In our recent investigations of diatom diversity,we studied three species,namely,Skeletonema costatum,Skeletonema subsalsum,and Skeletonema potamos.Although they have been found frequently in Changjiang(Yangtze)River ...In our recent investigations of diatom diversity,we studied three species,namely,Skeletonema costatum,Skeletonema subsalsum,and Skeletonema potamos.Although they have been found frequently in Changjiang(Yangtze)River Basin,their morphological and molecular identification is difficult in taxonomy.Therefore,to integrate morphological and molecular biological approaches,we compared systematically their morphological characters and performed phylogenetic analysis.Twelve strains of Skeletonema were collected and isolated from Shanghai and Jiangsu,China,and their morphological characteristics were examined by light microscopy(LM)and the scanning electron microscopy(SEM).Based on morphological comparison,we determined that S.potamos is easy to distinguish from the other two species.The heavily silicified areolae,undulated or cleft distal ends of terminal fultoportula processes(TFPPs),absence of basal pores of fultoportula processes(FPPs),the rootlike protrusions of FPPs,and no interlocking connection are the stable characteristics that can be used to identify S.potamos.However,there are only two features that can distinguish S.costatum from S.subsalsum,namely the location of terminal rimoportulae(TRPs)and the distal shape of TFPPs.In addition,we amplified and sequenced nine common genetic markers from the strains,from which 101 sequences were obtained,constructed phylogenetic trees based on the nine genes and evaluated that seven genes can be used to identify S.potamos,and revealed that S.subsalsum is the closest known relative of S.costatum,and only ATP synthetase beta-subunit gene(atp B)is able to distinguish them from each other,which strongly support that it is an effective molecular marker for Skeletonema.This work provided a theoretical basis for the taxonomic study of Skeletonema.展开更多
This review updates the present status of the field of molecular markers and marker-assisted selection(MAS),using the example of drought tolerance in barley.The accuracy of selected quantitative trait loci(QTLs),candi...This review updates the present status of the field of molecular markers and marker-assisted selection(MAS),using the example of drought tolerance in barley.The accuracy of selected quantitative trait loci(QTLs),candidate genes and suggested markers was assessed in the barley genome cv.Morex.Six common strategies are described for molecular marker development,candidate gene identification and verification,and their possible applications in MAS to improve the grain yield and yield components in barley under drought stress.These strategies are based on the following five principles:(1)Molecular markers are designated as genomic‘tags’,and their‘prediction’is strongly dependent on their distance from a candidate gene on genetic or physical maps;(2)plants react differently under favourable and stressful conditions or depending on their stage of development;(3)each candidate gene must be verified by confirming its expression in the relevant conditions,e.g.,drought;(4)the molecular marker identified must be validated for MAS for tolerance to drought stress and improved grain yield;and(5)the small number of molecular markers realized for MAS in breeding,from among the many studies targeting candidate genes,can be explained by the complex nature of drought stress,and multiple stress-responsive genes in each barley genotype that are expressed differentially depending on many other factors.展开更多
Flowering time is an important agronomic trait of Chinese cabbage with late flowering being a primary breeding objective.In our previous work,we obtained Chinese cabbage-cabbage translocation lines that contained seve...Flowering time is an important agronomic trait of Chinese cabbage with late flowering being a primary breeding objective.In our previous work,we obtained Chinese cabbage-cabbage translocation lines that contained several beneficial cabbage genes.Cabbage-specific molecular markers show that these genes were coming from chromosome C01 of cabbage.In this study,we investigated the inheritance of flowering time in a couple of translocation lines and analyzed the transmission rate of molecular markers in the offspring.Consequently,we obtained the late flowering Chinese cabbage-cabbage translocation line‘AT7–4’in which the flowering time was later than that of‘85–1’by about 7 days under 4-week vernalization.Based on previous studies of the genomes of Chinese cabbage and cabbage,we located the cabbage-specific molecular markers that were closely linked at the top of the chromosome A01 in the F2mapping population generated by self-crossing F1s derived from a cross between the translocation line‘AT7–4’and Chinese cabbage‘14–36’.Five flowering-related genes in the alien fragment were found by functional annotation and their molecular markers were developed.This study lays the foundation for the future improvement of Chinese cabbage varieties using A-C translocation lines.展开更多
We developed a molecular marker for MAS of mungbean resistant varieties against CLS from the consensus sequence(MB-CLsRG)of identified RGAs(MB-ClsRCaG1 and MB-ClsRCaG2).The MB-CLsRG sequence-specific primer pair was u...We developed a molecular marker for MAS of mungbean resistant varieties against CLS from the consensus sequence(MB-CLsRG)of identified RGAs(MB-ClsRCaG1 and MB-ClsRCaG2).The MB-CLsRG sequence-specific primer pair was used to screen Cercospora leaf spot(CLS)resistant varieties of mungbean in genomic analysis that showed congruency with phenotypic screening.Validation of molecular marker linkage with CLS resistance was performed using rtPCR in transcriptomic analysis.The sequenced PCR products showed 100%homology with MB-CLsRG sequence and putative disease resistance proteins that confirmed the linkage of molecular marker with CLS resistance in mungbean.The antifungal potential of MB-CLsRG gene encoding protein was assessed.The MB-CLsRG gene sequence was cloned in the E.coli expression vector for recombinant protein production.The recombinant protein was then investigated for its in vitro antifungal potential against Cercospora canescens.The in vitro investigation showed strong antifungal activity of recombinant protein as it restricted the growth of fungal mycelial mass.The results validated the linkage of developed marker with CLS-resistant mungbean varieties;therefore,it can be used to screen resistant varieties from a large population in MAS.Moreover,the recombinant protein of the MB-CLsRG gene sequence revealed antifungal potential,which proved the gene sequence could be suitable to use in transgenic plants technology to develop fungal-resistant transgenic crops.展开更多
Sesame(Sesamum indicum L.) plays a crucial role in Ethiopian agriculture,serving both subsistence and commercial purposes.However,our understanding of the extensive genetic diversity and population structure of Ethiop...Sesame(Sesamum indicum L.) plays a crucial role in Ethiopian agriculture,serving both subsistence and commercial purposes.However,our understanding of the extensive genetic diversity and population structure of Ethiopian sesame remains limited.To address this knowledge gap,we genotyped 368 Ethiopian sesame germplasms,categorizing into four distinct breeding groups:Accessions,landraces,improved varieties,and wild types,using a comprehensive set of 28 polymorphic markers,including 23 simple sequence repeat(SSR) and five Insertion-Deletion(InDel) markers.These markers ensured robust genomic representation,with at least two markers per linkage group.Our results unveiled substantial genetic diversity,identifying a total of 535 alleles across all accessions.On average,each locus displayed 8.83 alleles,with observed and expected heterozygosity values of 0.30 and 0.36,respectively.Gene Diversity and Polymorphic Information Content(PIC) were recorded at 0.37 and 0.35.The percentage of polymorphic loci varied significantly among breeding groups,ranging from8.00% to 82.40%,indicating high diversity in accessions(82.4%),moderate diversity in improved varieties(31.20%) and landraces(29.60%),and limited diversity in wild types(8.00).Analysis of Molecular Variance(AMOVA) results emphasized significant genetic differentiation among populations,with substantial diversity(P<0.001) within each population.Approximately 8% of the entire genetic diversity could be attributed to distinctions among populations,while the larger proportion of genetic diversity(92%) resided within each individual sesame population,showcasing heightened diversity within each group.Our study’s findings received support from both Bayesian clustering and Neighbor-joining(NJ) analysis,reaffirming the credibility of our genetic structure insights.Notably,Population structure analysis at its highest Δk value(k=2) revealed the existence of two primary genetic clusters,further subdivided into four sub-populations at k=4.Similarly,NJ analysis identified two prominent clusters,each displaying additional sub-clustering.In conclusion,our research provides a comprehensive understanding of genetic groups,subpopulations,and overall diversity within Ethiopian sesame populations.These findings underscore the significant genetic diversity and population structure within Ethiopian sesame germplasm collections.This genetic richness holds promise for breeding and conservation efforts,highlighting the importance of preserving genetic diversity to ensure adaptation to changing environments and meet the needs of farmers and consumers.展开更多
