Advantages And Disadvantages Of Prunus

For millions of years, repetitive DNA sequences such as the “Alu sequence” have been randomly inserted in the human genome. In this experiment, I will study whether or not the repetitive element such as the “Alu sequence” is present in the PV92 region of chromosome 16 of my DNA. I will then gather the data from my Biology Lab Class and compare it with those of the United States. To perform this experiment, the method of Polymerase Chain Reaction (PCR) will be used to amplify the DNA. The purpose of using PCR is to create enough mass in order for it to run on the agarose gel electrophoresis. Performing this

It is a type of polymorphism and repeated sequences in intergenic regions of DNA. SSLPs are used to understand the genetic variation between two individuals. Another type of genetic marker is Restriction Fragment Length Polymorphism (RFLP), in which restriction enzymes are used to be isolate specific fragments of DNA, then these fragments are separated by length using gel electrophoresis. RFLP is an important tool in localizing genes for genetic disorder, genome mapping, finding risk for disease, and paternity testing. A third type of genetic marker is Amplified Fragment Length Polymorphism (AFLP), which is a PCR-base tool. It is used in different fields such as genetics, DNA fingerprinting, and genetic engineering. A fourth type of genetic marker is Random Amplification of Polymorphic DNA (RAPD), it is a type of PCR but in the case of RAPD the segment of amplified DNA would be random. It is used to trace the phylogeny of various plants and animals. A fifth type of genetic marker is Single Nucleotide Polymorphism (SNP), it is a segment of DNA sequence in the genome. It is when a single nucleotide is changed in a genome. Most commonly SNPs have only two alleles. A sixth type of genetic marker is Variable Number Tandem Repeat (VNTR) is located in a genome where nucleotide sequence is arranged as tandem repeat and can be found on many


Bloom's Level: 1. Remember
Learning Outcome: 06.01.03 Predict the outcome of crosses involving genetic variation in chloroplast genomes.
Section: 06.01
Topic: Extranuclear Inheritance: Chloroplasts

Microsatellite and mitochondria DNA (mtDNA) genetic markers are often used in population genetic studies. Please detail the differences in their mode of inheritance, as well as what types of genetic information that these markers may provide.

Biological Background: It is scientifically proven that DNA (deoxyribonucleic acid) contains genetic material and highly specific to individual. DNA fingerprint can be tested by restriction fragment length polymorphism (RFLP) methods and Polymerase chain reaction (PCR) methods. Although RFLP is considered more accurate, due to the cost and requirement of longer period to complete, it is not commonly used. While only 1% of genetic materials are unique to individual, the short tandem repeats (STR) sequences called minisatellites can be used to distinguish all humans as it shows great variation between each person (What is DNA fingerprint? 2016).

In order to test whether the curry leaf possesses one of the 6 alleles and whether it has a Ruby gene promoter, PCR and gel electrophoresis was used. Primers, short DNA sequences designed specifically for each allele of the Ruby gene, were used to isolate the gene and amplify it for PCR. Multiple PCRs were performed, each using a different primer set. Primers attach to specific regions surrounding the gene and amplify only the region that is flanked. The forward primer is bound to a specific sequence before the Ruby promoter, found to precede the actual gene sequence, and the reverse primer is bound to the DNA after the gene. In order for visible bands for gel electrophoresis to be produced, a forward primer must bind to one strand of DNA and a reverse primer must bind to the strand complementary to the one the forward primer binds to. If both primers bind to the same strand, the PCR product formed will not produce a result after gel electrophoresis. The size of the gel band of the DNA amplified by the primer will determine the identity of the allele. Band sizes will

PCR technique for both polymorphisms was performed in 2µl genomic DNA, 10 µl buffer (pH 8.4) 0.8 µl MgCl2, 0.7 µl dNTPs, 1 µl of each primer and 0.5 U Taq DNA polymerase. Then 5µl of products were incubated with 0.4U of Taq1 restriction enzyme at 65 °C for 48 h. Finally the products of the Taq1B digestion were electrophoresed on 1.5% agarose gel.

PCR was performed in 1 × PCR amplification buffer with 1 mM MgCl2 (Applied Biosystems, Tunis, Tunisia), 1 μM of each primer, 50 μM of each deoxynucleotide triphosphate (Promega, Tunis, Tunisia), 0.2 μg of DNA template, and 1.2 U of Taq DNA polymerase (Applied Biosystems, Tunis, Tunisia), in a final volume of 50 μl, using a GeneAmp PCR System 2400 (Perkin Elmer, Tunis, Tunisia). Cycling parameters were 95 °C for 3 min followed by 35 cycles of 94 °C for 1 min, 52 °C for 40 s, and 72 °C for 1 min, and then a final extension at 72 °C for 10 min. Control reactions lacking template DNA were performed simultaneously to rule out any putative contamination of PCR products. The ITS amplified fragments were visualized on 1% agarose gels stained with ethidium bromide, purified using a GeneClean kit (Q-BIOgene, Tunis, Tunisia), ligated into the pGEM-T Easy vector (Promega, Tunis, Tunisia), transformed into E. coli strain DH5α and plated on Luria Bertani agar medium containing ampicillin (50 μg ml-1) and X-Gal (5-bromo-4-chloro-3-indoyl-β-D-galactopyranoside; 20 μg ml-1) (Sambrook et al., 1989). The presence of an insert encoding for ITS in the recombinants was confirmed by PCR amplification and sequenced using BigDye Terminator v3.1 Cycle Sequencing kit (Applied Biosystems, Tunis,

