Selection and use of molecular markers for evaluation of DNA polymorphism in plants are couple of the most important approaches in the field of molecular genetics.The assessment of genetic diversity using morphologica...Selection and use of molecular markers for evaluation of DNA polymorphism in plants are couple of the most important approaches in the field of molecular genetics.The assessment of genetic diversity using morphological markers is not sufficient due to little differentiating traits among the species,genera or their individuals.Morphological markers are not only highly influenced by environmental factors but skilled assessment is also prerequisite to find the variations in plant genetic resources.Therefore,molecular markers are considered as efficient tools for detailed DNA based characterization of fruit crops.Molecular markers provide new directions to the efforts of plant breeders particularly in genetic variability,gene tags,gene localization,taxonomy,genetic diversity,phylogenetic analysis and also play an important role to decrease the time required for development of new and excellent cultivars.The success of molecular markers technology in genetic improvement programs depends on the close relationship among the plant breeders,biotechnologists,skilled manpower and good financial support.The present review describes application and success of molecular markers technology used for genetic improvement in different fruit crops.展开更多
Background:This study aimed to develop a set of perfect simple sequence repeat(SSR)markers with a single copy in the cotton genome,to construct a DNA fingerprint database suitable for authentication of cotton cultivar...Background:This study aimed to develop a set of perfect simple sequence repeat(SSR)markers with a single copy in the cotton genome,to construct a DNA fingerprint database suitable for authentication of cotton cultivars.We optimized the polymerase chain reaction(PCR)system for multi-platform compatibility and improving detection efficiency.Based on the reference genome of upland cotton and 10×resequencing data of 48 basic cotton germplasm lines,single-copy polymorphic SSR sites were identified and developed as diploidization SSR markers.The SSR markers were detected by denaturing polyacrylamide gel electrophoresis(PAGE)for initial screening,then fluorescence capillary electrophoresis for secondary screening.The final perfect SSR markers were evaluated and verified using 210 lines from different sources among Chinese cotton regional trials.Results:Using bioinformatics techniques,1246 SSR markers were designed from 26626 single-copy SSR loci.Adopting a stepwise(primary and secondary)screening strategy,a set of 60 perfect SSR markers was selected with high amplification efficiency and stability,easy interpretation of peak type,multiple allelic variations,high polymorphism information content(PIC)value,uniform chromosome distribution,and single-copy characteristics.A multiplex PCR system was established with ten SSR markers using capillary electrophoresis detection.Conclusions:A set of perfect SSR markers of cotton was developed and a high-throughput SSR marker detection system was established.This study lays a foundation for large-scale and standardized construction of a cotton DNA fingerprint database for authentication of cotton varieties.展开更多
Nematode identification serves as an important param-eter to study their behaviour,importance and pathogenic-ity.Application of classical morphometric based identifica-tion methods prove to be lacking due to insuffici...Nematode identification serves as an important param-eter to study their behaviour,importance and pathogenic-ity.Application of classical morphometric based identifica-tion methods prove to be lacking due to insufficient knowledge on morphological variations among closely related taxa.Molecular approaches such as DNA and protein-based information,microarray,probing,sequence-based methods and others have been used to supplement morphology-based methods for nematode identification.Ascarosides and certain protein-based nematode-associated molecular patterns(NAMPs),can be perceived by the host plants,and can initiate a signalling cascade.This review primarily emphasizes on an updated account of different classical and modern tools used for the identification of nematodes.Besides we also summa-rize the mechanism of some important signalling pathways which are involved in the different plant nematode interactions.Nematodes constitute most diverse and least studied group of soil inhabiting invertebrates.They are ecologically and physiologically important,however,wide range of nematodes show harmful impact on the individuals that live within their vicinity.Plant parasitic nematodes(PPNs)are transparent,pseudocoelomate,free living or parasitic microorganisms.PPNs lack morphometric identification methods due to insufficient knowl-edge on morphological variations among closely related taxa.As such,molecular approaches such as DNA and protein-based information,microarray,probing,sequence-based methods and others have been used to supplement morphology-based methods for their identification.To invade the defense response of different plant species,parasitic nematodes have evolved different molecular strategies.Ascarosides and certain protein-based nematode-associated molecular patterns(NAMPs),can be perceived by the host plants,and can initiate a signaling cascade.To overcome the host confrontation and develop certain nematode feeding sites,some members can inject effectors into the cells of susceptible hosts to reprogram the basal resistance signaling.This review primarily emphasizes on an updated account of different classical and modem tools used for the identification of PPNs.Besides we also summarize the mechanism of some important signaling pathways which are involved in the different plant nematode interactions.展开更多