Objective: There is an ongoing debate about whether the management of gastroenteropancreatic(GEP)neuroendocrine carcinoma(NEC) should follow the guidelines of small-cell lung cancer(SCLC). We aim to identify the genet...Objective: There is an ongoing debate about whether the management of gastroenteropancreatic(GEP)neuroendocrine carcinoma(NEC) should follow the guidelines of small-cell lung cancer(SCLC). We aim to identify the genetic differences of GEPNEC and its counterpart.Methods: We recruited GEPNEC patients as the main cohort, with lung NEC and digestive adenocarcinomas as comparative cohorts. All patients undergone next-generation sequencing(NGS). Different gene alterations were compared and analyzed between GEPNEC and lung NEC(LNEC), GEPNEC and adenocarcinoma to yield the remarkable genes.Results: We recruited 257 patients, including 99 GEPNEC, 57 LNEC, and 101 digestive adenocarcinomas.Among the mutations, KRAS, RB1, TERT, IL7R, and CTNNB1 were found to have different gene alterations between GEPNEC and LNEC samples. Specific genes for each site were revealed: gastric NEC(TERT amplification),colorectal NEC(KRAS mutation), and bile tract NEC(ARID1A mutation). The gene disparities between small-cell NEC(SCNEC) and large-cell NEC(LCNEC) were KEAP1 and CDH1. Digestive adenocarcinoma was also compared with GEPNEC and suggested RB1, APC, and KRAS as significant genes. The TP53/RB1 mutation pattern was associated with first-line effectiveness. Putative targetable genes and biomarkers in GEPNEC were identified in22.2% of the patients, and they had longer progression-free survival(PFS) upon targetable treatment [12.5 months vs. 3.0 months, HR=0.40(0.21-0.75), P=0.006].Conclusions: This work demonstrated striking gene distinctions in GEPNEC compared with LNEC and adenocarcinoma and their clinical utility.展开更多
Clubroot caused by Plasmodiophora brassicae is a devastating disease of Cruciferous crops.Developing cultivars with clubroot resistance(CR)is the most effective control measure.For the two major Brassica vegetable spe...Clubroot caused by Plasmodiophora brassicae is a devastating disease of Cruciferous crops.Developing cultivars with clubroot resistance(CR)is the most effective control measure.For the two major Brassica vegetable species B.rapa and B.oleracea,several commercial cultivars with unclear CR pedigrees have been intensively used as CR donors in breeding.However,the continuous occurrence of CR-breaking makes the CR pedigree underlying these cultivars one of the breeders'most urgent concerns.The complex intraspecific diversity of these two major Brassica vegetables has also limited the applicability of CR markers in different breeding programs.Here we first traced the pedigree underlying two kinds of CR that have been widely applied in breeding by linkage and introgression analyses based on public resequencing data.In B.rapa,a major locus CRzi8 underlying the CR of the commercial CR donor‘DegaoCR117’was identified.CRzi8 was further shown to have been introgressed from turnip(B.rapa ssp.rapifera)and that it carried a potential functional allele of Crr1a.The turnip introgression carried CRb^(c),sharing the same coding sequence with the CRb that was also identified from chromosome C07 of B.oleracea CR cultivars with different morphotypes.Within natural populations,variation analysis of linkage intervals of CRzi8,PbBa8.1,CRb,and CRb^(c)yielded easily resolved InDel markers(>20 bp)for these fundamental CR genes.The specificity of these markers was tested in diverse cultivars panels,and each exhibited high reliability in breeding.Our research demonstrates the value of the practice of applying resequencing big data to solve urgent concerns in breeding programs.展开更多
Objective:Rheumatoid arthritis(RA)is a systemic autoimmune disease characterized by chronic erosive arthritis.Due to the lack of effective biomarkers for diagnosis and treatment,RA patients have many complications in ...Objective:Rheumatoid arthritis(RA)is a systemic autoimmune disease characterized by chronic erosive arthritis.Due to the lack of effective biomarkers for diagnosis and treatment,RA patients have many complications in the later stage,seriously affecting their quality of life.Thus,this study was conducted to investigate new therapeutic targets and to discover diagnostic biomarkers in RA.Methods:In this study,the expression profiles of GSE55235 and GSE55457 were downloaded from the Gene Expression Omnibus database to obtain DEGs between RA and healthy samples.Genetic Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed on the common genes existing in the RA-related modules.Additionally,we used the STRING database to construct the protein‒protein interaction network.Furthermore,we established the interaction analysis of Hub Genes and microRNA(miRNA)and verified the 10 Hub genes through the GSE77298 dataset and quantitative real-time polymerase chain reaction Results:276 and 69 DEGs were screened from the GSE55235 dataset and GSE55457 dataset,respectively.Then,we obtained 42 up-regulated genes in two chip datasets intersection.Genetic Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis of the 42 up-regulated genes showed that they were mainly concentrated in immune response-activating cell surface receptor signaling pathway,etc.Furthermore,the protein-protein interaction network indicated that 10 hub genes are closely related to RA,including MS4A1,CD27,LCK,CD79A,SDC1,CXCL9,CXCL10,CXCL13,IGLL5,and IGJ.In addition,we found that miR-4531 is the same target miRNAs between MS4A1 and SDC1 through messenger RNA-miRNA co-expression network.Finally,the GSE77298 gene chip and quantitative real-time polymerase chain reaction verified the expression of 10 Hub genes.The six Hub genes of CD27,SDC1,CXCL9,CXCL10,CXCL13,and IGJ are significantly increased.Conclusions:We found that SDC1 may be a novel molecular marker for the prevention and treatment of RA.The miR-4531/SDC1 regulatory axis may play a key role in this process.In conclusion,our study not only provides potential biomarkers for the diagnosis and treatment of RA,but also provides a basis and new targets for further revealing the potential mechanism of RA occurrence and development and discovering targeted drugs.展开更多
Metabolic reprogramming is a key feature driving oncogenesis in cancers. Recent studies have revealed that protein metabolism is largely altered in gliomas facilitating its malignant growth. Urea is the end product of...Metabolic reprogramming is a key feature driving oncogenesis in cancers. Recent studies have revealed that protein metabolism is largely altered in gliomas facilitating its malignant growth. Urea is the end product of nitrogen metabolism which is mainly produced by arginase. The interdependence of arginase and other biochemical mechanisms triggered scientific research interest. This research aimed to investigate the relationships between the urea as the main parameter of protein metabolism and glioma progression. It was also the most pronounced relationship between urea and the level of the nuclear protein Ki-67 as a marker of proliferative activity and O-6-methylguanine-DNA methyltransferase (MGMT), which performs DNA repair. Postoperative material from 20 patients with gliomas of different grades of anaplasia was analyzed.展开更多
