Identification of genes associated with low furanocoumarin content in grapefruit

Genome ◽  
2014 ◽  
Vol 57 (10) ◽  
pp. 537-545 ◽  
Author(s):  
Chunxian Chen ◽  
Qibin Yu ◽  
Xu Wei ◽  
Paul F. Cancalon ◽  
Fred G. Gmitter, Jr.
Keyword(s):  
Grapefruit Juice ◽  
Fragment Length Polymorphism ◽  
Sweet Orange ◽  
Single Gene ◽  
Digital Gene Expression ◽  
Differentially Expressed ◽  
Aflp Analysis ◽  
Citrus Paradisi ◽  
Aflp Fragment ◽  
Digital Gene Expression Profile

Some furanocoumarins in grapefruit (Citrus paradisi) are associated with the so-called grapefruit juice effect. Previous phytochemical quantification and genetic analysis suggested that the synthesis of these furanocoumarins may be controlled by a single gene in the pathway. In this study, cDNA-amplified fragment length polymorphism (cDNA-AFLP) analysis of fruit tissues was performed to identify the candidate gene(s) likely associated with low furanocoumarin content in grapefruit. Fifteen tentative differentially expressed fragments were cloned through the cDNA-AFLP analysis of the grapefruit variety Foster and its spontaneous low-furanocoumarin mutant Low Acid Foster. Sequence analysis revealed a cDNA-AFLP fragment, Contig 6, was homologous to a substrate-proved psoralen synthase gene, CYP71A22, and was part of citrus unigenes Cit.3003 and Csi.1332, and predicted genes Ciclev10004717m in mandarin and orange1.1g041507m in sweet orange. The two predicted genes contained the highly conserved motifs at one of the substrate recognition sites of CYP71A22. Digital gene expression profile showed the unigenes were expressed only in fruit and seed. Quantitative real-time PCR also proved Contig 6 was down-regulated in Low Acid Foster. These results showed the differentially expressed Contig 6 was related to the reduced furanocoumarin levels in the mutant. The identified fragment, homologs, unigenes, and genes may facilitate further furanocoumarin genetic study and grapefruit variety improvement.

scholarly journals Citrus asymmetric somatic hybrids produced via fusion of gamma-irradiated and iodoacetamide-treated protoplasts

2009 ◽  
Vol 44 (5) ◽  
pp. 454-462 ◽  
Author(s):  
Claudine Maria de Bona ◽  
Jean Howe Gould ◽  
J. Creighton Miller Jr ◽  
David Stelly ◽  
Eliezer Silva Louzada
Keyword(s):  
Gamma Rays ◽  
Fragment Length Polymorphism ◽  
Somatic Hybrids ◽  
Poncirus Trifoliata ◽  
Aflp Analysis ◽  
Citrus Paradisi ◽  
Suspension Cells ◽  
Rough Lemon ◽  
Embryogenic Suspension ◽  
Gamma Irradiated

The objective of this study was to produce citrus somatic asymmetric hybrids by fusing gamma-irradiated protoplasts with iodoacetamide-treated protoplasts. Protoplasts were isolated from embryogenic suspension cells of grapefruit (Citrus paradisi Macfad.) cultivars Ruby Red and Flame, sweet oranges (C. sinensis Osbeck) 'Itaboraí', 'Natal', Valencia', and 'Succari', from 'Satsuma' (C. unshiu Marcow.) and 'Changsha' mandarin (C. reticulata Blanco) and 'Murcott' tangor (C. reticulata x C. sinensis). Donor protoplasts were exposed to gamma rays and receptor protoplasts were treated with 3 mmol L-1 iodoacetamide (IOA), and then they were fused for asymmetric hybridization. Asymmetric embryos were germinated, and the resulting shoots were either grafted onto sour orange, rough lemon or 'Swingle' (C. paradisi x Poncirus trifoliata) x 'Sunki' mandarin rootstock seedlings, or rooted after dipping their bases in indol-butyric acid (IBA) solution. The products were later acclimatized to greenhouse conditions. Ploidy was analyzed by flow cytometry, and hybridity was confirmed by amplified fragment length polymorphism (AFLP) analysis of plantlet DNAsamples. The best treatment was the donor-recipient fusion combination of 80 Gy-irradiated 'Ruby Red' protoplasts with 20 min IOA-treated 'Succari' protoplasts. Tetraploid and aneuploid plants were produced. Rooting recalcitrance was solved by dipping shoots' stems in 3,000 mg L-1 IBA solution for 10 min.

cDNA-AFLP Analysis of Differentially Expressed Genes in Tobacco Infected by TMV

2013 ◽  
Vol 38 (1) ◽  
pp. 62-70 ◽  
Author(s):  
Rong-Ping CHEN ◽  
Lie LIU ◽  
Xiu-Qing WAN ◽  
En-Jian QIU ◽  
Chun-Jun WANG ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Aflp Analysis