Bottle gourd is an important cucurbit crop worldwide. To provide more available molecular markers for this crop, a bioinformatic approach was employed to develop insertion–deletions(In Dels) markers in bottle gourd b...Bottle gourd is an important cucurbit crop worldwide. To provide more available molecular markers for this crop, a bioinformatic approach was employed to develop insertion–deletions(In Dels) markers in bottle gourd based on restriction site-associated DNA sequencing(RAD-Seq)data. A total of 892 Indels were predicted, with the length varying from 1 bp to 167 bp. Single-nucleotide In Dels were the predominant types of In Dels. To validate these In Dels, PCR primers were designed from 162 loci where In Dels longer than 2 bp were predicated. A total of 112 In Dels were found to be polymorphic among 9 bottle gourd accessions under investigation. The rate of prediction accuracy was thus at a high level of72.7%. DNA fingerprinting for 4 cultivars were performed using 8 selected Indels markers, demonstrating the usefulness of these markers.展开更多
For the protection of consumers and developments of relevant industry, authentication of medicinal plants is a critical issue. This review covers various aspects of authentication methods and techniques based on molec...For the protection of consumers and developments of relevant industry, authentication of medicinal plants is a critical issue. This review covers various aspects of authentication methods and techniques based on molecular biology and genomics with special emphasis on molecular biology techniques including genome-based authentication, microchip-based authentication, DNA barcoding, and their applications.展开更多
In potato breeding,it is difficult to improve the traits of interest at the tetraploid level due to the tetrasomic inheritance.A promising alternative is diploid breeding.Thus it is necessary to assess the genetic div...In potato breeding,it is difficult to improve the traits of interest at the tetraploid level due to the tetrasomic inheritance.A promising alternative is diploid breeding.Thus it is necessary to assess the genetic diversity of diploid potato germplasm for efficient exploration and deployment of desirable traits.In this study,we used SSR markers to evaluate the genetic diversity of diploid potato cultivars.To screen polymorphic SSR markers,55 pairs of SSR primers were employed to amplify 39 cultivars with relatively distant genetic relationships.Among them,12 SSR markers with high polymorphism located at 12 chromosomes were chosen to evaluate the genetic diversity of 192 diploid potato cultivars.The primers produced 6 to 18 bands with an average of 8.2 bands per primer.In total,98 bands were amplified from 192 cultivars,and 97 of them were polymorphic.Cluster analysis using UPGMA showed the genetic relationships of all accessions tested:186 of the 192 accessions could be distinguished by only 12 pairs of SSR primers,and the 192 diploid cultivars were divided into 11 groups,and 83.3% constituted the first group.Clustering results showed relatively low genetic diversity among 192 diploid cultivars,with closer relationship at the molecular level.The results can provide molecular basis for diploid potato breeding.展开更多
A total of 10 non-repetitive multi-drug-resistant Acinetobacter strains were collected.With reference to A.calcoaceticus(ATCC23055),A.baumannii(ATCC19606),A.lwoffii(ATCC17986),and A.junii(NCTC5866),DNA fingerprint tec...A total of 10 non-repetitive multi-drug-resistant Acinetobacter strains were collected.With reference to A.calcoaceticus(ATCC23055),A.baumannii(ATCC19606),A.lwoffii(ATCC17986),and A.junii(NCTC5866),DNA fingerprint technique,amplified ribosomal DNA restriction analysis(ARDRA),and random amplified polymorphism DNA(RAPD)were carried out to identify the genomic species of Acinetobacter spp.The distances between them were calculated by the unweighted pair group method with arithmetic(UPGMA).Genotypes of Acinetobacter spp.were effectively classified and an A.junii together with nine A.baumannii isolates was genomically identified.The combination of ARDRA and RAPD DNA-fingerprint technique shows high complementarity,and could be a useful tool in Acinetobacter genomic species identification.展开更多
文摘Selection and use of molecular markers for evaluation of DNA polymorphism in plants are couple of the most important approaches in the field of molecular genetics.The assessment of genetic diversity using morphological markers is not sufficient due to little differentiating traits among the species,genera or their individuals.Morphological markers are not only highly influenced by environmental factors but skilled assessment is also prerequisite to find the variations in plant genetic resources.Therefore,molecular markers are considered as efficient tools for detailed DNA based characterization of fruit crops.Molecular markers provide new directions to the efforts of plant breeders particularly in genetic variability,gene tags,gene localization,taxonomy,genetic diversity,phylogenetic analysis and also play an important role to decrease the time required for development of new and excellent cultivars.The success of molecular markers technology in genetic improvement programs depends on the close relationship among the plant breeders,biotechnologists,skilled manpower and good financial support.The present review describes application and success of molecular markers technology used for genetic improvement in different fruit crops.
