Agriculture Reference
In-Depth Information
conserved. A comparison of potato genes with
those of
11
other plant genomes revealed more
than 8000 unique genes in some 1200 gene
families (
Fig. 17.2a)
(Potato Genome Sequen-
cing Consortium, 2011).
While comparative genomics is crucial to
identify mechanisms of evolution, it is also a tool
for molecular geneticists to identify genes coding
for functional proteins important for crop im-
provement. Comparative genomics can be the
base for gene identification in the postgenomic
era. The analysis of crop genomes and genetic
maps is crucial in understanding plant origin
and evolution, revealing ancestral rearrange-
ments and polyploidization events through
evidence of genome duplication. Scientists can
address fundamental questions about species
proliferation, adaptation, and functional modu-
lations (Ballvora
et al
., 2007).
Species within the Solanaceae harbor di-
verse phenotypes that have been exploited for
different agronomic purposes. Potato has been
bred for tubers (modified stems), while tomato,
pepper, and aubergine have been bred for en-
hanced fruit production. Likewise, petunia has
been bred and selected for floral phenotypes,
while tobacco has been bred for leaf size and sec-
ondary metabolism (Rensink
et al
., 2005c). Gen-
omes within the Solanaceae have undergone
relatively few rearrangements and duplications,
and therefore have similar gene content and
order. This exceptionally high level of conserva-
tion of genome organization at the macro and
micro levels makes this family a model to explore
the basis of phenotypic diversity and adaptation
to natural and agricultural environments (Mu-
eller
et al
., 2005).
Rensink
et al
. (2005c) documented a
genomic-scale comparison of the available coding
sequences (ESTs and ETs) from six solanaceous spe-
cies, comparing nucleotide sequences for potato,
tomato, pepper, aubergine, tobacco, and
Nicotiana
benthamiana
. Including ortholog analysis, they
confirmed a high level of sequence conservation.
Phylogenetic and comparative genomic analyses
with Arabidopsis, rice, and
21
other gene indices
revealed sequence divergence during speciation, as
evidenced by transcripts likely unique among the
Solanaceae and unique to individual Solanaceae
species (Rensink
et al
., 2005c).
Arabidopsis is often the model of choice for
anchoring comparative genomic studies at a
more detailed level, because it has been charac-
terized more completely, and is the first plant
species with its genome completely sequenced.
The Arabidopsis system, though, has its limita-
tions for studying certain biological processes.
The genome of potato has been compared with
those of Arabidopsis and grape, revealing vari-
ous degrees of syntenic blocks
(Fig. 17.2c
)
(Po-
tato Genome Sequencing Consortium, 2011).
Moore
et al
. (2005) examined the ripening of
fleshy fruits based in tomato microarrays. By
analyzing different stages of fruit development
in closely related heterologous species, they
identified candidate ESTs and genes implicated
in fruit ripening in the Solanaceae (Moore
et al
.,
2005). Most studies on comparative genomics of
solanaceous species have been performed gener-
ally by analyzing two species at a time (Ballvora
et al
., 2007; Guyot
et al
., 2012).
Wu and Tanksley (2010) used comparative
genomics based on a large set of single-copy
conserved orthologous markers (COSII) from
studies in tomato, potato, aubergine, pepper, and
diploid
Nicotiana
species, to deduce the broad
features and outcomes of chromosomal evolu-
tion in this family over the past
30
million years.
The authors concluded that a rate of 0.03-0.12
rearrangements per chromosome per million
years caused the chromosomal changes present
in the family. They determined that a higher fre-
quency of inversions rather than translocations
occurred, and identified hotspots of chromo-
somal breakage. They reconstructed the most
likely genome configuration for the ancestors of
the Solanaceae species.
Molecular markers, and more recently,
high-throughput genome sequencing efforts,
have increased dramatically the knowledge of
and ability to characterize genetic diversity in
the germplasm pool for essentially any crop spe-
cies (see Chapter
2,
this volume). The availability
of full genome sequences for several crop spe-
cies allows comparison between many acces-
sions within species, providing new keys
for biodiversity exploitation and interpretation.
High-throughput genotyping by re-sequencing
is enabling the identification of a wealth of SNPs
to produce the haplotype maps necessary to
associate molecular variation to phenotype ac-
curately. A genome sequence provides a useful
starting point for insight into genetic variation.
Genome-wide molecular tools can be used to
