RAPD is a PCR based technique which involves the use of single arbitrary short primers (8-12 nucleotid es), resulting in the amplification of many discrete DNA . The segments of DNA that are amplified are random. The technique was developed independently by two different laboratories and called as RAPD and AP-PCR (Arbitrary Primed PCR). This procedure detects nucl eotide sequence polymorphisms in a DNA amplification based assay using only a single prime r of arbitrary nucleotide sequence. The RAPD technology has provided a quick and efficient scree n for DNA-sequence polymorphisms at a very large no of loci. The present communication gives emphasis on basic knowledge about RAPD, procedure, its advantages disadvantages, limitations and applicati ons of RAPD.

Randomly amplified polymorphic dna-a brief review

The dramatic development of molecular genetics has laid the groundwork for genomics. It has introduced new generations of molecular markers for use in the genetic improvement of farm animals. These markers provide more accurate genetic information and better understanding of the animal genetic resources. Scientists, unfamiliar with the different molecular techniques tend to get lost as each has its own advantages and disadvantages. This review represents a trail to shade alight on the different types of molecular markers by introducing a brief summary on the development of genetic markers including both the classical genetic markers and more advanced DNA-based molecular markers. This review could be helpful to better understand the characteristics of different genetic markers and the genetic diversity of animal genetic resources.

http://ejournal8.com/journals_n/1445499510.pdf

Molecular Markers: an Introduction and Applications

The Arabian Peninsula is known to have a comprehensive and rich endowment of unique and genetically diverse plant genetic resources. Analysis and conservation of biological diversity is a crucial issue to the whole Arabian Peninsula. The rapid and accurate delimitation and identification of a species is crucial to genetic diversity analysis and the first critical step in the assessment of distribution, population abundance and threats related to a particular target species. During the last two decades, classical strategies of evaluating genetic variability, such as morphology and physiology, have been greatly complemented by phylogenetic, taxonomic, genetic diversity and breeding research molecular studies. At present, initiatives are taking place around the world to generate DNA barcode libraries for vascular plant flora and to make these data available in order to better understand, conserve and utilize biodiversity. The number of herbarium collection-based plant evolutionary genetics and genomics studies being conducted has been increasing worldwide. The herbaria provide a rich resource of already preserved and identified material, and these as well as freshly collected samples from the wild can be used for creating a reference DNA barcode library for the vascular plant flora of a region. This review discusses the main molecular and genomic techniques used in plant identification and biodiversity analysis. Hence, we highlight studies emphasizing various molecular techniques undertaken during the last 10 years to study the plant biodiversity of the Arabian Peninsula. Special emphasis on the role of DNA barcoding as a powerful tool for plant biodiversity analysis is provided, along with the crucial role of herbaria in creating a DNA barcode library.

/pdf/the-promise-of-molecular-and-genomic-techniques-for-4ijhxl086z.pdf

The Promise of Molecular and Genomic Techniques for Biodiversity Research and DNA Barcoding of the Arabian Peninsula Flora

Goat plays a crucial role in human livelihoods, being a major source of meat, milk, fiber, and hides, particularly under adverse climatic conditions. The goat genomics related to the candidate gene approach is now being used to recognize molecular mechanisms that have different expressions of growth, reproductive, milk, wool, and disease resistance. The appropriate literature on this topic has been reviewed in this article. Several genetic characterization attempts of different goats have reported the existence of genotypic and morphological variations between different goat populations. As a result, different whole-genome sequences along with annotated gene sequences, gene function, and other genomic information of different goats are available in different databases. The main objective of this review is to search the genes associated with economic traits in goats. More than 271 candidate genes have been discovered in goats. Candidate genes influence the physiological pathway, metabolism, and expression of phenotypes. These genes have different functions on economically important traits. Some genes have pleiotropic effect for expression of phenotypic traits. Hence, recognizing candidate genes and their mutations that cause variations in gene expression and phenotype of an economic trait can help breeders look for genetic markers for specific economic traits. The availability of reference whole-genome assembly of goats, annotated genes, and transcriptomics makes comparative genomics a useful tool for systemic genetic upgradation. Identification and characterization of trait-associated sequence variations and gene will provide powerful means to give positive influences for future goat breeding program.

/pdf/goat-genomic-resources-the-search-for-genes-associated-with-4r5a7eb4iv.pdf

Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits.

Population genetic structure and diversity analysis in Hedychium coronarium populations using morphological, phytochemical and molecular markers

