Development and Characterization of Novel EST-SSR Markers in Masson Pine (Pinus massoniana) Based on Transcriptome Data

Masson pine (Pinus massoniana Lamb.) is a versatile tree that can be used for timber, pulp, resin production and ecological maintenance. Although great progress has been made in its superior family selection and rapid propagation, little is known about its molecular genetics, primarily due to a lack of genomic information or reliable molecular markers. In the current study, 70896 unigenes derived from masson pine were analyzed, and 3317 SSR loci were identified from 3064 SSR-containing sequences. The most abundant repeat type was the mono-nucleotide (1337, 40.3%), followed by tri-nucleotide (1223, 36.87%) and di-nucleotide (695, 20.95%). In total, 1807 pairs of non-redundant primers were designed after filtering unqualified SSR loci. One hundred primer pairs were randomly selected to be validated among 6 masson pine clones. Seventy-one of 100 primer pairs amplified the expected products, of which 37 polymorphic EST-SSRs were used to genotype 53 masson pine clones. A cluster analysis revealed three major clusters, and most of the same excellent trait clones were assigned into the same inferred clusters. These SSR data are valuable for the discovery of novel EST-SSR markers, and will provide an effective tool for further genetic research on masson pine, such as genetic linkage map construction, QTL mapping and marker-assisted selection.