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Transcriptome sequencing and EST-SSR marker development in Salix babylonica and S. suchowensis

Tian, Xueyao, Zheng, Jiwei, Jiao, Zhongyi, Zhou, Jie, He, Kaiyue, Wang, Baosong, He, Xudong
Tree genetics & genomes 2019 v.15 no.1 pp. 9
Salix babylonica, breeding, databases, expressed sequence tags, genomics, microsatellite repeats, sequence analysis, transcriptome, transcriptomics, unigenes
As the largest genus in the family Salicaceae, Salix L. has great potential in industrial, ornamental, and bioenergy-related applications. Despite their comprehensive importance, the genetic and genomic resources available for various willow species are still insufficient. In the present study, the transcriptomes of S. babylonica and S. suchowensis were sequenced using Roche 454 pyrosequencing and screened for expressed sequence tagged simple sequence repeat (EST-SSR) markers. A total of 280,074 and 267,030 reads with an average length of 432 bp and 398 bp were obtained for S. babylonica and S. suchowensis, respectively. The de novo assemblies yielded 40,271 unigenes for S. babylonica and 55,083 unigenes for S. suchowensis, of which 32,506 and 42,482 unigenes were respectively annotated in at least one of the four reference databases. A total of 1479 differentially expressed genes were identified between the two species. A set of 1083 SSR markers (424 for S. babylonica and 659 for S. suchowensis) were developed from the expressed sequence assemblies. Of the 300 randomly selected EST-SSR markers, 295 (98.3%) were polymorphic among different individuals of S. babylonica and of S. eriocephala. High rates of cross-species/genus amplification were also observed within 16 different species. In conclusion, this transcriptomic analysis provides novel resources for functional genomic research and can be used to improve the efficiency of genetics and breeding applications for these Salix species.