The document discusses plant genomics, covering the history, study, and organization of plant genomes, including the significance of model organisms like Arabidopsis thaliana. It highlights the complexity and variability of plant genomes, the roles of chloroplast and mitochondrial DNA, and the impact of transposable elements. Additionally, it emphasizes the applications of genomics in improving crop productivity and quality, showcasing its relevance in food production and environmental sustainability.

1. PLANT GENOMICS
By
KAUSHAL KUMAR SAHU
Assistant Professor (Ad Hoc)
Department of Biotechnology
Govt. Digvijay Autonomous P. G. College
Raj-Nandgaon ( C. G. )

2. CONTENTS:
 Introduction
 History
 First model organism(Arabidopsis thaliana)
 Studying plant genome
 Plant nuclear genome composition
 Organization of plant genome
 Transposable elements
 Chloroplast genome & its evolution
 Mapping plant genomes
 Plant genome project
 Application
 Conclusion
 References

3. Introduction
 Genomics - the study of genomes.
 Genome -The word ‘’genome’’describes the total
repertoire of DNA in a particular organelle.
 Plant genomes dramatically vary in size and in
function.
 Plant chloroplasts and mitochondria maintain plant
genomes, and plant mitochondrial genomes are large,
variable and enormously interesting.
 Plant nuclear genomes have been sculpted by
interspecific hybridization ,polyploidy, transposition,
retro-transposition and translocation events.

4. History :
 Formal research into the function of the plant
genome started with mendel in 1866 .
 Arabidopsis thaliana (a dicot) was the first plant
chosen for genome sequencing, Rice was the
second genome sequenced and was the first
monocot.
 A small number of plant genomes have been
studied in great detail in the 1990s and early in the
twenty-first century and the DNA of their genomes
has been sequenced.


5. First eukaryotic model
organism(Arabidopsis thaliana)
 One of the first eukaryotic organisms that will be
completely sequenced is the small mustard species
Arabidopsis thaliana.
 During the past decade, Arabidopsis has emerged
as one of the most widely used model organisms for
studying the biology of higher plants.
 It was chosen for sequencing because it has a highly
compact genome of about 130 Mb with little
interspersed repetitive DNA.


6.  Fig.: Functional classification of predicted genes in
a 1.9-Mb region of the Arabidopsis genome.

7. Studying Plant genome:
 Plant genomes are more complex than other eukaryotic
genomes, and analysis reveals many evolutionary flips and
turns of the DNA sequences over time.

 Plant nuclear genome range in size from less than
100million base pairs to more than 100 billion base pairs.

 Plants show widely different chromosome numbers and
varied ploidy levels . Overall, the size of plant genomes
(both number of chromosomes and total nucleotide base-
pairs) exhibits the greatest variation of any kingdom in the
biological world. For example, tulips contain over 170 times
as much DNA as the small weed Arabidopsis thaliana.

8.  The DNA of plants, like animals, can also contain
regions of sequence repeats, sequence inversions, or
transposable element insertions, which further modify
their genetic content.Traditionally, variation in
chromosome inversions and ploidy has been used to
build up a picture of how plant species have evolved .

 Increasingly,researchers are turning to studying the
organization of plant DNA sequences to obtain
important information about the evolutionary history of
a plant species.


9.  FIGURE : Chromosome numbers possible in plant
genomes.

10. Nuclear Genomes and their Size
 The nuclear genome of rice consists of 450 million base
pairs (Mbp) of DNA divided among the 12 chromosome
pairs, and includes the genes that encode some 38 000
proteins.
 Along with their controlling sequences, these genes
represent less than 10% of the total amount of DNA, and
about half of all the DNA consists of repetitive motifs that
are present thousands of times in the genome.
 Another fully sequenced plant genome,Arabidopsis
(Arabidopsis thaliana) has a total of 157Mbp with about
31 000 genes on five chromosome pairs.


11.  It is currently anticipated that the complete genome
sequence of Arabidopsis will be available by the end of the
year 2000.

 Because Arabidopsis is only distantly related to the cereal
crops that provide the bulk of the world’s food supply, the
genome of rice will also be sequenced during the next
decade .

 Rice was chosen because, in addition to its importance as a
food source for about one-quarter of the human population,
it has one of the most compact genomes among the cereals.
 It contains about 3.5 times as much DNA as Arabidopsis but
only about 20% as much DNA as maize and about 3% as
much DNA as wheat .

12.  All higher plants, at the diploid level, require
approximately the same number of genes and
regulatory DNA sequences for physiological processes
like seed germination,growth, flowering and
reproduction.
 However, nuclear genome sizes, measured by the
number of base pairs of DNA, of different plant species
vary enormously between species, although each
species has a characteristic and relatively constant
genome size.
 The amount of nuclear DNA can be given as an
absolute weight of the DNA (in pg, picograms) or
converted into the number of base pairs represented by
that weight.

14. Plant Nuclear Genome Composition
 The plant nuclear genome consists of DNA divided
among the chromosomes within the cell nucleus.
 Plant genomes contain coding and regulatory
sequences for the genes and repetitive DNA.
 Genomes are evolutionarily dynamic and analysis
provides insights into the evolution of genes,
sequence families and genomes, and supports
studies of species phylogeny and relationships.

15.  The plant nuclear genome consists of
deoxyribonucleic acid (DNA) and is contained
within the nucleus, an organelle encased by a
double membrane in each cell.
 During cell division, mitosis, the genome
condenses into a characteristic number of
metaphase chromosomes, the nuclear membranes
break down, and the chromosomes divide, moving
into the two daughter cells before the nuclei reform.

