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My trait of choice is the song of mating sung by Koel bird during summer season .For this phenotype the contrasting traits are good song which can attract many birds and another trait is the song of not good quality .
1. PEDIGREE ANALYSIS:
The pedigree information is required for the association of Phenotypic and genotypic information. So the sweet song of one koel is selected as one parent and the bird with the harsh song is selected as another parent and the cross is made between these birds .To obtain f1 generation is obtained and the back cross is performed to obtain the F2 GENERATION individuals.
2. INFORMATION REGARDING MARKERS:
Random markers are selected for studying .the markers related to microsatellite are selected and their respective map position is obtained from UCSC browser.
3. INFORMATION OF PHENOTYPE:
The phenotype data of P1, P2, F1 and F2 individual is charted by observing the phenotypic variations.
4. ASSOCIATION OF GENOTYPIC AND PHENOTYPIC DATA:
For this interval mapping is used and the ANOVAs is used to link the information of both the genotypic and phenotypic data. Here the linking of markers with trait and the association between two markers for respective trait co variances are compared and maximum likelihood data is obtained.
5. QTL MAP:
5.1 Single marker analysis:
5.2 composite interval mapping:
5.3 Multiple interval mapping: The maximum likelihood data is taken on the x-axis and chromosomal map position of individual markers are drawn on y-axis. We had obtained a graph and the 5% threshold value is selected on x axis .the region which are significant i.e.; which crossed the threshold can be treated as QTL. Here the dominant and additive can be studied. The soft wares likes map marker and QTL cartographer can be used.
Snps have come about by mutations the transition and transversion are the agents which allowed them to creep.
FIXATION: When an allele reaches a frequency of 1 (100%) it is said to be "fixed" in the population and when an allele reaches a frequency of 0 (0%) it is lost. Once an allele becomes fixed, genetic drift comes to a halt, and the allele frequency cannot change unless a new allele is introduced in the population via mutation or gene flow. Thus even while genetic drift is a random, directionless process, it acts to eliminate genetic variation over time.
In RNA sequencing two approaches can be used
In cDNA sequencing,the RNA is reverse transcribed and the cDNA is obtained.the cDNA is sequenced by using high throughput sequencing methods like 454 ROCHE Â®,HELICOSÂ®,SOLiDÂ®.
DIRECT RNA SEQUENCING:
In this approach direct RNA is used for sequencing and this method is called as RNA sequencing.
The principle for both the methods is "HIGH THROUGHPUT SEQUENCING".
In microarray, the plastic/silicon wafer contains many pores and to this pores the known DNA sequence is coated. Later the test sample is passed on to this microarray .Based on color change we determine whether the hybridized one are matched or unmatched.
The principle in this approach is "HYBRIDIZATION".
For performing RNA sequencing we need NOT to know the initial sequence
For performing this we should have the knowledge of sequence used.
The sequencing involves higher expenditure
It is less expensive compared to RNA sequencing
The data obtained here is in universal format
The data differs with individual experiment.
The experiments involved with the methods are
Experiment for RNA SEQUENCING.
Expression in BHK cells
Experiment for RNA SEQUENCING.
Expression in HeLa cells
In gene duplication another copy of DNA is obtained .the causes for gene duplication are Homologous recombination, retro transposon.
The fates of Duplicated genes are of probably four types.
The gene gets duplicated and the duplicated copy gets either mutation or deleted .if it gets mutation the gene can be converted into Psuedogene.The psuedogene genes get selective advantages like they can reverted by mutation and gets functional.
CONSERVATION OF GENE FUNCTION:
Some proteins are needed in heavier number .for this reason the duplicated copies retain the original function and increase the amount of protein to be formed. The selective advantages with this are the gene function is conserved.
In this the duplicated copies subdivide the function of parent protein. Here the selective advantage is the function gets sub divided.
The duplicated copy gets new function compared to the parent gene from which it is formed. The selective advantage with this type is new function formation.
A1B1 A1B2 A2B1 A2B2
34 13 15 38
Hence significant linkage equilibrium is observed.
The myostatin is the negative regulator for muscle growth and the gene encoding for myostatin is on recessive alleles .so the breeders obtain the muscular hypertrophy in off springs by selective Breeding.
The three approaches which used today are
The transgene containing individuals have different post translational modifications compared to normal individuals. This property is used in protein profiling
CHANGE IN IMMUNE RESPONSES:
When the viral vectors are used the immune system show some responses and this are used in the detection of doping.
The doped individual proteins differ from normal individuals and the proteins of doped individual are used for detection of this method.
The transcription process is little bit different when we compare the embryonic stem cells compared to normal cells. Here the heterochromatin region is larger and where less in number. This might be the reason for poking hands at transcription for developmental defects.
LOD stands for logarithm of odds. It is used for linkage analysis and the value of unlinked to the linked markers is increased by using logarithm.
The relations A vs. B showed the statistical linkage with recombination fraction of 0. 1. And A vs. C showed the inconclusive linkage with the value of 0.5 recombination fraction.
The challenges in complex genetic diseases are
Some diseases are involved with Epistasis effects.
Environmental effects influence some diseases.
Time dependent expression of some proteins is in some disease.
The domestic animals as model animals, because of their complete or partial genomic information.
The phenotypic status is well studied regarding their purity of breed.
COLLIE EYE ABNORMALITY is disease in dogs and this disease is genetic disease with abnormalities in choroid plexus, optic nerve.
CANINE PEDIGREES, SAMPLE PREPARATION:
Canine pedigree for this disease is studied.
DISTRIBUTED MARKER AND CANDIDATE GENE:
Distributed marker and candidate gene approach is followed and the linkage map of this disease is determined.
SYNTENY BETWEEN gene AND HUMAN CHROMOSOME:
The synteny between human and the collie eye anomaly gene search is performed for any conserved reasons.