This document discusses genomics and the usage and effects of mutations in genomics. It begins by defining genomics and the different types including structural, functional, comparative, and mutation genomics. It then describes different types of mutations that can occur at the DNA level like transitions, transversions, deletions, and insertions. It also discusses how mutations can affect proteins by being neutral, silent, missense, nonsense, or causing frameshifts. The document outlines several ways mutation genomics is used, including determining gene function, demonstrating metabolic pathways, and understanding metabolic regulation. It concludes by covering applications of genomics in crop improvement like predicting gene-phenotype relationships and improving drought, salt, and disease tolerance.

1. Genomics & usage and effect of mutation in genomics
SUBMITTED BY:
Shivashish Verma
Department of Genetics and Plant Breeding
Naini Agricultural Institute (NAI)
Sam Higginbottom University of Agriculture, Technology & Sciences,
Prayagraj, UP, 211007,
2019

2. Introduction :
WHAT IS GENOMICS?
• Genomics is the branch of science which deals with the structure function
evolution of the genome
• A genome is an organism's complete set of DNA, including all of its genes.
• A major part of genomics is determining the sequence of molecules that
make up the genomic deoxyribonucleic acid (DNA) content of an
organism.
• The genomic DNA sequence is contained within an organism chromosome,
or more sets of which are found in each cell of an organism comprising of
the fundamentals unit of heredity i.e. genes

3. Types of genomics:
• Structural genomics: Aims to determine the structure of
every protein encoded by the genome.
• Functional genomics: Aims to collect and use data from
sequencing for describing gene and protein functions.
• Comparative genomics: Aims to compare genomic
features between different species.
• Mutation genomics: Studies the genome in terms of
mutations that occur in a person's DNA or genome.

4. Changes occuring at the genomic level:
• The changes occuring by mutation can be classified at the two
different levels :
A. At the DNA level:
1. Transition
2. Transversion
3. Deletion
4. Insertions

5. 1) Transition:
• Refers to a point mutation that changes a purine nucleotide to
another purine (A ↔ G), or a pyrimidine nucleotide to another
pyrimidine (C ↔ T).
2) Transversion:
• Transversion mutation is a specific kind of point mutation,
one in which a single purine is substituted for a pyrimidine or
vice versa. As the result of a transversion mutation,
the mutated position in the gene may for example have an
adenine where it had a thymine or cytosine.

7. • Deletion: Deletion (also called gene deletion, deficiency,
or deletion mutation) (sign: Δ) is a mutation (a genetic
aberration) in which a part of a chromosome or a sequence of
DNA is left out during DNA replication
• Eg : Turner syndrome, cystic fibrosis etc.
• Insertion: Insertion (also called an insertion mutation) is the
addition of one or more nucleotide base pairs into a DNA
sequence. This can often happen in microsatellite regions due
to the DNA polymerase slipping.
• Eg: Huntington disease etc.

8. B) Effect at the protein level:
1) Neutral : When the alteration in codon shows the minimal
effect on the protein structure. No loss of the protein function
takes place.
2) Silent: When the change in codon sequence doesn't affect the
protein sequence. Example: AGG (arg) replace by CGG (arg).
3) Missense : When alteration in codon sequence codes for
different amino acid. Protein function get altered.
4) Nonsense: Premature termination of the translation by the
involvement of the stop codon.(UAA, UGA, UAG)
5) Frameshift: Small additions and deletions in the codon
sequence. This in turn alters the expression of the protein
character.

9. Usage of mutation in genomics:
• 1. Determination of Function:
• A mutation defines a function. For example, a wild type E.coli cells
can uptake lactose from 10-5 M solution by a passive diffusion
through the cell membrane. But the mutants cannot uptake lactose
even at the concentration higher than 10-5 M. This shows that the
genetically determined process is involved in lactose uptake.
• 2. Demonstration of Metabolic Pathways in Microorganisms:
• It has been demonstrated by isolating the three different classes of
gal mutants that galactose is utilized by three distinct genes, galK,
galT and galE. The Gal+ cells are grown on medium containing
radioactive galactose (14C-Gal). As the 14C-Gal is metabolized,
many different radioactive compounds can be found in the growth
medium.

10. • 3. For Understanding The Metabolic Regulation:
• Several bacterial mutants have been isolated which show changes in
amount of a particular protein of its responses to external signals.
For example, the enzyme synthesized by galK, galT and galE genes
are normally not present in bacteria. These are synthesized only
when galactose is supplied in the growth medium.
• 4. Matching a Biochemical Entity with a Biological Function:
• E. coli synthesizes an enzyme, DNA polymerase which polymerizes
the DNA. It was thought that DNA polymerase I is also synthesizes
the bacterial DNA. In Pol A-mutant of E.coli the activity of
polymerase I has been found reduced by 50 time. After biochemical
analysis of cell extracts of Pol A- mutants of E.coli two other
enzymes, DNA polymerase II and DNA polymerase III were
isolated. The purified enzymes synthesized the DNA molecule.

11. • 5. For Locating the Site of Action of External Agents:
• Eg : An antibiotic, rifamycin is known to inhibit RNA synthesis. In
the beginning it was unknown about the precise activity of rifamycin
whether it acts by checking the synthesis of precursor molecule by
binding to DNA and in turn by inhibiting the transcription of DNA
into RNA, or by binding to RNA polymerase.
• 6. For the Production of Useful Products:
• In addition, mutation in microorganisms for beneficial products was
started since the time of Alexander Fleming during the end of 1920s.
By using ultraviolet rays penicillin production by a mold Pencillium
chrysogenum has been increased by about thousand fold greater to
what was produced at Fleming’s time.

12. Application of genomics in crop improvement:
• Prediction of gene-to-phenotype relationships-
• The quantitative trait loci(QTL) shows caliber to minimize the
genotype-phenotype gap in plant species. This QTL information has
been incorporated into plant models for analyzing the genotype-by-
environment interactions.
• Drought tolerance improvement in crop plants-
• There are three main approaches for creating drought resistance crop
species:
 i. Plant physiology helps us in understanding the complete network
of drought related traits with the development of new tools.
 ii. Molecular genetics on the other hand helps us discover QTL’s that
affect the yield under drought conditions.
 iii. Molecular biology that helps in providing genes which can be
further used as candidate sequences

13. • Improving salt tolerance in plants-
• The lack of availability of genes that confer salt resistance
along with the lack of knowledge in understanding the
molecular basis of salt tolerance has restricted the
development in breeding for salt tolerant plants. Thus
genomics provide suitable evidence regarding the
characteristics and variations in crop species that can be used
effectively to develop and improve salt tolerance in plants.
• Crop improvement through modification of plant’s own
genome-
• A plant derived (P-) DNA fragment was used to replace the
Agrobacterium transfer (T-) DNA. The method that was used
here could be able to produce multiple marker-free and
backbone free potato plants that could display less amount of
tuber-specific polyphenol oxidase gene in potato

14. References:
• Significant Role of Genomics in Crop Breeding: An Overview
Anoushka Kotra1*, Neetu Jabalia2 and Nidhee Chaudhary3 Amity Institute
of Biotechnology, Amity University, Uttar Pradesh, Noida
• Genomics for Crop Improvement – an Indian perspective
Sheel Yadav, Sundeep Kumar, Kirti Savita, Amit Kumar Singh and Rakesh
Singh Division of Genomic Resources, National Bureau of Plant Genetic
Resources, New Delhi, India 110012
• Principles of Genetics – by B.D.Singh
• www.slideshare.com