Dominant and codominant markers30nov

A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites.

1. Dominant and Codominant Markers Presented by : Ankit Tiwari M.Sc. (MBT) Final year Pt. J.N.M. Medical College, Raipur Department of Biochemistry Session:2018-19 1

2. Introduction Genetic Markers Dominant and Codominant Marker Restriction Fragment Length Polymorphism (RFLP) Random Amplified Polymorphic DNA (RAPD) Amplified Fragment Length Polymorphism (AFLP) Microsatellites Applications References Contents 2

3. What are markers ? In 1980, scientists studying human genetics observed that variation in the pattern of DNA fragments generated by restriction enzyme digestion of genomic DNA could be used as Genetic Marker . Markers are genetically linked with the gene of interest. If the gene of interest in not known, markers linked to the gene of interest can still be used to select for individuals with desirable alleles of the gene of interest. Introduction 3

4. Genetic Markers Genetic marker is a gene or DNA sequence with known location on chromosome that can be used to identify individuals or species. Generally they do not represent the target genes themselves but act as signs or flags . Fig. 1 : Genetic Makers Source : http://usda-ars-beaumont.tamu.edu/dblhelix.jpg All genetic markers occupy specific genomic position within the chromosome called ‘loci’ . 4

5. Dominant Marker : Dominant marker can't differentiate the homozygous and heterozygous. Indicate difference on the basis of present and absent. Examples : RAPD, AFLP. Codominant Marker : Codominant marker can differentiate the homozygous and heterozygous. Indicate differences in size. Examples : RFLP, Microsatellites. Dominant and Codominant Marker 5

6. RFLPs were the first type of DNA marker to be studied . Restriction Fragment Length Polymorphism  ( RFLP ) is a difference in homologous DNA sequences that can be detected by the presence of fragments of different lengths after digestion of the DNA samples with specific restriction endonucleases. Restriction Fragment Length Polymorphism (RFLP) Fig.2 A Restriction Fragment Length Polymorphism Source : Genomes, Brown TA ;2002. 6

7. Fig.3 Workflow of RFLP Source: https://www.slideshare.net/search/slideshow?searchfrom=header&q=Gentic+marker+&ud=any&ft=all&lang=**&sort= 7

8. PCR based technology. RAPD is a DNA polymorphism assay based on the amplification of random DNA segments with single primers of arbitory nucleotide sequence. It do not require any specific knowledge of DNA sequence of target organism. The primers will or will not amplify a segment of DNA depending on positions that are complementary to the primers sequence. Therefore, if a mutation has occurred in template DNA at site that was previously complementary to primer, a PCR product will not be produced. This results in different pattern of amplified DNA segments on gel. Random Amplified Polymorphic DNA (RAPD) 8

9. Fig.6 Workflow of RAPD Source : https://www.researchgate.net/figure/The-principle-of-RAPD-PCR-technique-Arrows-indicate-primer-annealing-sites-modified_fig4_44684171 9

10. Fig. 7 Analysis of RAPD Source : https://pmblab.wordpress.com/2013/09/22/qa-in-agh635-course-in-rapd-marker-analysis-what-is-called-the-locus-and-what-is-the-allele / 10

11. AFLP is based on the selectively amplifying the subset of restriction fragments from a complex of DNA fragments obtained after the digestion of genomic DNA with restriction endonucleases. This is the combination of RFLP and RAPD. Typically, two different restriction enzymes are used to cut the genomic DNA to produce large number of fragments. Restricted fragments are ligated with adapters (25-30 bp long). Primers are used to amplify the restricted fragments. These primers are complementary to adapters. Amplified Fragment Length Polymorphism (AFLP) 11

12. Fig.8 Workflow of AFLP Source : https://www.researchgate.net/figure/Schematic-representation-of-AFLP-workflow_fig2_298971868 12

13. Microsatellites are also known as short tandem repeats. Microsatellites, or short tandem repeats/simple sequence repeats are polymorphic loci present in DNA that consist of repeating units of one to six base pairs in length. The repeated sequence is often simple, consisting of two, three or four nucleotides ( di -, tri-, and tetra-nucleotide repeats) and can be repeated many times. Microsatellites can be amplified for identification by PCR using the unique sequences of flanking regions as primers. Microsatellites 13

14. 14 Fig.9 Variation in microsatellite alleles can be detected by analyzing polymerase chain reaction (PCR) products using agarose gel electrophoresis . Source : Genetic Linkage and Recombination through Mapping with Molecular Markers, Lisa M McDonnell and Jennifer Klenz,2014.

15. RFLPs have been widely used in gene mapping studies because of their high genomic abundance due to ample availability of different restriction enzymes and random distribution throughout the genome. RAPDs have been used for many purpose, ranging from studies at the individual level (e.g. Genetic identity) to studies involving closely related species. The AFLP technology has the capability to detect various polymorphism in different genomic regions simultaneously. Microsatellites are very informative markers that can be used for many population genetics studies, ranging from the individual level to that of closely related species. 15 Applications

16. 16 Genetic Maker Dominant (D) or Codominant (C) Advantages Disadvantages Restriction Fragment length polymorphism (RFLP) C Robust, Reliable. Transferable across populations Time consuming, laborious and expensive Large amount of DNA required Random Amplified Polymorphic DNA (RAPD) D Quick and simples, Inexpensive Generally not transferable Simple Sequence Repeats (SSR) or microsatellites C Technically simple, Reliable Large amount of time and labour required Amplified Fragment length polymorphism (AFLP) D Multiple loci, High level of polymorphism generated Large amount of DNA required Complicated

17. Satyanarayana U. Biotechnology. Book and allied (p) Ltd; 2013. 4:649-52. Lewin Benjamin. Genes VIII. Pearson Education International; 2004. 54-55 . Brown TA. Genomes.Oxford : Wiiley-Liss; 2002 ISBN-10: 0-471-25046-5 Lodish H, Berk A, Matsudaira P et al. Molecular cell biology; 2004. 5: 396-97. Pierce BA. Genetics: a conceptual approach. WH.Freeman and company; 2012. 4:186. Collard BCY, Jahufer Z and Kyong Pang EC. An introduction to markers, quantitative trait loci (QTL) mapping and marker- assisted selection for crop improvement: the basic concepts. Euphytica ; 2005. 142: 169-196. 17 References

18. I would like to express my sincere gratitude to Dr. Abhigyan Nath sir and Dr. Khushboo Bhange Ma’am for their guidance and help in preparation of this presentation. I would also like to thanks Dr. G.K. Sahu sir, Dr. Abhigyan Nath sir and Dr. Khushboo Bhange Ma’am for providing me the opportunity to present a seminar at this level . This power point presentation has been prepared from various text books (Biochemistry by U. Satyanarayan, Genes VIII by Lewin, Genetics by Benjamin A. Pierce etc.) and review articles . I am also thankful to my classmates for their support in completion of the assignment. 18 Acknowledgment

19. 19 THANK YOU