BACKGROUND: The carcinogenesis of hepatocellular carcinoma (HCC) is a multi-factorial, multistep and complex process. Its prognosis is poor, and early diagnosis and monitoring metastasis of HCC is of the utmost import...BACKGROUND: The carcinogenesis of hepatocellular carcinoma (HCC) is a multi-factorial, multistep and complex process. Its prognosis is poor, and early diagnosis and monitoring metastasis of HCC is of the utmost importance. Circulating diagnostic and prognostic biomarkers could be used in proper postoperative treatment of patients at an early stage of HCC development. This review summarizes recent studies of the specific biomarkers in diagnosis and monitoring metastasis or postoperative recurrence of HCC. DATA SOURCES: An English-language literature search was conducted using MEDLINE (June 1998 to Spetember 2006) on researches of some valuable specific biomarkers in diagnosis and monitoring metastasis or postoperative recurrence of HCC. RESULTS: Hepatoma tissues can synthesize various tumor-related proteins, polypeptides, and isoenzymes, such as alpha-fetoprotein (AFP), hepatoma-specific gamma-glutamyl transpeptidase (HS-GGT), etc, and then secrete into blood. The valuable early diagnostic and prognostic biomarkers could predict the development an metastases of HCC. Recent researches have confirmed that circulating hepatoma-specific AFP subfraction, transforming growth factor (TGF)-beta 1, HS-GGT, and free insulin-like growth factor (IGF)-II may be more specific markers than total AFP level for early diagnosis for HCC. The circulating genetic markers such as AFP-mRNA, TGF-beta 1-mRNA, IGF-II-mRNA, etc from peripheral blood mononuclear cells of HCC patients have been most extensively used in monitoring distal metastasis or postoperative recurrence of HCC. CONCLUSIONS: Hepatoma tissues synthesize and secrete valuable molecular markers into blood. The analyses of circulating hepatoma-specific biomarkers are useful to early diagnosis of HCC or monitoring metastasis or postoperative recurrence of HCC.展开更多
Five super hybrid rice combinations, i.e. HYS-1/R105, Pei'ai 64S/E32, Liangyoupeijiu (Pei'ai 64S/9311), 88S/0293, and J23A/Q611, and their parental lines were tested by means of SSR analysis. A total of 144 SS...Five super hybrid rice combinations, i.e. HYS-1/R105, Pei'ai 64S/E32, Liangyoupeijiu (Pei'ai 64S/9311), 88S/0293, and J23A/Q611, and their parental lines were tested by means of SSR analysis. A total of 144 SSR primer pairs distributed on 12 rice chromosomes were used, out of which 47 detected polymorphism among the tested rice lines. Among all these primers, RM337 and RM154 produced polymorphic patterns in four or more of the tested experimental materials respectively, and they could distinguish among most rice genotypes tested. Twenty-four primer pairs, two on each rice chromosome, were selected to make a reference SSR marker-based fingerprinting for the rice lines. For most of the primer pairs, F1 hybrids mainly showed complementary pattern of both parents, which could be very useful to distinguish the F1 from its parental lines. In addition, 5 primer pairs were selected as special primer pairs for five hybrid rice combinations respectively. By combining the rapid, simple method on DNA extraction, it is suggested that SSR technique has wide prospective in variety authentication and purity identification.展开更多
Eleven evaluating parameters for rice core collection were assessed based on genotypic values and molecular marke' information. Monte Carlo simulation combined with mixed linear model was used to eliminate the interf...Eleven evaluating parameters for rice core collection were assessed based on genotypic values and molecular marke' information. Monte Carlo simulation combined with mixed linear model was used to eliminate the interference from environment in order to draw more reliable results. The coincidence rate of range (CR) was the optimal parameter. Mean Simpson index (MD), mean Shannon-Weaver index of genetic diversity (M1) and mean polymorphism information content (MPIC) were important evaluating parameters. The variable rate of coefficient of variation (VR) could act as an important reference parameter for evaluating the variation degree of core collection. Percentage of polymorphic loci (p) could be used as a determination parameter for the size of core collection. Mean difference percentage (MD) was a determination parameter for the reliability judgment of core collection. The effective evaluating parameters for core collection selected in the research could be used as criteria for sampling percentage in different plant germplasm populations.展开更多
This paper reports the development of the first SSR marker-based sugarcane (Saccharum spp.) molecular identity database in the world. Since 2005, 1,025 sugarcane clones were genotyped, including 811 Louisiana, 45 Flor...This paper reports the development of the first SSR marker-based sugarcane (Saccharum spp.) molecular identity database in the world. Since 2005, 1,025 sugarcane clones were genotyped, including 811 Louisiana, 45 Florida, 39 Texas, 130 foreign, and eight consultant/seed company clones. Genotyping was done on a fluorescence-capillary electrophoresis detection platform involving 21 highly polymorphic SSR markers that could potentially amplify 144 distinctive DNA fragments. Genotyping data were processed with the GeneMapper? software to reveal electrophoregrams that were manually checked against the 144 fragments. The presence (A) or absence (C) of these 144 fragments in any sugarcane clone was recorded in an affixed sequence order as a DNAMAN? file to represent its molecular identity being achieved into a local molecular identity database. The molecular identity database has been updated annually by continued genotyping of newly assigned sugarcane clones. The database provides molecular descriptions for new cultivar registration articles, enables sugarcane breeders to identify mis-labeled sugarcane clones in crossing programs and determine the paternity of cross progeny, and ensures the desired cultivars are grown in farmers’ fields.展开更多
In this review we summarized recent historical records and molecular studies on evolutionary history and phylogeography of Scots pine with focus on the European highly fragmented distribution area of the species. Foss...In this review we summarized recent historical records and molecular studies on evolutionary history and phylogeography of Scots pine with focus on the European highly fragmented distribution area of the species. Fossilized pollen, plant micro- and macrofossil records provided evidences on the large-scale species’ range shifts and demographic changes during the Quaternary. Populations of Scots pine were documented both in the glacial (incl. full glaciation) and interglacial periods. Recolonization of Europe after the glaciation originated from the (Sub) Mediterranean areas like the Balkan Peninsula but also from around the Eastern Alps and the surroundings of the Danube plain. Fennoscandia and northern European Baltic regions were most probably colonized from two main directions, from Western Europe and from the Russian Plain. Modern history of Scots pine was hardly affected by anthropogenic activities that started to strengthen in the Bronze and Iron Age. Along with the fossil records, molecular genetic tools were used to infer the origin and putative history including migration, differentiation and demography of the species. In this paper we compiled the major publications (30) of molecular genetic studies of the past 20 years derived from distinctly inherited organelle genomes (mitochondrial, chloroplast, nuclear) revealed by different marker systems (mtDNA-cox1, -nad1, -nad3, -nad7, ISSR, cpSSR, nSSR, B-SAP, SNP). It is important to consider that different phylogeographic patterns can be drawn by the analysis of different DNA marker types. Accordingly the use of more than one marker simultaneously outlines the most sophisticated phylogeographical pattern on the genetic lineages and can reveal high differentiation of the European distribution. Combined marker systems and markers derived from coding sequences have also been used to detect species’ phylogeographic patterns, but these were rarely applied to Scots pine. Although new molecular techniques can provide higher resolution data for populations, the reviewed results can shape the direction of further studies.展开更多
Two yield-enhancing genes (yld1.1 and yld2.1) are located on chromosomes 1 and 2 respectivelyin a weedy relative of cultivated rice, Oryza rufipogon. SSR markers RM9 and RM166 are closelylinked with the two loci respe...Two yield-enhancing genes (yld1.1 and yld2.1) are located on chromosomes 1 and 2 respectivelyin a weedy relative of cultivated rice, Oryza rufipogon. SSR markers RM9 and RM166 are closelylinked with the two loci respectively. Minghui63 (MH63) has been a widely used restorationline in hybrid rice production in China during the past two decades. The F1 of cross 'MH63O.rufipogon' was backcrossed with MH63 generation by generation. RM9 and RM166 were used toselect the plants from the progeny of the backcross populations. The results were as follows:(1) In BC2F1 population, the percentage of the individuals which have RM9 and RM166 amplifiedbands simultaneously was 12.2%, while in the BC3F1 population, that was 16.3%. (2) Among 400individuals of BC3F1, four yield-promising plants were obtained, with yield being 30% more thanthat of MH63. (3) The products amplified by primer RM166 in O. rufipogon and MH63 weresequenced. It was found that the DNA fragment sequence amplified by RM166 from MH63 was 101 bpshorter than that from O. rufipogon. The 101bp sequence is a part of an intron of the PCNA(proliferating cell nuclear antigen) gene.展开更多