Furocoumarin Kinetics in Plasma and Urine of Healthy Adults Following Consumption of Grapefruit (Citrus paradisi Macf.) and Grapefruit Juice

2017 ◽  
Vol 65 (14) ◽  
pp. 3006-3012 ◽  
Author(s):  
Melissa M. Melough ◽  
Terrence M. Vance ◽  
Sang Gil Lee ◽  
Anthony A. Provatas ◽  
Christopher Perkins ◽  
...  
Keyword(s):  
Grapefruit Juice ◽  
Healthy Adults ◽  
Citrus Paradisi

scholarly journals Genetic Diversity of Rhubarb Cultivars

2008 ◽  
Vol 133 (4) ◽  
pp. 587-592 ◽  
Author(s):  
Joseph C. Kuhl ◽  
Veronica L. DeBoer
Keyword(s):  
Genetic Diversity ◽  
Central Asia ◽  
Length Polymorphism ◽  
Genetic Relationship ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
18Th Century ◽  
Pedigree Information ◽  
Aflp Analysis ◽  
Fingerprint Analysis

The genus Rheum L., commonly known as rhubarb, is composed of ≈60 species, primarily distributed throughout northern and central Asia. Rhubarb species have been used for medicinal purposes for thousands of years; however, it was not until the 18th century that the culinary use of petioles was first reported. Although the origin(s) of culinary rhubarb is not clear, it is thought that they originated from hybridization of rhubarb species originally brought to Europe for medicinal purposes. Most rhubarb cultivars lack pedigree information, and the genetic relationship among cultivars is largely unknown. Amplified fragment length polymorphism (AFLP) markers were generated for fingerprint analysis of 37 cultivars and four putative Rheum species accessions. Ten EcoRI and MseI primer combinations were analyzed for a total of 1400 scored polymorphisms, with an average of 140 polymorphisms per primer combination. Results show at least two clusters of related cultivars, as well as distantly related accessions. This study provides an estimate of rhubarb cultivar genetic diversity using AFLP analysis.

scholarly journals Genomic Relatedness of ChlamydiaIsolates Determined by Amplified Fragment Length Polymorphism Analysis

1999 ◽  
Vol 181 (15) ◽  
pp. 4469-4475 ◽  
Author(s):  
Adam Meijer ◽  
Servaas A. Morré ◽  
Adriaan J. C. Van Den Brule ◽  
Paul H. M. Savelkoul ◽  
Jacobus M. Ossewaarde
Keyword(s):  
Cluster Analysis ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Chlamydia Psittaci ◽  
Rrna Genes ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Genomic Relatedness

ABSTRACT The genomic relatedness of 19 Chlamydia pneumoniaeisolates (17 from respiratory origin and 2 from atherosclerotic origin), 21 Chlamydia trachomatis isolates (all serovars from the human biovar, an isolate from the mouse biovar, and a porcine isolate), 6 Chlamydia psittaci isolates (5 avian isolates and 1 feline isolate), and 1 Chlamydia pecorum isolate was studied by analyzing genomic amplified fragment length polymorphism (AFLP) fingerprints. The AFLP procedure was adapted from a previously developed method for characterization of clinical C. trachomatis isolates. The fingerprints of all C. pneumoniae isolates were nearly identical, clustering together at a Dice similarity of 92.6% (± 1.6% standard deviation). The fingerprints of the C. trachomatis isolates of human, mouse, and swine origin were clearly distinct from each other. The fingerprints of the isolates from the human biovar could be divided into at least 12 different types when the presence or absence of specific bands was taken into account. The C. psittacifingerprints could be divided into a parakeet, a pigeon, and a feline type. The fingerprint of C. pecorum was clearly distinct from all others. Cluster analysis of selected isolates from all species revealed groups other than those based on sequence data from single genes (in particular, omp1 and rRNA genes) but was in agreement with available DNA-DNA hybridization data. In conclusion, cluster analysis of AFLP fingerprints of representatives of all species provided suggestions for a grouping of chlamydiae based on the analysis of the whole genome. Furthermore, genomic AFLP analysis showed that the genome of C. pneumoniae is highly conserved and that no differences exist between isolates of respiratory and atherosclerotic origins.

Comparative Fingerprinting Analysis ofCampylobacter jejuni subsp. jejuni Strains by Amplified-Fragment Length Polymorphism Genotyping

2000 ◽  
Vol 38 (9) ◽  
pp. 3379-3387 ◽  
Author(s):  
Bjørn-Arne Lindstedt ◽  
Even Heir ◽  
Traute Vardund ◽  
Kjetil K. Melby ◽  
Georg Kapperud
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Epidemiological Surveillance ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Pcr Rflp ◽  
Pcr Products ◽  
Ofcampylobacter Jejuni

