Functional genomics is a general approach toward understanding how the genes of an organism work together by assigning new functions to unknown genes. Information about the hypothesized function of an unknown gene may be deduced from its sequence structure using already known functions of similar genes as the basis for comparison. Gene function analysis therefore necessitates the analysis of temporal and spatial gene expression patterns (Yunbi Xu et al , Plant Molecular Biology (2005) ).

1. ROLE OF FUNCTIONAL GENOMICS
IN CROP IMPROVEMENT
ASHISH GAUTAM
Department of Plant Breeding & Genetics
AAU, Jorhat, Assam

2. CONTENT
• INTRODUCTION
• IMPORTANCE OF FUNCTIONAL GENOMICS
TO CROP IMPROVEMENT.
• TECHNIQUES AND APPLICATIONS OF
FUNCTIONAL GENOMICS .
• GENOME SIZE AND NO OF GENES OF SOME
ORGANISMS.
• CASE STUDY
• CONCLUSION

3. INTRODUCTION

4. Genomics is the field of genetics that attempts to
understand the content, organisation, function and
evolution of genetic information contained in whole
genome.
Genomics

5. Types of genomics :

6. Functional Genomics
Development and application of globe wide or
system wide experimental approach to access the
function of gene by making use of information and
reagent provided by structural Genomics.
It characterizes the function of sequences
elucidated by structural genomics.
Functional genomics is a characterwise study.

7. Function(s) of Gene
Protein Synthesis
Ionic Homeostasis
40-60% genes unknown Functions
FUNCTIONAL GENEOMICS

9. IMPORTANCE OF FUNCTIONAL GENOMICS TO CROP
IMPROVEMENT

11. Knowing the exact sequence and location of
all the genes of a given organism is only the
first step towards understanding how all the
parts of a biological system work together. In
this respect functional genomics is the key
approach to transforming quantity into quality
to crop improvement.
Functional genomics is a general approach
toward understanding how the genes of an
organism work together by assigning new
functions to unknown genes.

12. Process of conventional plant breeding

14. TECHNIQUES OF
FUNCTIONAL GENOMICS

15. Insertional Mutagenesis:
• Transposons & T-DNA Tagging.
Sequence Based Mutagenesis:
• Physical & Chemical Mutagens.
1.CLASSICAL TECHNIQUES/ TOOLS:

16. Target Gene Mutagenesis:
• RNAi .
• VIGS.
• Sense and Antisence Expression

17. RNA interference

18. Example of Plant trait engineered through RNAi
ISAAA/Resources/Publications/Pocket K/RNAi for Crop Improvement.

19. VIGS
(A tool for gene silencing )
 Creation of engineered viruses carrying sequences
corresponding to the host gene to be silenced.
 Infection leads to synthesis of viral dsRNA.
 Results in Down regulation of the host gene transcript.
 It provides robust silencing , has a broad host range, can infect
meristematic tissue, and produces only mild disease
symptoms.
Examples:-
 Silencing of phytotene desaturase gene (PDS) in
N.benthamiana plants.
 Recently , the turnip yellow mosaic virus has been adopted for
VIGS in Arabidopsis and provides silencing following
mechanical inoculation with a plasmid carrying engineered
virus.(Pfliger et al.2008).

20. 2. MODERN TECHNIQUE /TOOLS:
 DNA level:
• Southern Hybridisation.
 RNA level:
• Micro array .
• SAGE .
• EST
• Northern hybridisation.
 PROTEIN LEVEL:
• AP/MS.
• Yeast two-hybrid (Y2H) System.

21. Micro array
A RNA microarray (also commonly known as
RNA chip or biochip) is a collection of
microscopic DNA spots attached to a solid
surface.
It is used to measure the expression levels of
large numbers of genes simultaneously or to
genotype multiple regions of a genome.

