Identification of AFLP makers linked to non-seed shattering locus (sht1) in buckwheat and conversion to STS markers for marker-assisted selection

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 469-474 ◽  
Author(s):  
K Matsui ◽  
Y Kiryu ◽  
T Komatsuda ◽  
N Kurauchi ◽  
T Ohtani ◽  
...  
Keyword(s):  
Marker Assisted Selection ◽  
Bulked Segregant Analysis ◽  
Aflp Markers ◽  
Aflp Analysis ◽  
Common Buckwheat ◽  
Gene Encoding ◽  
Sts Markers ◽  
Self Compatibility ◽  
Almost All

Shattering habit in buckwheat has two forms: brittle pedicel and weak pedicel. Brittle pedicel is observed in wild buckwheat, but not in cultivated buckwheat. Brittle pedicel in buckwheat is produced by two complementary, dominant genes, Sht1 and Sht2. The sht1 locus is linked to the S locus; almost all common buckwheat cultivars possess the allele sht1. To detect molecular makers linked to the sht1 locus, we used amplified fragment-length polymorphism (AFLP) analysis in combination with bulked segregant analysis of segregating progeny of a cross between a non-brittle common buckwheat and a brittle self-compatible buckwheat line. We screened 312 primer combinations and constructed a linkage map around the sht1 locus by using 102 F2 plants. Five AFLP markers were linked to the sht1 locus. Two of these, e54m58/610 and e55m46/320, cosegregated with the sht1 locus without recombination. The two AFLP markers were converted to STS markers according to the sequence of the AFLPs. The STS markers are useful for marker-assisted selection of non-brittle pedicel plants and provides a stepping-stone for map-based cloning and characterization of the gene encoding non-brittle pedicel.Key words: Fagopyrum esculentum, brittle pedicel, self-compatibility, bulked segregant analysis.

scholarly journals Release of Nonstop Ribosomes Is Essential

mBio ◽  
2014 ◽  
Vol 5 (6) ◽  
Author(s):  
Heather A. Feaga ◽  
Patrick H. Viollier ◽  
Kenneth C. Keiler
Keyword(s):  
Messenger Rna ◽  
Caulobacter Crescentus ◽  
Stop Codon ◽  
Selective Advantage ◽  
Gene Encoding ◽  
Content Type ◽  
Bacterial Phyla ◽  
Almost All

ABSTRACTBacterial ribosomes frequently translate to the 3′ end of an mRNA without terminating at a stop codon. Almost all bacteria use the transfer-messenger RNA (tmRNA)-basedtrans-translation pathway to release these “nonstop” ribosomes and maintain protein synthesis capacity.trans-translation is essential in some species, but in others, such asCaulobacter crescentus,trans-translation can be inactivated. To determine whytrans-translation is dispensable inC. crescentus, a Tn-seq screen was used to identify genes that specifically alter growth in cells lackingssrA, the gene encoding tmRNA. One of these genes,CC1214, was essential in ΔssrAcells. Purified CC1214 protein could release nonstop ribosomesin vitro. CC1214 is a homolog of theEscherichia coliArfB protein, and using the CC1214 sequence, ArfB homologs were identified in the majority of bacterial phyla. Most species in whichssrAhas been deleted contain an ArfB homolog, suggesting that release of nonstop ribosomes may be essential in most or all bacteria.IMPORTANCEGenes that are conserved across large phylogenetic distances are expected to confer a selective advantage. The genes required fortrans-translation,ssrAandsmpB, have been found in >99% of sequenced bacterial genomes, suggesting that they are broadly important. However, these genes can be deleted in some species without loss of viability. The identification and characterization ofC. crescentusArfB reveals whytrans-translation is not essential inC. crescentusand suggests that many other bacteria are likely to use ArfB to survive whentrans-translation is compromised.

scholarly journals (272) DNA Markers Linked to the Resistance Gene of Scab in Oriental Pear (Pyrus sp.)