In this study, an F2 segregated population obtained by hybridization between the aphid-sensitive sorghum strain Qiansan and aphid-resistant cultivar Henong 16 was used to establish an aphid-resistant pool and an aphid...In this study, an F2 segregated population obtained by hybridization between the aphid-sensitive sorghum strain Qiansan and aphid-resistant cultivar Henong 16 was used to establish an aphid-resistant pool and an aphid-sensitive pool. 192 pairs of AFLP (amplified fragment length polymorphism) marker primers were screened in these pools using BSA (bulked segregant analysis). Three pairs of EcoR I-CTG/Mse I-CCT, EcoR I-CTG/Mse I-CAT, and EcoR I-AGT/Mse I-CCC showed linkage with aphis resistance. EcoR I-CTG/Mse I-CCT-475, EcoR I-CTG/Mse I-CAT-390, and EcoR I-AGT/Mse I-CCC- 350 (E42/M52-350) were mapped within 6, 10, and 13 cM distances with the aphid-resistant gene by using Mapmaker 3.0 software. The bands amplified by EcoR I-CTG/Mse I-CCT-475 and EcoR I-CTG/Mse I-CAT-390 were extracted, cloned, and sequenced. Specific primers of SCAR (sequence characterized amplified regions) were then designed from these bands. A specific band of 300 bp was amplified by a pair of SCAR primers designed based on the sequence obtained from the EcoR I-CTG/Mse I-CAT-390 marker. The SCAR marker was named SCAS0. The marker was used to detect the F2, BC1, and F2:3 populations. The selective efficiency was 86.8, 91.1, and 86.3% in the BC1, F2, and F2:3 populations, respectively. The average selective efficiency was 88.2%.展开更多
The wild hawthorn species, Crataegus songorica K. Koch., is an important wild germplasm resource in Xinjiang, China that has been endangered in recent years. The genetic diversity of C. songorica K. Koch. germplasm in...The wild hawthorn species, Crataegus songorica K. Koch., is an important wild germplasm resource in Xinjiang, China that has been endangered in recent years. The genetic diversity of C. songorica K. Koch. germplasm in five populations from Daxigou, Xinjiang, China were evaluated based on phenotypic traits and ISSR molecular markers to provide basic infor- mation on resource protection, rational utilization and genetic improvement. The F-value for the phenotypic differentiation coefficient of the 33 traits measured ranged from 0.266 to 15.128, and mean value was 13.85%. The variation among populations was found to be lower than that within population. A total of 303 loci were detected within the five populations by 12 primers. Within 298,polymorphic loci, the polymorphism was 98.35%, showing a high genetic diversity in C. songorica K. Koch. The gene diversity within population, total population genetic diversity, genetic differentiation coefficient and gene flow were 0.2779, 0.3235, 0.1408, and 3.0511, respectively. Our results showed that C. songorica K. Koch. from Xinjiang has a high level of genetic diversity at both the phenotypic and molecular levels. Significant genetic differentiation existed within population and the differentiation trend showed a regional association. And in this study, in situ and ex situ conser- vation approaches were raised for wild hawthorn protection utilization.展开更多
Genetic variation in a species enhances the capability of organism to adapt to changing environment and is necessary for survival of the species. Genetic variation arises between individuals leading to differentiation...Genetic variation in a species enhances the capability of organism to adapt to changing environment and is necessary for survival of the species. Genetic variation arises between individuals leading to differentiation at the level of population, species and higher order taxonomic groups. The genetic diversity data has varied application in research on evolution, conservation and management of natural resources and genetic improvement programmes, etc. Development of Molecular genetic markers has powerful ability to detect genetic studies of individuals, populations or species. These molecular markers combined with new statistical developments have revolutionized the analytical power, necessary to explore the genetic diversity. Molecular markers and their statistical analysis revolutionized the analytical power, necessary to explore the genetic diversity. Various molecular markers, protein or DNA (mt-DNA or nuclear DNA such as microsatellites, SNP or RAPD) are now being used in fisheries and aquaculture. These markers provide various scientific observations which have importance in aquaculture practice recently such as: 1) Species Identification 2) Genetic variation and population structure study in natural populations 3) Comparison between wild and hatchery populations 4) Assessment of demographic bottleneck in natural population 5) Propagation assisted rehabilitation programmes. In this review article, we have concentrated on the basics of molecular genetics, overview of commonly used markers and their application along with their limitations (major classes of markers) in fisheries and aquaculture studies.展开更多
The feasibility of molecule markers' application in gene pyramiding has been proved,and obvious progresses in crop breeding have been made till now.Furthermore,different QTLs or molecular markers linked tightly to yi...The feasibility of molecule markers' application in gene pyramiding has been proved,and obvious progresses in crop breeding have been made till now.Furthermore,different QTLs or molecular markers linked tightly to yield,quality or resistance may be used for marker assisted selection.MAS will be applied widely in crop breeding due to the development of more gene-based markers and efficient quantitative trait locus(QTL) as well as lower cost marking systems.展开更多
Lablab purpureus (L.) Sweet is a multipurpose legume that combines use as human food and animal feed in addition to serving as a cover crop for soil conservation. In this work, molecular diversity in Lablab purpureus ...Lablab purpureus (L.) Sweet is a multipurpose legume that combines use as human food and animal feed in addition to serving as a cover crop for soil conservation. In this work, molecular diversity in Lablab purpureus was assessed using amplified fragment length polymorphism markers on fifty Kenyan lablab accessions obtained from farmers’ fields and the Kenya National gene bank. One hundred and eighty polymorphic bands were revealed using fifteen selective primer pairs. The overall mean expected heterozygosity (He) for the five populations was 0.189. Estimates of components of molecular variance revealed that most of the genetic variation resided within populations (99%) and only 1% variance was among the populations, while Principal Coordinate Analysis showed an overlap between accessions from different geographic origins. The UPGMA cluster analysis generated from the distance matrix of the 50 assayed accessions, revealed low diversity among most of the accessions. The low diversity observed may be due to the narrow genetic base for breeding stocks, and extensive exchange of germplasm among smallholder farmers across the country. Results obtained from this study are discussed in light of the need to enhance the genetic management and improvement of this multipurpose crop species.展开更多
基金Supported by the National Natural Science Foundation of China(No.32170205)the Natural Science Foundation of Shanghai(No.21ZR144730)。
文摘In our recent investigations of diatom diversity,we studied three species,namely,Skeletonema costatum,Skeletonema subsalsum,and Skeletonema potamos.Although they have been found frequently in Changjiang(Yangtze)River Basin,their morphological and molecular identification is difficult in taxonomy.Therefore,to integrate morphological and molecular biological approaches,we compared systematically their morphological characters and performed phylogenetic analysis.Twelve strains of Skeletonema were collected and isolated from Shanghai and Jiangsu,China,and their morphological characteristics were examined by light microscopy(LM)and the scanning electron microscopy(SEM).Based on morphological comparison,we determined that S.potamos is easy to distinguish from the other two species.The heavily silicified areolae,undulated or cleft distal ends of terminal fultoportula processes(TFPPs),absence of basal pores of fultoportula processes(FPPs),the rootlike protrusions of FPPs,and no interlocking connection are the stable characteristics that can be used to identify S.potamos.However,there are only two features that can distinguish S.costatum from S.subsalsum,namely the location of terminal rimoportulae(TRPs)and the distal shape of TFPPs.In addition,we amplified and sequenced nine common genetic markers from the strains,from which 101 sequences were obtained,constructed phylogenetic trees based on the nine genes and evaluated that seven genes can be used to identify S.potamos,and revealed that S.subsalsum is the closest known relative of S.costatum,and only ATP synthetase beta-subunit gene(atp B)is able to distinguish them from each other,which strongly support that it is an effective molecular marker for Skeletonema.This work provided a theoretical basis for the taxonomic study of Skeletonema.
