Molecular Genetics: Gene Sequence Homology

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Table of Contents

Introduction
Results and Discussion
Conclusion
References

Introduction

The emergence of the Mendelian genetics in the 19^th century and the discovery of DNA structure by James Watson and Francis Crick in the 20^th century have paved the way for the development of molecular genetics in the 20^th and 21^st centuries. The scientific protocols and advanced equipment have made it possible to extract, amplify, and sequence genetic material obtained from diverse sources. Polymerase Chain Reaction (PCR) has revolutionized molecular biology because it allows in vitro amplification of DNA material making it available for various genetic studies [1]. Currently, PCR has become a versatile technology for it applies in diverse fields ranging from biological research to medical diagnostics.

The evolution and advancement of genetic tools have made it possible to sequence genomes of different organisms for purposes of molecular genetics. Genome sequences from prokaryotic and eukaryotic organisms have enhanced understanding of evolutionary relationships of organisms. From the Human Genome Project (HGP), identification and characterization of genes show that individual genome reveals their genetic lineage and evolutionary processes they have undergone with time [2]. Continued sequencing of genomes necessitated creation of genome databases such as GenBank, DNA Data Bank of Japan (DDBJ), and European Molecular Biology Laboratory (EMBL), which store genome sequences for genetic studies.

In genome sequence homology, the comparative genomic mapping is a powerful evolutionary tool that determines the degree of similarity and divergence of genome sequences between organisms [3]. Moreover, comparative genomic mapping has become the basis of identifying variable and evolutionary conserved genes that confer certain traits of interest in plants and animals. The process of selecting genes of interests constitutes marker-assisted selection (MAS), and it plays a central role in plant and animal breeding. Identification and characterization of genes using quantitative trait loci (QTL) aid in the selection of required traits in both plants and animals.

This study was done to determine genetic homology between cattle and humans by comparing DNA obtained from blood and cheek cells respectively. Therefore, the lab report presents results and discusses their application in comparative genomic mapping, MAS, evolutionary studies, and QTL analysis.

Results and Discussion

Table 1 displays the results of homology analysis done using BioEdit. The results show that the genetic material of cattle obtained from blood and the one obtained from human cheek cells have 80% homology. These results reflect the expectation because earlier studies revealed that conserved genes in cattle and humans have percent homology ranging from 80% to 100% [4, 5]. A comparative study, which determined homology of genes that code for α2-fucosyltransferase in cattle, namely, FUT1, FUT2, and SEC1, exhibited percent homology with human genes of 81%, 84%, and 83% respectively [4]. Another comparative study revealed that genes coding for bovine prion protein in cattle have 81% homology with human genes [5]. Comparatively, the results obtained imply that human and cattle are highly similar because most of their genes (80%) are similar while some of the genes (20%) are dissimilar. In this view, human and cattle share conserved regions, which indicate that they are closely related and evolved from the same ancestor.

However, since the process of isolation and amplification is prone to contamination, genetic material from either human or cattle might have contaminated isolated genetic material resulting in the apparent high homology. Moreover, the amplification of regions that are not conserved might have caused such a high homology. Therefore, the isolation process requires caution to prevent contamination, and a highly specific set of primers are necessary to prevent amplification of regions that are not conserved.

Table 1: Identities of cheek and cattle blood DNA.

DNA type	Homology to cattle blood
Human cheek cells	0.8006873

Since an experimental procedure is prone to errors, the loss of DNA pellet, contamination, amplification inefficiency, poor cleaning of PCR product, and sequencing reaction failure are some of the factors, which contribute to erroneous results. Isolation of DNA is a delicate process that is susceptible to slight changes in temperature and chemical conditions. DNA isolation inefficiency coupled with the loss of DNA pellet might have reduced the amount and quality of DNA obtained. As the process of isolation and amplification is prone to contamination, genetic material from either human or cattle might have contaminated isolated genetic material resulting in the apparent high homology. Amplification inefficiency might have occurred due to the inability of primers to prime targeted sequences or suboptimal PCR conditions. Moreover, the amplification of regions that are not conserved might have led to a high homology. Essentially, isolation process requires caution to prevent contamination, and a highly specific set of primers are necessary to prevent amplification of regions that are not conserved. Poor cleaning of PCR product might have resulted in the loss of mixture of amplicons and DNA template, which could have affected sequencing process. As homology examines sequences of DNA, sequencing failure interferes with accurate determination of sequences thus giving a false homology.

