Q.

What do you mean by RAPD?

The Random Amplified Polymorphic DNA (RAPD) method is based on the Polymerase Chain Reaction (PCR) using short (usually 10 nucleotide) primers of arbitrary sequences. Polymorphism of amplified fragments are caused by: (1) base substitutions or deletions in the priming sites, (2) Insertions that render priming sites too distant to support amplification, or (3) insertions or deletions that change the size of the amplified fragment.

Short (10nt oligo) primers are randomly arbitrarily selected to amplify random DNA sequence throughout the genome.The resulting amplified products genarated at the region flanking a part of 10bp primer site in appropriate orientation.Often shows a dominant relationship due to primer being unable to bind on recessive allele. Q.2. How RAPD can be utilized in genome mapping? Random primer of 10nts having all probable combination of base is developed, then the PCR is run with those primer. The variety of PCR product obtained is obtained is then sequenced. By overlapping sequence analysis we can resolve genome map. In chromosome walking the technique of RAPD is used, in which the flanking sequence is revealed by random primer designing against known sequence

Q.3.What do you mean by SCAR? SCAR is sequence characterized amplified regions.In this technique the polymorphic band obtained in RAPD is further characterized. Obtaining a codominant marker may be an additional advantage of converting RAPDs into SCARs. Polymorphic band obtained in RAPD is cutted and cloned. Then the insert is sequenced and a specific primer is designed to amplify the band of interest.Reamplification of the template will show clear and easy to interperate pattern

Q.4. What is molecular polymorphism? Molecular polymorphism is variation in DNA sequence. Genetic variations occurring in more than 1% of a population would be considered useful polymorphisms for genetic linkageanalysis.

These polymorphism can be detected and amplified by RFLP RAPD AFLP

It is used in different Germplasm characterization Genetic diagnosis Characterization of transformants Study of genome Organization and phylogenic analysis

Q.5. What is marker assisted selection? Marker assisted selection or marker aided selection (MAS) is a process whereby a marker (morphological, biochemical or one based on DNA/RNA variation) is used for indirect selection of a genetic determinant or determinants of a trait of interest (i.e. productivity, disease resistance, abiotic stress tolerance, and/or quality). This process is used in plant and animal breeding. The major genes which are responsible for economically important characteristics are frequent in the Plant Kingdom. Such characteristics include disease resistance, male sterility, selfincompatibility, others related to shape, color, and architecture of whole plants and are often of mono- or oligogenic in nature. The marker loci which are tightly linked to major genes can be used for selection and are sometimes more efficient than direct selection for the target gene. Such vantages in efficiency may be due for example, to higher expression of the marker mRNA in such cases that the marker is actually a gene. Alternatively, in such cases that the target gene of interest differs between two alleles by a difficult-to-detect single nucleotide polymorphism, an external marker (be it another gene or a polymorphism that is easier to detect, such as a short tandem repeat) may present as the most realistic opti.

Q.6. How FISH technique is used for genome mapping? FISH involves the preparation of short sequences of single-stranded DNA, called probes, which are complementary to the DNA sequences the researchers wish to paint and examine. These probes hybridize, or bind, to the complementary DNA and, because they are labeled with fluorescent tags, allow researchers to see the location of those sequences of DNA. Unlike most other techniques used to study chromosomes, which require that the cells be actively dividing, FISH can also be performed on nondividing cells, making it a highly versatile procedure As in optical mapping, FISH enables the position of a marker on a chromosome or extended DNA molecule to be directly visualized

Q.7. What do you mean by biochemical marker? Biochemical markers are the marker used in genetic mapping which rely on biochemical phenotype. For example ADE2 is a yeast biochemical marker where yeast grows only in presence of adenine. Enzymes are also used as biochemical marker CYH1 is an enzyme marker which inactivate cycloheximide, hence yeast become resistant to it. In human the biochemical phenotypes that can be scored by blood typing. These include the standard blood groups such as the ABO series and also the human leukocyte antigens (the HLA system).

Q.8. What is Somatic Cell Hybridization technique? It is technique used for physical mapping of genome. It involves fusion of two cell lines by using either inactivated Sendai virus or polyethylene glycol.The hybrid cells unilaterally lose chromosome of the species under investigation.The cell stabilize with some part of chromosome. Cell line can be examined to see whether certain genes are in certain clone

Somatic cell hybrids are originally polyploid, containing the full chromosome complement of both the rodent and human parental cells. In time, however, many of the chromosomes of one of the species are lost because their continued presence is not required for hybrid survival. Only the chromosome carrying the gene for a marker being selected (for example, the X chromosome, carrying the HPRT gene) is necessarily present in all cells, although, in general, at least a few other donor chromosomes also persist. The basis for chromosome loss or retention is still unknown; the important characteristic of rodent/human somatic cell hybrids is that it is the human, not rodent, chromosomes that are preferentially lost, resulting in hybrid cells retaining different numbers and combinations of human chromosomes, as determined by a number of karyotyping techniques that distinguish between rodent and human chromosomes.

Q.9. What are utility of genome mapping/sequencing? Utility of genome mapping To find genes that are associated with traits of economic important(quantitative trait loci) Discover genes causing major physiological disorders Use genetic marker for marker assisted selection and introgression program To develop comparative maps To develop phylogenetic trees To find out the gene involved in particular genetic disease It is used in finger print analysis Q.10 What do you mean by Spectral Karyotyping? Spectral Karyotyping is a technique used for sorting of different chromosomes through fluorescent activated cell sorting procedure. Chromosomes stained with a fluorescentdye are passed through a laser beam. Each time, the amount of fluorescence is measured and the chromosome is deflected accordingly. The chromosomes are then collected as droplets. Mixtures of fluorophores used to separately label chromosome-specific probes. Mixtures of fluorophores used to separately label chromosome-specific probes.

It is used in making chromosome specific libraries and in finding new marker.