基金supported by Bolashak International Fellowships,Center for International Programs,Ministry of Education and Science,KazakhstanAP14869777 supported by the Ministry of Education and Science,KazakhstanResearch Projects BR10764991 and BR10765000 supported by the Ministry of Agriculture,Kazakhstan。
文摘This review updates the present status of the field of molecular markers and marker-assisted selection(MAS),using the example of drought tolerance in barley.The accuracy of selected quantitative trait loci(QTLs),candidate genes and suggested markers was assessed in the barley genome cv.Morex.Six common strategies are described for molecular marker development,candidate gene identification and verification,and their possible applications in MAS to improve the grain yield and yield components in barley under drought stress.These strategies are based on the following five principles:(1)Molecular markers are designated as genomic‘tags’,and their‘prediction’is strongly dependent on their distance from a candidate gene on genetic or physical maps;(2)plants react differently under favourable and stressful conditions or depending on their stage of development;(3)each candidate gene must be verified by confirming its expression in the relevant conditions,e.g.,drought;(4)the molecular marker identified must be validated for MAS for tolerance to drought stress and improved grain yield;and(5)the small number of molecular markers realized for MAS in breeding,from among the many studies targeting candidate genes,can be explained by the complex nature of drought stress,and multiple stress-responsive genes in each barley genotype that are expressed differentially depending on many other factors.
基金supported by the State Key Program of National Natural Science Foundation of China(Grant Nos.31930098,31772324)Hebei Provincial Natural Science Fund for Distinguished Young(Grant No.C2020204063)+6 种基金Natural Science Foundation and basic research project in Hebei Province(Grant No.18966925D)the Innovative Research Group Project of Hebei Natural Science Foundation(Grant No.C2020204111)the Agricultural Science and Technology Innovation Program of CAAS(Grant No.CAASXTCX2019025)the National Natural Science Foundation of China(Grant No.31672151)the Science and Technology Support Program of Hebei(Grant No.16226304D-2)Science and Technology Research Project of Universities in Hebei Province(BJ2019020)the International Science and Technology Cooperation base Special Project of Hebei(Grant No.20592901D)。
文摘Flowering time is an important agronomic trait of Chinese cabbage with late flowering being a primary breeding objective.In our previous work,we obtained Chinese cabbage-cabbage translocation lines that contained several beneficial cabbage genes.Cabbage-specific molecular markers show that these genes were coming from chromosome C01 of cabbage.In this study,we investigated the inheritance of flowering time in a couple of translocation lines and analyzed the transmission rate of molecular markers in the offspring.Consequently,we obtained the late flowering Chinese cabbage-cabbage translocation line‘AT7–4’in which the flowering time was later than that of‘85–1’by about 7 days under 4-week vernalization.Based on previous studies of the genomes of Chinese cabbage and cabbage,we located the cabbage-specific molecular markers that were closely linked at the top of the chromosome A01 in the F2mapping population generated by self-crossing F1s derived from a cross between the translocation line‘AT7–4’and Chinese cabbage‘14–36’.Five flowering-related genes in the alien fragment were found by functional annotation and their molecular markers were developed.This study lays the foundation for the future improvement of Chinese cabbage varieties using A-C translocation lines.
基金The Higher Education Commission(HEC)funded this work under“Transcriptomics Based Understanding of Cercospora Leaf Spot Resistance in Mungbean and Disease Management through Nanotechnology,”Project No.7425.
文摘We developed a molecular marker for MAS of mungbean resistant varieties against CLS from the consensus sequence(MB-CLsRG)of identified RGAs(MB-ClsRCaG1 and MB-ClsRCaG2).The MB-CLsRG sequence-specific primer pair was used to screen Cercospora leaf spot(CLS)resistant varieties of mungbean in genomic analysis that showed congruency with phenotypic screening.Validation of molecular marker linkage with CLS resistance was performed using rtPCR in transcriptomic analysis.The sequenced PCR products showed 100%homology with MB-CLsRG sequence and putative disease resistance proteins that confirmed the linkage of molecular marker with CLS resistance in mungbean.The antifungal potential of MB-CLsRG gene encoding protein was assessed.The MB-CLsRG gene sequence was cloned in the E.coli expression vector for recombinant protein production.The recombinant protein was then investigated for its in vitro antifungal potential against Cercospora canescens.The in vitro investigation showed strong antifungal activity of recombinant protein as it restricted the growth of fungal mycelial mass.The results validated the linkage of developed marker with CLS-resistant mungbean varieties;therefore,it can be used to screen resistant varieties from a large population in MAS.Moreover,the recombinant protein of the MB-CLsRG gene sequence revealed antifungal potential,which proved the gene sequence could be suitable to use in transgenic plants technology to develop fungal-resistant transgenic crops.
基金funded by the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(CAAS-ASTIP-2021-OCRI)China Agriculture Research System(CARS14)+2 种基金Hubei International Science and Technology Cooperation Project(2022EHB034)the Science and Technology Innovation Project of Hubei Province(2021-620-000-001-035)the Fundamental Research Funds for Central Non-profit Scientific Institution(2013).