16. Organization of Plant Genomes:-
 Most seed plants contain quantities of DNA that
greatly exceed their needs for coding and
regulatory function. Hence, for plants, a very small
percentage of the genome may actually encode
genes involved in the production of protein.
 This portion of the genome which encodes most of
the transcribed genes is often referred to as “low-
copy number DNA,” because the DNA sequences
comprising these genes are present in single or
small numbers of copies.

17.  “Medium-copy-number DNA” is composed largely
of DNA sequences that encode ribosomal RNA
(rRNA), a key element of the cellular machinery that
translates transcribed messenger RNA (mRNA) into
protein.
 In plant genomes, rRNA genes may be repeated
several hundred to several thousand times.
 Plant cells may also contain excess DNA in their
genomes in the form of highly repetitive sequences,
or “high-copy-number DNA.” At present, the
function of this high-copy-number DNA in plant
genomes is unknown.

18. Sequence Replication and
Inversion
 High-copy-number DNA sequences in the plant
genome may be short, such as the nucleotide sequence
“GAA,” or much longer, involving up to several hundred
nucleotides.
 Moreover, the number of copies of an individual high
copy repetitive DNA sequence can total from 10,000 to
100,000.There are several possibilities for how high-
copy repetitive DNA sequences may be organized
within a plant genome.
 Several copies of a single repetitive DNA sequence may
be present together in the same orientation, in a
pattern called “simple tandem array.”

19.  Alternatively, repetitive DNA sequences can be dispersed among
single-copy DNA in the same orientation (“repeat/single-copy
interspersion”) or the opposite orientation (“inverted repeats”).
 In addition, groups of repetitive DNA sequences can also occur
together in plant genomes in a variety of possible arrangements,
such as a“compound tandem array” or a “repeat/repeat
interspersion.”
 The presence of repetitive DNA can vastly increase the size of a
plant genome, making it difficult to find and characterize individual
single-copy genes.
 A variety of mechanisms can account for the presence of highly
repetitive DNA sequences in plant genomes.

20. Transposable Elements:
 Transposable elements, are special sequences of DNA with
the ability to move from place to place in the genome.

 They can excise from one site at unpredictable times and
reinsert in another site. For this reason, transposable
elements have been called “jumping genes.

 Transposable elements often insert into coding regions or
regulatory regions of a gene and so affect expression of that
gene, resulting in a mutation that may or may not be
detectable.

 Barbara McClintock won the Nobel Prize in 1983 for her
work describing transposable elements in corn.

21. 
 FIGURE : Organization of repeated DNA sequences and the
mechanism of transposable elements in altering gene function.

22. Chloroplast Genome and Its
Evolution
 The chloroplast is a plant organelle that functions in
photosynthesis,and it can independently replicate in the
plant cell.

 Plant chloroplasts have their own specific DNA, which is
separate from that present in the nucleus.

 This DNA is maternally inherited and encodes unique
chloroplast proteins.

 Many of the proteins encoded by chloroplast DNA are
involved in photosynthesis.


23.  Chloroplast DNA is present as circular loops of
double-stranded DNA similar to prokaryotic
chromosomal DNA.

 Moreover, chloroplast DNA contains genes for
ribosomes that are very similar to those present in
prokaryotes.The DNA in chloroplasts of all land
plants has about the same number of genes (~100),
and they are present in about the same order .

24.  FIGURE :Chloroplast genome.

25. Mapping plant genomes:
 RFLP and AFLP asTools to Map Genomes and Detect
Polymorphisms
 Genome mapping is a widely-Aplicable approach to
scanning the genetic information of an organism for genes
that are responsible for a specific trait.

 Higher plants are thought to have 25,000 or more genes,the
vast majority of which remain of unknown function.

 A particular strenghth of genome mapping.is that it
facilitates isolation of genes based simply on measurement
of their effects(s)on phenotype requiring no a priori
knowledge of the biochemical function performed by a
gene.

26.  Much more of the genome can be mapped using RFLPs
(restriction fragment length polymorphisms) which need
not have a macroscopic phenotype.
 This approach, involves analysis of the RFLP map, or the
pattern of DNA fragments, produced when DNA is treated
with restriction enzymes that cleave at specific sites.
 RFLP mapping can identify important regions of the
genome at a glance, while sequence data require
sophisticated computer- based searching and matching
systems.
 A comparison of the RFLP maps of parents and progeny
can give an indication of the heritability of gene traits and of
heritable loci that are characteristic of traits.

27.  Another tool that utilizes sequence variability is AFLPs,
or amplified fragment length polymorphisms.
 Hybridizing DNA primers with genomic DNA
fragments that have been cut with restriction enzymes,
usually EcoRI and MseI, and then subsequently
amplified using the polymerase chain reaction (PCR)
generates AFLP maps.
 The resulting PCR products, which represent each piece
of DNA cut by a restriction enzyme, are separated by
size via gel electrophoresis.
 The band sizes on an AFLP gel tend to show more
polymorphisms than those found with RFLP mapping
because the entire genome is visible on the gel .


28. Applications:
 Genomics research will lead to new and innovative ways
to
achieve such trait improvement. Clearly,genomics can
help in issues related to food safety, food quality,and
food diversity.
 Genomics provides objectivity in breeding as never
before possible; it allows hypothesis testing of
quantitative genetics applications in plant
improvement.
 It is useful to increase crop productivity, improve crop
quality, and maintain the environment.

29. Conclusion:
 Genomic organization is much more varied in plants
than in animals.The completely sequenced
Arabidopsis genome will have far-reaching uses in
agricultural breeding and evolutionary analysis.
 Plant genome research is more than biology; it is
also about producing food for our planet.

30. References
 Plant genomics and proteomics-Christopher
A.Cullis, A. Jhon & Sons,Inc.Publication (pdf).
 Biotechnology –vol-VII plant genome mapping
strategies & application – Andrew H.Peterson(pdf).