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two-fold more SNPs (1/32.1 bp) than coding sequences (1/62.8 bp). Fusari
et al. (2008) reported that one SNP was found in every 69 bp the 14,348-bp
aligned sequences of 28 candidate genes related to biotic and abiotic stresses
in 19 sunflower inbred lines. The abundance and interspersed nature of
SNPs in the sunflower genome together with the upcoming automatic high-
throughput analytic technology will make the construction of high-density
sunflower genetic maps possible in the near future. SNPs are also ideal for
fine mapping of QTL, marker-assisted selection and association mapping.
3.3.8 Markers from DNA Sequence Databases
The advent of high-throughput sequencing technology produced a large
volume of DNA sequence data, which provide a rich source for DNA
marker development. The Compositae Genome Program (CGP;
http://
cgpdb.ucdavis.edu/
),
supported jointly by grants from the National Science
Foundation Plant Genome Program and the United States Department of
Agriculture Plant Genome Program, has generated over two million ESTs
for many biologically and economically important plant species in the
Compositae (Asteraceae) family. The majority of the 284,745 sunflower ESTs
in GenBank were deposited by the CGP. Heesacker et al. (2008) described a
catalog of 16,643 EST-SSRs, a collection of 484 EST-SSR and 43 EST-INDEL
markers developed from common sunflower ESTs by data mining. They
found that approximately 11% (1,956/17,904) of the unigenes in the transcript
assembly harbored one or more SSRs with repeat counts of n
5. Among the
primers tested for 43 INDELs and 484 SSRs, 39 and 427 produced high
quality genotype data (Heesacker et al. 2008).
3.4 Mapping Populations and Tools
Linkage maps of molecular markers are constructed from segregating
populations with the aid of computer software packages. This section briefly
discusses the mapping populations, tools, and strategies that have been
used in sunflower genome mapping.
3.4.1 Mapping Populations
All the published sunflower linkage maps were constructed from two types
of mapping populations: F
2
and RIL (recombinant inbred line) populations
each having advantages that are useful in different situations for different
purposes. The two parental plants were usually selected by maximum
polymorphism based on molecular marker screening or by the difference in
the phenotypic trait of interest. After creating the F
1
hybrid, an F
2
or a RIL
population can be generated and used for molecular mapping. An F
2
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