Therefore short tandem repeats (STRs), or microsatellites, proved to be better suited for use in forensic analysis. STRs are similar to VNTRs in that they are portions of the noncoding DNA that contain various amounts of repeated units. But in regards to VNTRs, STRs have a much shorter repetitive sequence, usually between 2 to 6 nucleotides, but sometimes can be up to 10 base pairs (Figure 1). The small size of STRs in comparison to VNTRs allows for more efficient amplification of the DNA via PCR and enables scientists to use DNA that has been more significantly degraded. Forensic analysts compare 13 different STR locations plus one that determines gender of the obtained sample (Roewer, 2013). STRs vary highly between individuals; for example, one person could have an STR at a specific locus encoding the following: CGCGCGCGCGCG, whereas another person could have CGCG at the same locus.

STRs have become a main practice in DNA analysis due to the easily amplifiable structure. Enhancement methods such as polymerase chain reaction or PCR. PCR products for STRs are generally similar in amount, making analysis easier for analysis and amplification. An individual gets one copy of an STR from each of its parents that may have similar repeat sizes. The amount of repeats in STR markers can be a relatively high variable among an individual, which make STRs an effective strategy for identification of an

(Ferriol, Pico et al. 2004) analysed 47 accessions of C. moschata featuring the morphological characters which revealed considerable variability, comparable to that found in different C. moschata centers of diversity. Molecular analysis through AFLP (amplified fragment length polymorphism) markers which analyze neutral genetic diversity and SRAP (sequence-related amplified polymorphism) markers, which amplify gene regions both showed a genetic diversity in accordance with the morphological variability. With both markers clustered the genotypes according to their geographical origin: Central America, South America, and Spain, which suggested the existence of two independent domestications in both American areas, and/or introgressions from related species.

Jansen, R., Embden, J., Gaastra, W., & Schouls, L. (2002). Identification of genes that are associated with DNA repeats in prokaryotes. Molecular Microbiology, 43(6), 1565-1575. http://dx.doi.org/10.1046/j.1365-2958.2002.02839.x

CsA concentration varied between rounds (Table 1). Library was ordered from Integrated DNA Technologies (IDT). N30 library (30 unknown nucleotide bases): 5 '-GGA GGC TCT CGG GAC GAC NNN NNN NNN NNN NNN NNN NNN NNN NNN NNN GTC GTC CCG ATG CTG CAA TCG TAA-3 '. Capture Sequence: GTC GTC CCG AGA GCC ATA/3BioTEG/. Primer_P1: GGAGGCTCTCGGGACGAC. Primer_P2: TTACGATTGCAGCATCGGGACG. P2_biotin: /5BiosG/TTACGATTGCAGCATCGGGACG. All oligo’s (primers, library, and capture-strand) were ordered from IDT . Bio-capture used: 5’ biotin from IDT. Two SELEX buffers were used: SELEX 1 buffer (10 mM HEPES, 150mM NaCl, 5mM KCl, and 2mM MgCl2) and SELEX 2 buffer (10mM HEPES, 150mM NaCl, 5mM KCl). The composition of the PCR mix was as follows: 10% 10X buffer, .5% Taq, 1% P1, 1% P2, 2% dTNP, and 80.5% water. All gels were run in .5X TBE buffer and 3% agarose gel. Columns used: Micro Bio-Spin™ Chromatography Columns. PCR polymerase used was Choice Taq from Denville Scientific. DNTP is also from Denville Scientific. Streptavidin Beads are from Sigma Aldrich.

Along with the development of the PCR, a new type of polymorphism of DNA was discovered in the DNA structure known as hypervariable minisatellites. Large proportion of the eukaryotes genomes is consists of non-coding DNA. Usually, this non-coding region carries some regulatory elements such as promoters and enhancers but in many cases it also contains repetitive elements, e.g. multiple repeats (Turner et al., 1998). These repetitions include satellite DNA, which comprises thousands of tandem repeats in one site, as well as minisatellite and microsatellite DNA, depending on the number of repeats (Vanhala et al., 1998). These minisatellites are defined regions of DNA with polymorphisms in the number of repeated nucleotide

A molecular marker may be a short DNA sequence such as a sequence surrounding a single base-pair change like single nucleotide polymorphism (SNP) or a long one like minisatellites (Jeffreys et al., 1985) and microsatellites (Jarne and Lagoda, 1996). That leads to the development of a new type of marker that is single nucleotide polymorphism (SNP) (He et al., 2003). However, AFLP markers are devoid of dense marker maps, so still used for QTL mapping and genetic diversity studies in species (Nicholas, 1997; Van Haeringen et al., 2001). With time the RFLPs was replaced by microsatellites for building genetic maps in human and animal species. Factor responsible for development of microsatellites are firstly, at a single microsatellite locus large number of alleles are found thereby, developing a high heterozygosity values enabling to reduce the number of reference families to be used for building the map and secondly, the possibility to perform genotypes by simple PCR followed by allele sizing on polyacrylamide gels (Dinesh et al., 1995). Some points should be taken into consideration when using molecular markers for genetic studies. As for molecular biologists the genotyping procedure should be simple and cheap in order to generate the vast amount of genotyping data as often necessary. From the statistician's angle some characteristics are most important like the dominance relationships, information content, neutrality, map positions or genetic