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markers. Virtually all markers on this map were
sequence characterized. This, in combination
with the high proportion of low or single-copy
gene markers allowed the map to be aligned to
the fully sequenced genomes of
Lotus japoni-
cus
and
Medicago truncatula
(Sato et al. 2008;
www.medicago.org)
. These alignments revealed
surprising degrees of synteny considering the
time of species divergence (estimated at about
55 million years). Phylogenetically
Arachis
is an
outgroup to
Medicago
and
Lotus
, and for this
reason, comparisons are particularly informa-
tive for making evolutionary inferences. Using
genome plots
Arachis
versus
Lotus
,
Arachis
ver-
sus
Medicago
, and comparing to a previously
published plot between
Lotus
and
Medicago
genomes (Cannon et al. 2006; Bertioli et al.
2009), 10 distinct conserved synteny blocks and
also non-conserved regions could be observed
in all genome comparisons (Bertioli et al. 2009).
This clearly implies that certain legume genomic
regions are consistently more stable during evo-
lution than others. It is notable that these regions
are large scale, and apparently in some cases
consist of entire chromosomal arms.
Intriguingly, an analysis of the retrotranspo-
son distributions in
Lotus
and
Medicago
shed
further light on these observations. Retrotrans-
posons are unevenly distributed in both
Lotus
and
Medicago
, and retrotransposon-rich regions
tend to correspond to variable regions, interca-
lating with the synteny blocks, which are rela-
tively retrotransposon poor. Furthermore, while
the variable regions generally have lower den-
sities of single-copy genes than the more con-
served regions, some harbor high densities of
the fast-evolving disease resistance genes (Berti-
oli et al. 2009). For
Arachis
it was notable that
LGs 2 and 4, which harbor the most prominent
clusters of resistance gene analogs (RGAs) and
QTLs for late leaf spot resistance, showed shat-
tered synteny with both
Lotus
and
Medicago
.An
association between RGAs and retrotransposons
in
Arachis
has also been supported by studies on
two peanut retrotransposons FIDEL and Matita
(Nielen et al. 2010, 2011).
Genetic Maps Based on Cultivated x
Cultivated Crosses
Screening of isozyme, RFLP, and RAPD mark-
ers on accessions of
A. hypogaea
identified only
very low levels of polymorphism among culti-
vated peanut accessions (Kochert et al. 1991;
Halward et al. 1992; Lu and Pickersgill 1993;
Burow et al. 1996; Subramanian et al. 2000;
Dwivedi et al. 2001). The partial first link-
age map from a cross between accessions of
A. hypogaea
was constructed using an F
2
pop-
ulation (Herselman et al. 2004). Five linkage
groups with 12 markers spanning 139 cM of
the genome were reported. The first reasonably
complete genetic maps of cultivated peanut were
published by Hong et al. (2008) and Varshney
et al. (2009). Hong et al. (2008) tested 1,048 SSR
primer pairs and mapped 131 SSR loci onto 20
linkage groups for a total length of 670 cm on an
RIL population between the cultivars Yueyou 13
and Zhenzhuhei. Varshney et al. (2009) screened
1,145 SSR markers and mapped 135 loci onto 22
linkage groups spanning 1,271 cM onto an RIL
population developed from two parental geno-
types, TAG 24 and ICGV 86031. Later a com-
posite map containing 175 SSR markers in 22
linkage groups was developed from three culti-
vated crosses (Hong et al. 2010); of 901 primer
pairs screened, 146, 124, and 64 were polymor-
phic. The most saturated map so far was recently
published by Wang et al. (2012), containing 385
polymorphic SSRs covering 318 loci.
Attempts to develop maps with higher den-
sities have required screening several thousand
SSR markers. The SSR-based cultivated genetic
map with 135 marker loci developed by Varsh-
ney et al. (2009) was then further saturated up to
191 SSR loci (Ravi et al. 2011). Two new par-
tial genetic maps with 56 (TAG 24
×
GPBD
4) and 45 (TG 26
GPBD 4) marker loci
(Khedikar et al. 2010; Sarvamangala et al. 2011)
were constructed covering genome distances of
merely 462.24 and 657.9 cM, respectively. These
two maps were then saturated with enhanced
genome coverage up to 188 (1,922.4 cM) and
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