scholarly journals SEX IDENTIFICATION OF DATE PALM BY USING DNA MOLECULAR MARKERS

2017 ◽  
Vol 48 (5) ◽  
Author(s):  
Khierallah & et al.
Keyword(s):  
Molecular Markers ◽  
Dna Markers ◽  
Date Palm ◽  
Restriction Enzymes ◽  
Sex Identification ◽  
Candidate Region ◽  
Randomly Amplified Polymorphic Dna ◽  
Pcr Products ◽  
Polymorphic Bands ◽  
Gender Detection

This study was conducted to investigate the early detection of date palm gender, the current study was conducted using some DNA markers technology using Bulk Segregant Analysis (BSA) and three molecular markers including Randomly Amplified Polymorphic DNA (RAPDs), and Cleaved Amplified Polymorphic Sequence (CAPS) and Nested PCR. Results showed that RAPD primers used cleared different banding pattern. Fifty primers showed monomorphic bands while ten showed polymorphic bands for the two balks Males (MB) and females (FM). These primers showed 626 total bands in which 41 of them was polymorphic (6.54% polymorphism). OPD.10 primer gave the highest number of bands reached 118 bands and was the highest efficiency (18.85%). While the primer OPE04 was least efficient (3.51%), giving only 22 bands. A band with molecular weight of 143 bp appeared in six females of the total seven female varieties (85.71%) and did not appear in all males suggesting a positive marker which could be consider a candidate region for gender in date palm. Results of CAPS markers using three restriction enzymes: Bcl I, Hpa II and RsaI to digest the PCR products of OPD.10 primer. Results indicated that not all enzymes were useful for cutting DNA of samples. Bcl I enzyme cut the band of 143 bp which appeared in six female samples, while Hpa II enzyme cut the band of 180 bp in five males and six females. The former enzyme had also cut and the band of 433 bp in all female varieties. No response was noted when DNA was restricted with enzyme RsaI. The above results consider to be promising for gender detection in date palm.   

scholarly journals A Comparative Study of 5S rDNA Non-Transcribed Spacers in Elaeagnaceae Species

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 4
Author(s):  
Oleg S. Alexandrov ◽  
Olga V. Razumova ◽  
Gennady I. Karlov
Keyword(s):  
Polymerase Chain Reaction ◽  
Molecular Markers ◽  
Dna Markers ◽  
5S Rdna ◽  
Chain Reaction ◽  
Closely Related Species ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Species Specific ◽  
Shepherdia Canadensis

5S rDNA is organized as a cluster of tandemly repeated monomers that consist of the conservative 120 bp coding part and non-transcribed spacers (NTSs) with different lengths and sequences among different species. The polymorphism in the 5S rDNA NTSs of closely related species is interesting for phylogenetic and evolutional investigations, as well as for the development of molecular markers. In this study, the 5S rDNA NTSs were amplified with universal 5S1/5S2 primers in some species of the Elaeagnaceae Adans. family. The polymerase chain reaction (PCR) products of five Elaeagnus species had similar lengths near 310 bp and were different from Shepherdia canadensis (L.) Nutt. and Sh. argentea (Pusch.) Nutt. samples (260 bp and 215 bp, respectively). The PCR products were cloned and sequenced. An analysis of the sequences revealed that intraspecific levels of NTS identity are high (approximately 95–96%) and similar in the Elaeagnus L. species. In Sh. argentea, this level was slightly lower due to the differences in the poly-T region. Moreover, the intergeneric and intervarietal NTS identity levels were studied and compared. Significant differences between species (except E. multiflora Thunb. and E. umbellata Thunb.) and genera were found. Herein, a range of the NTS features is discussed. This study is another step in the investigation of the molecular evolution of Elaeagnaceae and may be useful for the development of species-specific DNA markers in this family.

