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Legume Genomics and Genetics (online), 2010, Vol. 1, No.6, 30-33
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32
cDNA library (Table 2).
Table 2 The most repeat motif of SSR loci in every type nucleotide
repeat
Frequency (%)
SSR motif
NCBI
cDNA library
AG/TC
8.65
13.42
AT/TA
4.10
0.47
CT/GA
8.49
12.95
AAG/TTC
5.64
9.36
AAT/TTA
3.05
0.94
AGA/TCT
4.30
8.42
CAA/GTT
2.03
2.81
CTT/GAA
6.70
13.42
CTC/GAG
1.42
2.18
CAC/GTG
1.30
1.56
AAAG/TTTC
0.77
0.78
AAAT/TTTA
1.26
0.00
AAAAG/TTTTC
1.34
0.31
The maximum repeat unit number of di-nucleotide
repeat motifs of AG/TC and CT/GA were 25 and 51
units in NCBI, respectively. And the numbers were 21
and 25 unit in cDNA library. In fact, in some studies,
the markers developed for longer repeat motifs were
found more informative for detection of polymer-
phism in cultivated groundnut germplasm (Moretz-
sohn et al. 2005).
2 Discussion
Peanut is one of important crops for both direct human
food and oil production in the world. One of the major
factors influencing peanut oil quality is the com-
position of polyunsaturated fatty acid. The linoleic
acid is one kind of polyunsaturated fatty acid, and its
acyl residues are susceptible to oxidation, which ad-
versely impacts on oil stability and increases deve-
lopment of off-flavors commonly associated with
rancidity in stored oil (Patel et al., 2004). So vali-
dating the mechanism of the polyunsaturated fatty
acid synthesis and metabolism is the central goal to
increase the peanut quality. In the recent research, we
made use of high-oil linoleic acid accession E12 to
construct the peanut cDNA library. This library con-
tained 12 501 ESTs and 4 074 Unigene, which took
part in many biological processes, such as ransporting
and metabolizing amino acid and carbohydrate, energy
metabolism process, transcription, protein translation
and modification et al., And 641 SSR loci had been
screened in this library, of which 624 ESTs had been
designed EST-SSR markers. The AG/TC, CT/GA and
CTT/GAA repeat motifs are the most SSR motifs in
all nucleotide repeat motifs.
ESTs are currently the most widely sequenced nucleo-
tide commodity from plant genomes in terms of num-
ber of sequences and total nucleotide count. During
the past few years a great deal of attention has been
directed towards discovering and characterizing the
range of protein-coding genes existing within the
genome of plant species with large genomes. The lar-
ger size of the peanut genome is a result of polyploidy
and the presence of regions with repeat motifs, both of
which make it difficult to sequence the complete ge-
nome. One possible method that could be used to invest-
tigate genome coding regions is cDNA sequencing,
which may be considered to be an alternative to the
complete sequencing of the genome in those plants
with large genomes. The availability of ESTs in public
databases provides the opportunity to identify SSRs
and to develop molecular markers. Consequently, the
large deal of peanut EST-SSRs available developed
from public databases is an important research resource
which can be used to analyze the functional portion of
the genomes. In the present study, there were 86 132
ESTs downloaded from Genbank in NCBI. 14 141
contigs and 9 892 singletons were obtained, these
sequences contained 2 463 SSR loci and 1 943 EST-
SSRs are developed. The type and frequency are as
same as cDNA library.
In general, molecular markers, and microsatellites or
simple sequence repeats (SSRs) in particular have
proven very useful for crop improvement in many spe-
cies (Gupta and Varshney, 2000). However, breeding
applications using molecular markers in groundnut,
which has been limited by the low level of the genetic
variation in this species. This low level of genetic
variation in cultivated groundnut is attributed to its
origin from a single polyploidization event that oc-
curred relatively recently on an evolutionary time scale
(Young et al., 1996). However, additional contributing
factors to the low levels of molecular polymorphism
observed to date could be the marker techniques used
and the amount of diversity of samples tested (Singh
et al., 1998). In recent years, significant efforts have
been made to develop the EST-SSR markers in groun-
dnut (Ferguson et al., 2004; Moretzsohn et al., 2005;