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1020D-1020
Author(s):  
Kang-Hee Cho ◽  
Il-Sheob Shin ◽  
Seong-Sig Hong ◽  
Ki-Taek Kim ◽  
Hwa-Suk Song ◽  
...  
Keyword(s):  
Dna Markers ◽  
Marker Assisted Selection ◽  
Bulked Segregant Analysis ◽  
Scab Resistance ◽  
Aflp Analysis ◽  
Practical Application ◽  
Selection Efficiency ◽  
Susceptible Parent ◽  
Breeding Programs ◽  
Resistant Parent

Pear scab caused by Venturianashicolais one of the most important diseases of oriental pear. Breeding a variety resistant to scab can be improved through marker-assisted selection (MAS). Bulked segregant analysis (BSA) and amplified fragment length polymorphic (AFLP) analysis were performed to identify DNA markers linked to the scab-resistant gene (Vn) using a population from a cross between PS2-93-3-98 (resistant parent) and Yali (susceptible parent). A total of 480 EcoR I/MseI primer combinations were used to identify markers specific to PS2-93-3-98 and resistant pool. Three AFLP markers linked to Vn, E-AGT/M-CCA245, E-ATT/M-CCG300, and E-GGT/M-TCT225, were selected. Linkage analysis between the selected markers and Vn locus was conducted with 51 individual plants. The selected markers, E-AGT/M-CCA245, E-ATT/M-CCG300, and E-GGT/M-TCT225, were located at 3.9, 3.8, and 1.2 cm away from Vn, respectively. For practical application, we are currently converting selected markers to simple PCR-based markers. The markers could be used to increase selection efficiency in pear-breeding programs for scab resistance.

Development of a CAPS marker for the Pvr4 locus: A tool for pyramiding potyvirus resistance genes in pepper

Genome ◽  
1999 ◽  
Vol 42 (6) ◽  
pp. 1111-1116 ◽  
Author(s):  
Carole Caranta ◽  
Arnaud Thabuis ◽  
Alain Palloix
Keyword(s):  
Resistance Genes ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Marker Assisted Selection ◽  
Fragment Length Polymorphism ◽  
Bulked Segregant Analysis ◽  
Amplified Fragment Length Polymorphism ◽  
Aflp Markers ◽  
Caps Marker ◽  
Using Data

The Pvr4 resistance gene in pepper confers a complete resistance to the three pathotypes of potato virus Y (PVY) and to pepper mottle virus (PepMoV). In order to use this gene in a marker-assisted selection (MAS) program and to permit the pyramiding of several potyvirus resistance genes in the same cultivar, tightly linked amplified fragment length polymorphism (AFLP) markers were obtained by the bulked segregant analysis method. Eight linked AFLP markers were mapped in an interval from 2.1 ± 0.8 to 13.8 ± 2.9 cM around this locus. The closest codominant AFLP marker was converted into a codominant CAPS (cleaved amplified polymorphic sequence) marker using data from the alignment of the two allele sequences. We have further characterized the relevance of the CAPS marker for MAS programs in different pepper breeding lines.Key words: amplified fragment length polymorphism markers, bulked segregant analysis, Capsicum annuum, marker-assisted selection, potyvirus resistance.

Identification of AFLP markers closely linked to the powdery mildew resistance genes Pm1c and Pm4a in common wheat (Triticum aestivum L.)

Genome ◽  
1999 ◽  
Vol 42 (2) ◽  
pp. 322-329 ◽  
Author(s):  
Lorenz Hartl ◽  
Volker Mohler ◽  
Friedrich J Zeller ◽  
Sai LK Hsam ◽  
Günther Schweizer
Keyword(s):  
Triticum Aestivum ◽  
Powdery Mildew ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Powdery Mildew Resistance ◽  
Bulked Segregant Analysis ◽  
Triticum Aestivum L ◽  
Aflp Markers ◽  
Aflp Analysis ◽  
Mildew Resistance