Molecular markers in entomology

1998 ◽  
Vol 88 (6) ◽  
pp. 577-600 ◽  
Author(s):  
H.D. Loxdale ◽  
G. Lushai
Keyword(s):  
Biological Sciences ◽  
Molecular Markers ◽  
Dna Markers ◽  
Great Promise ◽  
Randomly Amplified Polymorphic Dna ◽  
Protein Markers ◽  
General Reader ◽  
Banding Patterns ◽  
Diverse Range ◽  
Fields Of Study

AbstractA diverse range of novel molecular (DNA) markers are now available for entomological investigations. Both DNA and protein markers have revolutionized the biological sciences and have enhanced many fields of study, especially ecology. Relative to DNA markers, allozymes are cheap, often much quicker to isolate and develop, even from minute insects (aphids, thrips, parasitic wasps, etc.), and subsequently easy to use. They display single or multi-locus banding patterns of a generally easily interpretable Mendelian nature, and the statistics for their analysis are well established. DNA markers are also suitable for use with small amounts of insect material and can be used with stored, dry or old samples. They have an expanding range of applications, many involving intra- and interspecific discriminations. Like allozymes, they can be single or multilocus, whilst methods for their statistical analysis have recently been published. However, they can be considerably more expensive than allozymes, require more complex preparatory protocols, expensive equipment, may involve lengthy development procedures (e.g. isolating cloned oligonucleotides to develop primers to detect microsatellite regions) and some have complex multi-locus banding patterns which may be of a non-Mendelian nature (e.g. RAPDs, randomly amplified polymorphic DNA), and are in some cases, not easily repeatable. In this review, we hope to inform the general reader about the methodology and scope of the main molecular markers commonly in use, along with brief details of some other techniques which show great promise for entomological studies. Thereafter, we discuss their applications including suitability for particular studies, the methods used to load and run samples, subsequent band detection, band scoring and interpretation, the reliability of particular techniques, the issues of safety involved, cost effectiveness and the statistical analyses utilized.

scholarly journals Diversity Assessment and Cultivar Identification in Date Palm through Molecular Markers- A Review

2017 ◽  
Vol 5 (12) ◽  
pp. 1516
Author(s):  
Nadia Faqir ◽  
Aish Muhammad ◽  
Muhammad Zeeshan Hyder
Keyword(s):  
Molecular Markers ◽  
Environmental Factors ◽  
Dna Markers ◽  
Growth Stage ◽  
Date Palm ◽  
Environmental Changes ◽  
Morphological Properties ◽  
Length Variation ◽  
Diversity Assessment

Date palm has a long history of cultivation and a valuable germplasm with little knowledge about its genetic makeup and variation among the most cultivated cultivars. Diversity is the variability of a species. Plants show variation in yield, vegetative traits and morphological properties of fruits and seeds in response to environmental changes. Molecular markers or DNA markers have been in use since past three decades. The DNA profiles give information about the genotype, screen the whole genome and show variation in both the coding and noncoding region and hence give information about polymorphism. Since plastid genes are transferred mostly from the mother line, the identification of maternal lines is possible by the sequencing of plastid genes. Simple sequence repeats (SSRs) can detect length variation with the help of Polymerase Chain Reaction (PCR) and may be used as highly informative genetic markers. Single Nucleotide Polymorphism (SNPs) are the third generation of molecular markers. SNPs are more stable and have high fidelity of inheritance as compared to other marker systems. Molecular markers have been developed but they are not enough for sufficient diversity assessment. Therefore there is a need to increase the number of DNA markers in date palm. Previously, there are several studies to type various commercially important germplasm based on morphological or yield parameters. Morphological and biochemical markers are limited in number and are affected by environmental factors and growth stage of the plant which reduce their reliability in the assessment of diversity and characterization of the germplasm. This necessitates the use of genetic characterization, utilizing DNA markers, gene sequencing or SNP genotyping which can work independent of the plant growth stage and are not affected by environmental factors. A combination of morphological, biochemical and molecular characterization of the date palm cultivars can better assess the level of diversity and relationship among the cultivars.