Amplified-fragment length polymorphism (AFLP) analysis with the endonucleases BglII and MfeI was used to genotype 91 Campylobacter jejuni subsp. jejunistrains from outbreaks and sporadic cases. AFLP-generated fragments were labeled with fluorescent dye and separated by capillary electrophoresis. The software packages GeneScan and GelCompar II were used to calculate AFLP pattern similarities and to investigate phylogenetic relationships among the genotyped strains. The AFLP method was compared with two additional DNA-based typing methods, pulsed-field gel electrophoresis (PFGE) using SmaI and restriction fragment length polymorphism analysis on PCR products (PCR-RFLP) of theflaA and flaB genes. We found that AFLP analysis of C. jejuni strains is a rapid method that offers better discriminatory power than do both PFGE and PCR-RFLP. AFLP and, to a lesser extent, PCR-RFLP could differentiate strains within the same PFGE profiles, which also makes PCR-RFLP an alternative to PFGE. We were able to clearly distinguish 9 of 10 recognized outbreaks by AFLP and to identify similarities among outbreak and sporadic strains. Therefore, AFLP is suitable for epidemiological surveillance ofC. jejuni and will be an excellent tool for source identification in outbreak situations.

scholarly journals Relationships among Morphological Characters, Isozymes Polymorphism and DNA Variability – the Impact on Lactuca Germplasm Taxonomy

2011 ◽  
Vol 39 (No. 2) ◽  
pp. 59-67 ◽  
Author(s):  
I. Doležalová ◽  
A. Lebeda ◽  
M. Dziechciarková ◽  
E. Křístková ◽  
D. Astley ◽  
...  
Keyword(s):  
Dna Content ◽  
Fragment Length Polymorphism ◽  
Morphological Variability ◽  
Morphological Characters ◽  
Aflp Analysis ◽  
Dapi Staining ◽  
Lactuca Species ◽  
Relative Dna Content ◽  
The Impact

Fifty one accessions of nineteen Lactuca species, the hybrid L. serriola × L. sativa and the related species Mycelis muralis were evaluated for morphological variability, esterase (EST) polymorphism, Amplified Fragment Length Polymorphism (AFLP) and relative DNA content. Sixteen Lactuca accessions were classified taxonomically on the basis of morphology, isozyme analysis and AFLP. Twenty-eight bands (isoforms) of EST were recorded allowing 82% of accessions to be distinguished. The relative DNA content, measured using flow-cytometry (DAPI staining), ranged from 2.02 pg in L. capensis to 17.96 pg in L. canadensis. The results from AFLP analysis and the relative DNA content measurement corresponded well with recent taxonomic classification of the genus Lactuca.  

Genetic Variability in the Potato Pathogen Colletotrichum coccodes as Determined by Amplified Fragment Length Polymorphism and Vegetative Compatibility Group Analyses

2006 ◽  
Vol 96 (10) ◽  
pp. 1097-1107 ◽  
Author(s):  
Larry J. Heilmann ◽  
Nadav Nitzan ◽  
Dennis A. Johnson ◽  
Julie S. Pasche ◽  
Curt Doetkott ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Vegetative Compatibility ◽  
Colletotrichum Coccodes ◽  
Aflp Analysis ◽  
Aflp Data ◽  
Bootstrap Analysis ◽  
Nit Mutants

Amplified fragment length polymorphism (AFLP) using three primer sets was used to characterize 211 Colletotrichum coccodes isolates from North America, 112 of which were assigned to six vegetative compatibility groups (VCGs) using nitrate nonutilizing (nit) mutants. These isolates clustered into five corresponding groups by unweighted pairgroup method with arithmetic means-based cluster analysis of AFLP banding patterns. Isolates of C. coccodes belonging to NA-VCG1 and NA-VCG3 were closely related, as were isolates belonging to NA-VCG2 and NA-VCG5. Based on bootstrap analysis of AFLP data, the two isolates originally assigned to NA-VCG4 clustered with isolates belonging to NA-VCG2 and NA-VCG5. C. coccodes isolates that clustered with two isolates belonging to NA-VCG6 were the most diverged from other groups, including seven isolates collected from hosts other than potato. As opposed to the bootstrap analysis, a quadratic discriminant analysis (QDA) of AFLP data correctly categorized the two isolates of NA-VCG4. Furthermore, in isolates where VCG determinations had been made, this model correctly classified isolates of all VCGs. QDA classifications were identical to those made by the bootstrap analysis, with the exception of VCG4. Overall, classifications made by the QDA model were strongly correlated (r = 0.970, P < 0.001) to the VCGs assigned by traditional methods. All 99 C. coccodes isolates evaluated only by AFLP also were subjected to QDA, leading to the assignment of a presumptive VCG for each isolate. No isolates of VCG4 or VCG6 were identified by QDA within this population. Symptoms of black dot developed in plants inoculated with isolates collected from both potato and non-potato hosts. However, total yield was not significantly reduced by infection with non-potato isolates. The lack of any additional groups identified by AFLP analysis may be an indicator of a limited level of genetic variation among North American C. coccodes isolates. AFLP is a much more efficient technique for subspecific characterization in C. coccodes than VCG analysis utilizing nit mutants and will provide an effective means by which the population biology of this pathogen can be further investigated worldwide.

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