Owing to the existence of high homology between cattle and human, it is feasible to perform comparative genome mapping. Fundamentally, comparative genome mapping provides a way of identifying genomic positions of homologous sequences between related organisms with a view of establishing their structure and function [6]. The homology of sequences means that cattle and human have proteins that have similar structure and functions. Through comparative genome mapping, it is possible to map genes of cattle based human genes. In this view, the existence of biological databases with characterized and annotated genes provides templates for comparative genome mapping.

Evolutionary conservation of genome plays a central role in the comparative genome mapping because conserved sequences act as evolutionary markers. The existence of mutations in the conserved sequences signals diversity among species. Primers that flank conserved sequences are specific for they initiate specific amplification of the conserved regions, which effectively indicates the extent of variation in genomes. Evolutionary studies target conserved regions in the DNA sequences for they do not only indicate genomic sequences but also protein sequences and functions [6]. The homology of DNA sequences and protein sequences implies that compared organisms have similar genes, which codes for the proteins with the same structure and function. Homology analysis of the conserved sequences offers integral information for they indicate functional and evolutional conservation of genes [7]. In this case, as the conserved sequences have 80% homology, it implies that cattle and human have close evolutionary relationships inherited from a common ancestor.

QTL is an important molecular technique used in the analysis of genomes and prediction of genetic functions. Understanding of genomes requires the establishment of the relationship between genetic sequences and phenotypic characteristics [8]. The existence of high homology between cattle and human genetic material means that QTL analysis and MAS provide important information in the comparative analysis of the homologous genes. QTL mapping allows the establishment of the relationship between genotypes and phenotypes of a given genomic sequences [8]. Moreover, QLT mapping locates genes in their respective loci, thus improving comparative genome mapping of homologous sequences. The identification of the traits and their genetic loci enhances location of genes using specific markers. The markers identified by QTL are useful in MAS, which is applicable in both animal and plant breeding [8]. Thus, QLT and MAS are inseparable molecular techniques used in animal and plant breeding.

Conclusion

This study has demonstrated how isolation, amplification, sequencing, and homology analysis of human and cattle genetic material. The results indicate that the sequenced genetic material obtained from cattle and human have 80% homology, which shows that they are highly related and have a common ancestor. Moreover, the homology of the genetic material indicates that comparative genome mapping, evolutionary conservation of genome, QTL, and MAS are molecular genetics that applies in their analysis.

References

Valones, M., Guimaraes, R., Brandao, L., Souza, P., Carvalho, A. and Crovela, S. (2009). ‘Principles and applications of polymerase chain reaction in medical diagnostic fields: a review’. Brazilian Journal of Microbiology 40(1): 1-11.
Hood, L., and Rowen, L. (2013). ‘The Human Genome Project: big science transforms biology and medicine’. Genome Medicine 5(79): 1-8.
Schranz, M., Windsor, A., Song, B., Lawton-Rauh, A. and Mitchell-Olds. ‘Comparative Genetic Mapping in Boechera stricta, a Close Relative of Arabidopsis’. Plant Physiology 44(1): 286-298.
Choi, S., Kim, I., Kim, D., Kim, S., Chae, S., Choi, H., Choi, I., Yeo, J., Song, M. and Park, H. (2006). ‘Comparative genomic organization of the human and bovine PRNP locus’. Genomics 87(1), 598-607.
Barreaud, J., Saunier, K., Souchaire, J., Delourme, D., Oulmouden, A., Oriol, R., Leveziel, H., Julien, R. and Petit, J. (2000). ‘Three bovine α2-fucosyltransferase genes encode enzymes that preferentially transfer fucose on Galβ1-3GalNAc acceptor substrates’. Glycobiology 10(6), 611-621.
Thomas, J., Summers, T., Lee-Lin, S., Maduro, V., Idol, J., Mastrian, S., Ryan, J., Jamison, D., and Green, E. (2000). ‘Comparative Genome Mapping in the Sequence-based Era: Early Experience with Human Chromosome 7’. Genome Research 10(1): 624-633.
Kunin, V., Sorek, R., and Hugenholtz, P. (2007). ‘Evolutionary conservation of sequence and secondary structures in CRISPR repeats’. Genome Biology 8(61): 1-7.
Collard, B. and Mackill, D. (2008). ‘Marker-assisted selection: An approach for precision plant breeding in the twenty-first century’. Philosophical Transactions of the Royal Society 363(1491): 557-572.

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Molecular Genetics: Gene Sequence Homology

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