Variation in bacterial endosymbionts associated with the date palm hopper,Ommatissus lybicuspopulations

2017 ◽  
Vol 108 (2) ◽  
pp. 271-281 ◽  
Author(s):  
S. Karimi ◽  
H. Izadi ◽  
M. Askari Seyahooei ◽  
A. Bagheri ◽  
P. Khodaygan
Keyword(s):  
Date Palm ◽  
Multiple Infections ◽  
Infection Frequency ◽  
Pcr Assay ◽  
Specific Primers ◽  
Consensus Sequences ◽  
Pcr Products ◽  
Bacterial Endosymbionts ◽  
Different Populations ◽  
Polymerase Chain

AbstractThe date palm hopper,Ommatissus lybicus, is a key pest of the date palm, which is expected to be comprised of many allopatric populations. The current study was carried out to determine bacterial endosymbiont diversity in the different populations of this pest. Ten date palm hopper populations were collected from the main date palm growing regions in Iran and an additional four samples from Pakistan, Oman, Egypt and Tunisia for detection of primary and secondary endosymbionts using polymerase chain reaction (PCR) assay with their specific primers. The PCR products were directly sequenced and edited using SeqMan software. The consensus sequences were subjected to a BLAST similarity search. The results revealed the presence of ‘CandidatusSulcia muelleri’ (primary endosymbiont) andWolbachia,ArsenophonusandEnterobacter(secondary endosymbionts) in all populations. This assay failed to detect ‘CandidatusNasuia deltocephalinicola’ andSerratiain these populations. ‘Ca. S. muelleri’ exhibited a 100% infection frequency in populations andWolbachia,ArsenophonusandEnterobacterdemonstrated 100, 93.04 and 97.39% infection frequencies, respectively. The infection rate ofArsenophonusandEnterobacterranged from 75 to 100% and 62.5 to 100%, respectively, in different populations of the insect. The results demonstrated multiple infections by ‘Ca. Sulcia muelleri’,Wolbachia,ArsenophonusandEnterobacterin the populations and may suggest significant roles for these endosymbionts on date palm hopper population fitness. This study provides an insight to endosymbiont variation in the date palm hopper populations; however, further investigation is needed to examine how these endosymbionts may affect host fitness.

scholarly journals PCR amplification and sequence analyses of reverse transcriptase-like genes in Crinipellis perniciosa isolates

2007 ◽  
Vol 32 (5) ◽  
pp. 373-380 ◽  
Author(s):  
Jorge F. Pereira ◽  
Mariana D.C. Ignacchiti ◽  
Elza F. Araújo ◽  
Sérgio H. Brommonschenkel ◽  
Júlio C.M. Cascardo ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Pathogenic Fungus ◽  
Pcr Amplification ◽  
Restriction Enzymes ◽  
Sequence Comparisons ◽  
Copy Numbers ◽  
A Genome ◽  
Close Relationship ◽  
Pcr Products ◽  
Broom Disease

Reverse transcriptase (RT) sequence analysis is an important technique used to detect the presence of transposable elements in a genome. Putative RT sequences were analyzed in the genome of the pathogenic fungus C. perniciosa, the causal agent of witches' broom disease of cocoa. A 394 bp fragment was amplified from genomic DNA of different isolates of C. perniciosa belonging to C-, L-, and S-biotypes and collected from various geographical areas. The cleavage of PCR products with restriction enzymes and the sequencing of various RT fragments indicated the presence of several sequences showing transition events (G:C to A:T). Southern blot analysis revealed high copy numbers of RT signals, forming different patterns among C-, S-, and L-biotype isolates. Sequence comparisons of the predicted RT peptide indicate a close relationship with the RT protein from thegypsy family of LTR-retrotransposons. The possible role of these retrotransposons in generating genetic variability in the homothallic C. perniciosa is discussed.

scholarly journals First Report of a Group 16SrII Phytoplasma Infecting Chickpea in Oman

Plant Disease ◽  
2006 ◽  
Vol 90 (7) ◽  
pp. 973-973 ◽  
Author(s):  
N. A. Al-Saady ◽  
A. M. Al-Subhi ◽  
A. Al-Nabhani ◽  
A. J. Khan
Keyword(s):  
Nested Pcr ◽  
Animal Feed ◽  
Restriction Enzymes ◽  
Universal Primers ◽  
Polymorphism Analysis ◽  
Disease Symptoms ◽  
First Report ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Group 2

