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DNA marker can be used for precise plant cultivar identification. However, DNA markers have often not been used effectively for the identification of plant cultivars due to a lack of an effective analysis strategy. We used a novel strategy for effective identification of plant individuals based on a new way of recording DNA fingerprints of the genotyped plants; a cultivar identification diagram can be manually generated and used as key reference information for quick identification of plant and/or seed samples. Forty-seven pomegranate varieties popularly cultivated in various provinces of China were subjected to RAPD marker analysis. Using the cultivar identification diagram strategy, they were clearly separated by the fingerprints of 11 RAPD primers. The utility and accuracy of the cultivar identification diagram analysis results were confirmed by the identification of three randomly chosen groups of cultivars among the 47 varieties.
Genet Mol Res 2012 Aug 31
PMID:A novel strategy for identification of 47 pomegranate (Punica granatum) cultivars using RAPD markers. 2278 22

We studied the efficiency of maintaining and restoring cytoplasmic male sterility (CMS) systems in pepper (Capsicum annuum L.). An Rf-linked molecular marker was employed to analyze the interaction between 6 CMS lines (A), 5 maintainers (B), and 6 restorers (C). Sterility was maintained in the matings of lines 201A x 200B, 203A x 200B, 206A x 200B, 200A x 201B, 206A x 201B, 200A x 202B, 200A x 203B, 200A x 206B, and 201A x 206B. All 6 restorers restored the fertility of lines 200A, 202A, 203A, and 204A, except that 213C could not restore the fertility of lines 200A and 204A. However, the 6 restorers had diverse restoring abilities in individual CMS lines. The Rf-linked molecular marker was amplified by PCR in lines 207C, 208C, and 213C. This DNA marker was only found in the F1 hybrids M39, M14, M19, M25, M13, M20, and M22. We conclude that the restorers 208C and 207C can transmit the Rf gene or the Rf-linked marker to F1 hybrids.
Genet Mol Res 2013 Jul 08
PMID:Maintaining and restoring cytoplasmic male sterility systems in pepper (Capsicum annuum L.). 2331 67

The genetic backgrounds of many Citrus varieties are quite complex. Classifications and phylogenetic relationships of Citrus species have become the focus of researchs. Some conserved genes of chloroplast genome's research have been proven effective in determining the biosources of hybrids and phylogenetic analysis. Thus, we studied variations among the chloroplast trnL gene sequences of 10 Citrus species, including C. nobilis Lour. 'Gonggan'. The amplification results of different trnL target genes and identification of the double-enzyme cut after cloning show that lengths of all trnL sequences were within 895 to 935 bp and a total of 24 variation sites were detected among the 10 material samples. Clustering analysis revealed differences in trnL genes caused by systematic evolution and allowed the determination of variations among Citrus varieties. Variation sites of trnL sequences can be used in the phylogenetic classification and species identification of Citrus, and the results agreed with random amplified polymorphic DNA marker results. C. nobilis Lour. 'Gonggan' is closely associated with the other two varieties in Zhaoqing area, and C. nobilis Lour. 'Gonggan' and C. haniana Hort. ex Tseng 'Sihuihanggan' can be classified into the same category. C. nobilis Lour. 'Gonggan' as a natural hybrid is probably a hybrid with C. haniana Hort. ex Tseng 'Sihuihanggan' as its female parent.
Genet Mol Res 2013 Jan 30
PMID:Genetic background of Citrus nobilis Lour. 'Gonggan' based on the chloroplast trnL gene. 2340 51