22. Other Techniques used in Functional
Genomics
1. Association Mapping.
2. 2-D Electrophoresis.
3. Forward genetics.
(QTL Mapping)
4. Reverse genetics.
( TILLING)
5. NGSK.
6. MAS.

23. Bioinformatics Tools
• NCBI BLAST : To search homology between
sequences. It compares nucleotide or protein-protein
sequences to sequence databases .
• EMBL (European molecular biology lab) : Used for
Nucleotide sequence.
• Gene Bank: For Nucleotide Sequence.
• MAP MAKER: For Linkage map.

24. Contd..
• GenMAPP: To visualize gene expression and other
genomic data on maps representing biological
pathways and grouping of genes.
• TASSEL: To study Association mapping of
complex traits in diverse samples.
(Trait analysis by association, evolution and
linkage)
• GRAMENE Data base: Gramene is a curated,
open-source, integrated data resource for
comparative functional genomics in crops and
model plant species.

25. APLLICATION OF FUNCTIONAL
GENOMICS

26. Sequencing of crop-plant genomes.
Gene discovery for useful traits.
Genome wide regulatory networks to improve
Traits.
Diversity analysis.
Evolutionary.

27. Phylogenetic relationship.
Fine mapping.
Disease diagnosis.
Gene expression Study.

28. Genome Size and Number Of Genes
Organisms.
S.No. Organism Base Pair (Mbp) No Of Genes
1. Arabidopsis thaliana 125 25,706
2. Oryza sativa 425 16,941
3. E.coli 4.64 4289
4. Z.maize 2300 39,656
5. Glycine max 1115 46,430
6. Mouse 2627 26,762
7. S.cerevisiae 12 6144
8. Drosophila melanogaster 170 13,525
9. Ascaris megalocephala 103 20,598
10. Homo sapiens sapiens 3223 30,000
11. Solanum lycopersicum 900 34,727

29. 1.CASE STUDY

31. Genomics research generates new tools :
• Functional molecular markers
• Bioinformatics.
• Knowledge about Statistics and inheritance phenomenon.
In present Study case it has been presented:
• An overview of the status and availability of genomic
resources.
• Genomics research in crop plant species, and has been
discussed.
• Strategies and approaches for effectively exploiting
genomics research for crop improvement has been
discussed.

32. An integrated view of exploitation of genomic resources for crop improvement via
different genetic and genomic strategies
Abbreviations: AB-QTL, advanced backcross QTL; COS, conserved orthologous set; DHs, doubled haploids; eQTLs, expression QTLs; ESTs,
expressed sequence tags; ILs, introgression lines; LD, linkagedisequilibrium; NILs, near isogenic lines; QTL, quantitative trait locus; RILs,
recombinant inbred lines; SNP, single nucleotide polymorphism; SSR, simple sequence repeat or microsatellite; TILLING, targeted induced local
lesions in genome.

33. 2.CASE STUDY

35. It enables agricultural researchers to investigate
how gene expression and regulation contributes
to complex production traits at a genome-wide
level.
In this review, it has been highlighted some of
the different areas of functional genomics,
including some emerging techniques, with a
specific focus on how they are being applied to
production livestock and aquaculture systems.

36. It has been discussed how transcriptomics,
proteomics,metabolomics,interactomics,epigeneti
cs and nutrigenomics are applied to improve our
understanding of complex production traits and
how the environment affects these traits.
It has been shown how changing technologies
contribute to functional genomics and the
resources agricultural researchers require to
ensure that their functional genomics data are
effectively translated into benefits for society

37. Functional genomics approaches examine different aspects of
gene expression and gene expression regulation.

38. Conclusion
Functional genomics is a field of molecular
biology that attempts to make use of the vast
wealth of data produced by genomics and
transcriptomics to describe gene (and protein)
functions and interactions.
 It focuses on the dynamic aspects such as gene
regulation, transcription, translation, gene
expression and protein-protein interaction
 It attempts to answer questions about the
function of DNA at the levels of genes, RNA
transcripts, and protein products.

39. Thank you...