Chickpea (Cicer arietinum), locally known as “Dungo”, is grown for legume and animal feed mainly in the interior region of Oman. During February 2006, survey samples of chickpea leaves from plants showing yellows disease symptoms that included phyllody and little leaf were collected from the Nizwa Region (175 km south of Muscat). Total nucleic acid was extracted from asymptomatic and symptomatic chickpea leaves using a cetyltrimethylammoniumbromide method with modifications (3). All leaf samples from eight symptomatic plants consistently tested positive using a polymerase chain reaction assay (PCR) with phytoplasma universal primers (P1/P7) that amplify a 1.8-kb phytoplasma rDNA product and followed by nested PCR with R16F2n/R16R2 primers yielding a product of 1.2 kb (2). No PCR products were evident when DNA extracted from healthy plants was used as template. Restriction fragment length polymorphism analysis of nested PCR products by separate digestion with Tru9I, HaeIII, HpaII, AluI, TaqI, HhaI, and RsaI restriction enzymes revealed that a phytoplasma belonging to group 16SrII peanut witches'-broom group (2) was associated with chickpea phyllody and little leaf disease in Oman. Restriction profiles of chickpea phytoplasma were identical with those of alfalfa witches'-broom phytoplasma, a known subgroup 16SrII-B strain (3). To our knowledge, this is the first report of phytoplasma infecting chickpea crops in Oman. References: (1) A. J. Khan et al. Phytopathology, 92:1038, 2002. (2). I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998 (3) M. A. Saghai-Maroof et al. Proc. Natl. Acad. Sci. USA. 81:8014, 1984.

scholarly journals Genetic Variation among and within United States Collard Cultivars and Landraces as Determined by Randomly Amplified Polymorphic DNA Markers

1996 ◽  
Vol 121 (3) ◽  
pp. 374-379 ◽  
Author(s):  
Mark W. Farnham
Keyword(s):  
Genetic Variation ◽  
Dna Markers ◽  
Crop Improvement ◽  
Similarity Index ◽  
Randomly Amplified Polymorphic Dna ◽  
Brussels Sprouts ◽  
Breeding Lines ◽  
Intrapopulation Variation ◽  
Similarity Indices ◽  
Systematic Collection

A collection of collard (Brassica oleracea L., Acephala group) germplasm, including 13 cultivars or breeding lines and 5 landraces, was evaluated using randomly amplified polymorphic DNA (RAPD) markers and compared to representatives of kale (Acephala group), cabbage (Capitata group), broccoli (Italica group), Brussels sprouts (Gemmifera group), and cauliflower (Botrytis group). Objectives were to assess genetic variation and relationships among collard and other crop entries, evaluate intrapopulation variation of open-pollinated (OP) collard lines, and determine the potential of collard landraces to provide new B. oleracea genes. Two hundred nine RAPD bands were scored from 18 oligonucleotide decamer primers when collard and other B. oleracea entries were compared. Of these, 147 (70%) were polymorphic and 29 were specific to collard. Similarity indices between collard entries were computed from RAPD data and these ranged from 0.75 to 0.99 with an average of 0.83. Collard entries were most closely related to cabbage (similarity index = 0.83) and Brussels sprouts entries (index = 0.80). Analysis of individuals of an OP cultivar and landrace indicated that intrapopulation genetic variance accounts for as much variation as that observed between populations. RAPD analysis identified collard landraces as unique genotypes and showed them to be sources of unique DNA markers. The systematic collection of collard landraces should enhance diversity of the B. oleracea germplasm pool and provide genes for future crop improvement.

scholarly journals Identification of restriction enzyme in the FSHR gene of indonesian local cattle

2021 ◽  
Vol 888 (1) ◽  
pp. 012024
Author(s):  
P W Prihandini ◽  
A Primasari ◽  
M Luthfi ◽  
D Pamungkas ◽  
A P Z N L Sari ◽  
...  
Keyword(s):  
Restriction Enzyme ◽  
Restriction Site ◽  
Follicle Stimulating Hormone ◽  
Restriction Enzymes ◽  
Future Studies ◽  
Fshr Gene ◽  
Pcr Rflp ◽  
Mapping Analysis ◽  
Pcr Products ◽  
Enzyme Mapping

