Development and Characterization of EST-SSR Markers in Taxodium ‘zhongshansa’

Abstract

Taxodium ‘zhongshansa’, an extremely flood-tolerant tree species, has been widely planted in eastern China due to its environmental attributes. Although much progress has been made in understanding its physiological response to flooding stress, as well as its rapid propagation and variety selection, little is known regarding its molecular genetics due primarily to a lack of reliable molecular markers. In this paper, 108,692 expressed sequence tags (ESTs) with a total size of 69.3 Mb derived from T. ‘zhongshansa’ were analyzed. And 10,038 simple sequence repeat (SSR) loci were identified from 8137 SSR-containing EST sequences. The average SSR frequency in the transcriptome was one in 6.90 kb of EST sequences. The most abundant repeat type was mononucleotide (6581, 65.56 %), followed by trinucleotide (2246, 22.37 %) and dinucleotide (1080, 10.76 %). After filtering unqualified SSR loci, loci with mononucleotide repeats and compound SSRs, 1958 EST-SSR loci were selected to design SSR makers. To validate this set of SSR markers, 503 primer pairs were randomly selected to amplify across 12 genomic DNA templates from three Taxodium species. Two hundred fifty-seven (51.09 %) out of 503 primer pairs amplified the expected products, of which 81 and 176 could amplify polymorphic and monomorphic bands, respectively. The functional categorization of EST sequences containing randomly selected markers revealed that 264 (52.49 %) had homology with known proteins. This set of EST-SSR markers will provide a valuable genetic and genomic tool for further genetic research in Taxodium, such as genetic map construction, quantitative trait loci mapping, and marker assisted selection.