A total of 7654 DNA fragments were screened for linkage to wheat powdery mildew resistance gene Pm1c employing fluorescently based AFLP analysis and phenotypic pools from F3 families. F3 and derived F4 families were used for segregation analysis. Pool screening revealed several cosegregating and tightly linked (0.9 cM) AFLP markers for the Pm1c resistance gene. The previously reported RFLP locus Xwhs178 was integrated into the AFLP map in the vicinity of Pm1c. One AFLP marker, 18M2, was determined to be highly specific for the Pm1c gene in diverse genetic backgrounds. As Pm1c allele confers an effective resistance to powdery mildew, the marker 18M2 provides a valuable tool for enhancing marker assisted selection and pyramiding of powdery mildew resistance genes in wheat.Key words: Triticum aestivum, powdery mildew, disease resistance, AFLP, bulked segregant analysis

AFLP markers linked to resistance against Striga gesnerioides race 1 in cowpea (Vigna unguiculata)

Genome ◽  
2002 ◽  
Vol 45 (5) ◽  
pp. 787-793 ◽  
Author(s):  
Jeremy T Ouédraogo ◽  
Jean-Baptiste Tignegre ◽  
Michael P Timko ◽  
François J Belzile
Keyword(s):  
Molecular Markers ◽  
Vigna Unguiculata ◽  
Fragment Length Polymorphism ◽  
Bulked Segregant Analysis ◽  
Aflp Markers ◽  
Resistant Cultivar ◽  
Aflp Analysis ◽  
Striga Gesnerioides ◽  
Striga Resistance ◽  
Race 1

Amplified fragment length polymorphism (AFLP) analysis was used in combination with bulked segregant analysis (BSA) to identify molecular markers linked to two cowpea (Vigna unguiculata (L.) Walp.) genes conferring resistance to Striga gesnerioides race 1. After AFLP analysis of an F2 population derived from a cross between the resistant cultivar Gorom and the susceptible cultivar Tvx 3236, seven AFLP markers were identified that are linked to Rsg3, the gene conferring race 1 resistance in 'Gorom'. The distances between these markers and Rsg3 ranged from 9.9 to 2.5 cM, with two markers, E-AGA/M-CTA460 and E-AGA/M-CAG300, flanking Rsg3 at 2.5 and 2.6 cM, respectively. Analysis of a second F2 population derived from the cross between 'Tvx 3236' and the resistant cultivar IT81D-994 identified five AFLP markers linked to the race 1 resistance gene 994-Rsg present in 'IT81D-994'. The two markers showing the tightest linkage to the994-Rsg locus were E-AAG/M-AAC450 and E-AAG/M-AAC150 at 2.1 and 2.0 cM, respectively. Two of the markers linked to 994-Rsg, E-AGA/M-CAG300 and E-AGA/M-CAG450, were also linked to Rsg3. The identification of molecular markers in common between the two sources of race 1 resistance suggests that either Striga resistance genes are clustered in these plants or that these loci are allelic. Mapping of the resistance loci within the cowpea genome revealed that three markers linked to Rsg3 and (or) 994-Rsg are located on linkage group 6.Key words: cowpea, AFLP markers, Striga resistance, bulked segregant analysis.

Phylogeny Characterization of Seb Gene Encoding Enterotoxins in Staphylococcus aureus Isolated from Raw Milk and Cheese

2019 ◽  
Vol 9 (o3) ◽  
Author(s):  
Fatima N. Aziz ◽  
Laith Abdul Hassan Mohammed-Jawad
Keyword(s):  
Staphylococcus Aureus ◽  
Food Poisoning ◽  
Raw Milk ◽  
Staphylococcal Enterotoxin B ◽  
Human Pathogen ◽  
Conventional Pcr ◽  
Biochemical Tests ◽  
Specific Primers ◽  
Gene Encoding

