This document proposes a 3-year research project to study the gene networks and pathways involved in the pathogenicity of Fusarium oxysporum, which causes Fusarium wilt disease in many important crop plants. The objectives are to determine networks and pathways during different life cycle stages, compare protein relatedness between species, and detect horizontally transferred pathogenicity chromosomes. Methodologies include prediction tools, sequencing, blotting, and chemical analysis. The outcomes would provide insights into Fusarium biology and life cycles to aid disease management, with a total estimated budget of 16 lakhs.

1. UNIVERSITY OF
AGRICULTURAL
SCIENCES,BANGALORE.
Agricultural college ,Hassan

2. Submitted to,
Dept of Agri Biotechnology
Agricultural college, Hassan
Submitted by,
Ashwini,M. ( BLH 2007 )
Chandana,B.R. ( BLH 2010 )

3. Gene networks and pathways.
 A gene regulatory network is a set of genes, or parts
of genes, that interact with each other to control a
specific cell function. Gene regulatory networks are
important in development, differentiation and
responding to environmental cues.

5. Models of gene regulatory network
 Boolean network:
Boolean network can model a GRN together with its gene products (the
outputs) and the substances from the environment that affect it (the
inputs).
 Continuous networks:
Continuous network models of GRNs are an extension of the boolean
networks. Nodes still represent genes and connections between them
regulatory influences on gene expression. Genes in biological systems
display a continuous range of activity levels and it has been argued that
using a continuous representation captures several properties of gene
regulatory networks not present in the Boolean model.

6.  Stochastic gene networks:
Recent experimental results have demonstrated that
gene expression is a stochastic process. Works on
single gene expression and small synthetic genetic
networks. The first versions of stochastic models of
gene expression involved only instantaneous reactions.

7. Structure of GRN’s
Gene regulatory networks are generally thought to be
made up of a few highly connected nodes (hubs) and
many poorly connected nodes nested within a
hierarchical regulatory regime. Thus gene regulatory
networks approximate a hierarchical scale free
network topology.This structure is thought to evolve
due to the preferential attachment of duplicated genes
to more highly connected genes.

8. Evolution of GRN’s
 There are primarily two ways that networks can
evolve, first way by simultaneously. The first is that
network topology can be changed by the addition or
subtraction of nodes (genes) or parts of the network
(modules) may be expressed in different contexts.
The Drosophila Hippo signaling pathway provides a
good example.

9.  The second way networks can evolve is by changing
the strength of interactions between nodes, such as
how strongly a transcription factor may bind to a cis-
regulatory element. Such variation in strength of
network edges has been shown to underlie between
species variation in vulva cell fate patterning of
Caenorhabditis worms.

10. Importance

11. Development, hormone secretion, and
cellular communication.
prediction of adverse effects of new
drugs
Classification and clustering of genes.
studying interaction between
pathogen and its host.

12. Prediction of pathogenicity associated
network in Fusarium oxysporum using
transcriptomic and proteomic analysis
Title

13. Fusarium wilt
 Fusarium wilt is caused by
Fusarium oxysporum
Fusarium wilt is a common vascular
fungal disease. The fungal pathogen
Fusarium oxysporum affects a
wide variety of hosts of any age.

14. Continued…
Tomato, tobacco, legumes,
cucurbits, sweet potatoes
and banana are a few of the
most susceptible plants, but
it will also infect other
herbaceous plants.

15. symptoms
wilting
necrosis
Damping
off
Stunting
chlorosis
Premature
d leaf drop
Browning of
vascular
system

16. Infection
 Fungus invades plants through roots.
 Grows in plant xylem, which transports
water and nutrients from roots to foliage
 Xylem becomes obstructed and plant wilts and dies
 Older plants may survive but are often stunted.
 Infected plants usually show reddish brown
discoloration in cortex.

17. Economic importance
 The impacts of Fusarium wilt not only affects
biodiversity and health issues but also it affects socio
economic conditions of a country.
 Foc race 1 devastated
Bangladesh,Combodia,Srilanka,Vietnam agricultural
sectors.
 Foc race 1 also ruined the Latin American gros
Michel industries.

18. Literature search
 Fusarium wilt is most devastating disease of banana,
chilly, red gram and many other important crops. Its
been a major obstruct in global food production
since 18th century. It was 1st discovered in banana
plantations in Australia in 1874 then reported in
tropical America, Costa Rica and Panama.

19. Fusarium collectively represents the most imp group
of fungal plant pathogens, cause various diseases on
nearly every economically important crops and also
cause health hazards to humans and livestock by its
mycotoxins.

20.  The fusarium comparative genomics database
provides accesses to multiple sequenced fusarium
genomes simultaneously to facilitate the
comparative analysis among these closely related
fungal species.
 The study on fusarium comparative genomics
highlighted the existence of lineage specific
chromosomes that are rich in transposable
elements and encode genes that are pathogenicity
related.

21. Origin of the project proposal
 Still, its pathogenicity and interaction with other
pathogens is not being studied properly.
 Empowering the high throughput and cost effective
sequence technologies and optical mapping, and
gene networks and pathways prediction tools, we can
explore the genetic composition and evolutionary
origin of lineage specific chromosomes, which
capture the pathogenic and phenotypic diversity.

22. Novelty
 Transcriptomic analysis and proteomic analysis of
host and pathogen protein –protein interaction.
 To study role of supernumerary chromosomes in
pathogenicity that are inherited horizontally.
 To study gene networks and pathways that are
differentially expressed in the sexual and asexual life
cycle of Fusarium oxysporum.

23. Continued…
 To study secondary metabolite biosynthetic gene
clusters and pathways using complementary DNA
analysis in Fusarium.

24. OBJECTIVES
 To determine different networks and pathways
produced at different stages of life cycle by
complementary DNA analysis and Western blotting.
 To compare relatedness of proteins produced by
different species by complementary DNA analysis
and SNP studies through multiple sequence
alignment using ClustalW and Northern blotting.

25.  To detect whether other group pathogens have
horizontally inherited lineage specific pathogenicity
chromosomes by homology sequence search using
BLAST analysis.
 Chemical analysis of secondary metabolites and its
role in pathogenicity

26. Methodologies
 Prediction of gene networks and pathways using
Boolean networks and GeneMapp tool.
 Multiple sequence alignment using ClustalW.
 Western blotting and Northern blotting.

27.  It is a 3 year project
 1st and 2nd year different pathways and networks at
different stages of Fusarium oxysporum is studied.
 Secondary metabolites chemical analysis and 3rd
objective will be done by the end of 2nd year.
 Relatedness of proteins are studied at 3rd year.

28. Continued….
Series 1
Series 2
Series 3
series 4
0
0.5
1
1.5
2
2.5
3
Category 1
Category 2
Category 3
category 4

29. Outcome and deliverables..
 Better understanding of biology and life cycles of
( sexual and asexual stages ) of
Fusarium oxysporum.
 Fusarium as a model organism for study of other
fungal pathogens of Ascomycetes family.
 Study of gene networks and pathways of life cycle
helps in better management of disease, which is
major threat to global food production.

30. Tentative cost
 Total budget estimated for the completion of the
project estimated including man power and
equipment's and software is 16 lakhs.

31. ANY
QUIRIES ???