Agriculture Reference
In-Depth Information
nonautonomous elements of less than 600 bp in the genome, are also
used as DNA markers in plants (Grzebelus et al. 2009; Monden et al.
2009). For example, an
AhMITE1
insertion or excision (transposition)
has caused functional disruption of the fatty acid desaturase-encoding
gene
ahFAD2B
(Patel et al. 2004) and created more botanical diversity
and resistance to late leaf spot in peanut (Gowda et al. 2010, 2011).
Shirasawa et al. (2012a) reported 504
AhMITE1
s from the MITE-
enriched genomic libraries in peanut, of which 169 had polymorphisms
in peanuts. Using
in silico
analysis, Shirasawa et al. (2012b) developed
2702 SSR- and transposon-based markers, of which 926 (34.2%) were
polymorphic. This is probably the highest level of polymorphism
reported so far in cultivated peanut. Taken together, the polymorphic
DNA markers available in the public domain will be useful in peanut
diversity assessment, association genetics, linkage disequilibrium map-
ping, quantitative trait loci (QTL) detection, and genomics-led breeding.
Genetic linkage maps of varying density, based on cultivated
×
cultivated peanut crosses, have been published (Hong et al. 2008,
2010; Varshney et al. 2009; Khedikar et al. 2010; Qin et al. 2011;
Ravi et al. 2011; Gautami et al. 2012a,b; Shirasawa et al. 2012b; Sujay
et al. 2012; Wang et al. 2012). Gautami et al. (2012a) reported an
international reference consensus map based on 11 mapping popula-
tions of the cultivated peanut. This reference map contains 897 marker
loci (895 SSRs and 2 cleaved ampli
ed polymorphic sequence (CAPS)
markers) mapped on 20 linkage groups (LGs), with a total map distance
of 3863.6 cM and average marker density of 4.4 cM. The map is divided
into 20 cM long bins, which carry 1
20 loci with an average of 4 marker
loci per bin. Using 926 SSR- and transposon-based markers together
with another 253 SSRs from public domain, Shirasawa et al. (2012b)
constructed another high-density genetic linkage map that populated
1114 loci on 21 LGs, with a total map distance of 2166.4 cM and
average marker density of 1.9 cM, which ranged from 1.1 cM for
LG01.2 to 11.4 cM for LG10.1(t) in the 21 LGs. Using these resources,
several QTL associated with plant morphology and stress resistances
have been identi
-
ed, with a few of them having major effects
(Varshney et al. 2009; Khedikar et al. 2010; Qin et al. 2011; Ravi
et al. 2011; Fonceka et al. 2012; Gautami et al. 2012b; Sujay et al.
2012). These DNA markers and ensuing knowledge they provide will
be useful for selecting highly informative and uniformly distributed
markers for developing new genetic maps, performing QTL analysis in
a multipopulation design, assessing background effects on QTL expres-
sion, and assessing diversity and association mapping in germplasm
collections.
