Comparative genome mapping involves comparing genetic maps between closely related species to study genome evolution and understand relationships at the genetic level. Genomes can be compared by looking at features like gene location and order, as well as sequence similarity. Many model systems have been used for comparative mapping, including plants like rice and maize, Arabidopsis and Brassica, tomato and potato. These studies have revealed things like conserved synteny between species, rates of rearrangement, and the effects of polyploidization. Comparative mapping is a useful tool for understanding genomes and their relationships across species.

2. What Is Comparative Genome Mapping and
model systems ?
• Genetic mapping is the creation of a genetic map and
taking DNA fragments and assigning them to different
chromosomes. Recombining DNA to figure out the distance
between two genes.
• Map based cloning may be easier in some species than
others–e.g., rice (with a small genome) vs. wheat (with a
massive genome) thus model systems come into existence.

3. Why Comparative Genome Mapping ?
• Maps constructed in one species can be compared by means of common markers (or common single
gene traits) with closely related species.
Comparison of whole genome sequences provides a highly detailed view of
 These comparative maps can be used to study genome evolution–how the genome has been
rearranged through time–and to make inferences about gene organization, repeated sequences, etc.
 how organisms are related to each other at the genetic level.
 Understand the uniqueness between different species.
 overall structure of genes and gene function.
 inherited disease

4. How Are Genomes Compared?
• A simple comparison of the general features
of genomes such as
• genome size,
• number of genes, and
• chromosome number presents an entry point
into comparative genomic analysis.

5. Terms in comparative genome
mapping
• Colinearity:
Conservation of the gene order within a chromosomal segment between
different species.
• Microlinearity:
Conservation of the order of genes in DNA fragments that are bigger than 50
kb. Deletion, inversions and duplications are detected at this level.
• Orthologous loci:
Loci in different species originating from the same ancestral locus.
• Paralagous loci:
Loci in different (or the same) species that arose due to a duplication of an
ancestral locus.

6. What Is Compared?
 Gene location
 Gene structure
• Exon number
• Exon lengths
• Intron lengths
• Sequence similarity
 Gene characteristics
• Splice sites
• Codon usage
• Conserved synteny

7. Procedure for Whole-genome
sequencing:
1. Genome is cut into small sections.
2. Each section is hundreds or a few thousand bp of DNA.
3. Each section is sequenced and put in a database.
4. A computer aligns all sequences together (millions of them
from each chromosome) to form contigs.
5. Contigs are arranged (using markers, etc) to form scaffolds.

8. Genetic markers
1.Visible, or morphological markers
2 Protein markers
3. DNA markers
Types Of Genetic Markers Are
• RFLP (or Restriction fragment length
polymorphism)
• SSLP (or Simple sequence length
polymorphism)
• AFLP (or Amplified fragment length
polymorphism)
• RAPD (or Random amplification of
polymorphic DNA)
• VNTR (or Variable number tandem
repeat)
• SSR Microsatellite polymorphism, (or
Simple sequence repeat)
• SNP (or Single nucleotide
polymorphism)
• STR (or Short tandem repeat)
• SFP (or Single feature polymorphism)
• DArT (or Diversity Arrays Technology)
• RAD markers (or Restriction site
associated DNA markers)
Populations for genetic mapping
• Backcross/doubled haploid F2
• Recombinant inbred
• Intermated
• Near-Isogenic Lines
• F1 between heterozygous parents
Methods
• Single-Nucleotide Polymorphism
• Randomly Amplified Polymorphic DNA
• Amplified Fragment Length
Polymorphism
• Inter-Simple-Sequence Repeat
• Transposon Display
• Sequence-Related Amplified
Polymorphism
Physical mapping
• Clone-based physical mapping
approaches
• Radiation hybrid mapping
• Cytomolecular mapping