Within the genus Rosa numerous species have been described. Circumscription of the dogrose section Caninae is straightforward, but the delineation of species and subsections within this section is less clear, partly due to hybridisation between species. We have investigated the extent to which DNA marker-based information of wild populations corroborates present-day dogrose taxonomy and hypotheses about the origination of taxa. Sampling was conducted in a transect across Europe, collecting over 900 specimens of all encountered dogrose taxa. For comparison, we also included more than 200 samples of species belonging to other sections. Two lines of statistical analyses were used to investigate the genetic structure based on AFLP data: (1) an unstructured model with principal coordinate analysis and hierarchical clustering, and (2) a model with a superimposed taxonomic structure based on analysis of genetic diversity using a novel approach combining assignment tests with canonical discriminant analysis. Support was found for five of the seven subsections, whereas R. balsamica apparently belongs to subsection Caninae thus omitting the need for recognising subsection Tomentellae. For R. stylosa, a hybridogenic origin with a non-dogrose section member has been suggested, and it can be treated either as a separate subsection or within subsection Caninae. Within the subsection Rubigineae, a species cluster with low support for the taxa R. micrantha, R. rubiginosa and the putatively hybridogenous R. gremlii was identified. Similarly, several species in the subsection Caninae overlapped considerably, and are best regarded as one common species complex. This population genetic approach provides a general method to validate the taxonomic system in complex and polyploid taxa.
Mol Phylogenet Evol 2013 Jun
PMID:AFLP-based population structure analysis as a means to validate the complex taxonomy of dogroses (Rosa section Caninae). 2349 15

Estimating genetic variance is traditionally performed using pedigree analysis. Using high-throughput DNA marker data measured across the entire genome it is now possible to estimate and partition genetic variation from population samples. In this chapter, we introduce methods and a software tool called Genome-wide Complex Trait Analysis (GCTA) to estimate genomic relationships between pairs of conventionally unrelated individuals using genome-wide single nucleotide polymorphism (SNP) data, to estimate variance explained by all SNPs simultaneously on genomic or chromosomal segments or over the whole genome, and to perform a joint and conditional multiple SNPs association analysis using summary statistics from a meta-analysis of genome-wide association studies and linkage disequilibrium between SNPs estimated from a reference sample.
Methods Mol Biol 2013
PMID:Genome-wide complex trait analysis (GCTA): methods, data analyses, and interpretations. 2375 93

Genomic best linear unbiased prediction (gBLUP) is a method that utilizes genomic relationships to estimate the genetic merit of an individual. For this purpose, a genomic relationship matrix is used, estimated from DNA marker information. The matrix defines the covariance between individuals based on observed similarity at the genomic level, rather than on expected similarity based on pedigree, so that more accurate predictions of merit can be made. gBLUP has been used for the prediction of merit in livestock breeding, may also have some applications to the prediction of disease risk, and is also useful in the estimation of variance components and genomic heritabilities.
Methods Mol Biol 2013
PMID:Genomic best linear unbiased prediction (gBLUP) for the estimation of genomic breeding values. 2375 97

Tomato breeding and variety development have led to the generation of a large number of varieties in many countries worldwide. This has created a growing and urgent need for an improved strategy for genotyping and identification since the traditional methods based on phenotype are growing unreliable. DNA markers could provide distinct benefits in tomato variety identification; however, DNA fingerprint analyses have not made DNA marker data readily usable for identification of varieties in tomato and other crops. A manual cultivar and/or variety identification diagram (MCID) strategy has been developed and has been found to make DNA markers more usable for the identification of genotyped plant individuals. We adopted this strategy, using modified RAPD markers to identify 42 tomato varieties from different geographical origins and seed merchants. All of the varieties were clearly separated and individually identified by reproducible fingerprints of only 6 RAPD primers. The tomato MCID that is generated is usable for the identification of any two or more tomato varieties. In addition, fewer primers can be used to make a distinction between varieties using this approach, since the selected fingerprints from each primer are used after they have been generated. The information in this first version of the tomato MCID can be enriched through identification and incorporation of more varieties and adaptation to other molecular markers in order to provide a more comprehensive tomato variety identification service for the horticultural industry.
Genet Mol Res 2013 Jun 11
PMID:A novel and efficient strategy for practical identification of tomato (Solanum lycopersicon) varieties using modified RAPD fingerprints. 2391 74

