4. WHAT IS GENOME?
• A genome is an organism's complete set of DNA, including all of its genes.
• Genes carry the information for making all of the proteins required by the body for growth and
maintenance.
• The genome also encodes r-RNA and t-RNA which are involved in protein synthesis.
5. GENOMICS
• Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics
to sequence, assemble and analyze the function and structure of genomes (the complete set of DNA within a single
cell of an organism).
• The branch of molecular biology concerned with the structure, function, evolutionandmapping of genomes.
• It involves the study of all genes at the DNA, mRNA and proteome level as well as the cellular or tissue level.
• The term genomics was first coined in 1986 by Tom Roderick.
6. • Genomics is the study of the genomes (i.e. the entire hereditary information) of organisms and
includes:
- Determining the entire DNA sequence
- Fine-scale genetic mapping.
- Studies of intragenomic phenomena.
Usedto determine an ideal genotype insteadof just a few genes
The study of whole genomes of populations of individuals can reveal the genetic basis of different
responses to both biotic and abiotic stresses.
Requires a large amount of information per individual.
Expensive in agriculture where many individuals need to be analyzed.
7. GENETICS V/S GENOMICS
GENETICS
• Genetics is the study of heredity.
• “Gene” refers tto a specific sequence of
DNA on a single chromosome.
• Genetics involves the study of functions
and composition of single gene.
GENOMICS
• Genomics is the study of the entirety of an
organism’s genes.
• “Genome” refers to an organism's entire
genetic makeup.
• Genomics addresses all genes and their
inter relationships.
8. SUBFIELD OF GENOMICS
1. Structural genomics:
Construction of genomic sequence data
Gene discovery and localization
Construction of gene maps
Structural genomics seeks to describe the 3-dimensional structure of every protein encoded by a given genome.
2. Functional genomics:
Biological function of genes, Regulation, Products and Plant development studies.
Functional genomics focuses on the dynamic aspects such as gene transcription , translation and protein–protein
interactions.
3. Comparative genomics:
Compares gene sequences to elucidate functional or evolutionary relationships.
9. GOALS OF GENOMICS
• Sequence the entire genome by cutting it into small, manageable pieces (fragments).
• Assemble the entire genome from the pieces.
• Understand how gene expression takes place.
Why to sequence the genomes..?
• Sequencing genomes helps understand how the genome as a whole and how the genes work
together to direct the growth, development and maintenance of an entire organism.
• The genome sequence will represent a valuable shortcut, thus helping to find genes much
more easily and quickly.
11. FINDING THE GENES
• After sequencing, need to find the genes, using computer algorithms – this step is called
‘annotation’.
• Annotation identifies :
Protein-coding genes
Initiation sequences
Regulatory sequences
Termination sequences
Non protein-coding sequences
12. GENE FUNCTION
• After genome sequencing is annotated, functions need to be assigned to all genes in the
sequence.
• Some of the identified genes might have functions assigned already via classical methods of
mutagenesis and linkage mapping.
• Some may not have assigned functions – use homology searches.
• Computer-based comparisons of the sequence under study with known sequences from
other organisms.
14. BENEFITS OF GENOMICS TO CROP
IMPROVEMENT
• Unlimited possibilities for crop improvement, especially in combination with
genetic engineering:
Improved crop productivity
Increased nutritional quality and quantity
Tolerance to abiotic stresses – drought, low quality soils (acidity, low nutrient content)
Tolerance to biotic stresses - pests and diseases
• Other :
It can be used in the field of medicine for early detection of genetic diseases and its diagnosis and treatment.
To study evolution through mutation lineages.
In forensic science.
17. TRANSCRIPTOME
-The transcriptome is the complete set of transcripts in a cell and their quantity, for a specific
developmental stage or physiological condition.
-Understanding the transcriptome is essential for interpreting the functional elements of the
genome and revealing the molecular constituents of cells and tissues, and also for
understanding development and disease.
•
18. • It is the study of RNA in any of its forms.
• The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other
non-coding RNA produced in one or a population of cells.
19. SCOPE OF TRANSCRIPTOMICS
• The term can be applied to the total set of transcripts in a given organism, or to the specific
subset of transcripts present in a particular cell type.
• Unlike the genome, which is roughly fixed for a given cell line (excluding mutations), the
transcriptome can vary with external environmental conditions.
20. • Because it includes all mRNA transcripts in the cell, the transcriptome reflects the genes that
are being actively expressed at any given time, with the exception of mRNA degradation
phenomena such as transcriptional attenuation.
• The study of transcriptomics, also referred to as expression profiling, examines the
expression level of mRNAs in a given cell population, often using high-throughput
techniques based on DNA microarray technology.
21. AIMS OF TRANSCRIPTOMICS
I. To catalogue all species of transcripts, including mRNAs, noncoding RNAs and small
RNAs.
II. To determine the transcriptional structure of genes, in terms of their start sites, 5′ and 3′
ends, splicing patterns and other post-transcriptional modifications.
III. To quantify the changing expression levels of each transcript during development and
under different conditions.
22. APPLICATION OF TRANSCRIPTOMICS
IN PLANT BREEDING
1- Transcriptome assembly and profiling:
The widespread use of transcriptome sampling strategies is a complementary approach to
genome sequencing, and results in a large collection of expressed sequence tags (ESTs) for
almost all the important plant species
(http://www.ncbi.nlm.nih.gov/dbEST/dbEST_summary.html). The plant EST database has
recently passed the five million sequence landmark. More than 50 plant species, each with
>5000 ESTs, are represented.
23. 2- Small RNA characterization:
Small RNAs (sRNA) are non-protein-coding small RNA molecules ranging from 20
to 30 nt that have a role in development, genome maintenance and plant responses
to environmental stresses.
24. 3- eQTL:
Metabolite, protein and transcript profiles can also be directly mapped onto a segregating
population to provide information on loci that control gene expression levels, protein
modification or levels of a particular secondary metabolite. The QTLs associated with such
traits are known as expression (eQTL), protein (pQTL) or metabolite (mQTL)
