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DNA Markers in Forensic and Diagnostic Science
Published in Hajiya Mairo Inuwa, Ifeoma Maureen Ezeonu, Charles Oluwaseun Adetunji, Emmanuel Olufemi Ekundayo, Abubakar Gidado, Abdulrazak B. Ibrahim, Benjamin Ewa Ubi, Medical Biotechnology, Biopharmaceutics, Forensic Science and Bioinformatics, 2022
M. Y. Tatfeng, D. E. Agbonlahor, Ifeoma B. Enweani-Nwokelo, Ifeoma M. Ezeonu, Francisca Nwaokorie, E. A. Brisibe, D. Esiobu
The advancement in molecular genetics has laid the foundation for genomics studies. It has opened newer frontiers for the genetic improvement of crops and farm animals. These molecular signatures provide significant and accurate genetic information and better understanding of our biodiversity. A DNA or molecular (genetic) marker is a gene or DNA sequence with a known site on a chromosome and associated with a unique information or trait that can be used to characterize or identify individuals or species. In other terms, DNA markers represent a sequence, which may evolve from a mutation or alteration in the loci that can be noticed. Furthermore, they may be a short DNA sequence in which a single base-pair change (single nucleotide polymorphism, SNP) occurred, or a long one like mini and microsatellites and can be used in DNA-DNA hybridization, polymerase chain reaction (PCR) or restriction mapping experiments for DNA profiling. Recently, great interest towards molecular markers has been on the increase as they reveal polymorphism at the DNA level that is valuable in animal genetics studies (Van and Rodgers, 1996; Gizaw et al., 2007).
Genomics and Bionanotechnology
Published in Anil Kumar Anal, Bionanotechnology, 2018
Genome mapping is the process of locating the order of gene and their relative distance on the genome. It provides guidelines for the reconstruction of genome sequence after sequencing. DNA sequencing is a complex process due to which the genome needs to be fragmented before sequencing. The fragmented genome sequences are rearranged in original order using recognizable features. As genome map carries information about genome organization in terms of genes, restriction enzyme sites, and others, genome map is utilized to reconstruct the original genome after sequencing. There are two types of genome mapping that includes genetic mapping and physical mapping. For genetic mapping, commonly used markers are genes with visible phenotype and molecular markers, which is DNA sequence that shows polymorphism. Physical mapping involves direct location of DNA sequence on the chromosome using genome-wide unique DNA sequences, sequence-tagged site (STS), and expressed sequence tag (EST) as markers. Different physical mapping techniques include cytogenetic mapping, fluorescent in situ hybridization (FISH), restriction mapping, STS content mapping, and radiation hybrid mapping (Saraswathy and Ramalingam 2011).
Trends in Cancer Screening: Different Diagnostic Approaches
Published in Anjana Pandey, Saumya Srivastava, Recent Advances in Cancer Diagnostics and Therapy, 2022
Anjana Pandey, Saumya Srivastava
Any change in gene sequences, its level of expression, or change in structure and function of proteins can be used as a “molecular marker” which is used to detect cancer progression at an early stage (Sidransky, 2002; Edmondson et al., 2017; Arend et al., 2018; Nair et al., 2018; Bronkhorst et al., 2019; Moroney et al., 2019; Amelot et al., 2020; Doello et al., 2020; Rao et al., 2020; Mohanty et al., 2021). Many anatomical methods are designed to detect tumor masses such as mammography, physical examination, endoscopy, etc. Different molecular markers (Figure 3.4), on the other hand, independently rely on molecular signals present in the blood or other body fluids despite the presence of tumor mass. These markers are categorized into four classes (Baron, 2012):Carcinogenesis biomarker: These molecules are shed by tumor cells as a result of the carcinogenic process in form of methylated DNA or mutated DNA.Response biomarker: These molecules are produced by host cells in response to cancer. Examples include protein, antibodies, etc.Released biomarker: These are produced in response to damage caused by cancer like blood in the stool and PSA in serum.Risk biomarker: These are the factors associated with carcinogenic signals in the body like a high level of estradiol in breast cancer.
Prevalence of apomixis in Jatropha: Is it significant?
Published in Biofuels, 2022
Anoop Anand Malik, Vivek Kumar Singh, Shyam Sundar Sharma, Madan Singh Negi, Shashi Bhushan Tripathi
Apomixis-derived progeny can be detected by several methods. If fertile seeds are produced in the absence of pollen (e.g. emasculated flowers), apomixis is likely to be present. Cytological analysis, phenotypic and molecular markers have been used to detect apomixis. Cytological analysis is laborious but can identify and distinguish different types of apomixis such as apospory and parthenogenesis. Phenotypic and molecular markers can be used to screen a progeny array derived from a single mother plant heterozygous for one or more genetic loci or traits. Phenotypic analysis would, however, require that the trait displays incomplete dominance or codominance. As such traits are not readily available in the plant under investigation, molecular markers such as RAPD, AFLP and microsatellites have been used.
