A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study.
BACKGROUND
Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut).


RESULTS
A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.


CONCLUSIONS
We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.
INRA, UMR1202 BIOGECO, F-33610 Cestas, France.
Jérôme
J
Durand
Catherine
C
Bodénès
Emilie
E
Chancerel
Jean-Marc
JM
Frigerio
Giovanni
G
Vendramin
Federico
F
Sebastiani
Anna
A
Buonamici
Oliver
O
Gailing
Hans-Peter
HP
Koelewijn
Fiorella
F
Villani
Claudia
C
Mattioni
Marcello
M
Cherubini
Pablo G
PG
Goicoechea
Ana
A
Herrán
Ziortza
Z
Ikaran
Cyril
C
Cabané
Saneyoshi
S
Ueno
Florian
F
Alberto
Pierre-Yves
PY
Dumoulin
Erwan
E
Guichoux
Antoine
A
de Daruvar
Antoine
A
Kremer
Christophe
C
Plomion
D002874:Chromosome Mapping / Q000191:economics* / Q000379:methods*; D003362:Cost-Benefit Analysis; D057225:Data Mining; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D018745:Genome, Plant / Q000235:genetics; D018895:Microsatellite Repeats / Q000235:genetics; D018598:Minisatellite Repeats / Q000235:genetics*; D011110:Polymorphism, Genetic; D029963:Quercus / Q000235:genetics*
D005819:Genetic Markers