LEC.5- Finger printing with markers.pptx

Finger printing with markers

1. What is DNA fingerprinting? It is a technique, by which an individual can be identified at molecular level. With the advancement of science and technology STR analysis has become very popular in forensic laboratories. Scientists have chosen repeating sequences in the DNA, which are present in all individuals on different chromosomes, and are known to vary from individual to individual except in identical twins. These are used as genetic markers to identify the individual.  

2. The exploitation of DNA polymorphism techniques rendered easy and quick approach for genetic diversity analysis and fingerprinting of cultivars and hybrids using molecular markers, especially at early stages. Several types of molecular markers such as RAPD , AFLP, ISSR and SSR have been employed by researchers in DNA fingerprinting and genetic diversity studies in plants. However, SSR markers have been preferred over others and applied to peach ,apricot , rice sugarcane Brassica napus ,and cotton for genetic diversity and fingerprinting studies.

3. Markers derived from small, tandemly arranged repetitive elements offer a way around this limitation. Such markers are called micro- or mini-satellites or simple tandem repeats (STR), because their sequence organization resembles the tandem arrangement of classical satellite DNA.   Minisatellites (repeat units of 9-20 nucleotides) can be hybridized to restricted and electrophoretically separated DNA blotted on to nylon membranes ( Jeffreys et al., 1985). Minisatellites and Microsatellites

4. Microsatellites (repeat units of 1-5 nucleotides) can be hybridized to DNA in dried gels (Ali et al., 1986) or microsatellites can be cloned, sequenced, and amplification fragment length polymorphism detected by PCR, using oligonucleotides from the surrounding monomorphic DNA as primers. These sequenced tagged microsatellite sites (STMS; Beckman and Soller , 1990), like RFLP are co-dominant markers and therefore highly informative, which justifies the large amount of work needed for their generation. Microsatellites are present in different forms in plant genomes.

5. marker that screens many loci in the genome, as in the random amplified polymorphic DNA–polymerase chain reaction (RAPD–PCR), amplified fragment length polymorphism–PCR (AFLP–PCR) and minisatellite DNA fingerprinting. Multilocus marker: DNA fingerprinting in maize As a cash crop and a model biological system, maize is of great public interest. To facilitate maize molecular breeding and its basic biology research, we built a high-resolution physical map with two different fingerprinting methods on the same set of bacterial artificial chromosome clones.

6. The physical map was integrated to a high-density genetic map and further serves as a framework for the maize genome-sequencing project. Comparative genomics showed that the euchromatic regions between rice and maize are much conserved. Many genome rearrangementswere detected Duplication blocks were observed within the maize genome. These blocks allowed the reconstruct the chromosomes of the maize progenitor.

7. Maize genome has experienced two rounds of genome duplications, an ancient one before maize–rice divergence and a recent one after tetraploidization . In recent years, molecular marker techniques have gained widespread applications in many fields of plant genetics and breeding. Isozymes and restriction fragment length polymorphisms (RFLP) have provided valuable tools for linkage analysis and the establishment of genetic maps in all major crop plants, especially in maize (WALTON & HELENTJARIS, 1987). The discrimination power of restriction fragment length polymorphisms (RFLPs) has been extensively studied in maize, as has their use in establishing relationships with yield and heterosis ( Melchinger 1993).

8. Although a large number of SSRs are available in the maize GDB or PANZEA database, each SSR marker is not suitable for fingerprinting analysis. In maize, several sets of SSR markers have been published based on the standardization of fingerprinting analysis technology, genetic diversity of French varieties, or identification of North American varieties. However, a core set of SSR markers has not been established for DNA fingerprinting analysis based on Chinese maize varieties. .

9. RAPD analysis was used to verify the purity of maize hybrids . The use of three selective primers allowed the discrimination of two types of hybrids analyzed and purity was confirmed. RAPD analysis has been successfully used for hybrid and parentage verification of other crop plants. RAPD markers were also used to verify interspecific hybridisation (Benedetti et al ., 2000; Mei et al ., 2004). efficiency of RAPD technique for verification of hybridity and purity identification.   AFLP fingerprinting technique is a reliable genetic tool for achieving high discrimination rate among maize genotypes through determination of their genetic distances.

10. DNA fingerprinting in cotton Improved cotton cultivars which have been developed using traditional plant breeding procedures are mostly selections from intervarietal crosses and backcross programs. As these plants inherit much common genetic material, they often cannot be differentiated on the basis of growth and performance characteristics alone. In such cases, genetic fingerprinting can be employed to identify subtle differences between two closely-related plants, and so enable recognition of a unique cultivar.

11. To examine the genetic similarity of cotton cultivars available in Australia, twelve cultivars of Gossypium hirsutum , together with an American Pima cotton (G. barbadense ) cultivar, were subjected to genetic fingerprint analysis using the technique of RAPD-PCR 1. Genetic fingerprinting of parents and progeny, using techniques such as RAPD-PCR, can then be employed to identify genetic markers associated with the desired character. One useful strategy for detecting genetic markers linked with a character such as disease resistance is segregate fingerprint analysis.

12. Molecular markers such as simple sequence repeats (SSR) are a useful tool for characterizing genetic diversity of Gossypium germplasm . Genetic profiles by DNA fingerprinting of cotton accessions can only be compared among different collections if a common set of molecular markers are used by different laboratories and/or research projects.

13. The recent development of abundant cotton SSR markers has stimulated more effort in molecular characterization of cotton germplasm released from specific cotton breed­ing programs across the world ( Blenda et al ., 2006; Zhang et al ., 2005). But no SSR analysis of Bangladeshi cotton genotypes has been made till 2007 when 157 varieties of 20 crop genetic materials including cotton were studied and recorded in a government publication by Rahman et al. (2007). Zhang et al. (2005) reported genetic distance among ‘Acala1517’ genotypes ranged from 0.06 to 0.38 with an average of 0.18 on the basis of 189 SSR marker alleles, indicating a substantial genetic diversity among ‘Acala1517’ cotton germplasm .

14. Due to lack of patent application (patent­ing studies) at national level, the country may lose genetic resource and varietal identity of this important crop plant . It is essential to have proper genetic records and identity in maintaining conservation and cultivation of this plant species . Hence , the proposed plant variety protection lends added urgency to the search for solutions to the conser­vation of plant genetic diversity. Molecular markers have been successfully applied in registration activities Including cultivar identification (Mailer et al ., 1994).

15. However, with the necessity of varietal identity, present study was an attempt to reveal genetic diversity and varietal identification of eight cotton varieties in Bangladesh by DNA fingerprinting using microsatellite markers. Worldwide and national economic importance of the cotton crop, availability of large number of cultivars and hybrids for cultivation, bottleneck effect and narrow genetic base have necessitated the development of an authentic and unquestionable method i.e. DNA fingerprinting to ameliorate cotton germplasm resources, distinguish among distant elite cultivars and hybrids and to protect plant varieties owners’ intellectual property rights (IPRs) (Rojas et al., 2008).

16. In recent past, identification of cotton cultivars and hybrids has been executed based on - morphological and phenological traits such as plant stature, - number of sympodial branches, - boll weight, flowering time, - fiber length, fiber maturity, etc. Regarding morphological and phenological traits, it has always been befuddled to distinguish cultivars especially in the early stages of the cotton plant. Moreover, cultivar identification has been predicted to be complex in cotton because of polyploidy, simultaneous presence of lot of cultivars in a given time and area and narrow genetic base.