Black Bengal goat is a very valuable goat breed in India. The present investigation was proposed to be undertaken to evaluate gene flow, phylogeographic history, genetic structure and differentiation of both the goat populations to study genetic variation prevail ing among Black Bengal and Black Bengal type goat in west Bengal and Jharkhand respectively and to study genetic relationship between both goat populations and to study population structure and gene flow between th ese two goat populations. This experiment was conducted in the department of animal breeding and genetics ( molecular biology laboratory). DNA was extracted from 50 goats from each of the Black Bengal and Black Bengal type goats of Jharkhand and the extracted DNA was observed by gel electrophoresis. Ten specific goat specific primers were obtained from sigma. All the primers except for primers one and two were capable of priming polymorphic amplification pattern in both the b reeds. Random Amplification of Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) analysis was carried out using DNA samples of 50 Black Bengal goat and 50 Black Bengal type goats of Jharkhand (referred to as Jharkhand black) goat breeds. Only unambiguous, reproducible and scorable polymorphic fragments were taken into consideration for analysis. The amplific ation pattern of representative samples of Black Be ngal showed that primers 6,7,8,9 were highly polymorphic. Polymorphism Information Content (PIC) or expected heterozygosity scores varied from a minimum of 0.219 for primer sigma 06-3 to a maximum of 0.486 for primer sigma 04 with over all mean 0.411 in Black Bengal goat. Similarly for Jharkhand Black, the valu e of PIC ranged from a minimum of 0. 278 for primer sigma 06-3-0.496 for primer sigma10-2 with over all mea n value of 0.413. Data were analyzed by using a computer programe POPGENE (Version 1.31). A more appropriate measure of genetic variation within a p opulation is gene diversity .It was observed that, mean value of Nei,s Gene diversity value (h) was 0.3750 for Black Bengal and was 0.4022 for Jharkhand black. In case of Black Bengal, it was found that the maximum value of Nei’s gene diversity was 0.4861 for locus sigma 6-2 and sigma 9-2 while the minimum value of 0.0664 was found for locus Sigma 04. In Jharkhand Black t he maximum value of Nei’s gene diversity (h) was found to be 0.4965 for locus Sigma 10-2 and sigma06-1and the minimum value was 0.2491 for locus sigma 08-1. Dendrogram based on Nei’s genetic distance using Unweighted Pair Group Method of Arithmetic Means (UPGMA) indicated relative closeness and distance of the two goat breed. This study was mainly done on b reeds raised in marginal agricultural areas in orde r to assist in situ conservation. The result was importa nt with respect to puzzle of goat genetic diversity and conservation. Therefore it can be recommended that within breed diversity is actively maintained to en able these extensively unmanaged stocks to adapt to futu re demands and conditions and there is ample scope for further improvement in its productivity through app ropriate breeding strategies.

Molecular characterization of goats using random amplified polymorphic dna

Objective: Summary of breed characteristics of Black Bengal goats of Jharkhand (called as Jharkhand Black for ease) based on physical, cytogenetic and molecular parameters have been presented in the current study in order to characterize and conserve this unique germplasm. Findings: The physical parameters helped reveal the unique physical characteristics of Jharkhand Black goats with body weight of 18.64 and 17.75 kg respectively for the males and females. Cytogenetic characterization gave the length of all the autosomes (58) and sex (2) chromosomes of the total 60 chromosomes along with the karyotyping pattern of all 60 chromosomes. The X chromosome was found to be acrocentric and longest while the Y-chromosome was found to be smallest, dot like structure and suspected to be sub-metacentric. Molecular characterization showed the Mean na (observed number of alleles) was 2 while mean ne (effective number of alleles) was found to be 1.6935. Polymorphism information content (PIC) scores varied from 0.219 to 0.486 with over all over all mean 0.413. Evan’s Watterson’s Test of Neutrality indicated that F value for not even a single locus deviated from the standardized normal range of U95 and L95. Conclusions: The study might be further continued to provide additional information and evidence regarding the same which could be beneficial for conservation of this extremely important germplasm of Jharkhand and for the MAS.

Breed Characterization for Identification and Conservation of Black Bengal Goats of Jharkhand

TLRs (Toll like receptors) gene have a very important role in early defense against invading
pathogens, still we do not have sufficient literature available about them specially TLR6 gene in
swine. The current study deals with the characteristic polymorphic, sequencing and evolutionary
pattern of TLR6 gene in swine. SSCP based amplification and polymorphic pattern of TLR6 gene,
with the eight primers showed different polymorphism. Further, the evolutionary pattern of TLR6
gene was studied through phylogenetic tree analysis. Conclusively, the current comparative
phylogenetic and polymorphic analysis of vertebrate TLR6 gene in swine provided informative
insights into the process of gene evolution.

https://www.ijvsbt.org/index.php/journal/article/download/508/362

TLR6 Gene Polymorphism, Sequence Analysis, and Phylogenetic Tree in Susscrofa

FecB gene is first described gene which has been found to increase ovulation rate and litter size in sheep. But, work related to genetic mechanism and genetic markers for caprine proliferation has not been done so much. The present study was aimed to screen Black Bengal goat population for polymorphism of FecB gene and to study its effect on body weight at different growth stages. DNA samples from 96 animals were isolated and subjected to PCR. Amplified fragments obtained were allowed for polyacrylamide gel electrophoresis for the detection of single strand conformational polymorphism (SSCP) variants. Among all samples, three different SSCP variants were found which were marked as AA, AB and BB. The highest genotype frequency was observed for AB (0.38), which was followed by BB (0.33) and AA (0.29). Least-square analysis of variance showed significant (P<0.01) effect of genotype on body weight at birth only. The least square mean of body weights at birth for genotype BB (01.17±00.03 kg) was significantly lower than that of genotype AA (01.43±00.03 kg) and genotype AB (01.36±00.02 kg). It was also observed that genotype had non-significant effect on body weight at 4-week, 8-week, 12-week, 24-week, 36-week and 48-week of age. These results indicate that effect of FecB on body weight was limited at birth only. No significant effects were found on growth rate at later stage of life. FecB gene was hitherto linked to prolificacy. So, the effect of FecB gene on other traits has important bearing if the research is continued further with more number of species specific primers at other loci.

Nandani Kumari

Papers

Randomly amplified polymorphic dna-a brief review

Molecular characterization of goats using random amplified polymorphic dna

Breed Characterization for Identification and Conservation of Black Bengal Goats of Jharkhand

TLR6 Gene Polymorphism, Sequence Analysis, and Phylogenetic Tree in Susscrofa

Effect ofFecBGene on Body Weight in Black Bengal Goat