基金grants from the Thirteenth Five-Year Plan,National Key R&D Plan(2017YFD0102003–5)National Cotton Industry Technology System(CARS-15-25).
文摘Background:This study aimed to develop a set of perfect simple sequence repeat(SSR)markers with a single copy in the cotton genome,to construct a DNA fingerprint database suitable for authentication of cotton cultivars.We optimized the polymerase chain reaction(PCR)system for multi-platform compatibility and improving detection efficiency.Based on the reference genome of upland cotton and 10×resequencing data of 48 basic cotton germplasm lines,single-copy polymorphic SSR sites were identified and developed as diploidization SSR markers.The SSR markers were detected by denaturing polyacrylamide gel electrophoresis(PAGE)for initial screening,then fluorescence capillary electrophoresis for secondary screening.The final perfect SSR markers were evaluated and verified using 210 lines from different sources among Chinese cotton regional trials.Results:Using bioinformatics techniques,1246 SSR markers were designed from 26626 single-copy SSR loci.Adopting a stepwise(primary and secondary)screening strategy,a set of 60 perfect SSR markers was selected with high amplification efficiency and stability,easy interpretation of peak type,multiple allelic variations,high polymorphism information content(PIC)value,uniform chromosome distribution,and single-copy characteristics.A multiplex PCR system was established with ten SSR markers using capillary electrophoresis detection.Conclusions:A set of perfect SSR markers of cotton was developed and a high-throughput SSR marker detection system was established.This study lays a foundation for large-scale and standardized construction of a cotton DNA fingerprint database for authentication of cotton varieties.
文摘Nematode identification serves as an important param-eter to study their behaviour,importance and pathogenic-ity.Application of classical morphometric based identifica-tion methods prove to be lacking due to insufficient knowledge on morphological variations among closely related taxa.Molecular approaches such as DNA and protein-based information,microarray,probing,sequence-based methods and others have been used to supplement morphology-based methods for nematode identification.Ascarosides and certain protein-based nematode-associated molecular patterns(NAMPs),can be perceived by the host plants,and can initiate a signalling cascade.This review primarily emphasizes on an updated account of different classical and modern tools used for the identification of nematodes.Besides we also summa-rize the mechanism of some important signalling pathways which are involved in the different plant nematode interactions.Nematodes constitute most diverse and least studied group of soil inhabiting invertebrates.They are ecologically and physiologically important,however,wide range of nematodes show harmful impact on the individuals that live within their vicinity.Plant parasitic nematodes(PPNs)are transparent,pseudocoelomate,free living or parasitic microorganisms.PPNs lack morphometric identification methods due to insufficient knowl-edge on morphological variations among closely related taxa.As such,molecular approaches such as DNA and protein-based information,microarray,probing,sequence-based methods and others have been used to supplement morphology-based methods for their identification.To invade the defense response of different plant species,parasitic nematodes have evolved different molecular strategies.Ascarosides and certain protein-based nematode-associated molecular patterns(NAMPs),can be perceived by the host plants,and can initiate a signaling cascade.To overcome the host confrontation and develop certain nematode feeding sites,some members can inject effectors into the cells of susceptible hosts to reprogram the basal resistance signaling.This review primarily emphasizes on an updated account of different classical and modem tools used for the identification of PPNs.Besides we also summarize the mechanism of some important signaling pathways which are involved in the different plant nematode interactions.
