A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

Area of Science:

• Plant genetics and genomics
• Molecular marker development
• Forest tree breeding

Background:

• Expressed Sequence Tags (ESTs) are crucial for developing Simple Sequence Repeat (SSR) molecular markers.
• ESTs from Quercus robur and Quercus petraea offer opportunities for microsatellite marker development in long-lived oak species.
• Developing SSR markers aids research into adaptation and facilitates Quantitative Trait Locus (QTL) mapping.

Purpose of the Study:

• To mine and survey EST-SSRs in oak species.
• To develop a fast and cost-effective bin mapping approach for marker placement.
• To compare polymorphism levels between genomic and EST-derived SSRs and assess EST-SSR transferability.

Main Methods:

• Assembled 103,000 Sanger ESTs into 28,024 unigenes.
• Identified SSR motifs in 18.6% of unigenes, with trinucleotides being most common (>42%).
• Designed primers for 748 unigenes, validating 37.7% for single polymorphic loci in Quercus robur.

Main Results:

• Constructed bin maps for male and female oak parents using AFLP framework maps.
• Assigned 256 EST-SSRs to bins, with average bin lengths of 16.5 cM (female) and 20.99 cM (male).
• Found EST-SSRs to be less polymorphic than genomic SSRs but exhibited higher transferability to chestnut (Castanea sativa).

Conclusions:

• Generated a bin map for oak containing 256 EST-SSRs.
• This map is a foundational resource for establishing a gene-based map in Quercus.
• Facilitates dissection of QTLs for complex, ecologically relevant traits in oak.