Abstract The restriction enzyme is important for genotyping using the PCR-RFLP technique. Therefore, this study aims to identify the restriction enzyme mapping in the partial sequence of the follicle-stimulating hormone receptor (FSHR) gene in Indonesian local cattle. A total of 29 samples sized 306 bp, were aligned with Genbank sequence acc no. NC_032660, resulting three polymorphic sites, namely g.193G>C, g.227T>C, and g.275A>C. Furthermore, the restriction mapping analysis using the NEBcutter program V2.0 showed that no enzyme recognized the SNP g.275A>C, while the SNP g.193G>C and g.227T>C were identified by the AluI and MscI enzymes, respectively. The AluI enzyme cuts at two positions (193 bp and 243 bp) in the G allele sample producing three fragments namely 50 bp, 63 bp, and 193 bp, meanwhile, in the C allele, the AluI cuts only in position 243 bp, hence, the fragment products are 63 bp and 243 bp. In contrast, the MscI enzyme was only recognized in the T allele, producing fragments sized 77 bp and 229 bp but failed to identify the restriction site along with the PCR products in the C allele. Based on the results, the SNPs (g.193G>C and g.227T>C) and restriction enzymes (AluI and MscI) are applicable for genotyping local Indonesian cattle using the PCR-RFLP technique in future studies.

scholarly journals First Report of an Aster Yellows Phytoplasma Associated with Cabbage in Southern Texas

Plant Disease ◽  
2001 ◽  
Vol 85 (4) ◽  
pp. 447-447 ◽  
Author(s):  
I.-M. Lee ◽  
R. A. Dane ◽  
M. C. Black ◽  
Noel Troxclair
Keyword(s):  
16S Rdna ◽  
Nested Pcr ◽  
Restriction Enzymes ◽  
Diagnostic Procedures ◽  
Acid Extraction ◽  
Insect Vector ◽  
Aster Yellows ◽  
First Report ◽  
Pcr Products ◽  
Aster Yellows Phytoplasma

In early spring 2000 carrot crops in southwestern Texas were severely infected by an outbreak of phyllody associated with aster yellows phytoplasma. Cabbage crops that had been planted adjacent to these carrot fields began to display previously unobserved symptoms characteristic of phytoplasma infection. Symptoms included purple discoloration in leaf veins and at the outer edges of leaves on cabbage heads. Proliferation of sprouts also occurred at the base of the stem and between leaf layers of some plants, and sprouts sometimes continued to proliferate on extended stems. About 5% of cabbage plants in the field exhibited these symptoms. Two symptomless and four symptomatic cabbage heads were collected in early April from one cabbage field. Veinal tissues were stripped from each sample and used for total nucleic acid extraction. To obtain specific and sufficient amount of PCR products for analysis, nested PCR was performed by using primer pairs (first with P1/P7 followed by R16F2n/R16R2) (1,2) universal for phytoplasma detection. A specific 16S rDNA fragment (about 1.2 kb) was strongly amplified from the four symptomatic but not from the two asymptomatic samples. The nested PCR products obtained from the four symptomatic samples were then analyzed by restriction fragment length polymorphism (RFLP) using the restriction enzymes MseI, HhaI, and HpaII, and the RFLP patterns were compared to the published patterns of known phytoplasmas (1). The resulting RFLP patterns were identical to those of a phytoplasma belonging to subgroup B of the aster yellows phytoplasma group (16SrI). These RFLP patterns were also evident in putative restriction sites observed in a 1.5 kbp nucleotide sequence of the 16S rDNA. This is the first report of aster yellows phytoplasma associated disease symptoms in cabbage in Texas. The occurrence of cabbage proliferation coincided with the presence of high populations of the insect vector, aster leafhopper. References: (1) I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (2) B. Schneider et al. 1995. Molecular and Diagnostic Procedures in Mycoplasmology, Vol. I. Academic Press, San Diego, CA.

Sign in / Sign up

Export Citation Format

Share Document