HI

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Integration of Genetic and
physical map: from genomes to
interacting networks

Ashwini Samak N. R
ID no: PAK- 7188

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 Genetic map

•Constructed by measuring the meiotic

recombination frequencies between
different pairs of genetic markers.

•Primary task is to linking genes or their

surrogate genetic marker with trait of
interest

•Linkage analysis

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 Physical map

• Constructed by identifying the position of markers

along the chromosome
• Physical distance measured by techniques such
as Radiation hybrid mapping, Fluorescence in situ
hybridization, automated DNA sequencing.
• Primary task is to identification of genes

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Why physical map needed ? ??

• A genetic map has a limited degree of resolution:

In eukaryotes it is not possible to produce large
no. of progeny- less meiosis-resolving power
restricted

• Genetic maps have limited accuracy:

Recombination hot spots distribution

(Brown, 1999) 5
 Terms about Physical Map

•Chromosome = assembly of contigs

•Contig = assembly of clones
•Clone – the only physical entity (BAC or PAC clone)
•A veeerrry small chromosome piece sequenced; 100++ kb
DNA
•Gap = introduced by
•Recombination
•No data (assembly unfinished or data non-existent yet)
Anchor marker – molecular marker that is
•physically located on a clone (sequence is there)
•1 cM = ~247kb (from 420Mb japonica genome /
1700 cM total)

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 Centromere
Chromosome

Clones

ORFs

Components of physical map

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 A physical map of the rice genome that is
aligned with genetic map

Genetic Contig
Physical map
map Assembly
Cornell
“gap”

1 contig

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Construction of Integrated Map

• It depends on anchoring BAC/YAC contigs by

association with genetically mapped
probes/markers.
• Steps in Integration
o Screening YAC/ BAC libraries
o Hybridization of radioactive probes to BAC filters
o PCR based analysis of BAC DNA pools

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 Steps in integrating map

• BAC library construction and fingerprinting

•Manual editing of contigs

•Anchoring of BAC contigs to the genetic map

Rice physical Map

(Chromosome 1)

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 Integrated rice genome map

Singletons-2778 clones . This estimates 453Mb rice

genome
(Chen et al. 2002) 11
Manual editing of contigs

• Manual editing improves the physical map in 2

ways
1. For identification of potential joins b/n contigs &
performing merges
2. Identifies potential chimeric contigs by revealing
incorrectly overlapped fingerprint data or by
highlighting conflicting marker data.

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FPC Display of Contig 219.
Clones highlighted in green are in shotgun sequencing. Clones
highlighted in yellow are redigested finished clones from GenBank, and
the corresponding BAC clones are shown in gray.
(Chen et al. 2002) 13
Anchoring of rice BAC contigs to Rice
genetic map
• A contig can be assigned to a specific genetic
location if the contig is associated with a probe
that is mapped to one genetic location and the
probe does not hit BACs in another contig.
• It requires the high resolution genetic map

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2 approaches used in rice integrated map

1.DNA probes used for hybridization -which serves as

landmarks on the rice genome

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• In silico hybridization

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Integration helps us to
•It provide views that are highly complementary
with regard to cellular structure and function

•It will provide physical and genetic interaction

and provide biological pathway

•Correlation between physical and genetic map

will help full for efficient map based gene
cloning .

•It will help in associating candidate genes with

trait of interest
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 Biological Networks
Network: the interaction and integration of multiple
components in organisms using computational models
and visualized by node and connection diagrams.
• Components include genes, proteins, cis elements,
metabolites and other molecules.
• Four network types
• Gene-to-metabolite networks
• Protein–protein interaction networks
Static
• Transcriptional regulatory networks
• Gene regulatory networks.
Dynamic

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a) The gene-to-metabolite
network often derives from
correlation analysis of gene
and metabolite profiling under
multiple conditions.

(b) Interactomes can be derived

from genetic or protein-binding
assays.

(c) The transcriptional regulatory

network is highly diverse and
can be presented as a
hierarchical structure.

(d) The gene regulatory network

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Genetic interactome

• It is a network of genes characterized on the

basis of genetic interactions serving to elucidate
gene function within physiological processes .

• Genetic interaction- functional relationships

between genes, in which the phenotypic effect of
one gene is modified by another

• Genetic interactions define functional relationships

between genes, giving insight into how this physical
architecture translates into phenotype.

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Ex: Systematic genetic analysis (SGA) for yeast

In yeast genetic interactome , genes having

important cellular functions typically form
interaction hubs ( many genes with interaction)

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• Development of Genome wide genetic
interactome map is difficult.
• It depends on genome size, ploidy level,
generation time, data bases, computational
requirements, Statistical analysis, Bioinformatics,
algorithm development.

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Gene regulatory networks

• A gene regulatory network describes how genes

interact with one another during the biological
process to perform a function.
• The relationships among the genes in the network
can be defined in terms of activation &
repression.

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Development of network

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Construction of networks

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Physical interactome

• Physical interactions dictate the architecture of the

cell in terms of how direct associations between
molecules constitute protein complexes, signal
transduction pathways and other cellular
machinery.
• Physical interactions among proteins are
relatively easier to characterize in organisms.

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Physical interaction types

1. Protein-protein interaction
2. Protein- DNA interaction

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 The physical network
defines three
complexes Genetic
network defines
functional
dependencies
between prefoldin and
dynactin or the
kinetochore,
respectively

An integrated map of genetic and physical interactions for

the yeast cytoskeleton.
Solid lines - physical protein–protein interactions
dashed lines -synthetic-lethal genetic interactions

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The assembly and analysis of genetic and physical interaction networks

A complete picture of the cell must necessarily integrate both aspects .

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 Measuring physical interaction networks

• Networks of protein–protein:
 Yeast two-hybrid (Y2H) technology
 Tandem affinity purification coupled with mass
spectrometry (TAP–MS)
• Networks of protein–DNA
 Chromatin immunoprecipitation coupled with DNA
microchips (ChIP–chip) or sequencing (ChIP–PET)
 DNA adenine methylase identification (DamID)
Physical interactions can also be measured in vitro using
DNA or protein arrays, which have been used to identify
transcription factor binding sites and the substrates of yeast
kinases
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Measuring Genetic networks

• By comparing the effect of mutating each gene

individually to the effect of the double mutant.

• Ex: ‘synthetic sickness’ (Double mutant effect

more compare to single mutant )

• Synthetic genetic arrays (SGA)

Yeast
• Diploid-based synthetic-lethality analysis on
microarrays (dSLAM)

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• For higher eukaryotes:
• RNAi technology
• eQTL analysis (expression quantitative trait loci):
Genotyping

Phenotyping using microarray

Statistical analysis for linking marker to gene expression level of gene

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Interacting Networks and Genomes

• In

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Importance of networks

• It describe the physiology of an organism / a

biological process.
• To understand the inherent biological complexity
by identifying key components & interactions for
system regulation.
• It provides new perspectives for interpreting
omics data & can be applied to study a variety of
plant biological questions.

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Limitations of networks

• Difficulties in Data modeling, generalization.

• Networks in systems biology might never
completely represent the actual biological system.
•

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Importance of interacting networks in
plants

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