central Public-interest Scientific Institution Basal Research Fund,Chinese Academy of Agricultural Science(No.1610162021012)funded by DU Xiongming.
文摘Background:The lateral root is one of the most important organs that constitute the root architecture system in plants.It can directly affect the contact area between plants and soil and plays an important role in plant structural support and nutrient absorption.Optimizing root architecture systems can greatly increase crop yields.This study was designed to identify the molecular markers and candidate genes associated with lateral root development in cotton and to evaluate correlations with yield and disease traits.Result:The number of lateral roots for 14-day old seedlings was recorded for 215 Gossypium arboreum accessions.A correlation analysis showed that the number of lateral roots positively correlates with the sympodial branch node and seed index traits,but negatively correlates with lint percentage.A Genome-wide association study(GWAS)identified 18 significant SNPs with 19 candidate genes associated with the lateral root number.Expression analysis identified three genes(FLA 12,WRKY29,and RBOHA)associated with lateral root development.Conclusion:GWAS an alysis identified key SNPs and candidate gen esfor lateral root number,a nd gen es of FLA 12,WRKY29,and RBOHA may play a pivotal role in lateral root development in Asian cotton.
基金The present study was funded by National Key Research and Development Program of China(grants nos.2018YFD0101402,2018YFD0100300 and 2016YFD0101400)the Natural Science Foundation of Xinjiang Uygur Autonomous Region of China(grant no.2020D01A135)Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences.
文摘Background: Micronaire is a comprehensive index reflecting the fineness and maturity of cotton fiber.Micronaire is one of the important internal quality indicators of the cotton fiber and is closely related to the value of the cotton fiber.Understanding the genetic basis of micronaire is required for the genetic improvement of the trait.However,the genetic architecture of micronaire at the genomic level is unclear.The present genome-wide association study(GWAS)aimed to identify the genetic mechanism of the micronaire trait in 83 representa:tive upland cotton lines grown in multiple environments.Results GWAS of micronaire used 83 upland cotton accessions assayed by a Cotton 63 K Illumina Infinium single nucleotide polymorphism(SNP)array.A total of 11 quantitative trait loci(QTLs)for micronaire were detected on 10 chromosomes.These 11 QTLs included 27 identified genes with specific expression patterns.A novel QTL,qFM-A12–1,included 12 significant SNPs,and GhFLA9 was identified as a candidate gene based on haplotype block analysis and on strong and direct linkage disequilibrium between the significantly related SNPs and gene.GhFLA9 was expressed at a high level during secondary wall thickening at 20∼25 days post-anthesis.The expression level of GhFLA9 was significantly higher in the low micronaire line(Msco-12)than that in the high micronaire line(Chuangyou-9).Conclusions: This study provides a genetic reference for genetic improvement of cotton fiber micronaire and a foundation for verification of the functions of GhFLA9.
