Illumina sequencing of Lycium ruthenicum transcriptome

Chinese Lycium species have been extensively used as traditional medicinal plants due to their richness in health-promoting bioactive compounds. So far, marker-based exploitation of genetic diversity and marker-assisted breeding in the Lycium genus remain to be explored. Two transcriptomic data from Lycium ruthenicum Murr (LR) generated in this study and L. chinense Mill. (LC) retrieved from public database were utilized for the development of molecular markers. A total of 40,769 and 50,351 unigenes of LR and LC were generated to develop simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) markers, respectively. A total of 1,118 and 1,374 putative EST-SSRs markers were discovered for LR and LC, respectively. Out of the markers from LR, 975 of them were randomly selected for further validation. Finally, 766 (78.6%) primer pairs were successfully amplified in LR and 561 of them were tested in L. barbarum Linnaeus (LB) for cross-species transferability. Of the 66,862 SNPs identified, 62.8% (42,013 cases) were transitions, and 37.2% (24,849 cases) were transversions. A total of 96 SNPs were randomly chosen for SNPs validation and cross-species transferability test using three DNA pools, each pool representing DNA from one Lycium species, LR, LC or LB. Finally, Ninety-two SNPs markers could produce PCR product in at least one sample. Of these, 79 (82.3%) were confirmed by subsequent Sanger sequencing, suggesting that a total of 55,027 SNPs were effective and useful in Lycium species tested. These SSRs and SNPs markers are valuable resources for studying population genetics, constructing genetic map, and molecular breeding of Lycium species.