文摘Sesame(Sesamum indicum L.) plays a crucial role in Ethiopian agriculture,serving both subsistence and commercial purposes.However,our understanding of the extensive genetic diversity and population structure of Ethiopian sesame remains limited.To address this knowledge gap,we genotyped 368 Ethiopian sesame germplasms,categorizing into four distinct breeding groups:Accessions,landraces,improved varieties,and wild types,using a comprehensive set of 28 polymorphic markers,including 23 simple sequence repeat(SSR) and five Insertion-Deletion(InDel) markers.These markers ensured robust genomic representation,with at least two markers per linkage group.Our results unveiled substantial genetic diversity,identifying a total of 535 alleles across all accessions.On average,each locus displayed 8.83 alleles,with observed and expected heterozygosity values of 0.30 and 0.36,respectively.Gene Diversity and Polymorphic Information Content(PIC) were recorded at 0.37 and 0.35.The percentage of polymorphic loci varied significantly among breeding groups,ranging from8.00% to 82.40%,indicating high diversity in accessions(82.4%),moderate diversity in improved varieties(31.20%) and landraces(29.60%),and limited diversity in wild types(8.00).Analysis of Molecular Variance(AMOVA) results emphasized significant genetic differentiation among populations,with substantial diversity(P<0.001) within each population.Approximately 8% of the entire genetic diversity could be attributed to distinctions among populations,while the larger proportion of genetic diversity(92%) resided within each individual sesame population,showcasing heightened diversity within each group.Our study’s findings received support from both Bayesian clustering and Neighbor-joining(NJ) analysis,reaffirming the credibility of our genetic structure insights.Notably,Population structure analysis at its highest Δk value(k=2) revealed the existence of two primary genetic clusters,further subdivided into four sub-populations at k=4.Similarly,NJ analysis identified two prominent clusters,each displaying additional sub-clustering.In conclusion,our research provides a comprehensive understanding of genetic groups,subpopulations,and overall diversity within Ethiopian sesame populations.These findings underscore the significant genetic diversity and population structure within Ethiopian sesame germplasm collections.This genetic richness holds promise for breeding and conservation efforts,highlighting the importance of preserving genetic diversity to ensure adaptation to changing environments and meet the needs of farmers and consumers.
基金supported by the Major Program of National Natural Science Foundation of China (No. 91959205)National Natural Science Foundation of China (No. 82141117)+3 种基金The Capital’s Funds for Health Improvement and Research (CFH) (No. 2022-2-1023)Beijing Xisike Clinical Oncology Research Foundation Ypierrefabre (No. 202101-0099)Beijing Municipal Administration of Hospitals Incubating Program (No. PX2020045)Science Foundation of Peking University Cancer Hospital (No. 2020-4)。
文摘Objective: There is an ongoing debate about whether the management of gastroenteropancreatic(GEP)neuroendocrine carcinoma(NEC) should follow the guidelines of small-cell lung cancer(SCLC). We aim to identify the genetic differences of GEPNEC and its counterpart.Methods: We recruited GEPNEC patients as the main cohort, with lung NEC and digestive adenocarcinomas as comparative cohorts. All patients undergone next-generation sequencing(NGS). Different gene alterations were compared and analyzed between GEPNEC and lung NEC(LNEC), GEPNEC and adenocarcinoma to yield the remarkable genes.Results: We recruited 257 patients, including 99 GEPNEC, 57 LNEC, and 101 digestive adenocarcinomas.Among the mutations, KRAS, RB1, TERT, IL7R, and CTNNB1 were found to have different gene alterations between GEPNEC and LNEC samples. Specific genes for each site were revealed: gastric NEC(TERT amplification),colorectal NEC(KRAS mutation), and bile tract NEC(ARID1A mutation). The gene disparities between small-cell NEC(SCNEC) and large-cell NEC(LCNEC) were KEAP1 and CDH1. Digestive adenocarcinoma was also compared with GEPNEC and suggested RB1, APC, and KRAS as significant genes. The TP53/RB1 mutation pattern was associated with first-line effectiveness. Putative targetable genes and biomarkers in GEPNEC were identified in22.2% of the patients, and they had longer progression-free survival(PFS) upon targetable treatment [12.5 months vs. 3.0 months, HR=0.40(0.21-0.75), P=0.006].Conclusions: This work demonstrated striking gene distinctions in GEPNEC compared with LNEC and adenocarcinoma and their clinical utility.
基金supported by the China Agriculture Research System(Grant No.CARS-23-A13)Hubei Agrotechnical Major Project(Grant No.2021-620-000-001-01)+1 种基金Wuhan Major Project of Key Technologies in Biological Breeding and New Variety Cultivation(Grant No.2022021302024852)HZAU-AGIS Cooperation Fund(Grant No.SZYJY2023022).
文摘Clubroot caused by Plasmodiophora brassicae is a devastating disease of Cruciferous crops.Developing cultivars with clubroot resistance(CR)is the most effective control measure.For the two major Brassica vegetable species B.rapa and B.oleracea,several commercial cultivars with unclear CR pedigrees have been intensively used as CR donors in breeding.However,the continuous occurrence of CR-breaking makes the CR pedigree underlying these cultivars one of the breeders'most urgent concerns.The complex intraspecific diversity of these two major Brassica vegetables has also limited the applicability of CR markers in different breeding programs.Here we first traced the pedigree underlying two kinds of CR that have been widely applied in breeding by linkage and introgression analyses based on public resequencing data.In B.rapa,a major locus CRzi8 underlying the CR of the commercial CR donor‘DegaoCR117’was identified.CRzi8 was further shown to have been introgressed from turnip(B.rapa ssp.rapifera)and that it carried a potential functional allele of Crr1a.The turnip introgression carried CRb^(c),sharing the same coding sequence with the CRb that was also identified from chromosome C07 of B.oleracea CR cultivars with different morphotypes.Within natural populations,variation analysis of linkage intervals of CRzi8,PbBa8.1,CRb,and CRb^(c)yielded easily resolved InDel markers(>20 bp)for these fundamental CR genes.The specificity of these markers was tested in diverse cultivars panels,and each exhibited high reliability in breeding.Our research demonstrates the value of the practice of applying resequencing big data to solve urgent concerns in breeding programs.
基金This work was supported by grants from the National Natural Science Foundation of China(82130113)the National Key R&D Program of China(2017YFC1703904)+2 种基金the Regional Innovation and Cooperation Project of the Science&Technology Department of Sichuan Province(2020YFQ0032)the Key R&D and Transformation Program of the Science&Technology Department of Qinghai Province(2020-SF-C33)the“Xinglin Scholars”Research Promotion Program of Chengdu University of Traditional Chinese Medicine(BSH2021008).
文摘Objective:Rheumatoid arthritis(RA)is a systemic autoimmune disease characterized by chronic erosive arthritis.Due to the lack of effective biomarkers for diagnosis and treatment,RA patients have many complications in the later stage,seriously affecting their quality of life.Thus,this study was conducted to investigate new therapeutic targets and to discover diagnostic biomarkers in RA.Methods:In this study,the expression profiles of GSE55235 and GSE55457 were downloaded from the Gene Expression Omnibus database to obtain DEGs between RA and healthy samples.Genetic Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed on the common genes existing in the RA-related modules.Additionally,we used the STRING database to construct the protein‒protein interaction network.Furthermore,we established the interaction analysis of Hub Genes and microRNA(miRNA)and verified the 10 Hub genes through the GSE77298 dataset and quantitative real-time polymerase chain reaction Results:276 and 69 DEGs were screened from the GSE55235 dataset and GSE55457 dataset,respectively.Then,we obtained 42 up-regulated genes in two chip datasets intersection.Genetic Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis of the 42 up-regulated genes showed that they were mainly concentrated in immune response-activating cell surface receptor signaling pathway,etc.Furthermore,the protein-protein interaction network indicated that 10 hub genes are closely related to RA,including MS4A1,CD27,LCK,CD79A,SDC1,CXCL9,CXCL10,CXCL13,IGLL5,and IGJ.In addition,we found that miR-4531 is the same target miRNAs between MS4A1 and SDC1 through messenger RNA-miRNA co-expression network.Finally,the GSE77298 gene chip and quantitative real-time polymerase chain reaction verified the expression of 10 Hub genes.The six Hub genes of CD27,SDC1,CXCL9,CXCL10,CXCL13,and IGJ are significantly increased.Conclusions:We found that SDC1 may be a novel molecular marker for the prevention and treatment of RA.The miR-4531/SDC1 regulatory axis may play a key role in this process.In conclusion,our study not only provides potential biomarkers for the diagnosis and treatment of RA,but also provides a basis and new targets for further revealing the potential mechanism of RA occurrence and development and discovering targeted drugs.