Cadmium contamination in food crops: Risk assessment and control in smart age
Published in Critical Reviews in Environmental Science and Technology, 2023
Yan Huili, Zhang Hezifan, Hao Shuangnan, Wang Luyao, Xu Wenxiu, Ma Mi, Luo Yongming, He Zhenyan
For natural low-Cd superior variations, pyramiding is an approach of aggregating them into one rice cultivar, thus to produce a new germplasm with ultra-low-Cd trait. Hybridization is the major approach for pyramiding them. Marker-assisted selection (MAS) refers to indirect selection for a desired plant phenotype based on the banding pattern of linked molecular markers. By multi-generation backcross and MAS, researchers have created low-Cd cultivars by introducing single or multiple low-Cd superior alleles into high-accumulation cultivars. For example, introducing the low-Cd superior allele OsCd1V449 to substitute for OsCd1D449 in high-Cd background 9311 and GUICHAO-2 caused a significantly decrease of rice Cd accumulation in near iso-genic lines (NILs) (Yan et al., 2019). Yu et al., discovered that a duplication of OsNRAMP5 between SNP8881 and SNP8886 originated from a low-Cd cultivar Pokkali (Yu et al., 2022). By introducing the low-Cd duplication variation into Koshihikari using backcrossing, the rice Cd accumulation reduced by 64% when planted in high-contaminated soil. When pyramiding multiple low-Cd superior variations into one cultivar, breeders can achieve combining low-Cd and other superior traits. i.e., Liu et al. have created 2 rice lines pyramiding low-Cd QTL GCC7 with high-Zn or high-Se QTLs, which showed a significant decrease of rice grain Cd compared to wild type (Liu, Ding, et al., 2020). By introducing a segment on chromosome 7 which includes Cd-related genes OsHMA3-OsNRAMP5-OsNRAMP1jap originated from low-Cd japonica variety IRAT129 into 93-11, Wang et al. created an improved 93-11 line with 31.8% decrease in rice grain Cd accumulation and no negative effects on yield (Wang, Yan, et al., 2021). All these facts proved that hybrid pyramiding low-Cd related natural variation is an approachable way of creating low-Cd varieties.
Molecular and phytochemical assessment for some seedy strains of Alamar apricot rootstock under salinity stress
Published in Egyptian Journal of Basic and Applied Sciences, 2019
M. H. Abd El-Aziz, S. Y. Mohamed, Hadeer E. Magwaid
Molecular markers are premium tools for assessing genetic diversity, which help breeders to select important traits support the improving productivity of economic plants. It was shown that molecular marker data are very important for any breeding program to select promising varieties with traits of interest [9]. Markers such as ISSR and SCoT are used efficiently for genetic diversity assessment of plants [10]. Inter-simple sequence repeats (ISSRs), a class of molecular markers involves the use of microsatellite sequences as primers in a polymerase chain reaction to generate multilocus markers, were first described by Zietkiewicz et al. [11], and Kantety et al. [12]. These markers targets genome regions flanked by the simple sequence repeats (SSR or microsatellite sequences). So, they offer great potential for assessing genetic diversity compared to other arbitrary markers like RAPD, since they reveal variation within unique regions of the genome at several loci simultaneously. They exhibit specificity of sequence-tagged-site markers but need no sequence information for primer synthesis featuring the random markers advantages. ISSR-primers can be based on any of the SSR motifs (di-, tri-, tetra- or penta-nucleotides) found at microsatellite loci, giving a wide array of possible amplification products [11]. Having single primer, ISSR sequences can be amplified using Polymerase Chain Reaction (PCR) provided that within the amplifiable size domain. This reaction yields multiple amplification products (Amplicons) that can be used as a dominant multi-locus marker system for genetic diversity study in various organisms. Start Codon Targeted polymorphism (SCoT) is a new molecular marker technique, and not yet used in the apricot diversity studies except for study on native apricots in Southern Xinjiang of China [13]. It is a novel, simple, and reliable gene-targeted marker technique based on the short-conserved region flanking the ATG start codon (initiation codon) in plant genes. This technique uses single 18-mer primers designed to anneal with surrounding regions of the start codon on both DNA strands [14,15]. This technique was described by Collard and Mackill [16], it uses a single primer as a forward and reverse primer, like the RAPD or ISSR technique. Also, SCoT can generate dominant markers caused by sequence variations and co-dominant markers caused by insertions and deletions [17]. SCoT is superior over other dominant DNA marker systems like RAPD and ISSR in higher polymorphism and better marker resolvability [18].