Fusarium verticillioides is a pathogen of agriculturally important crops, especially maize. It is considered one of the most important pathogens responsible for fumonisin contamination of food products, which causes severe, chronic, and acute intoxication in humans and animals. Moreover, it is recognized as a cause of localized infections in immunocompetent patients and disseminated infections among severely immunosuppressed patients. Several molecular tools have been used to analyze the intraspecific variability of fungi. The objective of this study was to use molecular markers to compare pathogenic isolates of F. verticillioides and isolates of the same species obtained from clinical samples of patients with Fusarium mycoses. The molecular markers that we used were inter-simple sequence repeat markers (primers GTG5 and GACA4), intron splice site primer (primer EI1), random amplified polymorphic DNA marker (primer OPW-6), and restriction fragment length polymorphism-internal transcribed spacer (ITS) from rDNA. From the data obtained, clusters were generated based on the UPGMA clustering method. The amplification products obtained using primers ITS4 and ITS5 and loci ITS1-5.8-ITS2 of the rDNA yielded fragments of approximately 600 bp for all the isolates. Digestion of the ITS region fragment using restriction enzymes such as EcoRI, DraI, BshI, AluI, HaeIII, HinfI, MspI, and PstI did not permit differentiation among pathogenic and clinical isolates. The inter-simple sequence repeat, intron splice site primer, and random amplified polymorphic DNA markers presented high genetic homogeneity among clinical isolates in contrast to the high variability found among the phytopathogenic isolates of F. verticillioides.
Genet Mol Res 2013 Aug 12
PMID:Use of molecular markers to compare Fusarium verticillioides pathogenic strains isolated from plants and humans. 2406 42

In this study, we cloned and sequenced a 938-base pair polymorphic band, pHs27, in the tightly linked random amplified polymorphic DNA marker OPU10 and converted it into a sequence-characterized amplified region (SCAR) marker referred to as RHS141, which was specific for the Ns genome of Psathyrostachys huashanica. A GenBank basic local alignment search tool search showed that the sequence of pHs27 had no primary sequence homology with known sequences, and Southern blotting confirmed this result. This SCAR marker was used to detect Ns genome chromatin in wheat, and it was successfully amplified in P. huashanica itself, a complete set of wheat-P. huashanica disomic addition lines (1Ns-7Ns), and undetermined homoeologous group addition lines. This SCAR marker will be a powerful tool for the marker-assisted selection of P. huashanica chromosome(s) in a wheat background, and it should also allow wheat breeders to screen for the excellent traits found in P. huashanica chromatin.
Genet Mol Res 2013 Oct 18
PMID:A novel SCAR marker for detecting Psathyrostachys huashanica Keng chromatin introduced in wheat. 2422 54

Placental development is known for its resemblance with tumor development, such as in the expression of oncogenes (c-myc) and telomerase (hTERT). The expression of c-myc and hTERT is up-regulated during early pregnancy and gestational trophoblastic diseases (GTDs). To determine the role of DNA methylation [via methylation-sensitive high resolution melting (MS-HRM)] and histone modifications [via chromatin immunoprecipitation (ChIP assay)] in regulating the differential expression of c-myc and hTERT during normal gestation and their dysregulation during placental disorders, we obtained placental samples from 135 pregnant women, in five groups: normal first, second and third trimester (n = 30 each), pre-eclamptic pregnancy (n = 30) and molar pregnancy (n = 15). Two placental cell lines (JEG-3 and HTR-8/SVneo) and isolated first-trimester cytotrophoblasts were also studied. Quantitative RT-PCR revealed decreased mRNA expression levels of c-myc and hTERT, which were associated with a higher level of H3K9me3 (1.5-fold, P < 0.05) and H3K27me3 (1.9-fold, P < 0.05), respectively, in third-trimester placental villi versus first-trimester villi. A significantly lower level of H3K27me3 in molar placenta was associated with a higher mRNA expression of c-myc and hTERT. The development of pre-eclampsia (PE) was associated with increased methylation (P < 0.001) and H3K27me3 (P < 0.01) at the c-myc promoter and reduced H3K9me3 (P < 0.01) and H3K27me3 (P < 0.05) at the hTERT promoter. Further, mRNA expression of c-myc and hTERT was strongly correlated in molar villi (r = 0.88, P < 0.01) and JEG-3 cells (r = 0.99, P < 0.02). Moreover, on the basis of methylation data, we demonstrate the potential of c-myc as a fetal DNA epigenetic marker for pre-eclamptic pregnancies. Thus we suggest a role for epigenetic mechanisms in regulating differential expression of c-myc and hTERT during placental development and use of the c-myc promoter region as a potential fetal DNA marker in the case of PE.
Mol Hum Reprod 2014 Oct
PMID:Epigenetic mechanisms regulate placental c-myc and hTERT in normal and pathological pregnancies; c-myc as a novel fetal DNA epigenetic marker for pre-eclampsia. 2502 39


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