De novo transcriptome analysis of Dalbergia odorifera and transferability of SSR markers developed from the transcriptome

Abstract

Dalbergia odorifera T. Chen (Fabaceae), indigenous to Hainan Island, is a precious rosewood (Hainan hualimu) in China. However, only limited genomic information is available which has resulted in a lack of molecular markers, limiting the development and utilization of the germplasm resources. In this study, we aim to enrich genomic information of D. odorifera, and develop a series of transferable simple sequence repeat (SSR) markers for Dalbergia species. Therefore, we performed transcriptome sequencing for D. odorifera by pooling leaf tissues from three trees. A dataset of 138,516,418 reads was identified and assembled into 115,292 unigenes. Moreover, 35,774 simple sequence repeats (SSRs) were identified as potential SSR markers. A set of 19 SSR markers was successfully transferred across species of Dalbergia odorifera T. Chen, Dalbergia tonkinensis Prain, and Dalbergia cochinchinensis Pierre ex Laness. In total, 112 alleles (3-13 alleles/locus) were presented among 60 Dalbergia trees, and polymorphic information content ranged from 0.38 to 0.75. The mean observed and mean expected heterozygosity was 0.34 and 0.40 in D. odorifera, 0.27 and 0.32 in D. tonkinensis, and 0.29 and 0.33 in D. cochinchinensis, respectively. The cluster analysis classified these 60 trees into three major groups according to the three Dalbergia species based on the genetic similarity coefficients, indicating these newly developed transferable markers can be used to explore the relationships among Dalbergia species and assist genetic research. All these unigenes and SSR markers will be useful for breeding programs in the future.