基金supported by the National Natural Science Foundation of China (31401880)China Postdoctoral Science Foundation Funded Project (2015M571900)+2 种基金the Natural Science Foundation of Zhejiang Province (LY14C150004)Public Project of Zhejiang Province (2015C32042)grants from Zhejiang Academy of Agricultural Sciences (2016R23R08E04)
文摘Bottle gourd is an important cucurbit crop worldwide. To provide more available molecular markers for this crop, a bioinformatic approach was employed to develop insertion–deletions(In Dels) markers in bottle gourd based on restriction site-associated DNA sequencing(RAD-Seq)data. A total of 892 Indels were predicted, with the length varying from 1 bp to 167 bp. Single-nucleotide In Dels were the predominant types of In Dels. To validate these In Dels, PCR primers were designed from 162 loci where In Dels longer than 2 bp were predicated. A total of 112 In Dels were found to be polymorphic among 9 bottle gourd accessions under investigation. The rate of prediction accuracy was thus at a high level of72.7%. DNA fingerprinting for 4 cultivars were performed using 8 selected Indels markers, demonstrating the usefulness of these markers.
基金National Science and Technology Major Program (2008ZX 10005-004)Liaoning Education Department (2009A120)China Postdoctoral Science Foundation (20080440019 and 200902069)
文摘For the protection of consumers and developments of relevant industry, authentication of medicinal plants is a critical issue. This review covers various aspects of authentication methods and techniques based on molecular biology and genomics with special emphasis on molecular biology techniques including genome-based authentication, microchip-based authentication, DNA barcoding, and their applications.
基金funded by the National Natural Science Foundation of China(NSFC:31201257)the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(CAAS-ASTIP-AGISCAAS)
文摘In potato breeding,it is difficult to improve the traits of interest at the tetraploid level due to the tetrasomic inheritance.A promising alternative is diploid breeding.Thus it is necessary to assess the genetic diversity of diploid potato germplasm for efficient exploration and deployment of desirable traits.In this study,we used SSR markers to evaluate the genetic diversity of diploid potato cultivars.To screen polymorphic SSR markers,55 pairs of SSR primers were employed to amplify 39 cultivars with relatively distant genetic relationships.Among them,12 SSR markers with high polymorphism located at 12 chromosomes were chosen to evaluate the genetic diversity of 192 diploid potato cultivars.The primers produced 6 to 18 bands with an average of 8.2 bands per primer.In total,98 bands were amplified from 192 cultivars,and 97 of them were polymorphic.Cluster analysis using UPGMA showed the genetic relationships of all accessions tested:186 of the 192 accessions could be distinguished by only 12 pairs of SSR primers,and the 192 diploid cultivars were divided into 11 groups,and 83.3% constituted the first group.Clustering results showed relatively low genetic diversity among 192 diploid cultivars,with closer relationship at the molecular level.The results can provide molecular basis for diploid potato breeding.
基金This study was supported by the Natural Science Research Program of Universities and Colleges of Anhui Province,China(No.2006kj349B).
文摘A total of 10 non-repetitive multi-drug-resistant Acinetobacter strains were collected.With reference to A.calcoaceticus(ATCC23055),A.baumannii(ATCC19606),A.lwoffii(ATCC17986),and A.junii(NCTC5866),DNA fingerprint technique,amplified ribosomal DNA restriction analysis(ARDRA),and random amplified polymorphism DNA(RAPD)were carried out to identify the genomic species of Acinetobacter spp.The distances between them were calculated by the unweighted pair group method with arithmetic(UPGMA).Genotypes of Acinetobacter spp.were effectively classified and an A.junii together with nine A.baumannii isolates was genomically identified.The combination of ARDRA and RAPD DNA-fingerprint technique shows high complementarity,and could be a useful tool in Acinetobacter genomic species identification.
