Agriculture Reference
In-Depth Information
section
Petota
to facilitate the search for novel
sources of resistance to
Phytophthora infestans
.
The Solanaceae Source website publishes the
results of the National Science Foundation
(NSF) project to produce a worldwide taxonomic
monograph of all species in the genus
Solanum
,
divided into about
13
major clades, with molecu-
lar data from chloroplast NADH dehydrogenase
F (ndhF) sequences (Bohs, 2005). Spooner and
collaborators contributed data for section
Petota
.
Within the CBSG project, AFLP patterns of
4929 genotypes of more than 950 gene bank
accessions were generated, the largest data set
ever constructed for section
Petota
. The results
were reported in Jacobs
et al
. (2008 and 2011).
Jacobs
et al
. (2008) constructed a neighbor-
joining (NJ) tree of these 4929 genotypes (
Fig. 2.1
),
but due to the size of the data set, they were only
able to perform NJ and maximum parsimony (MP)
jackknife analyses on a reduced set consisting of
one genotype from each available accession (951
accessions, representing
196
taxa). Large parts of
both jackknife trees consisted of a polytomy, but
branches with jackknife support were used as the
basis for informal species groups. These partly co-
incided with a number of series from Mexico and
Central America, but most of the South American
material could not be subdivided. Jacobs
et al
.
(2008) consider it likely that the polytomy is indi-
cative of the real biological situation in section
Pe -
tota
. As reasons why the phylogenetic links be-
tween species are so difficult to establish, they put
forward the relatively fast spread of tuber-bearing
Solanum
species over South America, due to the
geographic conditions in the Andes, combined
with high levels of hybridization.
Jacobs
et al
. (2011) used population genetic
tools to establish the genetic structure in the
group of South American representatives of sec-
tion
Petota
(566 accessions representing
89
taxa).
They established the optimal partitioning of
the group, combining a Structure analysis with
maximizing the F-statistics (Fst) values among
subgroups, and found that the
89
species ar-
rangement had a lower Fst value than an ar-
rangement of the material in
16
clusters. Within
these clusters, they obtained support for add-
itional groups, arriving at a total of
44
groups.
They concluded that the South American part
of section
Petota
was overclassified and provided
a table with an estimate of the level of support of
all the species names in current use.
Recently, Vleeshouwers
et al
. (2011) re-
leased an online database, Sol
R
gene, which con-
tained the CBSG data on resistance to
P. infestans
and the presence of R genes and R gene ho-
mologs in
Solanum
section
Petota
. Phylogenetic
data of the entire Sol
R
gene collection are in-
cluded, and an interactive AFLP-based NJ tree is
presented that allows generating phylogenetic
trees of selected groups of germplasm. The col-
lection is classified according to the nomencla-
ture of Hawkes (1990), using his designations
of subsections and (super)series.
The NSF established the Planetary Biodiver-
sity Inventory (PBI) program in 2002 (
http://
research focused on the species-level taxonomy of
a monophyletic group and present the results on-
line. The Solanaceae Source website presents the
results of the PBI project “
Solanum
: a worldwide
treatment” (
http://solanaceaesource.org/content/
pbi-solanum-worldwide-treatment)
. Taxonomic
information on the whole genus
Solanum
will be
uploaded, including names lists, species descrip-
tions, specimen collections and publications. The
following statement on the site explains the status
of the information: “The names list on Solanace-
ae Source is a work in progress. Synonymy and
nomenclature information are considered au-
thoritative only for names that are accompanied
by a full species description. For accepted names
that do not yet have a species description, syn-
onymy should be considered provisional.” In the
potato clade, Spooner and co-workers recognize
156
species (
http://solanaceaesource.org/content/
pbi-solanum-worldwide-treatment)
. There is no
classification of these species in series, clades, or
species groups.
To highlight agreement and disagreement
between the approaches of the Solanaceae Source
website and the CBSG AFLP study, we discuss two
examples: first, the latest and perhaps “final”
comment on the classification of the
brevicaule
complex; and second, the treatment of a South
American group of species, series
Megistacroloba
.
The brevicaule complex
This complex is a prime example of overclassifi-
cation, as discussed above. More than
30
names
have been associated with material considered to
belong to this complex. Spooner and collaborators