9. Examples of comparative mapping.
• Gramineae
• Solanaceae
• Cruciferaceae
• Fabaceae

10. Gramineae
A. Rice and maize:(Ahn and Tanksley, 1993)
a. Diverged 50 Myr ago. Rice: x=12; maize: x=10; maize 6x more nuclear DNA.
b. Single copy gene of rice always duplicated in maize and 72% of the duplication still exist in maize
genome.
c. Loss of 28% of duplicated copy of maize genes could have resulted from deletions or
loss of entire chromosomes or chromosomal segments.
d. Pairs of homologous chromosomes in maize: ch 2 and 10 are similar and coliner to ricench 4. Ch 3
and 8 have the same gene content but shuffling of gene orders.
e. 6-fold more DNA but did not increase in recombination in the conserved region as
compared to that in rice. Same recombination rate.
f. But maize map length (1723 cM) , < 2x the rice map (1055 cM) - a bit less than 2x
(polyploidy) due to loss of dup. regions.
B. Grasses as a single genetic system
1. Grasses as a single genetic system [Bennetzen & Freeling’s (1993)].
a. 10-11 thousand species in the Gramineae.
b. Many of the species are cross compatible (allopolyploids, etc.).
C. Wheat, rye, barley: (Devos and Gale, 1997)
1. Wheat A, B, and D genomes are homologous.
2. Wheat shows synteny with barley and rye.
3. Regions of no synteny are “fast-evolving” and non-coding–i.e. more synteny seen with cDNA than
with random genomic probes.

11. Mapping Experiments shows
a. Large degree of collinearity among diverse grasses; within
5-10 cM regions, - good conservation across grass species.
b. Most genes are homologous across species--i.e. all grasses
have essentially the same genes.
c. All this led to the development of the circular grass genome
figure– “Grass genomes line up and form a circle”– (Moore
et al., 1995).
Reference : Devos and Gale (1997), Figs. 4 and 6.

13. Model Plants: RICE
Because Arabidopsis is only distantly related to the
cereals, the next plant species to be sequenced
was rice.
The data emerging are extensive, and some of the
most interesting discoveries include:
• Although 81% of predicted Arabidopsis genes
have a rice ortholog, only 49% of predicted rice
genes have an Arabidopsis ortholog. Although
gene order is hardly conserved between
Arabidopsis and rice, many gene functions are
conserved (light receptors, flowering pathways,
stress responses, developmental pathways, etc.)
• There are nearly 50,000 genes in the rice
genome, more than in the human genome.

15. Cruciferaceae
A. Brassica-Arabidposis (Lagercrantz, 1998)
1. Arabidopsis represents one copy of the ancestral Brassica genome, i.e., three copies of
Arabidopsis genes in Brassica .
2. B. nigra (B genome; x = 8), B. oleracea (C; x = 9), and B. rapa (A; x = 10). The B genome is
triplicated–others are too; therefore, all derived from hexaploid ancester
3. Conserved segments between species ~8 cM .
4. ~90 rearrangements since divergence much higher than other species.
The high number for the crucifers may be due to the recent polyploidization of Brassica,which
induces many rearrangements.
B. Arabidopsis–soybean (Grant et al., 2000)
1. Compared putative protein sequences of genes coded by soybean RFLP and flanking regions of
SSR markers with Arabidopsis databases.
2. Arabidopsis appears to be duplicated.
3. Strong synteny observed between soybean and Arabidopsis with few interchanges explaining
most of the map differences (only considered three soybean linkage groups).
4. This synteny may not be identified using either RFLP cross-hybridization or direct nucleotide
comparisons because too many alterations may have obscured the functional relationships.
• Gresshoff Group (2003) showed microlinearity in a region that contains a gene involved in
nodulaion.

