Genetic Linkage Maps: Strategies, Resources and Achievements - Genetics, Genomics and Breeding of Crop Plants - page 94

the time and cost for SSR development. The growing availability of expressed
sequence tag (EST) sequences from a range of crop plants allows large-scale
search for SSR motif and design of SSR primers using pipelined computer
programs. Numerous SSR markers have been developed from the EST
sequences in the public databases of several crop species (Holton et al.
2002; Thiel et al. 2003).
The laboratory of Steven Knapp at the Oregon State University (currently
at the University of Georgia, Athens) was among the pioneers in sunflower
SSR marker development and applying them to genome mapping (Huestis
et al. 1996; Tang et al. 2002; Yu at al. 2002, 2003), although the first report
appeared in 1994 (Brunel 1994), not much later than that in other crop
plants. However, the progress was slow in the following several years. The
total number of public sunflower SSR markers did not reach 100 before 2002
(Whitton et al. 1997; Hongtrakul et al. 1998a, b; Gedil 1999). Yu et al. (2002)
developed 131 unique SSRs from 970 clones isolated from the (CA) n - , (CT) n - ,
(CAA) n - , (CATA) n - , or (GATA) n - enriched genomic DNA libraries. The test of
allelic diversity among elite breeding lines revealed 3.7, 3.6, and 9.5 alleles
per locus for dinucleotide, trinucleotide, and tetranucleotide repeats,
respectively, and that the mean polymorphic information content (PIC)
scores were 0.53 for dinucleotide, 0.53 for trinucleotide, and 0.83 for
tetranucleotide repeats. These values are much higher than those for RFLP
in sunflower. Tang et al. (2002) mapped 462 of the 1,089 SSR markers (with
a prefix OSU) to a recombinant inbred line (RIL) population derived from a
cross of two USDA-ARS released sunflower lines, RHA 280 and RHA 801.
This map has been used as a public domain for linkage group assignment
of mapped QTL and genes.
CARTISOL, a collaborative research consortium of several public
research organizations and private seed companies in France also developed
SSR markers for sunflower. Mokrani et al. (2002) used 61 out of 465 SSR
primers from the CARTISOL source that were polymorphic between the two
inbred lines of the mapping population to locate QTLs underlying grain oil
content and agronomic traits in combination with 215 AFLP markers. Yu et
al. (2003) mapped 91 out of 156 screened for polymorphism to the public
RHA 280 × RHA 801 RIL map. Zhang et al. (2005) reported that they
identified 78 SSR markers from the 1,111 primer pairs provided by CARTISOL
as an effective set of SSR markers for sunflower variety identification and
diversity assessment. These 78 primers detected a total of 276 alleles across
the 124 elite inbred lines, with an average of 3.5 alleles per SSR locus.
3.3.6 TRAP
TRAP (target region amplification polymorphism) is a fairly new technique
(Hu and Vick 2003). TRAP is designed to harness the existing sequence