Food poisoning due to the bacteria is a big global problem in economically and human's health. This problem refers to an illness which is due to infection or the toxin exists in nature and the food that use. Milk is considered a nutritious food because it contains proteins and vitamins. The aim of this study is to detect and phylogeny characterization of staphylococcal enterotoxin B gene (Seb). A total of 200 milk and cheese samples were screened. One hundred ten isolates of Staphylococcus aureus pre-confirmed using selective and differential media with biochemical tests. Genomic DNA was extracted from the isolates and the SEB gene detects using conventional PCR with specific primers. Three staphylococcus aureus isolates were found to be positive for Seb gene using PCR and confirmed by sequencing. Sequence homology showed variety range of identity starting from (100% to 38%). Phylogenetic tree analyses show that samples (6 and 5) are correlated with S. epidermidis. This study discovered that isolates (A6-RLQ and A5-RLQ) are significantly clustered in a group with non- human pathogen Staphylococcus agnetis.

A Thorough Theoretical Exploration of Intriguing Characteristics of Cyclo[18]carbon: Geometry, Bonding Nature, Aromaticity, Weak Interaction, Reactivity, Excited States, Vibrations, Molecular Dynamics and Various Molecular Properties

2019 ◽  
Author(s):  
Tian Lu ◽  
Qinxue Chen ◽  
Zeyu Liu
Keyword(s):  
Molecular Dynamics ◽  
Excited States ◽  
Electronic Excitation ◽  
Ring Structure ◽  
Molecular Properties ◽  
Molecular Vibration ◽  
Full Characterization ◽  
Long Time ◽  
Almost All

Although cyclo[18]carbon has been theoretically and experimentally investigated since long time ago, only very recently it was prepared and directly observed by means of STM/AFM in condensed phase (Kaiser et al., <i>Science</i>, <b>365</b>, 1299 (2019)). The unique ring structure and dual 18-center π delocalization feature bring a variety of unusual characteristics and properties to the cyclo[18]carbon, which are quite worth to be explored. In this work, we present an extremely comprehensive and detailed investigation on almost all aspects of the cyclo[18]carbon, including (1) Geometric characteristics (2) Bonding nature (3) Electron delocalization and aromaticity (4) Intermolecular interaction (5) Reactivity (6) Electronic excitation and UV/Vis spectrum (7) Molecular vibration and IR/Raman spectrum (8) Molecular dynamics (9) Response to external field (10) Electron ionization, affinity and accompanied process (11) Various molecular properties. We believe that our full characterization of the cyclo[18]carbon will greatly deepen researchers' understanding of this system, and thereby help them to utilize it in practice and design its various valuable derivatives.

A Thorough Theoretical Exploration of Intriguing Characteristics of Cyclo[18]carbon: Geometry, Bonding Nature, Aromaticity, Weak Interaction, Reactivity, Excited States, Vibrations, Molecular Dynamics and Various Molecular Properties

2019 ◽  
Author(s):  
Tian Lu ◽  
Qinxue Chen ◽  
Zeyu Liu
Keyword(s):  
Molecular Dynamics ◽  
Excited States ◽  
Electronic Excitation ◽  
Ring Structure ◽  
Molecular Properties ◽  
Molecular Vibration ◽  
Full Characterization ◽  
Long Time ◽  
Almost All

Although cyclo[18]carbon has been theoretically and experimentally investigated since long time ago, only very recently it was prepared and directly observed by means of STM/AFM in condensed phase (Kaiser et al., <i>Science</i>, <b>365</b>, 1299 (2019)). The unique ring structure and dual 18-center π delocalization feature bring a variety of unusual characteristics and properties to the cyclo[18]carbon, which are quite worth to be explored. In this work, we present an extremely comprehensive and detailed investigation on almost all aspects of the cyclo[18]carbon, including (1) Geometric characteristics (2) Bonding nature (3) Electron delocalization and aromaticity (4) Intermolecular interaction (5) Reactivity (6) Electronic excitation and UV/Vis spectrum (7) Molecular vibration and IR/Raman spectrum (8) Molecular dynamics (9) Response to external field (10) Electron ionization, affinity and accompanied process (11) Various molecular properties. We believe that our full characterization of the cyclo[18]carbon will greatly deepen researchers' understanding of this system, and thereby help them to utilize it in practice and design its various valuable derivatives.

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