Development and characterization of EST-SSR markers for mapping reaction to Phytophthora cinnamomi in Castanea spp.

• We developed a new set of simple sequence repeats (SSRs) in chestnut species.
• Those SSRs were found in chestnut resistance genes to Phytophthora cinnamomi.
• The SSRs were transferable in four chestnut species and interspecific hybrids.
• They will improve the chestnut breeding programs in Fagaceae and related taxa

Utilizing recently released transcriptome data, we developed 43 simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) differentially expressed in European chestnut (Castanea sativa) and Japanese chestnut (Castanea crenata) in response to inoculation with the most severe chestnut pathogen in Europe, Phytophthora cinnamomi (Pc). We used 24 parent and progeny trees – representing Pc susceptible, European and American chestnut (C. dentata), and Pc resistant, Japanese and Chinese chestnut (C. mollissima), species and some of their inter-species hybrids – to evaluate the EST-SSR markers’ polymorphism and transferability rates within and among species, respectively. The set of EST-SSR markers showed a remarkably high interspecific transferability rate among the four Castanea species tested, ranging from 90.7% for Chinese chestnut and 100% for European chestnut. Only three EST-SSR markers were monomorphic (7%) and the average value of expected heterozygosity was 0.61, higher than that in other studies using EST-SSRs in chestnut.The novel EST-SSR markers developed and characterized here are useful for constructing genetic linkage maps, conducting QTL analyses of phenotypic traits, genotype–phenotype association studies (especially in relation of resistance to Pc), high-throughput genotyping for clonal identification or marker-assisted selection, and comparative genomics.