文摘Metabolic reprogramming is a key feature driving oncogenesis in cancers. Recent studies have revealed that protein metabolism is largely altered in gliomas facilitating its malignant growth. Urea is the end product of nitrogen metabolism which is mainly produced by arginase. The interdependence of arginase and other biochemical mechanisms triggered scientific research interest. This research aimed to investigate the relationships between the urea as the main parameter of protein metabolism and glioma progression. It was also the most pronounced relationship between urea and the level of the nuclear protein Ki-67 as a marker of proliferative activity and O-6-methylguanine-DNA methyltransferase (MGMT), which performs DNA repair. Postoperative material from 20 patients with gliomas of different grades of anaplasia was analyzed.
基金This study was supported by grants from the Key Project of Medical Science from Jiangsu Province (RC2003100)the Project of Medical Science from Department of Health, Jiangsu Province (H200523), China.
文摘BACKGROUND: The carcinogenesis of hepatocellular carcinoma (HCC) is a multi-factorial, multistep and complex process. Its prognosis is poor, and early diagnosis and monitoring metastasis of HCC is of the utmost importance. Circulating diagnostic and prognostic biomarkers could be used in proper postoperative treatment of patients at an early stage of HCC development. This review summarizes recent studies of the specific biomarkers in diagnosis and monitoring metastasis or postoperative recurrence of HCC. DATA SOURCES: An English-language literature search was conducted using MEDLINE (June 1998 to Spetember 2006) on researches of some valuable specific biomarkers in diagnosis and monitoring metastasis or postoperative recurrence of HCC. RESULTS: Hepatoma tissues can synthesize various tumor-related proteins, polypeptides, and isoenzymes, such as alpha-fetoprotein (AFP), hepatoma-specific gamma-glutamyl transpeptidase (HS-GGT), etc, and then secrete into blood. The valuable early diagnostic and prognostic biomarkers could predict the development an metastases of HCC. Recent researches have confirmed that circulating hepatoma-specific AFP subfraction, transforming growth factor (TGF)-beta 1, HS-GGT, and free insulin-like growth factor (IGF)-II may be more specific markers than total AFP level for early diagnosis for HCC. The circulating genetic markers such as AFP-mRNA, TGF-beta 1-mRNA, IGF-II-mRNA, etc from peripheral blood mononuclear cells of HCC patients have been most extensively used in monitoring distal metastasis or postoperative recurrence of HCC. CONCLUSIONS: Hepatoma tissues synthesize and secrete valuable molecular markers into blood. The analyses of circulating hepatoma-specific biomarkers are useful to early diagnosis of HCC or monitoring metastasis or postoperative recurrence of HCC.
文摘Five super hybrid rice combinations, i.e. HYS-1/R105, Pei'ai 64S/E32, Liangyoupeijiu (Pei'ai 64S/9311), 88S/0293, and J23A/Q611, and their parental lines were tested by means of SSR analysis. A total of 144 SSR primer pairs distributed on 12 rice chromosomes were used, out of which 47 detected polymorphism among the tested rice lines. Among all these primers, RM337 and RM154 produced polymorphic patterns in four or more of the tested experimental materials respectively, and they could distinguish among most rice genotypes tested. Twenty-four primer pairs, two on each rice chromosome, were selected to make a reference SSR marker-based fingerprinting for the rice lines. For most of the primer pairs, F1 hybrids mainly showed complementary pattern of both parents, which could be very useful to distinguish the F1 from its parental lines. In addition, 5 primer pairs were selected as special primer pairs for five hybrid rice combinations respectively. By combining the rapid, simple method on DNA extraction, it is suggested that SSR technique has wide prospective in variety authentication and purity identification.
基金the National Natural Science Foundation of China (Grant No. 30270759) the Science and Technology Department of Zhejiang Province (Grant No. 2005C32001).
文摘Eleven evaluating parameters for rice core collection were assessed based on genotypic values and molecular marke' information. Monte Carlo simulation combined with mixed linear model was used to eliminate the interference from environment in order to draw more reliable results. The coincidence rate of range (CR) was the optimal parameter. Mean Simpson index (MD), mean Shannon-Weaver index of genetic diversity (M1) and mean polymorphism information content (MPIC) were important evaluating parameters. The variable rate of coefficient of variation (VR) could act as an important reference parameter for evaluating the variation degree of core collection. Percentage of polymorphic loci (p) could be used as a determination parameter for the size of core collection. Mean difference percentage (MD) was a determination parameter for the reliability judgment of core collection. The effective evaluating parameters for core collection selected in the research could be used as criteria for sampling percentage in different plant germplasm populations.
文摘This paper reports the development of the first SSR marker-based sugarcane (Saccharum spp.) molecular identity database in the world. Since 2005, 1,025 sugarcane clones were genotyped, including 811 Louisiana, 45 Florida, 39 Texas, 130 foreign, and eight consultant/seed company clones. Genotyping was done on a fluorescence-capillary electrophoresis detection platform involving 21 highly polymorphic SSR markers that could potentially amplify 144 distinctive DNA fragments. Genotyping data were processed with the GeneMapper? software to reveal electrophoregrams that were manually checked against the 144 fragments. The presence (A) or absence (C) of these 144 fragments in any sugarcane clone was recorded in an affixed sequence order as a DNAMAN? file to represent its molecular identity being achieved into a local molecular identity database. The molecular identity database has been updated annually by continued genotyping of newly assigned sugarcane clones. The database provides molecular descriptions for new cultivar registration articles, enables sugarcane breeders to identify mis-labeled sugarcane clones in crossing programs and determine the paternity of cross progeny, and ensures the desired cultivars are grown in farmers’ fields.
基金supported by National Research,Development and Innovation Office,Hungary by a Grant of Hungarian Scientific Research Fund(OTKA K101600)
文摘In this review we summarized recent historical records and molecular studies on evolutionary history and phylogeography of Scots pine with focus on the European highly fragmented distribution area of the species. Fossilized pollen, plant micro- and macrofossil records provided evidences on the large-scale species’ range shifts and demographic changes during the Quaternary. Populations of Scots pine were documented both in the glacial (incl. full glaciation) and interglacial periods. Recolonization of Europe after the glaciation originated from the (Sub) Mediterranean areas like the Balkan Peninsula but also from around the Eastern Alps and the surroundings of the Danube plain. Fennoscandia and northern European Baltic regions were most probably colonized from two main directions, from Western Europe and from the Russian Plain. Modern history of Scots pine was hardly affected by anthropogenic activities that started to strengthen in the Bronze and Iron Age. Along with the fossil records, molecular genetic tools were used to infer the origin and putative history including migration, differentiation and demography of the species. In this paper we compiled the major publications (30) of molecular genetic studies of the past 20 years derived from distinctly inherited organelle genomes (mitochondrial, chloroplast, nuclear) revealed by different marker systems (mtDNA-cox1, -nad1, -nad3, -nad7, ISSR, cpSSR, nSSR, B-SAP, SNP). It is important to consider that different phylogeographic patterns can be drawn by the analysis of different DNA marker types. Accordingly the use of more than one marker simultaneously outlines the most sophisticated phylogeographical pattern on the genetic lineages and can reveal high differentiation of the European distribution. Combined marker systems and markers derived from coding sequences have also been used to detect species’ phylogeographic patterns, but these were rarely applied to Scots pine. Although new molecular techniques can provide higher resolution data for populations, the reviewed results can shape the direction of further studies.