16. Figure 2. Comparative genome organization of the inferred ancestral
karyotype (n 5 8) based on published genetic maps of A.
lyrata and C. rubella (A), and B. stricta using our F2 genetic mapping
results (B). A, Genome blocks of the ancestral karyotype (AK)
are labeled by the letters A to X. Each block is one of eight colors,
corresponding to each chromosome. Centromeric positions are
indicated by the colored circles. Since only the Arabidopsis genome is
currently sequenced, the boundaries of the blocks are
defined by their flanking Arabidopsis Genome Initiative At locus
names. Each block is considered to be in the upright orientation
in the ancestral karyotype. Blocks that are inverted relative to
Arabidopsis are indicated by upside-down text of the At locus
names. B, Genetic map and genomic blocks for B. stricta. The seven
LGs are labeled as BstLG1 to BstLG7. Marker positions (in
cM) are shown on the left hand and the corresponding marker name
shown on the right hand of each LG. Genomic blocks, as
defined above, are arranged onto the LGs based on sequence similarity
of the markers to Arabidopsis. Three LGs are completely
conserved (Bst4 5 AK4, BstLG6 5 AK6, and BstLG7 5 AK7). Incongruity
of color/letter order of the blocks indicates genomic
rearrangements in Boechera relative to the ancestral karyotype. Two
blocks (A and C) are subdivided in Boechera (A1 and A2; C1
and C2). Blocks that are inverted in Boechera (blocks C1 and C2) are
represented by their names being inverted and by a
downward pointing arrow.

17. Solanaceae
Initial comparative mapping work was done with the Solanaceae by Steve
Tanksley and colleagues at Cornell.
• A. Tomato and pepper (Tanksley et al., 1988)
1. Basic chromosome number x =12 for both species.
2. Most genes are conserved, but some are duplicated in pepper.
3. Linkage order is mixed up–i.e., many rearrangements since their common
ancestor.
4. Pepper has 4x DNA content of tomato–probably not due to gene
duplication (due to noncoding, repetitive DNA-retrotransposons?).
• B. Tomato and potato(Bonierbale et al., 1988; Tanksley et al., 1992)
1. much more closely related than tomato–pepper, x=12 for both
2. virtually identical maps with four paracentric inversions accounting for all
differences
3. potato has ½ as much recombination as tomato, despite similar physical
lengths (1200 vs 600 cM)
4. more closely related species (tomato-potato) have fewer rearrangements
than more distantly related taxa (tomato-pepper), as expected.

18. C. Tomato and Eggplant (Doganlar et al. 2002)
a. Much more closely related than tomato–pepper, x=12 for both.
b. Molecular genetic linkage map based on tomato cDNA, genomic DNA, and EST
markers was constructed for eggplant, Solanum melongena.
c. The map consists of 12 linkage groups, spans 1480 cM, and contains 233 markers.
d. Comparison of the eggplant and tomato maps revealed conservation of large tracts
of colinear markers, a common feature of genome evolution in the Solanaceae and
other plant families.
e. Overall, eggplant and tomato were differentiated by 28 rearrangements, which
could be explained by 23 paracentric inversions and five translocations during
evolution from the species' last common ancestor.
f. No pericentric inversions were detected. Thus, it appears that paracentric inversion
has been the primary mechanism for chromosome evolution in the Solanaceae. g.
On the basis of the number of chromosomal disruptions and an approximate
divergence time for Solanum, 0.19 rearrangements per chromosome per million
years occurred during the evolution of eggplant and tomato from their last
ancestor.
This result suggests that genomes in Solanaceae, or at least in Solanum, are evolving
at a moderate pace compared to other plant species.

21. Conclusions from comparative
genome mapping
A. Some conservations do exist among all plants.
B. Synteny increases as the divergence time
between species decreases.
C. Possible that small linkage blocks are well
conserved, but often shuffled.

22. Limitations
• Although the level of synteny in the grasses has`facilitated
research in these crops, there are limits to the extent of
synteny between more distantly related species.
• Little conservation of gene order exists between
Arabidopsis and maize, even though approximately 90% of
maize proteins have a homolog in Arabidopsis (Brendel et
al. 2002).
• Therefore sequencing more plant genomes will be not only
helpful but necessary.

23. Impact Of Comparative Genome
mapping
• The impact of comparative genomics will be far reaching.
• For example: "The genomic revolution is having a tremendous impact on the study
of natural variation.
• It is making it possible finally to discover the molecular basis of complex traits, a
fundamental question in evolutionary biology, and a question of immense practical
importance in many other fields."(Borevitz & Nordborg, 2003).
This will not only help us understand biology better, but aid in our exploitation of
natural diversity for:
• crop improvement,
• plant breeding efforts and
• biodiversity conservation.