Agriculture Reference
In-Depth Information
two main branches of eudicots, the asterids
and rosids, may share the same palaeo-hexaploid
duplication event (Tang
et al
., 2008). The
consortia suggest the second event occurred
after the divergence between dicots and
monocots (
185
±
55
million years ago) (Jail-
lon
et al
., 2007). Therefore, the recent dupli-
cation could have occurred ~
67
million years
ago, consistent with the WGD that occurred
near the Cretaceous-Tertiary boundary ~
65
million years ago (Busch
et al
., 2011). The di-
vergence of potato and grape occurred ~
89
million years ago, which was likely to repre-
sent the split between the rosids and asterids
(Potato Genome Sequencing Consortium,
2011). Barabaschi
et al
. (2012) compiled re-
cent data in monocots (Salse
et al
., 2009) and
in eudicots (Paterson
et al
., 2009) to support
the idea that “duplication-resistant” gene
families corresponded to transcriptional regu-
lators or disease resistance genes that were
usually maintained after WGD (Huang
et al
.,
2005; Guyot
et al
., 2012)
Completely sequenced genomes are indis-
pensable for comparative genomics; they offer
the possibility of utilizing the transcriptomes
of different species or different cultivars with
contrasting phenotypes to study a trait of
interest, to support crop improvement or sci-
entific research. An example of a downstream
application of comparative transcriptomics is
to evaluate inadvertent gene expression asso-
ciated with a transgenic; for example, in culti-
vars transformed with a gene for resistance to
P. infestans
(Gyetvai
et al
., 2012). With the re-
lease of the potato and tomato genome se-
quences, the efforts of mapping and cloning
disease-resistance genes from
Solanum
species
will increase. Resistance genes belonging to
the NBS-LRR class have a conserved protein
motif that enables the generation of resist-
ance gene analogs (RGA), polymerase chain
reaction fragments derived from
R
genes.
RGAs from
S. bulbocastanum
and other
Sola-
num
species were generated to perform com-
parative genomics meta-analysis of nearly
800 NBS-LRR gene sequences defining
R
gene
diversity bins to reflect evolutionary relation-
ships and DNA cross-hybridization. The results
demonstrate that all tested
R
gene lineages are
of ancient origin (Bedoya-Reina and Barrero,
2010).
Comparative genetics was used to study
the formation of tubers (the actual potatoes)
by modification of a stolon that was unique for
potato. Tomato is closely related to potato, but
does not produce stolons or modified stems for
tuber production. Transcript data from both
potato and tomato were analyzed to address
genetic regulation of the formation of stolons
and the transition of stolons to tubers. The
formation of stolons and tubers was found to
coincide with the upregulation of genes asso-
ciated with starch biosynthesis and storage
proteins, and Kunitz protease inhibitor genes
associated with pests and pathogens (Moore
et al
., 2005).
Now that sequenced plant genomes are
available, computer programs are under de-
velopment to exploit the information they
contain, as well as gene family data for ana-
lysis to aid comparative genomic studies for di-
verse applications. Such programs combine
plant genome databases in web portals that
are available as an aid to link model systems
with other plants of economic and ecological
importance for comparative translational gen-
omic studies (Goodstein
et al
., 2012). The SOL
Genomics Network collects and curates infor-
mation about Solanaceae-specific genes across
a range of species, and makes the information
available through a public portal (Menda
et al
., 2008).
17.
8
Conclusion
Potato breeding has not had the huge impact
on agricultural production that has been real-
ized in so many other crops where genetic im-
provement has been the major contributor to
agricultural productivity. Yield improvements
in potato over the past century have been due
more to improved cultural practices and sup-
porting technologies. However, potato breed-
ers have now been equipped with an enviable
array of genomic technologies that can be de-
ployed for cultivar improvement. It is likely
that the genetic gains that have already been
realized in other crops with more tractable
breeding systems can finally become a reality
for improvements to potato during the 21st
century.