文摘Two yield-enhancing genes (yld1.1 and yld2.1) are located on chromosomes 1 and 2 respectivelyin a weedy relative of cultivated rice, Oryza rufipogon. SSR markers RM9 and RM166 are closelylinked with the two loci respectively. Minghui63 (MH63) has been a widely used restorationline in hybrid rice production in China during the past two decades. The F1 of cross 'MH63O.rufipogon' was backcrossed with MH63 generation by generation. RM9 and RM166 were used toselect the plants from the progeny of the backcross populations. The results were as follows:(1) In BC2F1 population, the percentage of the individuals which have RM9 and RM166 amplifiedbands simultaneously was 12.2%, while in the BC3F1 population, that was 16.3%. (2) Among 400individuals of BC3F1, four yield-promising plants were obtained, with yield being 30% more thanthat of MH63. (3) The products amplified by primer RM166 in O. rufipogon and MH63 weresequenced. It was found that the DNA fragment sequence amplified by RM166 from MH63 was 101 bpshorter than that from O. rufipogon. The 101bp sequence is a part of an intron of the PCNA(proliferating cell nuclear antigen) gene.
基金the Natural Science Foundation, Hebei Province, China (C2010000758)the Science and Technology Department of Hebei Province,China (06547004D-2)
文摘In this study, an F2 segregated population obtained by hybridization between the aphid-sensitive sorghum strain Qiansan and aphid-resistant cultivar Henong 16 was used to establish an aphid-resistant pool and an aphid-sensitive pool. 192 pairs of AFLP (amplified fragment length polymorphism) marker primers were screened in these pools using BSA (bulked segregant analysis). Three pairs of EcoR I-CTG/Mse I-CCT, EcoR I-CTG/Mse I-CAT, and EcoR I-AGT/Mse I-CCC showed linkage with aphis resistance. EcoR I-CTG/Mse I-CCT-475, EcoR I-CTG/Mse I-CAT-390, and EcoR I-AGT/Mse I-CCC- 350 (E42/M52-350) were mapped within 6, 10, and 13 cM distances with the aphid-resistant gene by using Mapmaker 3.0 software. The bands amplified by EcoR I-CTG/Mse I-CCT-475 and EcoR I-CTG/Mse I-CAT-390 were extracted, cloned, and sequenced. Specific primers of SCAR (sequence characterized amplified regions) were then designed from these bands. A specific band of 300 bp was amplified by a pair of SCAR primers designed based on the sequence obtained from the EcoR I-CTG/Mse I-CAT-390 marker. The SCAR marker was named SCAS0. The marker was used to detect the F2, BC1, and F2:3 populations. The selective efficiency was 86.8, 91.1, and 86.3% in the BC1, F2, and F2:3 populations, respectively. The average selective efficiency was 88.2%.
基金supported by the Special Research Projects of National Forestry Industry of Public Benefit,China(201304701-1)the Key Discipline of Horticultural of Xinjiang Uygur Autonomous Region of China(2016-10758-3)the Key Laboratory of Characteristics of Fruit Trees Center of Xinjiang Agricultural University,China
文摘The wild hawthorn species, Crataegus songorica K. Koch., is an important wild germplasm resource in Xinjiang, China that has been endangered in recent years. The genetic diversity of C. songorica K. Koch. germplasm in five populations from Daxigou, Xinjiang, China were evaluated based on phenotypic traits and ISSR molecular markers to provide basic infor- mation on resource protection, rational utilization and genetic improvement. The F-value for the phenotypic differentiation coefficient of the 33 traits measured ranged from 0.266 to 15.128, and mean value was 13.85%. The variation among populations was found to be lower than that within population. A total of 303 loci were detected within the five populations by 12 primers. Within 298,polymorphic loci, the polymorphism was 98.35%, showing a high genetic diversity in C. songorica K. Koch. The gene diversity within population, total population genetic diversity, genetic differentiation coefficient and gene flow were 0.2779, 0.3235, 0.1408, and 3.0511, respectively. Our results showed that C. songorica K. Koch. from Xinjiang has a high level of genetic diversity at both the phenotypic and molecular levels. Significant genetic differentiation existed within population and the differentiation trend showed a regional association. And in this study, in situ and ex situ conser- vation approaches were raised for wild hawthorn protection utilization.
文摘Genetic variation in a species enhances the capability of organism to adapt to changing environment and is necessary for survival of the species. Genetic variation arises between individuals leading to differentiation at the level of population, species and higher order taxonomic groups. The genetic diversity data has varied application in research on evolution, conservation and management of natural resources and genetic improvement programmes, etc. Development of Molecular genetic markers has powerful ability to detect genetic studies of individuals, populations or species. These molecular markers combined with new statistical developments have revolutionized the analytical power, necessary to explore the genetic diversity. Molecular markers and their statistical analysis revolutionized the analytical power, necessary to explore the genetic diversity. Various molecular markers, protein or DNA (mt-DNA or nuclear DNA such as microsatellites, SNP or RAPD) are now being used in fisheries and aquaculture. These markers provide various scientific observations which have importance in aquaculture practice recently such as: 1) Species Identification 2) Genetic variation and population structure study in natural populations 3) Comparison between wild and hatchery populations 4) Assessment of demographic bottleneck in natural population 5) Propagation assisted rehabilitation programmes. In this review article, we have concentrated on the basics of molecular genetics, overview of commonly used markers and their application along with their limitations (major classes of markers) in fisheries and aquaculture studies.
基金Supported by National 863 Plan (2006AA100108-4-9)
文摘The feasibility of molecule markers' application in gene pyramiding has been proved,and obvious progresses in crop breeding have been made till now.Furthermore,different QTLs or molecular markers linked tightly to yield,quality or resistance may be used for marker assisted selection.MAS will be applied widely in crop breeding due to the development of more gene-based markers and efficient quantitative trait locus(QTL) as well as lower cost marking systems.
文摘Lablab purpureus (L.) Sweet is a multipurpose legume that combines use as human food and animal feed in addition to serving as a cover crop for soil conservation. In this work, molecular diversity in Lablab purpureus was assessed using amplified fragment length polymorphism markers on fifty Kenyan lablab accessions obtained from farmers’ fields and the Kenya National gene bank. One hundred and eighty polymorphic bands were revealed using fifteen selective primer pairs. The overall mean expected heterozygosity (He) for the five populations was 0.189. Estimates of components of molecular variance revealed that most of the genetic variation resided within populations (99%) and only 1% variance was among the populations, while Principal Coordinate Analysis showed an overlap between accessions from different geographic origins. The UPGMA cluster analysis generated from the distance matrix of the 50 assayed accessions, revealed low diversity among most of the accessions. The low diversity observed may be due to the narrow genetic base for breeding stocks, and extensive exchange of germplasm among smallholder farmers across the country. Results obtained from this study are discussed in light of the need to enhance the genetic management and improvement of this multipurpose crop species.